title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2023-11 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Major biotic stresses affecting maize production in Kenya and their implications for food security link: https://peerj.com/articles/15685 last-modified: 2023-11-30 description: Maize (Zea mays L.) is a staple food for many households in sub-Saharan Africa (SSA) and also contributes to the gross domestic product (GDP). However, the maize yields reported in most SSA countries are very low and this is mainly attributed to biotic and abiotic stresses. These stresses have been exacerbated by climate change which has led to long periods of drought or heavy flooding and the emergence of new biotic stresses. Few reports exist which compile the biotic stresses affecting maize production in SSA. Here, five major biotic stresses of maize in Kenya are presented which are attributed to high yield losses. They include Maize lethal necrosis, fall armyworm, gray leaf spot, turcicum leaf blight and desert locusts. Maize lethal necrosis and fall armyworm are new biotic stresses to the Kenyan maize farmer while gray leaf spot, and turcicum leaf blight are endemic to the region. The invasion by the desert locusts is speculated to be caused by climate change. The biotic stresses cause a reduction in maize yield of 30–100% threatening food security. Therefore, this review focuses on the cause, control measures employed to control these diseases and future prospective. There should be deliberate efforts from the government and researchers to control biotic stresses affecting maize yields as the effect of these stresses is being exacerbated by the changing climate. creator: Faith Njeru creator: Angeline Wambua creator: Edward Muge creator: Geert Haesaert creator: Jan Gettemans creator: Gerald Misinzo uri: https://doi.org/10.7717/peerj.15685 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Njeru et al. title: Gene mutation analysis of oral submucous fibrosis cancerization in Hainan Island link: https://peerj.com/articles/16392 last-modified: 2023-11-30 description: ObjectiveThe sequencing panel composed of 61 target genes was used to explore the related mutation genes of oral squamous cell carcinoma (OSCC) and oral submucous fibrosis (OSF) cancerization, so as to provide a theoretical basis for the early diagnosis of oral submucous fibrosis cancerization, find the most important mutations in OSF cancerization, and more targeted prevention of OSF cancerization.MethodsA total of 74 clinically diagnosed samples were included, including 36 cases of OSCC and 38 cases of OSF cancer patients. DNA was extracted, and targeted gene panel sequencing technology was used to analyze the gene frequency of pathogenic mutation sites in clinical samples.ResultsGene panel sequencing analysis showed that there were 69 mutations in 18 genes in OSCC and OSF cancerous specimens. The results of gene panel sequencing were screened, and 18 mutant genes were finally screened out and their mutation frequencies in the samples were analyzed. According to the frequency of gene mutations from high to low, they were TP53, FLT4, PIK3CA, CDKN2A, FGFR4, HRAS, BRCA1, PTPN11, NF1, KMT2A, RB1, PTEN, MSH2, MLH1, KMT2D, FLCN, BRCA2, APC. The mutation frequency of FLT4 gene was significantly higher than that of OSCC group (P < 0.05).ConclusionFLT4 gene may be related to OSF cancerization and is expected to be an early diagnostic biomarker for OSF cancerization. creator: Bingxia Li creator: Xinyu Chen creator: Haiyu Xian creator: Qitao Wen creator: Tao Wang uri: https://doi.org/10.7717/peerj.16392 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Potential of psychrotolerant rhizobacteria for the growth promotion of wheat (Triticum aestivum L.) link: https://peerj.com/articles/16399 last-modified: 2023-11-30 description: Wheat is the second most important staple crop grown and consumed worldwide. Temperature fluctuations especially the cold stress during the winter season reduces wheat growth and grain yield. Psychrotolerant plant growth-promoting rhizobacteria (PGPR) may improve plant stress-tolerance in addition to serve as biofertilizer. The present study aimed to isolate and identify PGPR, with the potential to tolerate cold stress for subsequent use in supporting wheat growth under cold stress. Ten psychrotolerant bacteria were isolated from the wheat rhizosphere at 4 °C and tested for their ability to grow at wide range of temperature ranging from −8 °C to 36 °C and multiple plant beneficial traits. All bacteria were able to grow at 4 °C to 32 °C temperature range and solubilized phosphorus except WR23 at 4 °C, whereas all the bacteria solubilized phosphorus at 28 °C. Seven bacteria produced indole-3-acetic acid at 4 °C, whereas all produced indole-3-acetic acid at 28 °C. Seven bacteria showed the ability to fix nitrogen at 4 °C, while all the bacteria fixed nitrogen at 28 °C. Only one bacterium showed the potential to produce cellulase at 4 °C, whereas four bacteria showed the potential to produce cellulase at 28 °C. Seven bacteria produced pectinase at 4 °C, while one bacterium produced pectinase at 28 °C. Only one bacterium solubilized the zinc at 4 °C, whereas six bacteria solubilized the zinc at 28 °C using ZnO as the primary zinc source. Five bacteria solubilized the zinc at 4 °C, while seven bacteria solubilized the zinc at 28 °C using ZnCO3 as the primary zinc source. All the bacteria produced biofilm at 4 °C and 28 °C. In general, we noticed behavior of higher production of plant growth-promoting substances at 28 °C, except pectinase assay. Overall, in vitro testing confirms that microbes perform their inherent properties efficiently at optimum temperatures rather than the low temperatures due to high metabolic rate. Five potential rhizobacteria were selected based on the in vitro testing and evaluated for plant growth-promoting potential on wheat under controlled conditions. WR22 and WR24 significantly improved wheat growth, specifically increasing plant dry weight by 42% and 58%, respectively. 16S rRNA sequence analysis of WR22 showed 99.78% similarity with Cupriavidus campinensis and WR24 showed 99.9% similarity with Enterobacter ludwigii. This is the first report highlighting the association of C. campinensis and E. ludwigii with wheat rhizosphere. These bacteria can serve as potential candidates for biofertilizer to mitigate the chilling effect and improve wheat production after field-testing. creator: Muhammad Abdullah creator: Mohsin Tariq creator: Syeda Tahseen Zahra creator: Azka Ahmad creator: Marriam Zafar creator: Shad Ali uri: https://doi.org/10.7717/peerj.16399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Abdullah et al. title: Alveolar antral artery: cone beam computed tomography study and clinical context link: https://peerj.com/articles/16439 last-modified: 2023-11-30 description: PurposeAnastomosis between posterior superior alveolar artery and infraorbital artery can go through bony canal in the lateral wall of the maxilla. This artery is called alveolar antral artery. It can complicate lateral sinus lift procedure by bleeding and hemosinus formation or bone graft wash out. The artery can also go in soft tissues where is not visible on cone beam computed tomography. In previous studies, the relation of this artery to sinus floor or alveolar process was measured. These structures are highly unstable during lifetime and after tooth loss. The aim of this study is to study presence and relations of bony canal in the lateral maxillary wall, to characterize the group of patients which is more likely to have bone canal in the lateral maxilla. The aim and the novelty of this study is the describing of the relationship of the bony canal to the more stable structure of hard palate and describing the relation of presence of bony canal on width of maxillary sinus, and to facilitate the prediction of presence of the alveolar antral artery.MaterialsThe cone beam computed tomography scans of the patients (251 in number) of the university hospital were examined for presence of alveolar antral artery (148 was fulfilled inclusion criteria), patient were characterized by gender, age, and sinus type (wide, average, narrow). The diameter of the bony canal and its relation to the level of sinus floor and hard palate were measured.ResultsThe cone beam computed tomography scans of 148 patients, out of it 55 man (37,2%) and 93 women (62,8%). Bony canal containing alveolar anastomosis was found in 69 cases (57,0%). Presence of the bony canal in the lateral wall of maxillae showed statistical probability depending on age with p = 0, 064 according to Mann-Whitney test. The older patients have more likely the bony canal. The presence of the alveolar antral artery was found more likely in the wide sinuses. The hard palate level can serve as a prediction point of alveolar antral artery only in first molar and second premolar region. In accordance with previous studies the width of bony canal is significantly higher in group of man (p = 0, 015). There was found a correlation between smaller distance of bony canal from sinus floor in the presence of teeth (p = 0, 067). After tooth loss the distance between sinus floor and bony canal increases, but the distance of bony canal to hard palate level stays constant. This can be explained hypothetically so that periodontal ligaments and root surface acts as a barrier for sinus pneumatization.ConclusionLateral sinus lifting in some cases can be unenviable, the knowledge about alveolar antral artery anatomy can reduce the risk of arterial bleeding. The cone-beam computed tomography is a routine examination prior to augmentation surgery and therefore the data obtained from it has an impact on clinical practice. creator: Ján Staněk creator: Kateřina Machálková creator: Magdalena Staňková creator: Jana Zapletalová creator: Tat’ána Kocurová uri: https://doi.org/10.7717/peerj.16439 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Staněk et al. title: Amlodipine and lufenuron as repurposing drugs against Sporothrix brasiliensis link: https://peerj.com/articles/16443 last-modified: 2023-11-30 description: BackgroundSporotrichosis caused by Sporothrix brasiliensis is a globally emerging infectious disease with limited therapeutic options. Thus, we aimed to evaluate the in vitro activity of amlodipine (AML) and lufenuron (LUF) alone and their interaction with itraconazole (ITZ), the first-choice drug against S. brasiliensis.MethodsTwenty clinical isolates of S. brasiliensis from two hyperendemic regions were tested through a microdilution assay to evaluate the minimal inhibitory concentration (MIC) and minimal fungicidal concentration (MFC) of AML and LUF. Checkerboard assay was performed with 10 isolates for both drug interactions with ITZ.ResultsAML showed inhibitory and fungicidal activity against all isolates included, with MIC values ranging from 32 to 256 µg/mL, and MFC from 64 to 256 µg/mL. However, none of the S. brasiliensis isolates were inhibited by the highest soluble concentration of LUF (MIC >64 µg/mL for all strains). Synergic interaction of AML and LUF with ITZ occurred in 50% and 40% of the isolates tested, without any antagonistic effects.ConclusionBoth repurposing drugs evaluated in our study showed a promising in vitro activity, especially in synergy with ITZ against S. brasiliensis, warranting future in vivo investigations regarding its activity. creator: Vanice Rodrigues Poester creator: Jéssica Estefania Dávila Hidalgo creator: Lara Severo Jardim creator: Mariana Rodrigues Trápaga creator: Vanessa Brito de Souza Rabello creator: Rodrigo Almeida-Paes creator: Rosely Maria Zancope-Oliveira creator: Melissa Orzechowski Xavier uri: https://doi.org/10.7717/peerj.16443 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Poester et al. title: Morphology and molecular phylogeny of Neolentinus in northern China link: https://peerj.com/articles/16470 last-modified: 2023-11-30 description: Neolentinus is a significant genus, belonging to Gloeophyllaceae, with important economic and ecological values, which are parasites on decaying wood of broad-leaf or coniferous trees, and will cause brown rot. However, the taxonomic study is lagging behind to other groups of macrofungi, especially in China. In view of this, we conducted morphological and molecular phylogenetic studies on this genus. We have discovered new types of cheilocystidia and with extremely long lamellae in Neolentinus, and, thus proposed it as a new species—Neolentinus longifolius. At the same time, we clarified the distribution of Neolentinus cyathiformis in China and provided a detailed description. Moreover, we also described two common species, viz. Neolentinus lepideus and Neolentinus adhaerens. All the species are described based on the Chinese collections. The key to the reported species of Neolentinus from China is provided. And the phylogeny of Neolentinus from China is reconstructed based on DNA sequences of multiple loci including the internal transcribed spacer (ITS) regions, the large subunit nuclear ribosomal RNA gene (nLSU), and the translation elongation factor 1-α gene (tef-1α). In addition, full morphological descriptions, illustrations, color photographs, taxonomic notes, and all the available sequences of Neolentinus species are provided. creator: Lei Yue creator: Yong-lan Tuo creator: Zheng-xiang Qi creator: Jia-jun Hu creator: Ya-jie Liu creator: Xue-fei Li creator: Ming-hao Liu creator: Bo Zhang creator: Shu-Yan Liu creator: Yu Li uri: https://doi.org/10.7717/peerj.16470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yue et al. title: Role of Pink1-mediated mitophagy in adenomyosis link: https://peerj.com/articles/16497 last-modified: 2023-11-30 description: Abstract BackgroundRecent studies indicate that endometrial hypoxia plays a critical role in adenomyosis (AM) development. Mitochondria are extremely sensitive to hypoxic damage, which can result in both morphological and functional impairment. Mitophagy is a crucial mechanism for preserving mitochondrial quality by selectively removing damaged mitochondria, thus ensuring the proper functioning of the entire mitochondrial network. In response to hypoxia, PINK1 is activated as a regulator of mitophagy, but its role in AM requires further study.ObjectiveTo explore the potential mechanism of mitophagy mediated by PINK1 in the pathogenesis of AM.MethodThe study compared PINK1, Parkin, OPTIN, P62, and NDP52 protein expression levels in patients with or without AM using clinical specimens and an AM mouse model. Pathological changes were compared using HE staining. Immunofluorescence and western blot were used to detect protein expression levels. Endometrial stromal cells (ESC) were isolated and examined for mitophagy, protein expression level, and cell invasion ability.ResultsBoth the endometrial tissue from patients with AM and AM ESC displayed an upregulation of protein levels for PINK1, Parkin, OPTIN, P62, and NDP52 when compared with the control group. Then, HE staining confirmed the successful establishment of the AM mouse model. Moreover, the ultrastructural analysis using transmission electron microscopy revealed that AM mice’s endometrial glandular epithelial and stromal cells had exhibited swollen, deformed, and reduced mitochondria along with an increase in the number of lysosomes and mitochondrial autophagosomes. The protein levels of PINK1, Parkin, OPTIN, P62, and NDP52 in uterine tissue from AM mice were noticeably increased, accompanied by a considerable upregulation of ROS levels compared to the control group. In addition, cells in the AM group showed remarkably elevated mitophagy and invasion potentials compared to the control group. In contrast, the cell invasion ability decreased following PINK1 knockdown using the RNA interference technique.ConclusionThe high levels of PINK1-mediated mitophagy have been found in AM. The upregulation in mitophagy contributes to mitochondrial damage, which may result in the abnormal invasion characteristic of AM. creator: Minmin Chen creator: Wei Wang creator: Xianyun Fu creator: Yongli Yi creator: Kun Wang creator: Meiling Wang uri: https://doi.org/10.7717/peerj.16497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Circular RNA hsa_circ_0051246 acts as a microRNA-375 sponge to promote the progression of gastric cancer stem cells via YAP1 link: https://peerj.com/articles/16523 last-modified: 2023-11-30 description: BackgroundGastric cancer (GC) stem cells play an important role in GC progression. Circular RNAs (circRNAs) act as microRNA (miRNA) sponges and inhibit the biological function of miRNAs in GC cytoplasm. MiRNAs also participate in GC progress. circ_0051246 was shown to be associated with miR-375 after analyzing GC microarray data GSE78091 and GSE83521. The oncoprotein Yes-associated protein 1 (YAP1) is targeted by miR-375 and can be inactivated via the Hippo tumor suppressor pathway. Due to insufficient research on circ_0051246, this study aimed to investigate its relationship with miR-375 and YAP1 in cancer stem cells (CSCs).MethodsSGC-7901 CSCs were used to establish knockdown/overexpression models of circ_0051246, miR-375, and YAP1. Malignant phenotypes of CSCs were assessed using Cell Counting Kit 8, colony/sphere formation, 5-Ethynyl-2′-deoxyuridine assay, flow cytometry, Transwell, and wound healing assays. To detect the interactions between circ_0051246, miR-375, and YAP1 in CSCs, a dual-luciferase reporter assay and fluorescence in situ hybridization were performed. In addition, 24 BALB/c nude mice were used to establish orthotopic xenograft tumor models. Four groups of mice were injected with CSCs (1 × 106 cells/100 µL) with circ_0051246 knockdown, miR-375 overexpression, or their respective control cells, and tumor progression and gene expression were observed by hematoxylin-eosin staining, immunohistochemistry. Western blot and quantitative real-time PCR were utilized to examine protein and gene expression, respectively.ResultsCirc_0051246 silencing reduced viability, promoted apoptosis, and inhibited proliferation, migration and invasion of CSCs. The functional effects of miR-375 mimics were comparable to those of circ_0051246 knockdown; however, the opposite was observed after miR-375 inhibitors treatment of CSCs. Furthermore, circ_0051246-overexpression antagonized the miR-375 mimics’ effects on CSCs. Additionally, YAP1 overexpression promoted CSC features, such as self-renewal, migration, and invasion, inhibited apoptosis and E-cadherin levels, and upregulated the expression of N-cadherin, vimentin, YAP1, neurogenic locus notch homolog protein 1, and jagged canonical notch ligand 1. Conversely, YAP1-silenced produced the opposite effect. Moreover, miR-375 treatment antagonized the malignant effects of YAP1 overexpression in CSCs. Importantly, circ_0051246 knockdown and miR-375 activation suppressed CSC tumorigenicity in vivo.ConclusionThis study highlights the promotion of circ_0051246-miR-375-YAP1 axis activation in GC progression and provides a scientific basis for research on the molecular mechanism of CSCs. creator: Minghui Deng creator: Yefeng Xu creator: Yongwei Yao creator: Yiqing Wang creator: Qingying Yan creator: Miao Cheng creator: YunXia Liu uri: https://doi.org/10.7717/peerj.16523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Deng et al. title: Water-use characteristics of Syzygium antisepticum and Adinandra integerrima in a secondary forest of Khao Yai National Park in Thailand with implications for environmental management link: https://peerj.com/articles/16525 last-modified: 2023-11-30 description: BackgroundSoutheast Asia has experienced widespread deforestation and change in land use. Consequently, many reforestation projects have been initiated in this region. However, it is imperative to carefully choose the tree species for planting, especially in light of the increasing climate variability and the potential alteration of plantation on the watershed water balance. Thus, the information regarding water-use characteristics of various tree species and sizes is critical in the tree species selection for reforestation.MethodsWe estimated tree water use (T) of dominant species including Syzygium antisepticum and Adinandra integerrima, hereafter Sa and Ai, respectively, in a secondary tropical forest in Khao Yai National Park, Thailand, using sap flow data, and compared T between species and size classes. Additionally, we evaluated the responses of T of both species in each size class to environmental factors including soil moisture and vapor pressure deficit (VPD).ResultsResults showed consistently higher T in Sa compared to Ai across ranges of VPD and soil moisture. Under low soil moisture, T of Sa responded to VPD, following a saturating exponential pattern while Ai maintained T across different VPD levels, irrespective of tree size. No responses of T to VPD were observed in either species when soil water was moderate. When soil moisture was high, T of both species significantly increased and saturated at high VPD, albeit the responses were less sensitive in large trees. Our results imply that Ai may be suitable for reforestation in water-limited areas where droughts frequently occur to minimize reforestation impact on water availability to downstream ecosystems. In contrast, Sa should be planted in regions with abundant and reliable water resources. However, a mixed species plantation should be generally considered to increase forest resilience to increasing climate variation. creator: Ratchanon Ampornpitak creator: Anuttara Nathalang creator: Pantana Tor-ngern uri: https://doi.org/10.7717/peerj.16525 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ampornpitak et al. title: Niraparib restrains prostate cancer cell proliferation and metastasis and tumor growth in mice by regulating the lncRNA MEG3/miR-181-5p/GATA6 pathway link: https://peerj.com/articles/16314 last-modified: 2023-11-29 description: BackgroundPoly (ADP-ribose) polymerase (PARP) inhibitors (PARPi), have gained approval for treating patients with castration-resistant prostate cancer (CRPC). Maternally expressed gene 3 (MEG3), a long non-coding RNA (lncRNA), plays a role in inhibiting tumorigenesis through regulating DNA repair genes. This study aimed to investigate the association between the anti-prostate cancer (PCa) effect of niraparib, a representative PARPi, and MEG3 expression, as well as explore the downstream pathway involved.MethodsThe levels of MEG3, miR-181-5p, GATA binding protein 6 (GATA6) in clinical samples from PCa patients were accessed by RT-qPCR. PC3 cells were treated with niraparib, and the expression of MEG3, miR-181-5p, GATA6 expression was tested. PC3 cell proliferation, migration, and invasion were tested by CCK-8, wound healing, and Transwell assays, respectively. The bindings between miR-181-5p and MEG3/GATA6 were determined by dual-luciferase reporter gene assay. Furthermore, rescue experiments were conducted to investigate the underlying mechanism of MEG3/miR-181-5p/GATA6 axis in PCa progression. Additionally, mice were injected with PC3 cells transfected with sh-MEG3 and treated with niraparib, and the xenograft tumor growth was observed.ResultsMEG3 and GATA6 were upregulated and miR-181-5p was downregulated in PCa patients. Niraparib treatment substantially upregulated MEG3 and GATA6, and downregulated miR-181-5p expression in PCa cells. Niraparib effectively restrained PC3 cell proliferation, migration, and invasion. MiR-181-5p targeted to MEG3, and the inhibitory effects of MEG3 overexpression on PC3 cell proliferation and metastasis were abrogated by miR-181-5p overexpression. Moreover, GATA6 was identified as a target of miR-181-5p, and GATA6 silencing abolished the inhibitory effects of miR-181-5p inhibition on PC3 cell proliferation and metastasis. Besides, MEG3 silencing could abrogate niraparib-mediated tumor growth inhibition in mice.ConclusionsNiraparib restrains prostate cancer cell proliferation and metastasis and tumor growth in mice by regulating the lncRNA MEG3/miR-181-5p/GATA6 pathway. creator: Ji Cheng creator: Yi Sun creator: Huacai Zhao creator: Wei Ren creator: Dan Gao creator: Zhigang Wang creator: Wei Lv creator: Qingchuan Dong uri: https://doi.org/10.7717/peerj.16314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cheng et al. title: Interactive bioacoustic playback as a tool for detecting and exploring nonhuman intelligence: “conversing” with an Alaskan humpback whale link: https://peerj.com/articles/16349 last-modified: 2023-11-29 description: Here we report on a rare and opportunistic acoustic turn-taking with an adult female humpback whale, known as Twain, in Southeast Alaska. Post hoc acoustic and statistical analyses of a 20-min acoustic exchange between the broadcast of a recorded contact call, known as a ‘whup/throp’, with call responses by Twain revealed an intentional human-whale acoustic (and behavioral) interaction. Our results show that Twain participated both physically and acoustically in three phases of interaction (Phase 1: Engagement, Phase 2: Agitation, Phase 3: Disengagement), independently determined by blind observers reporting on surface behavior and respiratory activity of the interacting whale. A close examination of both changes to the latency between Twain’s calls and the temporal matching to the latency of the exemplar across phases indicated that Twain was actively engaged in the exchange during Phase 1 (Engagement), less so during Phase 2 (Agitation), and disengaged during Phase 3 (Disengagement). These results, while preliminary, point to several key considerations for effective playback design, namely the importance of salient, dynamic and adaptive playbacks, that should be utilized in experimentation with whales and other interactive nonhuman species. creator: Brenda McCowan creator: Josephine Hubbard creator: Lisa Walker creator: Fred Sharpe creator: Jodi Frediani creator: Laurance Doyle uri: https://doi.org/10.7717/peerj.16349 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 McCowan et al. title: An ecological transcriptome approach to capture the molecular and physiological mechanisms of mass flowering in Shorea curtisii link: https://peerj.com/articles/16368 last-modified: 2023-11-29 description: Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation. creator: Ahmad Husaini Suhaimi creator: Masaki J. Kobayashi creator: Akiko Satake creator: Ching Ching Ng creator: Soon Leong Lee creator: Norwati Muhammad creator: Shinya Numata creator: Tatsuya Otani creator: Toshiaki Kondo creator: Naoki Tani creator: Suat Hui Yeoh uri: https://doi.org/10.7717/peerj.16368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Suhaimi et al. title: Assessing lead and cadmium tolerance of Chenopodium ambrosioides during micropropagation: an in-depth qualitative and quantitative analysis link: https://peerj.com/articles/16369 last-modified: 2023-11-29 description: The tolerance of Chenopodium ambrosioides to some heavy metals under in vitro environment was thoroughly investigated. A micropropagation protocol was developed to facilitate the mass production of plants and to identify metals-tolerant species for potential use in the restoration of polluted areas. Nodal explants exhibited callus formation when treated with N6-benzyladenin (BA) (1.5 mg/l) and a combination of BA/α-naphthalene acetic acid (NAA) at concentrations of 1.5/1.0 mg/l on the Murashige and Skoog (MS) medium. The optimal shoot formation was achieved with the callus grown on a medium enriched with 1.5/1.0 mg/l BA/NAA, resulting in an impressive number (21.89) and length (11.79 cm) of shoots. The in vitro shoots were rooted using NAA (1.0 and 1.5 mg/l) and were acclimatized in pots with 71% survival rate. After standardizing micropropagation protocol, the in vitro shoots were subjected to various doses of lead nitrate (Pb(NO3)2 and cadmium chloride (CdCl2). Pb(NO3)2 and CdCl2 in the media let to a reduction in shoot multiplication, decreasing from 18.73 in the control group to 11.31 for Pb(NO3)2 and 13.89 for CdCl2 containing medium. However, Pb(NO3)2 and CdCl2 promoted shoot length from 5.61 in the control to 9.86 on Pb(NO3)2 and 12.51 on CdCl2 containing medium. In the case of Pb(NO3)2 treated shoots, the growth tolerance index (GTI) ranged from117.64% to 194.11%, whereas for CdCl2 treated shoots, the GTI ranged from 188.23% to 264.70%. Shoots treated with high level of Pb(NO3)2induced reddish-purple shoots, while a low level of Pb(NO3)2 induced shoots displayed both green and reddish-purple colors in the same explants. In CdCl2 treated culture, the toxic effects were narrow leaf lamina, elongated petiole and a dark reddish purple coloration. These findings highlight the remarkable potential of C. ambrosioides to maintain growth and organogenesis even in the presence Pb(NO3)2 and CdCl2 on the MS medium, indicating a high degree of metal tolerance. creator: Tour Jan creator: Nasrullah Khan creator: Muhammad Wahab creator: Mohammad K. Okla creator: Mostafa A. Abdel-Maksoud creator: Ibrahim A. Saleh creator: Hashem A. Abu-Harirah creator: Tareq Nayef AlRamadneh creator: Hamada AbdElgawad uri: https://doi.org/10.7717/peerj.16369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jan et al. title: Hypertension doctors’ awareness and practice of medication adherence in hypertensive patients: a questionnaire-based survey link: https://peerj.com/articles/16384 last-modified: 2023-11-29 description: BackgroundPoor adherence to antihypertensive drugs is a major cause of unsatisfactory blood pressure control. Hypertension doctors play an integral role in improving medication adherence in hypertensive patients. Although most existing studies have recognized the status quo and influencing factors of medication adherence, little attention has been paid to hypertension doctors’ awareness and practice in hypertension management. Therefore, in this study, we aimed to investigate hypertension doctors’ awareness and practice of medication adherence in hypertensive patients.MethodsThis is a cross-sectional survey. A self-reported questionnaire was developed and sent to hypertension doctors in Hunan province, China, between May 1, 2022 and July 1, 2022. Univariate and generalized linear models were used to identify the factors influencing hypertension doctors’ awareness and practice. The correlation between awareness and practice was determined using Spearman’s correlation coefficient.ResultsIn total, 236 valid questionnaires were collected (valid response rate, 73.5%). Of the respondents, 44.1% were chief physicians and 64.4% were females. Approximately half of the respondents were ≥40 years old and had over 14 years of working experience. Most respondents (87.7%) did not have hypertension, but 54.2% had a family history of hypertension. The average awareness and practice scores were 29.8 ± 8.8 and 39.4 ± 7.1, respectively, out of 50, with higher scores indicating higher levels of awareness or practice. More hypertension consultations and more antihypertensive prescriptions issued were associated with better awareness and practice among respondents (ps < 0.05). Respondents with higher education and professional titles had higher awareness (ps < 0.05). Moreover, respondents with 6–13 years of work experience had better practice than those with <5 years of work experience (p = 0.017). There was a significant correlation between hypertension doctors’ awareness and practice of medication adherence in hypertensive patients (R = 0.682, p < 0.001). These findings indicate that misconceptions persist in hypertension doctors’ awareness and practice of patient medication adherence.ConclusionHypertension doctors lack sufficient and correct awareness and practice of medication adherence in hypertensive patients. creator: Tao Liu creator: Xiexiong Zhao creator: Miao Huang creator: Yan Yang creator: Zhi Chen creator: Xin He creator: Xiaogang Li creator: Weihong Jiang uri: https://doi.org/10.7717/peerj.16384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA) link: https://peerj.com/articles/16446 last-modified: 2023-11-29 description: BackgroundThe mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.MethodsThe recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.Results and DiscussionmPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22–24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers. creator: Genki Kobayashi uri: https://doi.org/10.7717/peerj.16446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kobayashi title: First specific detection and validation of tomato wilt caused by Fusarium brachygibbosum using a PCR assay link: https://peerj.com/articles/16473 last-modified: 2023-11-29 description: Tomato wilt is a widespread soilborne disease of tomato that has caused significant yield losses in many tomato growing regions of the world. Previously, it was reported that tomato wilt can be caused by many pathogens, such as Fusarium oxysporum, Ralstonia solanacearum, Ralstonia pseudosolanacearum, Fusarium acuminatum, and Plectosphaerella cucumerina. In addition, we have already reported that Fusarium brachygibbosum caused symptomatic disease of tomato wilt for the first time in China. The symptoms of tomato wilt caused by these pathogens are similar, making it difficult to distinguish them in the field. However, F. brachygibbosum specific identification method has not been reported. Therefore, it is of great importance to develop a rapid and reliable diagnostic method for Fusarium brachygibbosum to establish a more effective plan to control the disease. In this study, we designed F. brachygibbosum-specific forward primers and reverse primers with a fragment size of 283bp located in the gene encoding carbamoyl phosphate synthase arginine-specific large chain by whole genome sequence comparison analysis of the genomes of eight Fusarium spp.. We then tested different dNTP, Mg2+ concentrations, and annealing temperatures to determine the optimal parameters for the PCR system. We evaluated the specificity, sensitivity and stability of the PCR system based on the optimized reaction system and conditions. The PCR system can specifically identify the target pathogens from different fungal pathogens, and the lower detection limit of the target pathogens is at concentrations of 10 pg/uL. In addition, we can accurately identify F. brachygibbosum in tomato samples using the optimized PCR method. These results prove that the PCR method developed in this study can accurately identify and diagnose F. brachygibbosum. creator: Siyi Deng creator: Quanke Liu creator: Wei Chang creator: Jun Liu creator: Hua Wang uri: https://doi.org/10.7717/peerj.16473 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Deng et al. title: Excessive aggregation of fine particles may play a crucial role in adolescent spontaneous pneumothorax pathogenesis link: https://peerj.com/articles/16484 last-modified: 2023-11-29 description: BackgroundThe pathogenesis of primary spontaneous pneumothorax (PSP) is unclear. Fine particles aggregated in the lung can be phagocytosed by alveolar macrophages (AMs) to induce an inflammatory reaction and damage local pulmonary tissue, which could be a mechanism of PSP. This project aimed to explore the pathological association between fine particulate matter and PSP.MethodsThirty pulmonary bullae tissues were obtained from surgery of PSP patients (B group). The adjacent normal tissues of the lungs were defined as the control S group. Another 30 normal lung tissues with nonpneumothorax disease (NPD) were applied as the control N group. Hematoxylin and eosin (H & E), Wright-Giemsa (W-G), Victoria blue, and immunohistochemical (IHC) staining experiments were performed to measure the levels of fine particulate matter, alveolar macrophages (AMs), pulmonary elastic fibers, monocyte chemoattractant protein-1 (MCP-1), and matrix metalloproteinase-9 (MMP-9) in the lung tissues. The serum levels of MCP-1 and MMP-9 were prospectively analyzed as well.ResultsHistopathological examinations revealed obvious deposition of fine particulate matter and inflammatory reactions (proliferation of AMs) in the B group, compared with those in the S group and the N group. These alterations were significantly associated with PSP. The numbers of AMs and pulmonary elastic fibers, the positive area of the H-score, as well as the concentrations of MCP-1 and MMP-9 in the lungs of the experimental group were obviously raised compared with the controls (P < 0.05).ConclusionsFine particulate matter aggregation, inflammation (macrophage hyperplasia), and overexpression of MCP-1 and MMP-9 may contribute to the pathogenesis of PSP. The overaccumulation of fine particulate matter may play a crucial part in the occurrence of adolescent and young adult PSP.Trial registrationThis project was enrolled on the Chinese Clinical Trial Registry: ChiCTR2100051460. creator: Sibo Wang creator: Jun Li creator: Mengjiao Qian creator: Jing Wang creator: Yongxing Tan creator: Haibo Ou creator: Zhongyin Wang creator: Xiao Chen creator: Yunjiao Tu creator: Kai Xu uri: https://doi.org/10.7717/peerj.16484 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Rhizocompartmental microbiomes of arrow bamboo (Fargesia nitida) and their relation to soil properties in Subalpine Coniferous Forests link: https://peerj.com/articles/16488 last-modified: 2023-11-29 description: Arrow bamboo (Fargesia nitida) is a pioneer plant in secondary forest succession in the Sichuan Province mountains. To comprehensively investigate the microbial communities and their functional variations in different rhizocompartments (root endosphere, rhizosphere, and root zone) of arrow bamboo (Fargesia nitida), a high-throughput metagenomic study was conducted in the present study. The results showed that the abundances of the dominant bacterial phyla Proteobacteria and Actinobacteria in the bamboo root endosphere were significantly lower than those in the rhizosphere and root zones. In contrast, the dominant fungal phyla, Ascomycota and Basidiomycota, showed the opposite tendency. Lower microbial diversity, different taxonomic composition and functional profiles, and a greater abundance of genes involved in nitrogen fixation (nifB), cellulose degradation (beta-glucosidase), and cellobiose transport (cellulose 1, 4-beta-cellobiosidase) were found in the bamboo root endosphere than in the other rhizocompartments. Greater soil total carbon, total nitrogen, NH4+-N, microbial biomass carbon, and greater activities of invertase and urease were found in the bamboo root zone than in the adjacent soil (spruce root zone). In contrast, the soil microbial community and functional profiles were similar. At the phylum level, invertase was significantly related to 31 microbial taxa, and the effect of NH4+-N on the microbial community composition was greater than that of NO3−-N. The soil physicochemical properties and enzyme activities were significantly correlated with microbial function. These results indicate that the root endosphere microbiomes of arrow bamboo were strongly selected by the host plant, which caused changes in the soil nutrient properties in the subalpine coniferous forest. creator: Nan Nan Zhang creator: Xiao Xia Chen creator: Jin Liang creator: Chunzhang Zhao creator: Jun Xiang creator: Lin Luo creator: En Tao Wang creator: Fusun Shi uri: https://doi.org/10.7717/peerj.16488 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Insights on Pinna nobilis population genetic structure in the Aegean and Ionian Sea link: https://peerj.com/articles/16491 last-modified: 2023-11-29 description: The fan mussel Pinna nobilis Linnaeus, 1758 is an endemic species of the Mediterranean Sea, protected by international agreements. It is one of the largest bivalves in the world, playing an important role in the benthic communities; yet it has been recently characterized as Critically Endangered by the IUCN, due to mass mortality events. In this context, the assessment of the genetic variation of the remaining P. nobilis populations and the evaluation of connectivity among them are crucial elements for the conservation of the species. For this purpose, samples were collected from six regions of the Eastern Mediterranean Sea; the Islands of Karpathos, Lesvos and Crete; the Chalkidiki and Attica Peninsulas; and the Amvrakikos Gulf. Sampling was performed either by collecting tissue from the individuals or by using a non-invasive method, i.e., by scraping the inside of their shells aiming to collect their mucus and thus avoid stress induction to them. Conventional molecular techniques with the use of the COI and 16S rRNA mitochondrial markers were selected for the depiction of the intra-population genetic variability. The analyses included 104 samples from the present study and publicly available sequences of individuals across the whole Mediterranean Sea. The results of this work (a) suggest the use of eDNA as an efficient sampling method for protected bivalves and (b) shed light to the genetic structure of P. nobilis population in the Eastern Mediterranean; this latter knowledge might prove to be fundamental for the species conservation and hence the ecosystem resilience. The haplotype analyses reinforced the evidence that there is a certain degree of connectivity among the distinct regions of the Mediterranean; yet there is evidence of population distinction within the basin, namely between the Western and the Eastern basins. The combination of both genetic markers in the same analysis along with the inclusion of a large number of individuals produced more robust results, revealing a group of haplotypes being present only in the Eastern Mediterranean and providing insights for the species’ most suitable conservation management. creator: Georgia Sarafidou creator: Dimitris Tsaparis creator: Yiannis Issaris creator: Giorgos Chatzigeorgiou creator: Panos Grigoriou creator: Eva Chatzinikolaou creator: Christina Pavloudi uri: https://doi.org/10.7717/peerj.16491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sarafidou et al. title: Using transplantation to restore seagrass meadows in a protected South African lagoon link: https://peerj.com/articles/16500 last-modified: 2023-11-29 description: BackgroundSeagrass meadows provide valuable ecosystem services but are threatened by global change pressures, and there is growing concern that the functions seagrasses perform within an ecosystem will be reduced or lost without intervention. Restoration has become an integral part of coastal management in response to major seagrass declines, but is often context dependent, requiring an assessment of methods to maximise restoration success. Here we investigate the use of different restoration strategies for the endangered Zostera capensis in South Africa.MethodsWe assessed restoration feasibility by establishing seagrass transplant plots based on different transplant source materials (diameter (ø) 10 cm cores and anchored individual shoots), planting patterns (line, dense, bullseye) and planting site (upper, upper-mid and mid-intertidal zones). Monitoring of area cover, shoot length, and macrofaunal diversity was conducted over 18 months.ResultsMixed model analysis showed distinct effects of transplant material used, planting pattern and site on transplant survival and area cover. Significant declines in seagrass cover across all treatments was recorded post-transplantation (2 months), followed by a period of recovery. Of the transplants that persisted after 18 months of monitoring (~58% plots survived across all treatments), seagrass area cover increased (~112%) and in some cases expanded by over >400% cover, depending on type of transplant material, planting arrangement and site. Higher bioturbator pressure from sandprawns (Kraussillichirus kraussi) significantly reduced transplant survival and area cover. Transplant plots were colonised by invertebrates, including seagrass specialists, such as South Africa’s most endangered marine invertebrate, the false-eelgrass limpet (Siphonaria compressa). For future seagrass restoration projects, transplanting cores was deemed the best method, showing higher long-term persistence and cover, however this approach is also resource intensive with potentially negative impacts on donor meadows at larger scales. There is a clear need for further research to address Z. capensis restoration scalability and improve long-term transplant persistence. creator: Katie M. Watson creator: Deena Pillay creator: Sophie von der Heyden uri: https://doi.org/10.7717/peerj.16500 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Watson et al. title: Centre of pressure changes during stance but not during gait in young women after alcohol intoxication link: https://peerj.com/articles/16511 last-modified: 2023-11-29 description: BackgroundWomen are underrepresented in research focused on alcohol (e.g., Brighton, Moxham & Traynor, 2016; DOI 10.1097/JAN.0000000000000136) despite the changing patterns of alcohol consumption, which has been increasing in women in recent decades. The purpose of this study was to analyse the relationship between habitual alcohol consumption and centre of pressure (CoP) parameters during stance and gait while intoxicated by alcohol.MethodsThirty women (24.39 ± 2.93 years) participated in this study. All participants were asked to answer the AUDIT questionnaire. Stance and gait analysis were repeated under two conditions on a Zebris platform (FDM GmbH; Munich, Germany): when the participants were sober (0.00% breath alcohol concentration, BrAC) and when they were in an intoxicated state (0.11% BrAC). Participants were divided by their AUDIT score into a low-risk alcohol consumption group (n = 15; AUDIT score: 3 to 6) and a hazardous alcohol consumption group (n = 15; AUDIT score: 7 to 13).ResultsNo statistical difference was observed in stance and gait parameters when comparing the low-risk and hazardous groups under 0.00% BrAC and 0.11% BrAC conditions. A statistically significant difference was observed when comparing 0.00% BrAC and 0.11% BrAC conditions within each group. This significant difference was found in CoP path length and CoP average velocity during quiet stance. However, no statistically significant differences were observed in CoP parameters during gait. An alcohol intoxication of 0.11% BrAC was not sufficient to cause statistically significant impairments in butterfly parameters of gait. creator: Marta Gimunová creator: Michal Bozděch creator: Jan Novák uri: https://doi.org/10.7717/peerj.16511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gimunová et al. title: Significant improvement in survival outcomes of trisomy 18 with neonatal intensive care compared to non-intensive care: a single-center study link: https://peerj.com/articles/16537 last-modified: 2023-11-29 description: BackgroundTrisomy 18 syndrome, also known as Edwards syndrome, is a chromosomal trisomy. The syndrome has historically been considered lethal owing to its poor prognosis, and palliative care was primarily indicated for trisomy 18 neonates. Although there have been several reports on the improvement of survival outcomes in infants with trisomy 18 syndrome through neonatal intensive care, few studies have compared the impact of neonatal intensive care on survival outcomes with that of non-intensive care. Therefore, we compared the survival-related outcomes of neonates with trisomy 18 between intensive and non-intensive care.MethodsSeventeen infants of trisomy 18 admitted to our center between 2007 and 2019 were retrospectively studied. We divided the patients into a non-intensive group (n = 5) and an intensive group (n = 12) and evaluated their perinatal background and survival-related outcomes of the two groups.ResultsThe 1- and 3-year survival rates were both 33% in the intensive group, which was significantly higher than that in the non-intensive group (p < 0.001). Half of the infants in the intensive care group were discharged alive, whereas in the non-intensive care group, all died during hospitalization (p = 0.049).ConclusionsNeonatal intensive care for neonates with 18 trisomy significantly improved not only survival rates but also survival-discharge rates. Our findings would be helpful in providing 18 trisomy neonates with standard neonatal intensive care when discussing medical care with their parents. creator: Shigeki Koshida creator: Kentaro Takahashi uri: https://doi.org/10.7717/peerj.16537 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Koshida and Takahashi title: A novel long noncoding RNA (lncRNA), LINC02657(LASTR), is a prognostic biomarker associated with immune infiltrates of lung adenocarcinoma based on unsupervised cluster analysis link: https://peerj.com/articles/16167 last-modified: 2023-11-28 description: Non-small cell lung cancer (NSCLC) has long been the deadliest malignancy worldwide, with adenocarcinoma (AD) being the most common pathological subtype. Here we focused on the value of LASTR in LUAD. Using expression analysis, enrichment analysis, immune cell infraction analysis, we found that the expression level of LASTR was significantly increased in LUAD tissue. Meanwhile, LASTR was significantly associated with differential infiltration of various immune cells. Kaplan-Meier survival analysis showed that LUAD related with a poor prognosis in terms of OS, PFI, and DSS compared with high-expression LASTR. The enrichment analysis showed that LASTR is related to the pathays like PI3K-AKT signaling pathway. Thus, the present findings could be helpful in a better understand of LASTR in LUAD. RT-PCR was used to verify the high expression of LASTR in LUAD tissues, and the apoptosis of LUAD cell lines was promoted by CCK8 and Transwell experiments to verify the ability of LASTR to promote the migration and invasion of lung cancer cells in vitro. creator: Fanming Kong creator: Xinyu Yang creator: Zhichao Lu creator: Zongheng Liu creator: Yang Yang creator: Ziheng Wang uri: https://doi.org/10.7717/peerj.16167 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kong et al. title: An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae link: https://peerj.com/articles/16340 last-modified: 2023-11-28 description: Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae—a microbial cell widely used industrially for ethanol production—is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose. creator: Beatriz de Oliveira Vargas creator: Jade Ribeiro dos Santos creator: Gonçalo Amarante Guimarães Pereira creator: Fellipe da Silveira Bezerra de Mello uri: https://doi.org/10.7717/peerj.16340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Vargas et al. title: Diversity and ice nucleation activity of Pseudomonas syringae in drone-based water samples from eight lakes in Austria link: https://peerj.com/articles/16390 last-modified: 2023-11-28 description: Bacteria from the Pseudomonas syringae complex (comprised of at least 15 recognized species and more than 60 different pathovars of P. syringae sensu stricto) have been cultured from clouds, rain, snow, streams, rivers, and lakes. Some strains of P. syringae express an ice nucleation protein (hereafter referred to as ice+) that catalyzes the heterogeneous freezing of water. Though P. syringae has been sampled intensively from freshwater sources in the U.S. and France, little is known about the genetic diversity and ice nucleation activity of P. syringae in other parts of the world. We investigated the haplotype diversity and ice nucleation activity at −8 °C (ice+) of strains of P. syringae from water samples collected with drones in eight freshwater lakes in Austria. A phylogenetic analysis of citrate synthase (cts) sequences from 271 strains of bacteria isolated from a semi-selective medium for Pseudomonas revealed that 69% (188/271) belonged to the P. syringae complex and represented 32 haplotypes in phylogroups 1, 2, 7, 9, 10, 13, 14 and 15. Strains within the P. syringae complex were identified in all eight lakes, and seven lakes contained ice+ strains. Partial 16S rDNA sequences were analyzed from a total of 492 pure cultures of bacteria isolated from non-selective medium. Nearly half (43.5%; 214/492) were associated with the genus Pseudomonas. Five of the lakes (ALT, GRU, GOS, GOL, and WOR) were all distinguished by high levels of Pseudomanas (p ≤ 0.001). HIN, the highest elevation lake, had the highest percentage of ice+ strains. Our work highlights the potential for uncovering new haplotypes of P. syringae in aquatic habitats, and the use of robotic technologies to sample and characterize microbial life in remote settings. creator: Regina Hanlon creator: Celia Jimenez-Sanchez creator: James Benson creator: Ken Aho creator: Cindy Morris creator: Teresa M. Seifried creator: Philipp Baloh creator: Hinrich Grothe creator: David Schmale uri: https://doi.org/10.7717/peerj.16390 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hanlon et al. title: A multicentre study to determine the in vitro efficacy of flomoxef against extended-spectrum beta-lactamase producing Escherichia coli in Malaysia link: https://peerj.com/articles/16393 last-modified: 2023-11-28 description: BackgroundThe high burden of extended-spectrum beta-lactamase-producing (ESBL)-producing Enterobacterales worldwide, especially in the densely populated South East Asia poses a significant threat to the global transmission of antibiotic resistance. Molecular surveillance of ESBL-producing pathogens in this region is vital for understanding the local epidemiology, informing treatment choices, and addressing the regional and global implications of antibiotic resistance.MethodsTherefore, an inventory surveillance of the ESBL-Escherichia coli (ESBL-EC) isolates responsible for infections in Malaysian hospitals was conducted. Additionally, the in vitro efficacy of flomoxef and other established antibiotics against ESBL-EC was evaluated.ResultsA total of 127 non-repetitive ESBL-EC strains isolated from clinical samples were collected during a multicentre study performed in five representative Malaysian hospitals. Of all the isolates, 33.9% were isolated from surgical site infections and 85.8% were hospital-acquired infections. High rates of resistance to cefotaxime (100%), cefepime (100%), aztreonam (100%) and trimethoprim-sulfamethoxazole (100%) were observed based on the broth microdilution test. Carbapenems remained the most effective antibiotics against the ESBL-EC, followed by flomoxef. Antibiotic resistance genes were identified by PCR. The blaCTX-M-1 was the most prevalent ESBL gene, with 28 isolates (22%) harbouring blaCTX-M-1 only, 27 isolates (21.3%) co-harbouring blaCTX-M-1 and blaTEM, and ten isolates (7.9%) co-harbouring blaCTX-M-1,blaTEM and blaSHV. A generalised linear model showed significant antibacterial activity of imipenem against different types of infection. Besides carbapenems, this study also demonstrated a satisfactory antibacterial activity of flomoxef (81.9%) on ESBL-EC, regardless of the types of ESBL genes. creator: Polly Soo Xi Yap creator: Chun Wie Chong creator: Sasheela Ponnampalavanar creator: Ramliza Ramli creator: Azian Harun creator: Tengku Zetty Maztura Tengku Jamaluddin creator: Anis Ahmed Khan creator: Soo Tein Ngoi creator: Yee Qing Lee creator: Min Yi Lau creator: Shiang Chiet Tan creator: Zhi Xian Kong creator: Jia Jie Woon creator: Siew Thong Mak creator: Kartini Abdul Jabar creator: Rina Karunakaran creator: Zalina Ismail creator: Sharifah Azura Salleh creator: Siti Suraiya Md Noor creator: Siti Norbaya Masri creator: Niazlin Mohd Taib creator: Azmiza Syawani Jasni creator: Loong Hua Tee creator: Kin Chong Leong creator: Victor Kok Eow Lim creator: Sazaly Abu Bakar creator: Cindy Shuan Ju Teh uri: https://doi.org/10.7717/peerj.16393 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yap et al. title: Intraspecific body size variation and allometry of genitalia in the orb-web spider—Argiope lobata link: https://peerj.com/articles/16413 last-modified: 2023-11-28 description: The current consensus is that sexual selection is responsible for the rapid and diverse evolution of genitalia, with several mutually exclusive mechanisms under debate, including non-antagonistic, antagonistic and stabilizing mechanisms. We used the orb-web spider, Argiope lobata (Araneidae), as a study model to quantify the allometric relationship between body size and genitalia, and to test for any impact of genital structures on male mating success or outcome in terms of copulation duration, leg loss or cannibalism. Our data do not support the ‘one-size-fits-all’ hypothesis that predicts a negative allometric slope between genitalia and body size. Importantly, we measured both male and female genitalia, and there was no sex specific pattern in allometric slopes. Unexpectedly, we found no predictor for reproductive success as indicated by copulation duration, cannibalism, and leg loss. creator: Chathuranga Dharmarathne creator: Donald James McLean creator: Marie E. Herberstein creator: Jutta M. Schneider uri: https://doi.org/10.7717/peerj.16413 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dharmarathne et al. title: Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions link: https://peerj.com/articles/16414 last-modified: 2023-11-28 description: RNA structure has been increasingly recognized as a critical player in the biogenesis and turnover of many transcripts classes. In eukaryotes, the prediction of RNA structure by thermodynamic modeling meets fundamental limitations due to the large sizes and complex, discontinuous organization of eukaryotic genes. Signatures of functional RNA structures can be found by detecting compensatory substitutions in homologous sequences, but a comparative approach is applicable only within conserved sequence blocks. Here, we developed a computational pipeline called PHRIC, which is not limited to conserved regions and relies on RNA contacts derived from RNA in situ conformation sequencing (RIC-seq) experiments. It extracts pairs of short RNA fragments surrounded by nested clusters of RNA contacts and predicts long, nearly perfect complementary base pairings formed between these fragments. In application to a panel of RIC-seq experiments in seven human cell lines, PHRIC predicted ~12,000 stable long-range RNA structures with equilibrium free energy below −15 kcal/mol, the vast majority of which fall outside of regions annotated as conserved among vertebrates. These structures, nevertheless, show some level of sequence conservation and remarkable compensatory substitution patterns in other clades. Furthermore, we found that introns have a higher propensity to form stable long-range RNA structures between each other, and moreover that RNA structures tend to concentrate within the same intron rather than connect adjacent introns. These results for the first time extend the application of proximity ligation assays to RNA structure prediction beyond conserved regions. creator: Sergey Margasyuk creator: Lev Zavileyskiy creator: Changchang Cao creator: Dmitri Pervouchine uri: https://doi.org/10.7717/peerj.16414 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2023 Margasyuk et al. title: Lymphoid-specific helicase inhibits cervical cancer cells ferroptosis by promoting Nrf2 expression link: https://peerj.com/articles/16451 last-modified: 2023-11-28 description: BackgroundCervical cancer is a major cause of morbidity and mortality in women worldwide. The underlying mechanisms of its progression are not well understood. In this study, we investigated the role of lymphoid-specific helicase (HELLS) in cervical cancer.MethodsWe measured HELLS expression in cervical cancer and assessed its function using gain- and loss-of-function experiments. Cell viability was measured using the Cell Counting Kit-8 (CCK8 ) assay, and cell proliferation was analyzed using colony formation and EdU assays.ResultsWe found that HELLS was significantly increased in cervical cancer and that its overexpression promoted cell viability (P < 0.01) and colony formation (P < 0.001). In contrast, si-HELLS suppressed these effects. Moreover, HELLS overexpression inhibited cell death induced by the ferroptosis inducer erastin (P < 0.01). Mechanistically, we found that HELLS promoted cervical cancer proliferation by regulating nuclear factor erythroid 2-related factor 2 (Nrf2)-mediated ferroptosis.ConclusionOur data suggest that HELLS promotes cervical cancer proliferation by inhibiting Nrf2 expression. Therefore, HELLS knockdown may be an effective treatment for cervical cancer. creator: Weiwei Tie creator: Fenfen Ge uri: https://doi.org/10.7717/peerj.16451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Tie and Ge title: Co-inoculation of mycorrhizal fungi and plant growth-promoting rhizobacteria improve growth, biochemical and physiological attributes in Dracocephalum kotschyi Boiss. under water deficit stress link: https://peerj.com/articles/16474 last-modified: 2023-11-28 description: BackgroundBecause of swift climate change, drought is a primary environmental factor that substantially diminishes plant productivity. Furthermore, the increased use of chemical fertilizers has given rise to numerous environmental problems and health risks. Presently, there is a transition towards biofertilizers to enhance crops’ yield, encompassing medicinal and aromatic varieties.MethodsThis study aimed to explore the impacts of plant growth-promoting rhizobacteria (PGPR), both independently and in conjunction with arbuscular mycorrhizal fungi (AMF), on various morphological, physiological, and phytochemical characteristics of Dracocephalum kotschyi Boiss. This experimentation took place under different irrigation conditions. The irrigation schemes encompassed well watering (WW), mild water stress (MWS), and severe water stress (SWS). The study evaluated the effects of various biofertilizers, including AMF, PGPR, and the combined application of both AMF and PGPR (AMF + PGPR), compared to a control group where no biofertilizers were applied.ResultsThe findings of the study revealed that under water-stress conditions, the dry yield and relative water content of D. kotschyi Boiss. experienced a decline. However, the application of AMF, PGPR, and AMF + PGPR led to an enhancement in dry yield and relative water content compared to the control group. Among the treatments, the co-application of AMF and PGPR in plants subjected to well watering (WW) exhibited the tallest growth (65 cm), the highest leaf count (187), and the most elevated chlorophyll a (0.59 mg g−1 fw) and b (0.24 mg g−1 fw) content. Regarding essential oil production, the maximum content (1.29%) and yield (0.13 g plant −1) were obtained from mild water stress (MWS) treatment. The co-application of AMF and PGPR resulted in the highest essential oil content and yield (1.31% and 0.15 g plant−1, respectively). The analysis of D. kotschyi Boiss. essential oil identified twenty-six compounds, with major constituents including geranyl acetate (11.4–18.88%), alpha-pinene (9.33–15.08%), Bis (2-Ethylhexyl) phthalate (8.43-12.8%), neral (6.80–9.32%), geranial (9.23–11.91%), and limonene (5.56–9.12%). Notably, the highest content of geranyl acetate, geranial, limonene, and alpha-pinene was observed in plants subjected to MWS treatment following AMF + PGPR application. Furthermore, the co-application of AMF, PGPR, and severe water stress (SWS) notably increased the total soluble sugar (TSS) and proline content. In conclusion, the results indicate that the combined application of AMF and PGPR can effectively enhance the quantity and quality of essential oil in D. kotschyi Boiss., particularly when the plants are exposed to water deficit stress conditions. creator: Saeid Gasemi creator: Hassan Mahdavikia creator: Esmaeil Rezaei-Chiyaneh creator: Farzad Banaei-Asl creator: Aria Dolatabadian creator: Amir Sadeghpour uri: https://doi.org/10.7717/peerj.16474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gasemi et al. title: Modeling ocean distributions and abundances of natural- and hatchery-origin Chinook salmon stocks with integrated genetic and tagging data link: https://peerj.com/articles/16487 last-modified: 2023-11-28 description: BackgroundConsiderable resources are spent to track fish movement in marine environments, often with the intent of estimating behavior, distribution, and abundance. Resulting data from these monitoring efforts, including tagging studies and genetic sampling, often can be siloed. For Pacific salmon in the Northeast Pacific Ocean, predominant data sources for fish monitoring are coded wire tags (CWTs) and genetic stock identification (GSI). Despite their complementary strengths and weaknesses in coverage and information content, the two data streams rarely have been integrated to inform Pacific salmon biology and management. Joint, or integrated, models can combine and contextualize multiple data sources in a single statistical framework to produce more robust estimates of fish populations.MethodsWe introduce and fit a comprehensive joint model that integrates data from CWT recoveries and GSI sampling to inform the marine life history of Chinook salmon stocks at spatial and temporal scales relevant to ongoing fisheries management efforts. In a departure from similar models based primarily on CWT recoveries, modeled stocks in the new framework encompass both hatchery- and natural-origin fish. We specifically model the spatial distribution and marine abundance of four distinct stocks with spawning locations in California and southern Oregon, one of which is listed under the U.S. Endangered Species Act.ResultsUsing the joint model, we generated the most comprehensive estimates of marine distribution to date for all modeled Chinook salmon stocks, including historically data poor and low abundance stocks. Estimated marine distributions from the joint model were broadly similar to estimates from a simpler, CWT-only model but did suggest some differences in distribution in select seasons. Model output also included novel stock-, year-, and season-specific estimates of marine abundance. We observed and partially addressed several challenges in model convergence with the use of supplemental data sources and model constraints; similar difficulties are not unexpected with integrated modeling. We identify several options for improved data collection that could address issues in convergence and increase confidence in model estimates of abundance. We expect these model advances and results provide management-relevant biological insights, with the potential to inform future mixed-stock fisheries management efforts, as well as a foundation for more expansive and comprehensive analyses to follow. creator: Alexander J. Jensen creator: Ryan P. Kelly creator: William H. Satterthwaite creator: Eric J. Ward creator: Paul Moran creator: Andrew Olaf Shelton uri: https://doi.org/10.7717/peerj.16487 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Amphibian diversity across three adjacent ecosystems in Área de Conservación Guanacaste, Costa Rica link: https://peerj.com/articles/16185 last-modified: 2023-11-27 description: Amphibians are the most threatened species-rich vertebrate group, with species extinctions and population declines occurring globally, even in protected and seemingly pristine habitats. These ‘enigmatic declines’ are generated by climate change and infectious diseases. However, the consequences of these declines are undocumented as no baseline ecological data exists for most affected areas. Like other neotropical countries, Costa Rica, including Área de Conservación Guanacaste (ACG) in north-western Costa Rica, experienced rapid amphibian population declines and apparent extinctions during the past three decades. To delineate amphibian diversity patterns within ACG, a large-scale comparison of multiple sites and habitats was conducted. Distance and time constrained visual encounter surveys characterised species richness at five sites—Murciélago (dry forest), Santa Rosa (dry forest), Maritza (mid-elevation dry-rain forest intersect), San Gerardo (rainforest) and Cacao (cloud forest). Furthermore, species-richness patterns for Cacao were compared with historic data from 1987–8, before amphibians declined in the area. Rainforests had the highest species richness, with triple the species of their dry forest counterparts. A decline of 45% (20 to 11 species) in amphibian species richness was encountered when comparing historic and contemporary data for Cacao. Conservation efforts sometimes focus on increasing the resilience of protected areas, by increasing their range of ecosystems. In this sense ACG is unique containing many tropical ecosystems compressed in a small geographic space, all protected and recognised as a UNESCO world heritage site. It thus provides an extraordinary platform to understand changes, past and present, and the resilience of tropical ecosystems and assemblages, or lack thereof, to climate change. creator: Alex W. Edwards creator: Xavier A. Harrison creator: M. Alex Smith creator: Maria Marta Chavarría Díaz creator: Mahmood Sasa creator: Daniel H. Janzen creator: Winnie Hallwachs creator: Gerardo Chaves creator: Roberto Fernández creator: Caroline Palmer creator: Chloe Wilson creator: Alexandra North creator: Robert Puschendorf uri: https://doi.org/10.7717/peerj.16185 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Edwards et al. title: Predictive value of machine learning for the risk of acute kidney injury (AKI) in hospital intensive care units (ICU) patients: a systematic review and meta-analysis link: https://peerj.com/articles/16405 last-modified: 2023-11-27 description: BackgroundRecent studies suggest machine learning represents a promising predictive option for patients in intensive care units (ICU). However, the machine learning performance regarding its actual predictive value for early detection in acute kidney injury (AKI) patients remains uncertain.ObjectiveThis study represents the inaugural meta-analysis aiming to investigate the predictive value of machine learning for assessing the risk of AKI among ICU patients.MethodsPubMed, Web of Science, Embase, and the Cochrane Library were all thoroughly searched from inception to June 25, 2022. Eligible studies for inclusion were those concentrating on the predictive value and the development, validation, or enhancement of a prediction model for AKI patients in the ICU. Measures of effects, including c-index, sensitivity, specificity, and their corresponding 95% confidence intervals (CIs), were employed for analysis. The risk of bias in the included original studies was assessed using Probst. The meta-analysis in our study was carried out using R version 4.2.0.ResultsThe systematic search yielded 29 articles describing 13 machine-learning models, including 86 models in the training set and 57 in the validation set. The overall c-index was 0.767 (95% CI [0.746, 0.788]) in the training set and 0.773 (95% CI [0.741, 0.804]) in the validation set. The sensitivity and specificity of included studies are as follows: sensitivity [train: 0.66 (95% CI [0.59, 0.73]), validation: 0.73 (95% CI [0.68, 0.77])]; and specificity [train: 0.83 (95% CI [0.78, 0.87])], validation: 0.75 (95% CI [0.71, 0.79])].ConclusionThe machine learning-based method for predicting the risk of AKI in hospital ICU patients has excellent predictive value and could potentially serve as a prospective application strategy for early identification. PROSPERO Registration number ID: CRD42022362838. creator: Yuan Hong Du creator: Cheng Jing Guan creator: Lin Yu Li creator: Ping Gan uri: https://doi.org/10.7717/peerj.16405 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Du et al. title: The potential impact of advanced footwear technology on the recent evolution of elite sprint performances link: https://peerj.com/articles/16433 last-modified: 2023-11-27 description: BackgroundElite track and field sprint performances have reached a point of stability as we near the limits of human physiology, and further significant improvements may require technological intervention. Following the widely reported performance benefits of new advanced footwear technology (AFT) in road-running events, similar innovations have since been applied to sprint spikes in hope of providing similar performance enhancing benefits. However, it is not yet clear based on current evidence whether there have been subsequent improvements in sprint performance. Therefore, the aims of this study were to establish if there have been recent year-to-year improvements in the times of the annual top 100 and top 20 athletes in the men’s and women’s sprint events, and to establish if there is an association between the extensive use of AFT and potential recent improvements in sprint performances.MethodsFor the years 2016–19 and 2021–2022, the season best performances of the top 100 athletes in each sprint event were extracted from the World Athletics Top lists. Independent t-tests with Holm corrections were performed using the season’s best performance of the top 100 and top 20 athletes in each year to identify significant differences between years for each sprint discipline. Following the classification of shoes worn by the top 20 athletes in each event during their annual best race (AFT or non-AFT), separate linear mixed-model regressions were performed to determine the influence of AFT on performance times.ResultsFor the top 100 and top 20 athletes, there were no significant differences year-to-year in any sprint event prior to the release of AFT (2016–2019). There were significant differences between AFT years (2021 or 2022) and pre-AFT years (2016–2019) in eight out of 10 events. These differences ranged from a 0.40% improvement (men’s 100 m) to a 1.52% improvement (women’s 400 m hurdles). In the second analysis, multiple linear mixed model regressions revealed that the use of AFT was associated with improved performance in six out of ten events, including the men’s and women’s 100 m, women’s 200 m, men’s 110 m hurdles, women’s 100 m hurdles and women’s 400 m hurdles (estimate range: −0.037 – 0.521, p = <0.001 – 0.021). Across both analyses, improvements were more pronounced in women’s sprint events than men’s sprint events.ConclusionFollowing a period of stability, there were significant improvements in most sprint events which may be partly explained by advances in footwear technology. These improvements appear to be mediated by event, sex and potentially level of athlete. creator: Joel Mason creator: Dominik Niedziela creator: Jean-Benoit Morin creator: Andreas Groll creator: Astrid Zech uri: https://doi.org/10.7717/peerj.16433 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mason et al. title: kakapo: easy extraction and annotation of genes from raw RNA-seq reads link: https://peerj.com/articles/16456 last-modified: 2023-11-27 description: kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed for targeted assembly, to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of GenBank’s single-gene databases and help assemble datasets for a variety of phylogenetic analyses. creator: Karolis Ramanauskas creator: Boris Igić uri: https://doi.org/10.7717/peerj.16456 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ramanauskas and Igić title: Functional response of Neoseiulus californicus (Acari: Phytoseiidae) to Tetranychus urticae (Acari: Tetranychidae) at different temperatures link: https://peerj.com/articles/16461 last-modified: 2023-11-27 description: Environmental factors like temperature have a great impact on the predation potential of biological control agents. In the present study, the functional response of the predatory mite Neoseiulus californicus (Acari: Phytoseiidae) to the pest mite Tetranychus urticae (Acari: Tetranychidae) at moderate to high temperatures under laboratory conditions was determined. The study aimed to understand the prey-predator interaction under different temperatures and prey densities. Five constant temperatures (24 °C, 27 °C, 30 °C, 33 °C, and 36 °C), and thirteen prey densities (4, 5, 8, 10, 12, 15, 16, 20, 24, 25, 30, 32, and 40) of each stage (adult, nymph, larvae, and egg stage) were employed in the experiment. Observations were made 24 h after the start of each experiment. Results revealed that the predatory mites showed type II functional response to adult females of T. urticae, whereas type I to other stages (nymphs, larvae, and eggs) of T. urticae. The predation capability of adult predatory mites on T. urticae was significant at 24–36 °C. The instantaneous attack rate (a) of N. californicus increased and the handling time (Th) decreased with an increase in temperature. The maximum attack rate was recorded at 36 °C (1.28) for the egg stage. The longest handling time was (0.78) for the larval stage of T. urticae at 30 °C. Daily consumption increased with increasing prey density. Maximum daily consumption was observed at 33 °C (30.00) at the prey density of 40. Searching efficiency decreased with the increase in prey density but was found to increase with the rise in temperature. N. californicus was found to be voracious on the larval and egg stages. Conclusively, the incorporation of N. californicus at earlier stages (larvae and eggs) of T. urticae would be beneficial under warm conditions because managing a pest at its initial stage will save the crop from major losses. The results presented in this study at various temperatures will be helpful in different areas with different temperature extremes. The results of the functional response can also be applied to mass rearing, quality testing, and integrated pest management programmes. creator: Maryam Mumtaz creator: Vattakandy Jasin Rahman creator: Tahseen Saba creator: Tingting Huang creator: Yuxin Zhang creator: Chunxian Jiang creator: Qing Li uri: https://doi.org/10.7717/peerj.16461 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mumtaz et al. title: Ropivacaine inhibits the malignant behavior of lung cancer cells by regulating retinoblastoma-binding protein 4 link: https://peerj.com/articles/16471 last-modified: 2023-11-27 description: BackgroundRopivacaine is a local anesthetic commonly used in regional nerve blocks to manage perioperative pain during lung cancer surgery. Recently, the antitumor potential of ropivacaine has received considerable attention. Our previous study showed that ropivacaine treatment inhibits the malignant behavior of lung cancer cells in vitro. However, the potential targets of ropivacaine in lung cancer cells have not yet been fully identified. This study aimed to explore the antitumor effects and mechanisms of action of ropivacaine in lung cancer.MethodsLung cancer A549 cells were treated with or without 1 mM ropivacaine for 48 h. Quantitative proteomics was performed to identify the differentially expressed proteins (DEPs) triggered by ropivacaine treatment. STRING and Cytoscape were used to construct protein-protein interaction (PPI) networks and analyze the most significant hub genes. Overexpression plasmids and small interfering RNA were used to modulate the expression of key DEPs in A549 and H1299 cells. MTS, transwell assays, and flow cytometry were performed to determine whether the key DEPs were closely related to the anticancer effect of ropivacaine on the malignant behavior of A549 and H1299 cells.ResultsQuantitative proteomic analysis identified 327 DEPs (185 upregulated and 142 downregulated proteins) following ropivacaine treatment. Retinoblastoma-binding protein 4 (RBBP4) was one of the downregulated DEPs and was selected as the hub protein. TCGA database showed that RBBP4 was significantly upregulated in lung cancer and was associated with poor patient prognosis. Inhibition of RBBP4 by siRNA resulted in a significant decrease in the proliferation and invasive capacity of lung cancer cells and the induction of cell cycle arrest. Additionally, the results indicated RBBP4 knockdown enhanced antitumor effect of ropivacaine on A549 and H1299 cells. Conversely, the overexpression of RBBP4 using plasmids reversed the inhibitory effects of ropivacaine.ConclusionOur data suggest that ropivacaine suppresses lung cancer cell malignancy by downregulating RBBP4 protein expression, which may help clarify the mechanisms underlying the antitumor effects of ropivacaine. creator: Weiai Jia creator: Junmei Shen creator: Sisi Wei creator: Chao Li creator: Jingpu Shi creator: Lianmei Zhao creator: Huiqun Jia uri: https://doi.org/10.7717/peerj.16471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jia et al. title: Mitochondrial and nuclear gene sequencing confirms the presence of the invasive sea anemone Diadumene lineata (Verrill, 1869) (Cnidaria: Actiniaria) in Argentina link: https://peerj.com/articles/16479 last-modified: 2023-11-27 description: BackgroundDiadumene lineata is one of the most widespread sea anemone species worldwide. Although this species has been reported a few times on the Argentine coast since 2004, its identification has traditionally been based on external morphological characteristics, and in most cases no voucher specimens are available to support previous records.MethodsIn this study, we obtained DNA sequences of two mitochondrial markers (12S and 16S) and two nuclear markers (18S and 28S) from specimens of D. lineata collected in two locations on the Argentine coast separated by almost 800 km. Additionally, we conducted an analysis of the morphology, as well as the types and size ranges of cnidae, using specimens collected at three different locations along the Argentine coast. Furthermore, since introduced populations of D. lineata are presumably ephemeral and only reproduce asexually outside their native range, we examined the internal anatomy of representatives from the Argentine coast for gametogenic tissue as an indication of whether they might be capable of sexual reproduction.ResultsDNA data support our morphological identification, including cnidae analyses, of the specimens as D. lineata. Furthermore, all specimens examined were determined to be sterile.DiscussionGenetic sequence comparisons, phylogenetic reconstruction, and cnidae data support the identification of individuals of D. lineata from Mar Chiquita and Garipe Beach, confirming the presence of the species on the Argentine coast using both morphological and molecular tools. The absence of fertile specimens suggests that each sampled population is likely reproducing only by asexual reproduction and possibly composed of clones. The presence of an additional category of longer p-mastigophores B2a in the actinopharynx and filaments, as well as holotrichs in the column, is also reported.ConclusionsFor the first time, we have confirmed the presence of D. lineata in Argentina through molecular data. Additionally, our findings indicate that the analyzed specimens are sterile, suggesting that this species is not engaging in sexual reproduction in the studied localities. It is crucial to continue monitoring the populations of D. lineata along the Argentine coast to assess whether they establish sexual reproduction, expand their distribution range or disappear, or potentially cause any harm to local species or alterations in benthic communities. creator: Ricardo González Muñoz creator: Daniel Lauretta creator: María Cielo Bazterrica creator: Francisco Alejandro Puente Tapia creator: Agustín Garese creator: Gregorio Bigatti creator: Pablo E. Penchaszadeh creator: Betina Lomovasky creator: Fabián H. Acuña uri: https://doi.org/10.7717/peerj.16479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 González Muñoz et al. title: Sirtuin 1 alleviates alcoholic liver disease by inhibiting HMGB1 acetylation and translocation link: https://peerj.com/articles/16480 last-modified: 2023-11-27 description: BackgroundAlcoholic liver disease (ALD) encompasses a spectrum of liver disorders resulting from prolonged alcohol consumption and is influenced by factors such as oxidative stress, inflammation, and apoptosis. High Mobility Group Box 1 (HMGB1) plays a pivotal role in ALD due to its involvement in inflammation and immune responses. Another key factor, Sirtuin 1 (SIRT1), an NAD+-dependent deacetylase, is known for its roles in cellular stress responses and metabolic regulation. Despite individual studies on HMGB1 and SIRT1 in ALD, their specific molecular interactions and combined effects on disease advancement remain incompletely understood.MethodsAlcohol-induced liver injury (ALI) models were established using HepG2 cells and male C57BL/6 mice. HMGB1 and SIRT1 expressions were assessed at the mRNA and protein levels usingreverse transcription-quantitative polymerase chain reaction, western blot, and immunofluorescence staining. The physical interaction between HMGB1 and SIRT1 was investigated using co-immunoprecipitation and immunofluorescence co-expression analyses. Cellular viability was evaluated using the CCK-8 assay.ResultsIn patients with clinical ALI, HMGB1 mRNA levels were elevated, while SIRT1 expression was reduced, indicating a negative correlation between the two. ALI models were successfully established in cells and mice, as evidenced by increased markers of cellular and liver damage. HMGB1 acetylation and translocation were observed in both ALI cells and mouse models. Treatment with the SIRT1 agonist, SRT1720, reversed the upregulation of HMGB1 acetylation, nuclear translocation, and release in the ethyl alcohol (EtOH) group. Furthermore, SIRT1 significantly attenuated ALI. Importantly, in vivo binding was confirmed between SIRT1 and HMGB1.ConclusionsSIRT1 alleviates HMGB1 acetylation and translocation, thereby ameliorating ALI. creator: Juan Fu creator: Wei Deng creator: Jun Ge creator: Shengqi Fu creator: Panpan Li creator: Huazhi Wu creator: Jiao Wang creator: Yi Gao creator: Hui Gao creator: Tao Wu uri: https://doi.org/10.7717/peerj.16480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Fu et al. title: Context of substance initiation among urban Native Americans: an exploratory retrospective case-control study link: https://peerj.com/articles/16482 last-modified: 2023-11-27 description: BackgroundAddiction is a significant problem among many Native American groups but has rarely been examined in urban populations. In particular, little is known about the context in which urban Native Americans first use substances. This study compares cases (people with a history of addiction) to controls (people without a history of addiction) on demographics, substance use history, context of first substance use, and polysubstance use. In addition, this appears to be the first study to overcome the lack of Native American professionals by employing and training lay community members to identify criteria of substance use disorders in survey participants. Employing community members helped foster trust that enabled the revelation of sensitive and often illegal activity. As a result, the investigators were able to recruit participants who likely would not have engaged with traditional researchers.MethodsThe trained Native American lay research assistants recruited community members and administered surveys. They first asked questions regarding the criteria for substance use disorders. Individuals who were determined to have met criteria for a substance use disorder in the past were classified as cases (n = 38) and those who never met such criteria were classified as controls (n = 42). They then asked demographic, substance use, and polysubstance use questions. Lastly, eight cases and eight controls were randomly selected for a second interview by a licensed drug and alcohol counselor (LDAC) who conducted a blinded assessment regarding the presence or absence of a history of a substance use disorder.ResultsBoth groups reported a relatively young age of first substance use (age 16 years for cases and age 15 years for controls). Alcohol was the first substance most commonly used in both groups. Controls reported first benzodiazepine use at a younger age than cases but no other significant differences were found. Both groups reported first obtaining their first drug from family, friends, or at home (rather than a party, bar, or store). Most commonly, the location of their first use of drugs occurred at a friend’s home, a party, a bar, or school rather than at their own home. Cases were marginally more likely to report that their first drug use occurred with a friend rather than with a family member when compared with controls. The majority of both groups reported that their first drug use occurred with other Native Americans rather than with non-Native Americans. Polysubstance use was common in both groups (43–45%). There were no significant differences between the groups regarding polysubstance use. The LDAC arrived at the same determination as the trained research assistants on all eight cases and eight controls. creator: Nicholas Guenzel creator: Hongying Daisy Dai creator: Lyndsay Dean uri: https://doi.org/10.7717/peerj.16482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guenzel et al. title: Clinicopathologic features and prognosis of 71 patients with gastric cancer and disseminated intravascular coagulation link: https://peerj.com/articles/16527 last-modified: 2023-11-27 description: BackgroundGastric cancer consists of solid tumors with a tendency for disseminated intravascular coagulation (DIC). DIC is rare in patients with stomach cancer, and there have been few studies on this condition. We aimed to perform comprehensive analyses of the prognosis and clinicopathologic characteristics of stomach cancer patients with DIC.MethodsBetween June 2006 and March 2020, 14,016 patients at Fujian Cancer Hospital were diagnosed with stomach cancer. We reviewed their medical records and found that 105 of these patients were diagnosed with DIC. After excluding patients who were lost to follow-up, 71 patients with DIC remained. The clinical data were retrospectively analyzed to observe clinical characteristics and prognostic factors, and the Kaplan–Meier survival analysis was performed. Prognostic variables were investigated by the Cox proportional hazards method.ResultsThe median age was 54 (range, 21–83) years, and 38 patients (53.5%) were male. The histological category was poorly differentiated gastric cancer in 58 patients (81.7%). Eleven patients (15.5%) developed DIC after curative gastric resection. Sixty patients (84.5%) had DIC at the initial presentation of gastric cancer or developed DIC when the tumor progressed during treatment. Fifty-one patients (71.8%) had bleeding symptoms, and 43 (60.6%) patients had comorbidities at the time of DIC diagnosis. Among the 71 patients, 42 (59.2%) had multiple metastatic patterns. Twenty-one (29.6%) patients received chemotherapy. The median overall survival (OS) was 57.0 days (95% confidence interval [CI] [33.1–80.9] days). Tumor status (P = 0.000) and treatment (P = 0.003) were found to be significant variables associated with OS by univariate analysis. Multivariate analysis showed that tumor status (P = 0.000) and treatment (P = 0.000) had independent effects on OS.ConclusionsGastrointestinal bleeding, multiple metastatic patterns and comorbidities at diagnosis with DIC are common in patients with gastric cancer complicated with DIC. Patients with poorly differentiated gastric cancer are more likely to develop DIC. Treatment and tumor status are separate risk variables for the survival of gastric cancer patients with DIC.DIC patients without tumors have a good prognosis and can be cured by appropriate etiological correction and symptomatic treatment. Chemotherapy can improve the prognosis of DIC patients with tumors. creator: Ling Chen creator: Jing Lin creator: Yu Chen creator: Jiami Yu creator: Xiaojie Wang uri: https://doi.org/10.7717/peerj.16527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chen et al. title: Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs link: https://peerj.com/articles/16381 last-modified: 2023-11-24 description: Sponges are widely spread organisms in the tropical reefs of the American Northwest-Atlantic Ocean, they structure ecosystems and provide services such as shelter, protection from predators, and food sources to a wide diversity of both vertebrates and invertebrates species. The high diversity of sponge-associated fauna can generate complex networks of species interactions over small and large spatial-temporal gradients. One way to start uncovering the organization of the sponge host-guest complex networks is to understand how the accumulated geographic area, the sponge morphology and, sponge taxonomy contributes to the connectivity of sponge species within such networks. This study is a meta-analysis based on previous sponge host-guest literature obtained in 65 scientific publications, yielding a total of 745 host-guest interactions between sponges and their associated fauna across the Caribbean Sea and the Gulf of Mexico. We analyzed the sponge species contribution to network organization in the Northwest Tropical Atlantic coral reefs by using the combination of seven complementary species-level descriptors and related this importance with three main traits, sponge-accumulated geographic area, functional sponge morphology, and sponges’ taxonomy bias. In general, we observed that sponges with a widespread distribution and a higher accumulated geographic area had a greater network structural contribution. Similarly, we also found that Cup-like and Massive functional morphologies trend to be shapes with a greater contribution to the interaction network organization compared to the Erect and Crust-like morphos. Lastly, we did not detect a taxonomy bias between interaction network organization and sponges’ orders. These results highlight the importance of a specific combination of sponge traits to promote the diversity of association between reef sponges and their guest species. creator: Antar Mijail Pérez-Botello creator: Wesley Dáttilo creator: Nuno Simões uri: https://doi.org/10.7717/peerj.16381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pérez Botello et al. title: Environmental dissemination of respiratory viruses: dynamic interdependencies of respiratory droplets, aerosols, aerial particulates, environmental surfaces, and contribution of viral re-aerosolization link: https://peerj.com/articles/16420 last-modified: 2023-11-24 description: During the recent pandemic of COVID-19 (SARS-CoV-2), influential public health agencies such as the World Health Organization (WHO) and the U.S. Centers for Disease Control and Prevention (CDC) have favored the view that SARS CoV-2 spreads predominantly via droplets. Many experts in aerobiology have openly opposed that stance, forcing a vigorous debate on the topic. In this review, we discuss the various proposed modes of viral transmission, stressing the interdependencies between droplet, aerosol, and fomite spread. Relative humidity and temperature prevailing determine the rates at which respiratory aerosols and droplets emitted from an expiratory event (sneezing, coughing, etc.) evaporate to form smaller droplets or aerosols, or experience hygroscopic growth. Gravitational settling of droplets may result in contamination of environmental surfaces (fomites). Depending upon human, animal and mechanical activities in the occupied space indoors, viruses deposited on environmental surfaces may be re-aerosolized (re-suspended) to contribute to aerosols, and can be conveyed on aerial particulate matter such as dust and allergens. The transmission of respiratory viruses may then best be viewed as resulting from dynamic virus spread from infected individuals to susceptible individuals by various physical states of active respiratory emissions, instead of the current paradigm that emphasizes separate dissemination by respiratory droplets, aerosols or by contaminated fomites. To achieve the optimum outcome in terms of risk mitigation and infection prevention and control (IPAC) during seasonal infection peaks, outbreaks, and pandemics, this holistic view emphasizes the importance of dealing with all interdependent transmission modalities, rather than focusing on one modality. creator: M. Khalid Ijaz creator: Syed A. Sattar creator: Raymond W. Nims creator: Stephanie A. Boone creator: Julie McKinney creator: Charles P. Gerba uri: https://doi.org/10.7717/peerj.16420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ijaz et al. title: Differentiating wild from captive animals: an isotopic approach link: https://peerj.com/articles/16460 last-modified: 2023-11-24 description: BackgroundWildlife farming can be an important but complex tool for conservation. To achieve conservation benefits, wildlife farming should meet a variety of criteria, including traceability conditions to identify the animals’ origin. The traditional techniques for discriminating between wild and captive animals may be insufficient to prevent doubts or misdeclaration, especially when labels are not expected or mandatory. There is a pressing need to develop more accurate techniques to discriminate between wild and captive animals and their products. Stable isotope analysis has been used to identify animal provenance, and some studies have successfully demonstrated its potential to differentiate wild from captive animals. In this literature review, we examined an extensive collection of publications to develop an overall picture of the application of stable isotopes to distinguish between wild and captive animals focusing on evaluating the patterns and potential of this tool.Survey methodologyWe searched peer-reviewed publications in the Web of Science database and the references list from the main studies on the subject. We selected and analyzed 47 studies that used δ13C, δ15N, δ2H, δ18O, and δ34S in tissues from fish, amphibians, reptiles, birds, and mammals. We built a database from the isotope ratios and metadata extracted from the publications.ResultsStudies have been using stable isotopes in wild and captive animals worldwide, with a particular concentration in Europe, covering all main vertebrate groups. A total of 80.8% of the studies combined stable isotopes of carbon and nitrogen, and 88.2% used at least one of those elements. Fish is the most studied group, while amphibians are the least. Muscle and inert organic structures were the most analyzed tissues (46.81% and 42.55%). δ13C and δ15N standard deviation and range were significantly higher in the wild than in captive animals, suggesting a more variable diet in the first group. δ13C tended to be higher in wild fishes and in captive mammals, birds, reptiles, and amphibians. δ15N was higher in the wild terrestrial animals when controlling for diet. Only 5.7% of the studies failed to differentiate wild and captive animals using stable isotopes.ConclusionsThis review reveals that SIA can help distinguish between wild and captive in different vertebrate groups, rearing conditions, and methodological designs. Some aspects should be carefully considered to use the methodology properly, such as the wild and captivity conditions, the tissue analyzed, and how homogeneous the samples are. Despite the increased use of SIA to distinguish wild from captive animals, some gaps remain since some taxonomic groups (e.g., amphibians), countries (e.g., Africa), and isotopes (e.g., δ2H, δ18O, and δ34S) have been little studied. creator: Luiza Brasileiro creator: Rodrigo Ribeiro Mayrink creator: André Costa Pereira creator: Fabio José Viana Costa creator: Gabriela Bielefeld Nardoto uri: https://doi.org/10.7717/peerj.16460 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Brasileiro et al. title: Development of a 5-mRNAsi-related gene signature to predict the prognosis of colon adenocarcinoma link: https://peerj.com/articles/16477 last-modified: 2023-11-24 description: AimTo create a prognosis model based on mRNA-based stem index (mRNAsi) for evaluating the prognostic outcomes of colon adenocarcinoma (COAD).BackgroundGeneration of heterogeneous COAD cells could be promoted by the self-renewal and differentiation potential of cancer stem cells (CSCs). Biomarkers contributing to the development of COAD stem cells remained to be discovered.ObjectiveTo develop and validate an mRNAsi-based risk model for estimating the prognostic outcomes of patients suffering from COAD.MethodsSamples were collected from Rectal Adenocarcinoma (TCGA-READ) PanCancer Atlas datasets, The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD), and the GSE87211 dataset. MRNAsi was calculated by one-class logistic regression (OCLR) algorithm. Under the criterion of correlation greater than 0.4, genes related to mRNAsi were screened and clustered. Meanwhile, differentially expressed genes (DEGs) between molecular subtypes were identified to establish a risk model. According to the median risk score value for immunotherapy and results from immune cell infiltration and clinicopathological analyses, clusters and patients were divided into high-RiskScore and low-RiskScore groups. Cell apoptosis and viability were detected by flow cytometer and Cell Counting Kit-8 (CCK-8) assay, respectively.ResultsA negative correlation between mRNAsi and clinical stages was observed. Three clusters of patients (C1, C2, and C3) were defined based on a total of 165 survival-related mRNAsi genes. Specifically, C1 patients had greater immune cell infiltration and a poorer prognosis. A 5-mRNAsi-gene signature (HEYL, FSTL3, FABP4, ADAM8, and EBF4) served as a prediction index for COAD prognosis. High-RiskScore patients had a poorer prognosis and higher level of immune cell infiltration. In addition, the five genes in the signature all showed a high expression in COAD cells. Knocking down HEYL promoted COAD cell apoptosis and inhibited viability.ConclusionOur mRNAsi risk model could better predict the prognosis of COAD patients. creator: Haifu Huang creator: Lin Lu creator: Yaoxuan Li creator: Xiumei Chen creator: Meng Li creator: Meiling Yang creator: Xuewu Huang uri: https://doi.org/10.7717/peerj.16477 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding link: https://peerj.com/articles/16486 last-modified: 2023-11-24 description: The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts. creator: Habib Khemira creator: Mosbah Mahdhi creator: Muhammad Afzal creator: Mohammed D.Y. Oteef creator: Taieb Tounekti creator: Zarraq AL-Faifi creator: Wail Alsolami uri: https://doi.org/10.7717/peerj.16486 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Khemira et al. title: Antioxidant activity, anti-tyrosinase activity, molecular docking studies, and molecular dynamic simulation of active compounds found in nipa palm vinegar link: https://peerj.com/articles/16494 last-modified: 2023-11-24 description: Tyrosinase is a key enzyme in melanogenesis and its inhibitors have become increasingly because of their potential activity as hypopigmenting agents which have less side effects. Nipa palm vinegar is an aqueous product that is normally used as a food supplement. The aim of this study was to study the determination of antioxidant activity and tyrosinase inhibitory activities of aqueous extract of original nipa palm vinegar (AE O-NPV), nipa palm vinegar powder (NPV-P) and aqueous extract of nipa palm vinegar powder (AE NPV-P) were examined. Nipa palm vinegars were evaluated the phenolic and flavonoid content, and the active compounds which were submitted to molecular docking and molecular dynamic simulation, chemoinformatics, rule of five, skin absorption and toxicity. The highest phenolic and flavonoid contents in the AE O-NPV were 2.36 ± 0.23 mg gallic acid equivalents/g extract and 5.11 ± 0.59 mg quercetin equivalents/g, and the highest ABTS radical cation scavenging activity was also found. The AE O-NPV, NPV-P and AE NPV-P showed anti-mushroom tyrosinase activity. The HPLC analysis showed that there were vanillic acid and three flavonoids (catechin, rutin and quercetin). The molecular docking study revealed that the binding of the vanillic acid and three flavonoids occurred in the active site residues (histidine and other amino acids). Moreover, the number of hydrogen bond acceptors/donors, solubility, polar surface area and bioavailability score of the vanillic acid and three flavonoids were acceptable compared to Lipinski’s Rule of Five. The molecular dynamic simulation showed that vanillic acid interacts with HIS284 through π–π stacking hydrophobic interactions and forms a metal-acceptor interaction with the copper molecule at the tyrosinase active site. All compounds revealed good skin permeability and nontoxicity. Nipa palm vinegar could be a promising source of a new ingredient for tyrosinase inhibition for cosmetics or pharmaceutical products. creator: Moragot Chatatikun creator: Aman Tedasen creator: Nawanwat Chainuwong Pattaranggoon creator: Wilawan Palachum creator: Sirithip Chuaijit creator: Amron Mudpan creator: Supawita Pruksaphanrat creator: Sasirat Sohbenalee creator: Kenshi Yamasaki creator: Wiyada Kwanhian Klangbud uri: https://doi.org/10.7717/peerj.16494 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chatatikun et al. title: Behavioral dominance interactions between two species of burying beetles (Nicrophorus orbicollis and Nicrophorus pustulatus) link: https://peerj.com/articles/16090 last-modified: 2023-11-23 description: Closely related species with ecological similarity often aggressively compete for a common, limited resource. This competition is usually asymmetric and results in one species being behaviorally dominant over the other. Trade-offs between traits for behavioral dominance and alternative strategies can result in different methods of resource acquisition between the dominant and subordinate species, with important consequences for resource partitioning and community structure. Body size is a key trait thought to commonly determine behavioral dominance. Priority effects (i.e., which species arrives at the resource first), however, can also determine the outcome of interactions, as can species-specific traits besides size that give an advantage in aggressive contests (e.g., weapons). Here, we test among these three alternative hypotheses of body size, priority effects, and species identity for what determines the outcome of competitive interactions among two species of burying beetles, Nicrophorus orbicollis and N. pustulatus. Both overlap in habitat and seasonality and exhibit aggressive competition over a shared breeding resource of small vertebrate carrion. In trials, we simulated what would happen upon the beetles’ discovery of a carcass in nature by placing a carcass and one beetle of each species in a container and observing interactions over 13 h trials (n = 17 trials). We recorded and categorized interactions between beetles and the duration each individual spent in contact with the carcass (the key resource) to determine which hypothesis predicted trial outcomes. Body size was our only significant predictor; the largest species won most aggressive interactions and spent more time in contact with the carcass. Our results offer insight into the ecology and patterns of resource partitioning of N. orbicollis and N. pustulatus, the latter of which is unique among local Nicrophorus for being a canopy specialist. N. pustulatus is also unique among all Nicrophorus in using snake eggs, in addition to other carrion, as a breeding resource. Our results highlight the importance of body size and related trade-offs in ecology and suggest parallels with other coexisting species and communities. creator: Yohanna D. Vangenne creator: Brendan Sheppard creator: Paul R. Martin uri: https://doi.org/10.7717/peerj.16090 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Vangenne et al. title: Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change? link: https://peerj.com/articles/16366 last-modified: 2023-11-23 description: BackgroundWe compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) via NGS analysis.MethodsWe prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used.ResultsAmong the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups.ConclusionHere, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC via NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data. creator: Hee Yeon Kim creator: Tae Hyun Kim creator: Jeong Hwan Shin creator: Kwangrae Cho creator: Heon-Kyun Ha creator: Anbok Lee creator: Young Jin Kim uri: https://doi.org/10.7717/peerj.16366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kim et al. title: The impact of obesity on static and proactive balance and gait patterns in sarcopenic older adults: an analytical cross-sectional investigation link: https://peerj.com/articles/16428 last-modified: 2023-11-23 description: BackgroundObesity is increasingly recognized as a significant factor in the susceptibility of older adults to falls and related injuries. While existing literature has established a connection between obesity and reduced postural stability during stationary stances, the direct implications of obesity on walking dynamics, particularly among the older adults with sarcopenia, are not yet comprehensively understood.ObjectiveFirstly, to investigate the influence of obesity on steady-state and proactive balance, as well as gait characteristics, among older adults with sarcopenic obesity (SO); and secondly, to unearth correlations between anthropometric characteristics and balance and gait parameters in the same demographic.MethodsA cohort of 42 participants was categorized into control (CG; n = 22; age = 81.1 ± 4.0 years; BMI = 24.9 ± 0.6 kg/m²) and sarcopenic obese (SOG; n = 20; age = 77.7 ± 2.9 years; BMI = 34.5 ± 3.2 kg/m²) groups based on body mass index (BMI, kg/m²). Participants were assessed for anthropometric data, body mass, fat and lean body mass percentages (%), and BMI. Steady-state balance was gauged using the Romberg Test (ROM). Proactive balance evaluations employed the Functional Reach (FRT) and Timed Up and Go (TUG) tests. The 10-m walking test elucidated spatiotemporal gait metrics, including cadence, speed, stride length, stride time, and specific bilateral spatiotemporal components (stance, swing, 1st and 2nd double support, and single support phases) expressed as percentages of the gait cycle.ResultsThe time taken to complete the TUG and ROM tests was significantly shorter in the CG compared to the SOG (p < 0.05). In contrast, the FRT revealed a shorter distance achieved in the SOG compared to the CG (p < 0.05). The CG exhibited a higher gait speed compared to the SOG (p < 0.05), with shorter stride and step lengths observed in the SOG compared to the CG (p < 0.05). Regarding gait cycle phases, the support phase was longer, and the swing phase was shorter in the SOG compared to the CG group (p < 0.05). LBM (%) showed the strongest positive correlation with the ROM (r = 0.77, p < 0.001), gait speed (r = 0.85, p < 0.001), TUG (r = −0.80, p < 0.001) and FRT (r = 0.74, p < 0.001).ConclusionObesity induces added complexities for older adults with sarcopenia, particularly during the regulation of steady-state and proactive balance and gait. The percentage of lean body mass has emerged as a crucial determinant, highlighting a significant impact of reduced muscle mass on the observed alterations in static postural control and gait among older adults with SO. creator: Hamza Ferhi creator: Wael Maktouf uri: https://doi.org/10.7717/peerj.16428 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ferhi and Maktouf title: Diversity of bacteria associated with lichens in Mt. Yunmeng in Beijing, China link: https://peerj.com/articles/16442 last-modified: 2023-11-23 description: Lichens host highly complex and diverse microbial communities, which may perform essential functions in these symbiotic micro-ecosystems. In this research, sequencing of 16S rRNA was used to investigate the bacterial communities associated with lichens of two growth forms (foliose and crustose). Results showed that Pseudomonadota, Actinomycetota and Acidobacteriota were dominant phyla in both types of lichens, while Acetobacterales and Hyphomicrobiales were the dominant orders. Alpha diversity index showed that the richness of bacteria hosted by foliose lichens was significantly higher than that hosted by crustose ones. Principal co-ordinates analysis showed a significant difference between beta diversity of the foliose lichen-associated bacterial communities and those of crustose lichen-associated ones. Gene function prediction showed most functions, annotated by the lichen-associated bacteria, to be related to metabolism, suggesting that related bacteria may provide nutrients to their hosts. Generally, our results propose that microbial communities play important roles in fixing nitrogen, providing nutrients, and controlling harmful microorganisms, and are therefore an integral and indispensable part of lichens. creator: Yimeng Li creator: Yinzhi Huang creator: Torsten Wronski creator: Manrong Huang uri: https://doi.org/10.7717/peerj.16442 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Glyceraldehyde-3-phosphate dehydrogenase Gh_GAPDH9 is associated with drought resistance in Gossypium hirsutum link: https://peerj.com/articles/16445 last-modified: 2023-11-23 description: BackgroundGlyceraldehyde-3-phosphate dehydrogenase (GAPDH) is the central enzyme of glycolysis and plays important regulatory roles in plant growth and development and responses to adverse stress conditions. However, studies on the characteristics and functions of cotton GAPDH family genes are still lacking.MethodsIn this study, genome-wide identification of the cotton GAPDH gene family was performed, and the phylogeny, gene structures, promoter progenitors and expression profiles of upland cotton GAPDH gene family members were explored by bioinformatics analysis to highlight potential functions. The functions of GhGAPDH9 in response to drought stress were initially validated based on RNA-seq, qRT‒PCR, VIGS techniques and overexpression laying a foundation for further studies on the functions of GAPDH genes.ResultsThis study is the first systematic analysis of the cotton GAPDH gene family, which contains a total of 84 GAPDH genes, among which upland cotton contains 27 members. Quantitative, phylogenetic and covariance analyses of the genes revealed that the GAPDH gene family has been conserved during the evolution of cotton. Promoter analysis revealed that most cis-acting elements were related to MeJA and ABA. Based on the identified promoter cis-acting elements and RNA-seq data, it was hypothesized that Gh_GAPDH9, Gh_GAPDH11, Gh_GAPDH19 and Gh_GAPDH21 are involved in the response of cotton to abiotic stress. The expression levels of the Gh_GAPDH9 gene in two drought-resistant and two drought-sensitive materials were analyzed by qRT‒PCR and found to be high early in the treatment period in the drought-resistant material. The silencing of Gh_GAPDH9 based on virus-induced gene silencing (VIGS) technology resulted in significant leaf wilting or whole-plant dieback in silenced plants after drought stress compared to the control. The content of—malondialdehyde (MDA) in cotton leaves was significantly increased, and the content of proline (Pro) and chlorophyll (Chl) was reduced. In addition, the leaf wilting and dryness of transgenic lines under drought stress were lower than those of wild-type Arabidopsis, indicating that Gh_GAPDH9 is a positive regulator of drought resistance. In conclusion, our results demonstrate that GAPDH genes play an important role in the response of cotton to abiotic stresses and provide preliminary validation of the function of the Gh_GAPDH9 gene under drought stress. These findings provide an important theoretical basis for further studies on the function of the Gh_GAPDH9 gene and the molecular mechanism of the drought response in cotton. creator: Shiwei Geng creator: Shengmei Li creator: Jieyin Zhao creator: Wenju Gao creator: Qin Chen creator: Kai Zheng creator: Yuxiang Wang creator: Yang Jiao creator: Yilei Long creator: Pengfei Liu creator: Yanying Qu creator: Quanjia Chen uri: https://doi.org/10.7717/peerj.16445 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Geng et al. title: Individual and combined ecotoxic effects of water-soluble polymers link: https://peerj.com/articles/16475 last-modified: 2023-11-23 description: Water-soluble polymers (WSPs) are a class of high-molecular-weight compounds which are widely used in several applications, including water treatment, food processing, and pharmaceuticals. Therefore, they pose a potential threat for water resources and aquatic ecosystems. We assessed the ecotoxicity of four WSPs—non-ionic polyacrylamide (PAM) and polyethylene glycol (PEG-200), anionic homopolymer of acrylic acid (P-AA), and cationic polyquaternium-6 (PQ-6)—as single compounds and in mixture. For this purpose in vitro and in vivo assays were used to record baseline toxicity, mutagenic potential, endocrine effects, and growth inhibition in the freshwater alga Raphidocelis subcapitata. Furthermore, the mixture toxicity of the two polymers P-AA and PQ-6 which showed effects in the algae tests was evaluated with the concentration addition (CA), independent action (IA), and generalized concentration addition (GCA) model and compared with experimental data. No toxic effects were observed among the polymers and their mixtures in the in vitro assays. On the contrary, in the growth inhibition test with R. subcapitata the cationic PQ-6 caused high inhibition while the anionic P-AA and its mixture with the cationic polymer caused low inhibition. The non-ionic polymers PEG-200 and PAM showed no effect in R. subcapitata in the tested concentration range up to 100 mg/L. The IA model represented the mixture effect of the combination experiment better than the CA and GCA models. The results indicate (1) that the toxic effects of anionic and cationic polymers are most likely due to interactions of the polymers with the surfaces of organisms or with nutrients in the water and (2) that the polymers elicit their effects through different mechanisms of action that do not interact with each other. creator: Olcay Hisar creator: Jörg Oehlmann uri: https://doi.org/10.7717/peerj.16475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hisar and Oehlmann title: Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change link: https://peerj.com/articles/16498 last-modified: 2023-11-23 description: Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation. creator: Matt J. Nimbs creator: Curtis Champion creator: Simon E. Lobos creator: Hamish A. Malcolm creator: Adam D. Miller creator: Kate Seinor creator: Stephen D.A. Smith creator: Nathan Knott creator: David Wheeler creator: Melinda A. Coleman uri: https://doi.org/10.7717/peerj.16498 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Nimbs et al. title: Predicting carrying capacity of a large carnivore from prey densities: a new approach link: https://peerj.com/articles/15914 last-modified: 2023-11-22 description: BackgroundLarge carnivores play a crucial role in maintaining the balance of the ecosystem. Successful conservation initiatives have often led to a huge increase in predators which has often led to negative interactions with humans. Without the knowledge of the carrying capacity of the top predator, such decisions become challenging. Here, we have derived a new equation to estimate the carrying capacity of tigers based on the individual prey species density.MethodsWe used tiger densities and respective prey densities of different protected areas. Relative prey abundance was used instead of absolute prey density as this could be a better surrogate of the prey preference. We used a regression approach to derive the species-wise equation. We have also scaled these coefficients accordingly to control the variation in the standard error (heteroscedasticity) of the tiger density. Furthermore, we have extended this regression equation for different species to different weight classes for more generalized application of the method.ResultsThe new equations performed considerably better compared to the earlier existing carrying capacity equations. Incorporating the species-wise approach in the equation also reflected the preference of the prey species for the tiger. This is the first carrying capacity equation where the individual prey densities are used to estimate the carnivore population density. The coefficient estimates of the model with the comparison with prey-predator power laws also reflect the differential effect of tigers on different prey species. The carrying capacity estimates will aid in a better understanding of the predator-prey interaction and will advance better management of the top predator. creator: Nilanjan Chatterjee creator: Indranil Mukhopadhyay creator: Parag Nigam creator: Bilal Habib uri: https://doi.org/10.7717/peerj.15914 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chatterjee et al. title: Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains link: https://peerj.com/articles/16276 last-modified: 2023-11-22 description: PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed bacterial contamination within intragenic regions of Arthropoda binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07 Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this article we demonstrate that in this case the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of gene contamination increased with lower coverage. Future work should focus on developing reference free pre-binning approaches for HiFi reads produced from eukaryotic based metagenomic samples. creator: Alfredo Rodriguez Ruiz creator: Alex R. Van Dam uri: https://doi.org/10.7717/peerj.16276 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rodriguez Ruiz and Van Dam title: Basic psychological need satisfaction and aggressive behavior: the role of negative affect and its gender difference link: https://peerj.com/articles/16372 last-modified: 2023-11-22 description: BackgroundBasic psychological need satisfaction (BPNS) is a significant factor in a person’s development, especially for adolescents, and the failure to satisfy these basic needs may contribute to individuals’ aggressive behavior. However, it is still unclear about the underlying mechanism by which BPNS is negatively associated with aggressive behavior. This study aimed to explore the relationship between BPNS and aggressive behavior in Chinese adolescents, with a focus on the mediating role of negative affect and its gender differences.MethodA sample of 1,064 junior high school students from three schools in China were selected randomly for the cross-sectional survey. The revised Need Satisfaction Scale, the Positive and Negative Affect Schedule, and Youth’s Self-Report were used to measure BPNS, affect, and aggressive behavior. The proposed model was examined by the structural equation modeling test and multi-group comparison analysis.ResultsThe results showed that BPNS was negatively linked with adolescents’ aggressive behavior, and this effect was mediated by negative affect. Moreover, multigroup analysis demonstrated that there existed a stronger negative association between BPNS and negative affect in female group. Also, the mediating effect of negative affect in the model was greater for girls.ConclusionsOur findings highlighted the importance of BPNS in adolescents’ social behavior (i.e., aggressive behavior), and reveal disparate patterns in how BPNS affects aggressive behavior in girls as compared to boys. creator: Fen Dou creator: Qinglin Wang creator: Minghui Wang creator: Entao Zhang creator: Guoxiang Zhao uri: https://doi.org/10.7717/peerj.16372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dou et al. title: The effect of polypharmacy on rheumatoid and psoriatic arthritis treatment: retrospective study link: https://peerj.com/articles/16418 last-modified: 2023-11-22 description: BackgroundRheumatoid arthritis (RA) and psoriatic arthritis (PsA) are chronic, progressive inflammatory diseases that can be accompanied by other diseases. In recent years, with the increase in the lifespan of individuals, the concept of polypharmacy has become more prominent. We aimed to show the prevalence of polypharmacy and the effects of polypharmacy on disease activity in RA and PsA.MethodsThis study included PsA patients who had peripheral joint involvement and, RA patients. Since PsA has a heterogeneous clinical picture, only patients with peripheral joint involvement were included in the study and patients with inflammatory low back pain or radiological sacroiliitis or spondylitis, dactylitis or enthesitis were not included in the study due to homogeneity concerns. The numbers of medications used by the patients at the onset of their treatment and at sixth months into their treatment were recorded. Polypharmacy was accepted as the simultaneous use of at least five medications by the person. The Disease Activity Score 28 joints C-Reactive Protein (DAS-28 CRP) was used to assess disease activity for both disease. The modified Charlson Comorbidity Index (CCI) scores of the patients were calculated based on their chronic diseases.ResultsThe sample of the study included 232 RA and 73 PsA patients. Polypharmacy was present at the treatment onset in 115 (49.6%) of the RA patients and 28 (38.4%) of the PsA patients. At the sixth month of treatment, polypharmacy was present in the sixth month of the treatment in 217 (93.5%) RA and 61 (83.6%) PsA patients. The mean ages of the RA and PsA patients who were receiving polypharmacy treatment at the beginning were significantly older than the mean ages of those who were not receiving polypharmacy treatment. In both the RA and PSA groups, the patients with polypharmacy at the beginning had statistically significantly higher DAS-28 CRP scores at six months of treatment than those without polypharmacy at the beginning (p < 0.001).ConclusionPolypharmacy was present both at the time of diagnosis and in the treatment process in the RA and PsA patients, and the presence of polypharmacy at the beginning of the treatment was among the factors that affected the treatment of these patients by significantly affecting their 6th-month DAS-28 CRP values. creator: Mete Kara creator: Gülay Alp creator: Seher Palanbek Yavaş creator: Anıl Taşdemir creator: Sertaç Ketenci creator: Müge Mercan Kara creator: Erkan Ozduran uri: https://doi.org/10.7717/peerj.16418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kara et al. title: Research progress on the predictive role of sarcopenia in the course and prognosis of inflammatory bowel disease link: https://peerj.com/articles/16421 last-modified: 2023-11-22 description: Sarcopenia is a syndrome characterized by a progressive and extensive decrease in skeletal muscle quality and function. With the development of imaging technology in recent years, the understanding and research on the pathogenesis, diagnosis, and evaluation of sarcopenia have gradually improved. More than one-third of patients with inflammatory bowel disease (IBD) have sarcopenia (Ryan et al., 2019), and as a new and unique body composition evaluation index, it is critical for predicting the clinical course, prognosis and postoperative complications of patients with IBD. However, there are limited research summarizing the prevalence of sarcopenia among IBD. Furthermore, there is a scarcity of studies establishing the precise criteria for diagnosing sarcopenia in these patients. This article summarizes the evaluation of sarcopenia and its recent advancements in predicting the course and prognosis of IBD. creator: Yang Liu creator: Linglin Tian uri: https://doi.org/10.7717/peerj.16421 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu and Tian title: Interaction effects of significant risk factors on low bone mineral density in ankylosing spondylitis link: https://peerj.com/articles/16448 last-modified: 2023-11-22 description: BackgroundTo analyze individually and interactively critical risk factors, which are closely related to low bone mineral density (BMD) in patient with ankylosing spondylitis (AS).MethodsA total of 249 AS patients who visited China-Japan Friendship Hospital were included in this training set. Patients with questionnaire data, blood samples, X-rays, and BMD were collected. Logistic regression analysis was employed to identify key risk factors for low BMD in different sites, and predictive accuracy was improved by incorporating the selected significant risk factors into the baseline model, which was then validated using a validation set. The interaction between risk factors was analyzed, and predictive nomograms for low BMD in different sites were established.ResultsThere were 113 patients with normal BMD, and 136 patients with low BMD. AS patients with hip involvement are more likely to have low BMD in the total hip, whereas those without hip involvement are more prone to low BMD in the lumbar spine. Chest expansion, mSASSS, radiographic average grade of the sacroiliac joint, and hip involvement were significantly associated with low BMD of the femoral neck and total hip. Syndesmophytes, hip involvement and higher radiographic average grade of the sacroiliac joint increases the risk of low BMD of the femoral neck and total hip in an additive manner. Finally, a prediction model was constructed to predict the risk of low BMD in total hip and femoral neck.ConclusionsThis study identified hip involvement was strongly associated with low BMD of the total hip in AS patients. Furthermore, the risk of low BMD of the femoral neck and total hip was found to increase in an additive manner with the presence of syndesmophytes, hip involvement, and severe sacroiliitis. This finding may help rheumatologists to identify AS patients who are at a high risk of developing low BMD and prompt early intervention to prevent fractures. creator: Wenting Sun creator: Wenjun Mu creator: Caroline Jefferies creator: Thomas Learch creator: Mariko Ishimori creator: Juan Wu creator: Zeran Yan creator: Nan Zhang creator: Qingwen Tao creator: Weiping Kong creator: Xiaoping Yan creator: Michael H. Weisman uri: https://doi.org/10.7717/peerj.16448 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sun et al. title: The prevalence and common risk indicators of root caries and oral health service utilization pattern among adults, a cross-sectional study link: https://peerj.com/articles/16458 last-modified: 2023-11-22 description: BackgroundRoot caries is a prevalent oral health concern among adults, yet there remains a need for a comprehensive understanding of its occurrence and associated risk indicators. The present study was aimed to investigate the prevalence of root caries and to determine significantly associated indicators with it among adults.MethodsThe residents aged 35–74 years old were enrolled in a cross-sectional study in which dental examination were taken and structured questionnaires were collected in Zhejiang Province, China. All data were recorded in an electronic system and analyzed.ResultsThe prevalence of decayed and filled root caries in 1,076 respondents was 31.9%. Elder age, greater attachment loss, and exposed root surface were associated with higher odds of incidence for decayed/filled roots and decayed roots. In the last 12 months, 27.4% of adults with decayed or filled roots and 23.2% of others utilized oral health services. Carious adults who had a very poor/poor oral health status were 2.905 times likely to report dental visits. People with sound roots who were female (OR = 2.103, P < 0.001), perceived their oral health status as moderate (OR = 1.802, P = 0.015), or poor/very poor (OR = 4.103, P < 0.001) were more likely to visit a dentist in the past 12 months.ConclusionsAge, attachment loss and root exposure were most significantly associated with the prevalence of root caries. Individuals who recognize their poor or very poor oral health status should feel encouraged to make use of oral health services. creator: Weixing Chen creator: Tianer Zhu creator: Denghui Zhang uri: https://doi.org/10.7717/peerj.16458 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chen et al. title: Metabolomic analyses uncover an inhibitory effect of niclosamide on mitochondrial membrane potential in cholangiocarcinoma cells link: https://peerj.com/articles/16512 last-modified: 2023-11-22 description: BackgroundNiclosamide is an oral anthelminthic drug that has been used for treating tapeworm infections. Its mechanism involves the disturbance of mitochondrial membrane potential that in turn inhibits oxidative phosphorylation leading to ATP depletion. To date, niclosamide has been validated as the potent anti-cancer agent against several cancers. However, the molecular mechanisms underlying the effects of niclosamide on the liver fluke Opisthorchis viverrini (Ov)-associated cholangiocarcinoma (CCA) cell functions remain to be elucidated. The aims of this study were to investigate the effects of niclosamide on CCA cell proliferation and on metabolic phenoconversion through the alteration of metabolites associated with mitochondrial function in CCA cell lines.Materials and MethodsThe inhibitory effect of niclosamide on CCA cells was determined using SRB assay. A mitochondrial membrane potential using tetramethylrhodamine, ethyl ester-mitochondrial membrane potential (TMRE-MMP) assay was conducted. Liquid chromatography-mass spectrometry-based metabolomics was employed to investigate the global metabolic changes upon niclosamide treatment. ATP levels were measured using CellTiter-Glo® luminescent cell viability assay. NAD metabolism was examined by the NAD+/NADH ratio.ResultsNiclosamide strongly inhibited CCA cell growth and reduced the MMP of CCA cells. An orthogonal partial-least square regression analysis revealed that the effects of niclosamide on suppressing cell viability and MMP of CCA cells were significantly associated with an increase in niacinamide, a precursor in NAD synthesis that may disrupt the electron transport system leading to suppression of NAD+/NADH ratio and ATP depletion.ConclusionOur findings unravel the mode of action of niclosamide in the energy depletion that could potentially serve as the promising therapeutic strategy for CCA treatment. creator: Thanaporn Kulthawatsiri creator: Yingpinyapat Kittirat creator: Jutarop Phetcharaburanin creator: Jittima Tomacha creator: Bundit Promraksa creator: Arporn Wangwiwatsin creator: Poramate Klanrit creator: Attapol Titapun creator: Watcharin Loilome creator: Nisana Namwat uri: https://doi.org/10.7717/peerj.16512 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kulthawatsiri et al. title: Osmotic response during kidney perfusion with cryoprotectant in isotonic or hypotonic vehicle solution link: https://peerj.com/articles/16323 last-modified: 2023-11-21 description: Organ cryopreservation would revolutionize transplantation by overcoming the shelf-life limitations of conventional organ storage. To prepare an organ for cryopreservation, it is first perfused with cryoprotectants (CPAs). These chemicals can enable vitrification during cooling, preventing ice damage. However, CPAs can also cause toxicity and osmotic damage. It is a major challenge to find the optimal balance between protecting the cells from ice and avoiding CPA-induced damage. In this study, we examined the organ perfusion process to shed light on phenomena relevant to cryopreservation protocol design, including changes in organ size and vascular resistance. In particular, we compared perfusion of kidneys (porcine and human) with CPA in either hypotonic or isotonic vehicle solution. Our results demonstrate that CPA perfusion causes kidney mass changes consistent with the shrink-swell response observed in cells. This response was observed when the kidneys were relatively fresh, but disappeared after prolonged warm and/or cold ischemia. Perfusion with CPA in a hypotonic vehicle solution led to a significant increase in vascular resistance, suggesting reduced capillary diameter due to cell swelling. This could be reversed by switching to perfusion with CPA in isotonic vehicle solution. Hypotonic vehicle solution did not cause notable osmotic damage, as evidenced by low levels of lactate dehydrogenase (LDH) in the effluent, and it did not have a statistically significant effect on the delivery of CPA into the kidney, as assessed by computed tomography (CT). Overall, our results show that CPA vehicle solution tonicity affects organ size and vascular resistance, which may have important implications for cryopreservation protocol design. creator: Ross M. Warner creator: Jun Yang creator: Andrew Drake creator: Youngjoo Lee creator: Sarah Nemanic creator: David Scott creator: Adam Z. Higgins uri: https://doi.org/10.7717/peerj.16323 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Warner et al. title: Testing the effectiveness of different wash protocols to remove body surface contaminants in invertebrate food web studies link: https://peerj.com/articles/16018 last-modified: 2023-11-21 description: Molecular gut content analysis via diagnostic PCR or high-throughput sequencing (metabarcoding) of consumers allows unravelling of feeding interactions in a wide range of animals. This is of particular advantage for analyzing the diet of small invertebrates living in opaque habitats such as the soil. Due to their small body size, which complicates dissection, microarthropods are subjected to whole-body DNA extraction-step before their gut content is screened for DNA of their food. This poses the problem that body surface contaminants, such as fungal spores may be incorrectly identified as ingested food particles for fungivorous species. We investigated the effectiveness of ten methods for body surface decontamination in litter-dwelling oribatid mites using Steganacarus magnus as model species. Furthermore, we tested for potential adverse effects of the decontamination techniques on the molecular detection of ingested prey organisms. Prior to decontamination, oribatid mites were fed with an oversupply of nematodes (Plectus sp.) and postmortem contaminated with fungal spores (Chaetomium globosum). We used diagnostic PCR with primers specific for C. globosum and Plectus sp. to detect contaminants and prey, respectively. The results suggest that chlorine bleach (sodium hypochloride, NaClO, 5%) is most efficient in removing fungal surface contamination without significantly affecting the detection of prey DNA in the gut. Based on these results, we provide a standard protocol for efficient body surface decontamination allowing to trace the prey spectrum of microarthropods using molecular gut content analysis. creator: Melissa Jüds creator: Kerstin Heidemann creator: Bernhard Eitzinger creator: Stefan Scheu uri: https://doi.org/10.7717/peerj.16018 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jüds et al. title: Identification of key genes in sepsis-induced cardiomyopathy based on integrated bioinformatical analysis and experiments in vitro and in vivo link: https://peerj.com/articles/16222 last-modified: 2023-11-21 description: IntroductionSepsis is a life-threatening disease that damages multiple organs and induced by the host’s dysregulated response to infection with high morbidity and mortality. Heart remains one of the most vulnerable targets of sepsis-induced organ damage, and sepsis-induced cardiomyopathy (SIC) is an important factor that exacerbates the death of patients. However, the underlying genetic mechanism of SIC disease needs further research.MethodsThe transcriptomic dataset, GSE171564, was downloaded from NCBI for further analysis. Gene expression matrices for the sample group were obtained by quartile standardization and log2 logarithm conversion prior to analysis. The time series, protein-protein interaction (PPI) network, and functional enrichment analysis via Gene Ontology and KEGG Pathway Databases were used to identify key gene clusters and their potential interactions. Predicted miRNA-mRNA relationships from multiple databases facilitated the construction of a TF-miRNA-mRNA regulatory network. In vivo experiments, along with qPCR and western blot assays, provided experimental validation.ResultsThe transcriptome data analysis between SIC and healthy samples revealed 221 down-regulated, and 342 up-regulated expressed genes across two distinct clusters. Among these, Tpt1, Mmp9 and Fth1 were of particular significance. Functional analysis revealed their role in several biological processes and pathways, subsequently, in vivo experiments confirmed their overexpression in SIC samples. Notably, we found TPT1 play a pivotal role in the progression of SIC, and silencing TPT1 showed a protective effect against LPS-induced SIC.ConclusionIn our study, we demonstrated that Tpt1, Mmp9 and Fth1 have great potential to be biomarker of SIC. These findings will facilitated to understand the occurrence and development mechanism of SIC. creator: Dehua Liu creator: Tao Wang creator: Qingguo Wang creator: Peikang Dong creator: Xiaohong Liu creator: Qiang Li creator: Youkui Shi creator: Jingtian Li creator: Jin Zhou creator: Quan Zhang uri: https://doi.org/10.7717/peerj.16222 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Genomic assembly, characterization, and quantification of DICER-like gene family in Okra plants under dehydration conditions link: https://peerj.com/articles/16232 last-modified: 2023-11-21 description: BackgroundOkra is a plant farmed for its pods, leaves, and stems all of which are edible. It is famous for its ability to tolerate long desiccation periods. It belongs to the Malvaceae family and is a sister species to hibiscus, cotton, and cacao plants.MethodsIn the current study, okra plants were used as a model to sequence, assemble, and analyze the evolutionary and functional characteristics of the Dicer-like protein gene family (DCL) based on DNAseq and qPCR techniques.ResultsFour Dicer-like (DCL) single-copy genes of the okra plant Abelmoschus esculentus (L.) Moench (AeDCL) were successfully assembled. The lengths of the AeDCL copies were 8,494, 5,214, 4,731, and 9,329 bp. The detected exons in these samples ranged from a single exon in AeDCL3 to 24 exons in AeDCL4. AeDCLs had five functional domains of two DEAD-like helicase superfamilies, N and C; one Dicer domain; one ribonuclease III domain (a and b); and one double-stranded RNA-binding domain. The PAZ domain was completely annotated only for AeDCL1 and AeDCL3. All AeDCLs were up-regulated under drought conditions, with leaves showing more extensive fold changes than roots. The study focused on a comprehensive genome-wide identification and analysis of the DCL gene family in naturally drought-tolerant okra plants, an orphan crop that can be used as a model for further genomic and transcriptomic studies on drought-tolerance mechanisms in plants. creator: Hagar Tarek Elhefnawi creator: Mohamed Abdel Salam Rashed creator: Ayman Atta creator: Rana M. Alshegaihi creator: Khairiah Mubarak Alwutayd creator: Diaa Abd El-Moneim creator: Mahmoud Magdy uri: https://doi.org/10.7717/peerj.16232 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Elhefnawi et al. title: Gender-specific linkages: frailty, polypharmacy, anti-cholinergic burden, and 5-year mortality risk—a real-world analysis link: https://peerj.com/articles/16262 last-modified: 2023-11-21 description: BackgroundWith higher age, frailty escalates the risk of falls, unexpected physical dysfunction, hospitalization, and mortality. Polypharmacy in the older population is a major challenge that not only increases medical costs, but also may worsen the risk of hospitalization and death. More importantly, the properties of anti-cholinergic drugs contribute various negative effects. This study aimed to investigate the sex difference in the association of polypharmacy, anticholinergic burden, and frailty with mortality.MethodsParticipants older than 65 years who attended the geriatric outpatient clinic of the study center between January 2015 and July 2020 were invited to participate in this retrospective study. Comprehensive geriatric assessment data were collected and the phenotype of frailty was determined by Fried’s criteria. Cox regression and the Kaplan–Meier curve were used to identify risk factors of 5-year survival along with intergroup differences in the risks.ResultsOf the 2,077 participants, 47.5% were female. The prevalence of frailty and the rate of polypharmacy were 44.7% and 60.6%, respectively. Higher age, male sex, low body mass index, low Mini-Mental State Examination scores, low activities of daily living, frailty status, polypharmacy, and a high Charlson Comorbidity Index score, and greater anticholinergic burden were significant risk factors that were associated with the 5-year all-cause mortality. Male patients with frailty exhibited the highest risks of mortality compared with male patients without frailty and female patients with or without frailty. Polypharmacy was significantly associated with a higher 5-year mortality rate in the frail male group compared with the non-frail male. In frail female group, individuals with a higher anticholinergic burden (as indicated by the Anticholinergic Cognitive Burden Scale) from drug usage exhibited an elevated 5-year mortality rate.ConclusionsPolypharmacy and greater anticholinergic burden, synergistically interacted with frailty and intensified the 5-year mortality risk in a gender-specific manner. To mitigate mortality risks, clinicians should prudently identify polypharmacy and anticholinergic burden in the older population. creator: Yin Yi Chou creator: Yu Shan Lee creator: Chu Sheng Lin creator: Jun Peng Chen creator: Fu-Hsuan Kuo creator: Cheng-Fu Lin creator: Yi-Ming Chen creator: Shih-Yi Lin uri: https://doi.org/10.7717/peerj.16262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chou et al. title: Sulforaphene suppressed cell proliferation and promoted apoptosis of COV362 cells in endometrioid ovarian cancer link: https://peerj.com/articles/16308 last-modified: 2023-11-21 description: AimN6-methyladenosine (m6A) RNA methylation exerts a regulatory effect on endometrioid ovarian cancer (EOC), but the specific m6A regulator genes in EOC remain to be explored. This study investigated that sulforaphene (Sul) is implicated in EOC development by regulating methyltransferase-like 3 (METTL3).MethodsThe dysregulated m6A RNA methylation genes in EOC were determined by methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing. The roles of METTL3 and/or Sul on viability, proliferative ability, cell cycle, and apoptosis of EOC cells were determined by MTT, colony formation, flow cytometry, and TUNEL staining assay, respectively. The expression of METTL3 and apoptosis-related proteins in EOC cells was detected by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot assays.ResultsFive m6A RNA methylation regulators (METTL3, ELF3, IGF2BP2, FTO, and METTL14) were differentially expressed in EOC, among which METTL3 had the highest expression level. Silencing METTL3 reduced the clonal expansion and viability of EOC cells, and caused the cells to arrest in the G0/G1 phase. This also promoted apoptosis in the EOC cells and activated the FAS/FADD and mitochondrial apoptosis pathways. In contrast, overexpressing METTL3 had the opposite effect. Sul, in a dose-dependent manner, reduced the viability of EOC cells but promoted their apoptosis. Sul also increased the levels of IGF2BP2 and FAS, while decreasing the levels of KRT8 and METTL3. Furthermore, Sul was able to reverse the effects of METTL3 overexpression on EOC cells.ConclusionsSul could suppress cell proliferation and promote apoptosis of EOC cells by inhibiting the METTL3 to activate the FAS/FADD and apoptosis-associated pathways. creator: Hui-Yan Yu creator: Li Yang creator: Yuan-Cai Liu creator: Ai-Jun Yu uri: https://doi.org/10.7717/peerj.16308 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yu et al. title: Evidence for the adaptive parsing of non-communicative eye movements during joint attention interactions link: https://peerj.com/articles/16363 last-modified: 2023-11-21 description: During social interactions, the ability to detect and respond to gaze-based joint attention bids often involves the evaluation of non-communicative eye movements. However, very little is known about how much humans are able to track and parse spatial information from these non-communicative eye movements over time, and the extent to which this influences joint attention outcomes. This was investigated in the current study using an interactive computer-based joint attention game. Using a fully within-subjects design, we specifically examined whether participants were quicker to respond to communicative joint attention bids that followed predictive, as opposed to random or no, non-communicative gaze behaviour. Our results suggest that in complex, dynamic tasks, people adaptively use and dismiss non-communicative gaze information depending on whether it informs the locus of an upcoming joint attention bid. We also went further to examine the extent to which this ability to track dynamic spatial information was specific to processing gaze information. This was achieved by comparing performance to a closely matched non-social task where eye gaze cues were replaced with dynamic arrow stimuli. Whilst we found that people are also able to track and use dynamic non-social information from arrows, there was clear evidence for a relative advantage for tracking gaze cues during social interactions. The implications of these findings for social neuroscience and autism research are discussed. creator: Ayeh Alhasan creator: Nathan Caruana uri: https://doi.org/10.7717/peerj.16363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Alhasan et al. title: Head and neck squamous cell carcinoma-specific prognostic signature and drug sensitive subtypes based on programmed cell death-related genes link: https://peerj.com/articles/16364 last-modified: 2023-11-21 description: BackgroundAs a complex group of malignancies, head and neck squamous cell carcinoma (HNSC) is one of the leading causes of cancer mortality. This study aims to establish a reliable clinical classification and gene signature for HNSC prognostic prediction and precision treatments.MethodsA consensus clustering analysis was performed to group HNSC patients in The Cancer Genome Atlas (TCGA) database based on genes linked to programmed cell death (PCD). Differentially expressed genes (DEGs) between subtypes were identified using the “limma” R package. The TCGA prognostic signature and PCD-related prognostic genes were found using a least absolute shrinkage and selection operator (LASSO) regression analysis and univariate Cox regression analysis. The robustness of the LASSO analysis was validated using datasets GSE65858 and GSE41613. A cell counting kit-8 (CCK-8) test, Western blot, and real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) were used to evaluate the expression and viability of prognostic genes.ResultsFour molecular subtypes were identified in PCD-related genes. Subtype C4 had the best prognosis and the highest immune score, while subtype C1 exhibited the most unfavorable outcomes. Three hundred shared DEGs were identified among the four subtypes, and four prognostic genes (CTLA4, CAMK2N1, PLAU and CALML5) were used to construct a TCGA-HNSC prognostic model. High-risk patients manifested poorer prognosis, more inflammatory pathway enrichment, and lower immune cell infiltration. High-risk patients were more prone to immune escape and were more likely to be resistant to Cisplatin and 5-Fluorouracil. Prognosis prediction was validated in external datasets. The expression of CTLA4, CAMK2N1, PLAU and CALML5 was enhanced in CAL-27 and SCC-25 cell lines, and CALML5 inhibited CAL-27 and SCC-25 cell viability.ConclusionThis study shares novel insights into HNSC classification and provides a reliable PCD-related prognostic signature for prognosis prediction and treatment for patients with HNSC. creator: Chengbo Xu creator: Hongfang Xu creator: Baimei Liu uri: https://doi.org/10.7717/peerj.16364 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Light wavelength and pulsing frequency affect avoidance responses of Canada geese link: https://peerj.com/articles/16379 last-modified: 2023-11-21 description: Collisions between birds and aircraft cause bird mortality, economic damage, and aviation safety hazards. One proposed solution to increasing the distance at which birds detect and move away from an approaching aircraft, ultimately mitigating the probability of collision, is through onboard lighting systems. Lights in vehicles have been shown to lead to earlier reactions in some bird species but they could also generate attraction, potentially increasing the probability of collision. Using information on the visual system of the Canada goose (Branta canadensis), we developed light stimuli of high chromatic contrast to their eyes. We then conducted a controlled behavioral experiment (i.e., single-choice test) to assess the avoidance or attraction responses of Canada geese to LED lights of different wavelengths (blue, 483 nm; red, 631 nm) and pulsing frequencies (steady, pulsing at 2 Hz). Overall, Canada geese tended to avoid the blue light and move towards the red light; however, these responses depended heavily on light exposure order. At the beginning of the experiment, geese tended to avoid the red light. After further exposure the birds developed an attraction to the red light, consistent with the mere exposure effect. The response to the blue light generally followed a U-shape relationship (avoidance, attraction, avoidance) with increasing number of exposures, again consistent with the mere exposure effect, but followed by the satiation effect. Lights pulsing at 2 Hz enhanced avoidance responses under high ambient light conditions; whereas steady lights enhanced avoidance responses under dim ambient light conditions. Our results have implications for the design of lighting systems aimed at mitigating collisions between birds and human objects. LED lights in the blue portion of the spectrum are good candidates for deterrents and lights in the red portion of the spectrum may be counterproductive given the attraction effects with increasing exposure. Additionally, consideration should be given to systems that automatically modify pulsing of the light depending on ambient light intensity to enhance avoidance. creator: Ryan Lunn creator: Patrice E. Baumhardt creator: Bradley F. Blackwell creator: Jean Paul Freyssinier creator: Esteban Fernández-Juricic uri: https://doi.org/10.7717/peerj.16379 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lunn et al. title: Zooplankton biodiversity and temporal dynamics (2005–2015) in a coastal station in western Portugal (Northeastern Atlantic Ocean) link: https://peerj.com/articles/16387 last-modified: 2023-11-21 description: Long-term monitoring of zooplankton assemblages provides essential knowledge to assess key factors impacting marine ecosystems. Despite the importance of this type of data, monitoring stations worldwide are spatially and temporally limited due to the difficulty of maintaining them. In the northeastern Atlantic area, Cascais-Watch is one monitoring site operating since 2005, despite some constraints throughout the years, and has allowed the collection of important data on the zooplankton communities of the area. The present work summarizes the knowledge collected until 2015 on the biodiversity and dynamics of zooplankton in the site. The results showed a year-round high productivity of the zooplankton abundance, biomass and diversity for the area, with no significant general trends or periodicity, despite the relatively lower winter and higher spring values. The results revealed two main transition periods with marked changes in species composition and dominance of the most abundant taxa. This shift was tentatively attributed to the extended annual dry season verified in Portugal after 2011, the low values of upwelling and precipitation, and the warmer waters. The zooplankton abundance presented an interannual increase for spring periods, and the proportion of Copepoda, the dominant taxa, was lower during summer months, corresponding to increased abundances of Mollusca, Diplostraca (Cladocera) and Cnidaria. In particular, the study shows an increasing abundance of the gelatinous species (particularly Cnidaria) for spring/summer months in recent years, suggesting changes in primary production and prey dynamics. Other relevant tendencies were the higher abundance of meroplankton, such as Bivalvia and fish larvae/eggs, and the decreasing trend in the abundance of the meroplanktonic coastal crustaceans, Decapoda and Cirripedia taxa, highlighting possible changes in the benthic coastal populations in the study region. The present study highlights probable changes and trends in the zooplankton community that should be monitored in the following years. creator: Antonina Dos Santos creator: Raquel Marques creator: Rita F.T. Pires uri: https://doi.org/10.7717/peerj.16387 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dos Santos et al. title: Gamma-rays induced mutations increase soybean oil and protein contents link: https://peerj.com/articles/16395 last-modified: 2023-11-21 description: Mutation breeding is one of the effective techniques used for improving desired traits such as yield quality and quantity in economic crops. The present study aims to develop oil and protein contents in addition to high yield attributes in soybean using gamma rays as a mutagen. Seeds of the soybean genotypes Giza 21, Giza 22, Giza 82, Giza 83 and 117 were treated with gamma rays doses 50, 100, 200 and 300 Gy. Plants were then scored based on morphological parameters correlated with yield quantity including plant height, seed weight and valuable protein and oil contents. Mutant lines exhibiting the highest yield attributes were selected and used as parents for M2 generation. The M2 progeny was further assessed based on their ability to maintain their yield attributes. Twenty mutant lines were selected and used as M3 lines. The yield parameters inferred a positive effect of gamma irradiation on the collected M3 mutant lines compared to their parental genotypes. 100 Gy of gamma rays gave the highest effect on the number of pods, branches and seeds per plant in addition to protein content, while 200 Gy was more effective in increasing plant height, number of pods per plant, and oil content. Six mutant lines scored the highest yield parameters. Further assessment inferred an inverse relationship between oil and protein content in most of the tested cultivars with high agronomic features. However, four mutant lines recorded high content of oil and protein besides their high seed yield as well, which elect them as potential candidates for large-scale evaluation. The correlation among examined parameters was further confirmed via principal component analysis (PCA), which inferred a positive correlation between the number of pods, branches, seeds, and seed weight. Conversely, oil and protein content were inversely correlated in most of yielded mutant lines. Together, those findings introduce novel soybean lines with favorable agronomic traits for the market. In addition, our research sheds light on the value of using gamma rays treatment in enhancing genetic variability in soybean and improving oil, protein contents and seed yield. creator: Geehan Mohsen creator: Said S. Soliman creator: Elsayed I. Mahgoub creator: Tarik A. Ismail creator: Elsayed Mansour creator: Khairiah M. Alwutayd creator: Fatmah A. Safhi creator: Diaa Abd El-Moneim creator: Rahma Alshamrani creator: Osama O. Atallah creator: Wael F. Shehata creator: Abdallah A. Hassanin uri: https://doi.org/10.7717/peerj.16395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mohsen et al. title: Effect of various concentrations of common organic solvents on the growth and proliferation ability of Candida glabrata and their permissible limits for addition in drug susceptibility testing link: https://peerj.com/articles/16444 last-modified: 2023-11-21 description: ObjectivesDimethyl sulfoxide (DMSO), acetone, ethanol, and methanol are organic solvents commonly used for dissolving drugs in antimicrobial susceptibility testing. However, these solvents have certain antimicrobial activity. Currently, standardized criteria for the selection and dosage of drug solvents in drug susceptibility testing research are lacking. The study aims to provide experimental evidence for the selection and addition limit of drug solvents for the in vitro antifungal susceptibility test of Candida glabrata (C. glabrata).MethodsAccording to the recommendation of the Clinical and Laboratory Standards Institute (CLSI) M27-A3, a 0.5 McFarland C. glabrata suspension was prepared and then diluted 1:1,000. Next, a gradient dilution method was used to prepare 20%, 10%, 5%, and 2.5% DMSO/acetone/ethanol/methanol. The mixture was plated onto a 96-well plate and incubated at a constant temperature of 35 °C for 48 h. The inhibitory effects of DMSO, acetone, ethanol, and methanol on C. glabrata growth and proliferation were analyzed by measuring optical density values at 600 nm (OD600 values).ResultsAfter 48 h incubation, the OD600 values of C. glabrata decreased to different extents in the presence of the four common organic solvents. The decrease in the OD600 values was greater with increasing concentrations within the experimental concentration range. When DMSO and acetone concentrations were higher than 2.5% (containing 2.5%) and methanol and ethanol concentrations were higher than 5.0% (containing 5.0%), the differences were statistically significant compared with the growth control wells without any organic solvent (P < 0.05).ConclusionAll four organic solvents could inhibit C. glabrata growth and proliferation. When used as solvents for drug sensitivity testing in C. glabrata, the concentrations of DMSO, acetone, ethanol, and methanol should be below 2.5%, 2.5%, 5%, and 5%, respectively. creator: Juan Liu creator: Hongxin Zhang creator: Lifang Zhang creator: Ting Li creator: Na Liu creator: Qing Liu uri: https://doi.org/10.7717/peerj.16444 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: Targeting B4GALT7 suppresses the proliferation, migration and invasion of hepatocellular carcinoma through the Cdc2/CyclinB1 and miR-338-3p/MMP2 pathway link: https://peerj.com/articles/16450 last-modified: 2023-11-21 description: BackgroundAs a three-dimensional network involving glycosaminoglycans (GAGs), proteoglycans (PGs) and other glycoproteins, the role of extracellular matrix (ECM) in tumorigenesis is well revealed. Abnormal glycosylation in liver cancer is correlated with tumorigenesis and chemoresistance. However, the role of galactosyltransferase in HCC (hepatocellular carcinoma) is largely unknown.MethodsHere, the oncogenic functions of B4GALT7 (beta-1,4-galactosyltransferase 7) were identified in HCC by a panel of in vitro experiments, including MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide), colony formation, transwell and flow cytometry assay. The expression of B4GALT7 in HCC cell lines and tissues were examined by qPCR (real-time quantitative polymerase chain reaction) and western blot assay. The binding between B4GALT7 and miR-338-3p was examined by dual-luciferase reporter assay.ResultsB4GALT7 encodes galactosyltransferase I and it is highly expressed in HCC cells and human HCC tissues compared with para-tumor specimens. MiR-338-3p was identified to bind the 3′ UTR (untranslated region) of B4GALT7. Highly expressed miR-338-3p suppressed HCC cell invasive abilities and rescued the tumor-promoting effect of B4GALT7 in HCC. ShRNA (short hairpin RNA) mediated B4GALT7 suppression reduced HCC cell invasive abilities, and inhibited the expression of MMP-2 and Erk signaling.ConclusionThese findings identified B4GALT7 as a potential prognostic biomarker and therapeutic target for HCC. creator: Chang Liu creator: Yuqi Jia creator: Xinan Zhao creator: Zifeng Wang creator: Xiaoxia Zhu creator: Chan Zhang creator: Xiaoning Li creator: Xuhua Zhao creator: Tao Gong creator: Hong Zhao creator: Dong Zhang creator: Yuhu Niu creator: Xiushan Dong creator: Gaopeng Li creator: Feng Li creator: Hongwei Zhang creator: Li Zhang creator: Jun Xu creator: Baofeng Yu uri: https://doi.org/10.7717/peerj.16450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Future habitat changes of Bactrocera minax Enderlein along the Yangtze River Basin using the optimal MaxEnt model link: https://peerj.com/articles/16459 last-modified: 2023-11-21 description: BackgroundBactrocera minax (Enderlein, 1920) (Diptera: Tephritidae) is a destructive citrus pest. It is mainly distributed throughout Shaanxi, Sichuan, Chongqing, Guizhou, Yunnan, Hubei, Hunan, and Guangxi in China and is considered to be a second-class pest that is prohibited from entering that country. Climate change, new farming techniques, and increased international trade has caused the habitable area of this pest to gradually expand. Understanding the suitable habitats of B. minax under future climate scenarios may be crucial to reveal the expansion pattern of the insect and develop corresponding prevention strategies in China.MethodsUsing on the current 199 distribution points and 11 environmental variables for B. minax, we chose the optimal MaxEnt model to screen the dominant factors that affect the distribution of B. minax and to predict the potential future distribution of B. minax in China under two shared socio-economic pathways (SSP1-2.6, SSP5-8.5).ResultsThe current habitat of B. minax is located at 24.1–34.6°N and 101.1–122.9°E, which encompasses the provinces of Guizhou, Sichuan, Hubei, Hunan, Chongqing, and Yunnan (21.64 × 104 km2). Under future climate scenarios, the potential suitable habitat for B. minax may expand significantly toward the lower-middle reaches of the Yangtze River. The land coverage of highly suitable habitats may increase from 21.64 × 104 km2 to 26.35 × 104 × 104 km2 (2050s, SSP5-8.5) ~ 33.51 × 104 km2 (2090s, SSP5-8.5). This expansion area accounts for 29% (2050s, SSP1-2.6) to 34.83% (2090s, SSP1-2.6) of the current habitat. The center of the suitable habitat was predicted to expand towards the northeast, and the scenario with a stronger radiative force corresponded to a more marked movement of the center toward higher latitudes. A jackknife test showed that the dominant variables affecting the distribution of B. minax were the mean temperature of the driest quarter (bio9), the annual precipitation (bio12), the mean diurnal range (bio2), the temperature annual range (bio7), and the altitude (alt).DiscussionCurrently, it is possible for B. minax to expand its damaging presence. Regions with appropriate climate conditions and distribution of host plants may become potential habitats for the insects, and local authorities should strengthen their detection and prevention strategies. Climate changes in the future may promote the survival and expansion of B. minax species in China, which is represented by the significant increase of suitable habitats toward regions of high altitudes and latitudes across all directions but with some shrinkage in the east and west sides. creator: Chun Fu creator: Xian Wang creator: Tingting Huang creator: Rulin Wang uri: https://doi.org/10.7717/peerj.16459 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fu et al. title: How tank-mix adjuvant type and concentration influence the contact angle on wheat leaf surface link: https://peerj.com/articles/16464 last-modified: 2023-11-21 description: Currently, the utilization of unmanned aerial vehicles (UAVs) for spraying pesticides is a prevalent issue in Asian countries. Improving the pesticide efficiency of UAV spraying is a major challenge for researchers. One of the factors that affect the efficiency is the wetting property of the spraying solutions on crop leaves. Tank-mix adjuvants, which can modify the wetting ability of the solutions, are often used for foliar application. However, different types and concentrations of tank-mix adjuvants may have different impacts on the wetting properties of droplets. In this article, we investigated the effects of four tank-mix adjuvants, Beidatong (BDT), Velezia Pro (VP), Nongjianfei (NJF), and Lieying (LY), on the dynamic contact angle (CA) values of droplets on the adaxial surface of wheat leaves. We measured the dynamic CA values of various concentrations of each adjuvant solution and determined the optimal concentrations based on the CA values, droplet spreading time, and cost. The results showed that adding any of the four adjuvants decreased the CA values, but the patterns of decrease varied among them. The CAs of BDT and VP solutions decreased slowly during the observation time (0–8.13 s), while those of NJF and LY solutions decreased rapidly throughout the observation period. According to the dynamic CA values of different concentrations, the optimal concentrations of BDT, VP, NJF, and LY for wheat field application were 12%, 16%, 6‰, and 0.3‰, respectively. Alkoxy-modified polytrisiloxane adjuvant (LY) could be recommended as an appropriate tank-mix adjuvant for wheat field application, considering spreading efficiency and cost. This study provides theoretical and practical guidance for selecting and optimizing tank-mix adjuvants for UAV spraying. creator: Yanhua Meng creator: Qiufang Wu creator: Hanxue Zhou creator: Hongyan Hu uri: https://doi.org/10.7717/peerj.16464 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Meng et al. title: Intensive sea urchin harvest rescales Paracentrotus lividus population structure and threatens self-sustenance link: https://peerj.com/articles/16220 last-modified: 2023-11-20 description: The harvest of the edible sea urchin Paracentrotus lividus is intensively practiced in some regions of the Western Mediterranean Sea. The removal of the largest individuals can determine an overall reduction in population size and a size class truncation that can lead to a drastic drop the self-sustenance. The aim of this study is to evaluate the variability of the population reproductive potential across 5 years in one of the main harvest hotspots of Sardinia (Western Mediterranean Sea). The breeding stock consists of commercial and under-commercial size individuals which were sampled on a monthly basis to estimate their GonadoSomatic Index (GSI) and the Individual Gamete Output (IGO). In addition, the reproductive potential of the population—Total Gamete Output (TGO)—was calculated across the 5-year period in relation with the variation of the density of the breeding stock. During the last year, the reproductive potential was also estimated in a well-conserved population of a nearby Marine Protected Area. No significant variability in GSI and IGO was found over the 5 years nor when compared with the ones of protected population in the last year. However, the intensive harvest drastically rescaled the population body-size: although density of the commercial size class remained low, density of the under-commercial size-class halved from the beginning to the end of the study. Accordingly, the proportional decrease of their gamete output contribution led to a 40% loss of the reproductive potential of the whole population in the 5-year period. Interestingly, despite the loss of reproductive potential due to the decrease of the breeding stock density, the average values of IGO slightly increased across the years leading to the highest Annual Gamete Output (AGO) during the fourth year of sampling. This positive pattern could suggest a mechanism of reproductive investments of the survivors in terms of gonad production rate or increase in spawning intensity. This work provides evidence of the direct effect of size-selective harvesting on the rapid loss of population self-sustenance. Furthermore, it lays new prospective for future research of the indirect effects of the rescaling population body-size in functional traits of the sea urchin P. lividus and that could become important for both, sustainable exploitation and ecosystem conservation management. creator: Nicole Ruberti creator: Gianni Brundu creator: Giulia Ceccherelli creator: Daniele Grech creator: Ivan Guala creator: Barbara Loi creator: Simone Farina uri: https://doi.org/10.7717/peerj.16220 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ruberti et al. title: Gait and dynamic pedobarographic analyses in hallux rigidus patients treated with Keller’s arthroplasty, arthrodesis or cheilectomy 22 years after surgery link: https://peerj.com/articles/16296 last-modified: 2023-11-20 description: BackgroundKeller’s arthroplasty, arthrodesis and cheilectomy are well-known surgical interventions for hallux rigidus. This study aimed to evaluate the effects of these surgical interventions on gait, plantar pressure distribution and clinical outcome in patients treated for hallux rigidus 22 years after surgery.MethodsSpatio-temporal gait parameters and plantar pressure distribution, determined as pressure time integrals (PTIs) and peak pressures (PPs), were analyzed using a 7-foot tone analysis model. Patient-reported outcome was assessed using the Manchester-Oxford Foot Questionnaire (MOXFQ). Of the 73 patients (89 feet) from the original study, 27 patients (33 feet) and 13 healthy controls (26 feet) were available for evaluation 22 years after hallux rigidus surgery.ResultsSpatio-temporal gait parameters were comparable between all groups and were in line with healthy controls (P > 0.05). No differences (P > 0.05) in PTIs and PPs were found in the seven plantar zones between groups and as compared to healthy controls. MOXFQ scores in all domains (walking/standing, range 21.4–24.1; pain, range 16.5–22.2 and social interaction, range 23.8–35.4) were not clinically and statistically different (P > 0.05) between the three different surgical interventions.ConclusionThese results suggest no long-term functional and biomechanical differences after these surgical interventions for hallux rigidus correction. The interventions seem to be appropriate treatment options for a selective group of patients with symptomatic hallux rigidus. creator: Robin de Bot creator: Jasper Stevens creator: Thijs Smeets creator: Adhiambo Witlox creator: Wieske Beertema creator: Roel Hendrickx creator: Kenneth Meijer creator: Martijn Schotanus uri: https://doi.org/10.7717/peerj.16296 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 de Bot et al. title: Cloning and functional characterization of porcine AACS revealing the regulative roles for fat deposition in pigs link: https://peerj.com/articles/16406 last-modified: 2023-11-20 description: Fat deposition is a quantitative trait controlled by multiple genes in pigs. Using transcriptome sequencing, we previously reported that AACS is differentially expressed in the subcutaneous fat tissue of Dingyuan pigs with divergent backfat thickness. Therefore, with the aim of further characterizing this gene and its protein, we cloned the entire 3286-bp mRNA sequence of the porcine AACS, and the encoded AACS protein is a hydrophilic protein without a signal peptide or transmembrane sequence. Our findings suggested that among various tissues and pig breeds, AACS was highly expressed in subcutaneous fat. We have identified three completely linked SNP loci in the AACS gene: A-1759C, C-1683T, and A-1664G. The double luciferase activity test in the 5′ flanking region indicated that the flanking region of AACS contained several active regulatory elements. The three linked SNPs that were identified in one of the critical active elements, and might serve as important molecular markers regulating backfat thickness. Finally, we observed that AACS overexpression inhibited the proliferation and differentiation of subcutaneous preadipocytes. Collectively, our results suggest that AACS inhibits subcutaneous fat deposition in pigs. This study provides a new molecular marker for understanding the mechanism of porcine fat deposition. creator: Pan Zhang creator: Bo Zhang creator: Yu Fu creator: Pan Li creator: Hao Zhang uri: https://doi.org/10.7717/peerj.16406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Quantifying the land and population risk of sewage spills overland using a fine-scale, DEM-based GIS model link: https://peerj.com/articles/16429 last-modified: 2023-11-20 description: Accidental releases of untreated sewage into the environment, known as sewage spills, may cause adverse gastrointestinal stress to exposed populations, especially in young, elderly, or immune-compromised individuals. In addition to human pathogens, untreated sewage contains high levels of micropollutants, organic matter, nitrogen, and phosphorus, potentially resulting in aquatic ecosystem impacts such as algal blooms, depleted oxygen, and fish kills in spill-impacted waterways. Our Geographic Information System (GIS) model, Spill Footprint Exposure Risk (SFER) integrates fine-scale elevation data (1/3 arc-second) with flowpath tracing methods to estimate the expected overland pathways of sewage spills and the locations where they are likely to pool. The SFER model can be integrated with secondary measures tailored to the unique needs of decision-makers so they can assess spatially potential exposure risk. To illustrate avenues to assess risk, we developed risk measures for land and population health. The land risk of sewage spills is calculated for subwatershed regions by computing the proportion of the subwatershed’s area that is affected by one modeled footprint. The population health risk is assessed by computing the estimated number of individuals who are within the modeled footprint using fine-scale (90 square meters) population estimates data from LandScan USA. In the results, with a focus on the Atlanta metropolitan region, potential strategies to combine these risk measures with the SFER model are outlined to identify specific areas for intervention. creator: Emma L. McDaniel creator: Samuel F. Atkinson creator: Chetan Tiwari uri: https://doi.org/10.7717/peerj.16429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 McDaniel et al. title: Insight from the association between critical thinking and English argumentative writing: catering to English learners’ writing ability link: https://peerj.com/articles/16435 last-modified: 2023-11-20 description: IntroductionEnglish argumentative writing (EAW) is a ‘problem-solving’ cognitive process, and its relationship with critical thinking has drawn attention in China. This is because fostering EAW proficiency is a crucial element but a challenging task for Chinese high school English teaching and learning. The present study examined how critical thinking is related to Chinese high school students’ EAW performance. The study identified eight critical thinking disposition (CTD) subscales and aims to determine whether EAW and CTD are correlated.MethodsA questionnaire modified from the Chinese Version Critical Thinking Disposition Inventory (CTDI-CV) and the Evaluation Criteria for English Argumentative Writing (ECEAW) were employed in this study. Both instruments were administered to 156 students from Grade 12. A purposive sampling of high school students was used in this study. Student EAW performance was scored by two experts based on the Evaluation Criteria for English Argumentative Writing.ResultsA significant relationship was found between students’ CTD and EAW abilities. Furthermore, among the eight CTD subdispositions, cognitive maturity, truth-seeking, analyticity, and justice were found to be positively correlated with EAW, and they all were found to be the main predictors of EAW proficiency among high school students.ConclusionZhangzhou high school students’ CTDs were overall positive, and students’ EAW performance correlated significantly with the overall CTD and its four subdispositions of cognitive maturity, truth-seeking, analyticity, and justice. These four subdispositions showed a significantly predictive validity on EAW performance as well. creator: Yanfang Hu creator: Atif Saleem uri: https://doi.org/10.7717/peerj.16435 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hu and Saleem title: Genome-wide identification of 2-oxoglutarate and Fe (II)-dependent dioxygenase family genes and their expression profiling under drought and salt stress in potato link: https://peerj.com/articles/16449 last-modified: 2023-11-20 description: The 2-Oxoglutatrate-dependent dioxygenases (2OGDs) comprise the 2-Oxoglutatrate and Fe(II)-dependent dioxygenases (2ODD) enzyme families that facilitate the biosynthesis of various compounds like gibberellin, ethylene, etc. The 2OGDs are also involved in various catabolism pathways, such as auxin and salicylic acid catabolism. Despite their important roles, 2ODDs have not been studied in potato, which is the third most important crop globally. In this study, a comprehensive genome wide analysis was done to identify all 2ODDs in potatoes, and the putative genes were analysed for the presence of the signature 2OG-FeII_Oxy (PF03171) domain and the conserved DIOX_N (PF14226) domain. A total of 205 St2ODDs were identified and classified into eight groups based on their function. The physiochemical properties, gene structures, and motifs were analysed, and gene duplication events were also searched for St2ODDs. The active amino acid residues responsible for binding with 2-oxoglutarate and Fe (II) were conserved throughout the St2ODDs. The three-dimensional (3D) structures of the representative members of flavanol synthase (FNS), 1-aminocyclopropane-1-carboxylic acid oxidases (ACOs), and gibberellin oxidases (GAOXs) were made and docked with their respective substrates, and the potential interactions were visualised. The expression patterns of the St2ODDs under abiotic stressors such as heat, salt, and drought were also analysed. We found altered expression levels of St2ODDs under abiotic stress conditions, which was further confirmed for drought and salt stress using qRT-PCR. The expression levels of St2ODD115, St2ODD34, and St2ODD99 were found to be upregulated in drought stress with 2.2, 1.8, and 2.6 fold changes, respectively. After rewatering, the expression levels were normal. In salt stress, the expression levels of St2ODD151, St2ODD76, St2ODD91, and St2ODD34 were found to be upregulated after 24 hours (h), 48 hours (h), 72 hours (h), and 96 hours (h). Altogether, the elevated expression levels suggest the importance of St2ODDs under abiotic stresses, i.e., drought and salt. Overall, our study provided a knowledge base for the 2ODD gene family in potato, which can be used further to study the important roles of 2ODDs in potato plants. creator: Hanny Chauhan creator: Aiana creator: Kashmir Singh uri: https://doi.org/10.7717/peerj.16449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chauhan et al. title: Self-control mediates the relationship between time perspective and mobile phone addiction in Chinese college students link: https://peerj.com/articles/16467 last-modified: 2023-11-20 description: BackgroundMobile phone addiction (MPA) is a prevalent problem among college students, and Chinese college students are a high-risk group for smartphone addiction. MPA has a negative impact on the physical and mental health and academic performance of college students. Studies have explored the influence of many factors on MPA, such as the characteristics of the smartphone itself, the characteristics of the smartphone user, and the environment. However, to date, no studies have explored the protective and risk factors for MPA from the perspective of personality traits. From this perspective, this study explored the influence of time perspective and trait self-control on MPA to identify effective measures to prevent and intervene in MPA in college students.MethodsThe participants in this cross-sectional study were 526 Chinese college students. They completed the Zimbardo Time Perspective Inventory, the Self-Control Scale and the Mobile Phone Addiction Tendency Scale using an online questionnaire tool. Pearson correlation analysis was used to explore the relationships among time perspective, self-control and MPA. A latent variable mediation analysis of the structural equation model was used to examine the mediating role of self-control in the relationship between time perspective and MPA.ResultsVarious dimensions of time perspective were strongly associated with MPA. Among these dimensions, past negative (r = 0.397, p < 0.001), present hedonistic (r = 0.207, p < 0.001), and present fatalistic perspectives (r = 0.444, p < 0.001) were positively associated with MPA, while a future time perspective (r = −0.200, p < 0.001) was negatively associated with MPA. Mediation effects analysis showed that past negative (β = 0.034, p < 0.001, 95% CI [0.020–0.051]), present hedonistic (β = 0.038, p < 0.001, 95% CI [0.02–0.06]), present fatalistic (β = 0.047, p < 0.001, 95% CI [0.031–0.065]) and future orientation perspectives (β = −0.093, p < 0.001, 95% CI [−0.123–0.069]) indirectly influenced MPA through the mediating effect of self-control.ConclusionThis study confirmed that a future time perspective and self-control are protective factors for MPA and that past negative, present hedonistic and present fatalistic perspectives are risk factors for MPA. College educators can prevent MPA in college students directly by cultivating their self-control ability, as well as indirectly by increasing their use of future time perspective and reducing past negative, present fatalistic and present hedonistic perspectives. creator: Weigang Pan creator: Yingzhi Ma creator: Yihong Long creator: Ying Wang creator: Yujie Zhao uri: https://doi.org/10.7717/peerj.16467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pan et al. title: Minimally invasive pyeloplasty versus open pyeloplasty for ureteropelvic junction obstruction in infants: a systematic review and meta-analysis link: https://peerj.com/articles/16468 last-modified: 2023-11-20 description: BackgroundTo compare the perioperative outcomes and success rates of minimally invasive pyeloplasty (MIP), including laparoscopic and robotic-assisted laparoscopic pyeloplasty, with open pyeloplasty (OP) in infants.Materials and MethodsIn September 2022, a systematic search of PubMed, EMBASE, and the Cochrane Library databases was undertaken. The systematic review and meta-analysis were conducted in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, with the study registered prospectively in the PROSPERO database (CRD42022359475).ResultsEleven studies were included. Dichotomous and continuous variables were presented as odds ratios (OR) and standard mean differences (SMD), respectively, with their 95% confidence intervals (CI). Compared to OP, a longer operation time and shorter length of stay were associated with MIP (SMD: 0.96,95% CI: 0.30 to 1.62, p = 0.004, and SMD: −1.12, 95% CI: −1.82 to −0.43, p = 0.002, respectively). No significant differences were found between the MIP and OP in terms of overall postoperative complications (OR:0.84, 95% CI: 0.52 to 1.35, p = 0.47), minor complications (OR: 0.76, 95% CI: 0.40 to 1.42, p = 0.39), or major complications (OR: 1.10, 95% CI: 0.49 to 2.50, p = 0.81). In addition, a lower stent placement rate was related to MIP (OR: 0.09, 95% CI: 0.02 to 0.47, p = 0.004). There was no statistical difference for success rate between the MIP and OP (OR: 1.35, 95% CI: 0.59 to 3.07, p = 0.47). Finally, the results of subgroup analysis were consistent with the above.ConclusionsOur meta-analysis demonstrates that MIP is a feasible and safe alternative to OP for infants, presenting comparable perioperative outcomes and similar success rates, albeit requiring longer operation times. However, it is essential to consider the limitations of our study, including the inclusion of studies with small sample sizes and the combination of both prospective and retrospective research designs. creator: Min Wang creator: Yu Xi creator: Nanxiang Huang creator: Pengli Wang creator: Li Zhang creator: Mingjia Zhao creator: Siyi Pu uri: https://doi.org/10.7717/peerj.16468 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Long-term toxicity of chlorpromazine, diclofenac and two lanthanides on three generations of Ceriodaphnia dubia link: https://peerj.com/articles/16472 last-modified: 2023-11-20 description: Amultigenerational study on Ceriodaphnia dubia was carried out by exposing three subsequent generations to pharmaceuticals chlorpromazine (CPZ) and diclofenac (DCF), and two lanthanide chlorides, gadolinium as GdCl3 and europium as EuCl3. As the treatments, environmentally relevant concentrations were chosen (0.001, 0.01 and 0.1 mg/L for CPZ; 0.1, 1 and 10 mg/L for DCF; 0.425, 4.25 and 42.5 µg/L for Gd and 0.41, 4.1 and 41 µg/L for Eu). Survival, population growth and reproduction success were evaluated at 21 and 30 days of exposure, and the whole observation period lasted 40 days. The least sensitive to all selected substances was the first daphnid generation (F1). Within 21-day exposure, no significant effects of the psychotropic drug CPZ on C. dubia survival were observed in generations F1–F3. The anti-inflammatory drug DCF did not affect survival in the F1 generation; however, it significantly reduced survival in the F3 generation at 1–10 mg/L. Both lanthanides did not affect survival in the F1 and F2 generations of C. dubia but considerably decreased survival in the F3 at 4–42 µg/L. Both pharmaceuticals stimulated the reproduction of C. dubia in the F1 generation, while inhibition occurred at the highest tested concentrations in generations F2 and F3. The inhibitory effect on the reproductive success of lanthanides in the F2 generation resembled that for CPZ but not for DCF. The dynamics of adverse effects during the 21–30-day period revealed that despite increased mortality in the controls (up to 30%), concentrations used in the study minified, in most instances, the survival and aggravated population growth and reproduction success of C. dubia. Our data suggest that C. dubia as a test organism can be used for 21 days in multigenerational investigations, especially when testing close to environmental concentrations. In this respect, the standard C. dubia chronic toxicity assay seems limited since prolonged observations and several generations of daphnids are required to obtain reliable information for the risk assessment of potentially aggressive chemicals. creator: Brigita Gylytė creator: Viktoria Martinyuk creator: Reda Cimmperman creator: Rolandas Karitonas creator: Oksana Stoliar creator: Levonas Manusadžianas uri: https://doi.org/10.7717/peerj.16472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gylytė et al. title: Factors affecting the relative abundance in an overfished stock: red grouper (Epinephelus morio) in the Southeastern Gulf of Mexico link: https://peerj.com/articles/16490 last-modified: 2023-11-20 description: The most important fisheries are recording catches below their historical averages despite increased effort. This level of overfishing is worrying and requires the establishment of feasible and precise measures to prevent a continuing decrease in biomass. Determining the factors that lead to changes in the abundance and distribution of overfished resources would allow us to identify the strengths and weaknesses of management schemes; this approach would also make it possible to estimate more accurate parameters for their evaluation. We hypothesize that environmental, temporal, spatial, and operational components contribute to the variation in the relative abundance. Thus, we analyzed the red grouper fishery, the most important demersal fishery in the southeastern Gulf of Mexico (SGM); it is locally known as escama. We employed the catch per unit effort (CPUE) as an index of relative abundance recorded by the semi-industrial fleet (kilogram per effective fishing day) and the small-scale fleet (kilogram per effective fishing hour) during the overexploitation phase (from 1996 to 2019). We fitted several variables of the components using generalized additive models (GAM) and used multi-model inference to determine the best GAM for each fleet. For both fleets, the operational and temporal components (fishing gear and year) have had a greater impact on the distribution and abundance of red grouper in the SGM than the spatial and environmental components (the place of origin and sea surface temperature). These findings encourage the exploration of métier schemes for more efficient fishery management. In addition, we have identified several strategies that would support the recovery of the resource, such as restricting fishing in the quadrants located to the northeast or regulating scuba diving. We recommend that in the future, researchers use the indices we have generated in the present study to evaluate the red grouper fishery. creator: Iván Oribe-Pérez creator: Iván Velázquez-Abunader creator: Carmen Monroy-García uri: https://doi.org/10.7717/peerj.16490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Oribe-Pérez et al. title: TMUB1 expression is associated with the prognosis of colon cancer and immune cell infiltration link: https://peerj.com/articles/16334 last-modified: 2023-11-17 description: BackgroundTMUB1 is a transmembrane protein involved in biological signaling and plays an important role in the stability and transcription of P53. However, its role in tumor remains unknown.MethodsUsing R language, the expression level of 33 cancer spectrum TMUB1 was analyzed by the public database TCGA, GEO and HPA, the differential expressed gene (DEG) screening and protein interaction (PPI) network was constructed, and the differential genes of TMUB1 in colon cancer were identified. The relevant signaling pathways were identified by gene functional annotation and enrichment analysis. The ssGSEA algorithm in GSVA were used for immune infiltration analysis. The Kaplan-Meier analysis, univariate and multivariate Cox regression analysis, nomogram and calibration map analysis were constructed to evaluate the correlation between TMUB1 expression and clinical prognosis. The expression levels of TMUB1 in intestinal cancer cell lines as well as in 10 intestinal cancer tissues were verified by qPCR experiments.ResultsThrough the bioinformatics analysis of multiple databases and preliminary experimental studies, we found that the expression of TMUB1 was significantly increased in colon cancer tumors, and was correlated with the clinical N stage, pathological grade, lymphatic metastasis and BMI of colon cancer. TMUB1 may be involved in the regulation of the malignant progression of colon cancer. Meanwhile, patients with high expression of TMUB1 mRNA had worse OS and DSS, and TMUB1 expression was an independent prognostic factor for OS and DSS. It was further found that highly expressed TMUB1 tissues showed low levels of immune infiltration and stromal infiltration.ConclusionWe reported the expression level of TMUB1 in colon cancer and analyzed its potential prognostic value in colon cancer through the bioinformatics analysis and preliminary experimental studies. The high expression of TMUB1 is a negative prognostic factor for colon cancer patients. TMUB1 may be a potential target for colon cancer. creator: Yan Lu creator: Kang Wang creator: Yuanhong Peng creator: Jun Zhang creator: Qinuo Ju creator: Qihuan Xu creator: Manzhao Ouyang creator: Zhiwei He uri: https://doi.org/10.7717/peerj.16334 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lu et al. title: Microbes within the building envelope—a case study on the patterns of colonization and potential sampling bias link: https://peerj.com/articles/16355 last-modified: 2023-11-17 description: Humans are exposed to diverse communities of microbes every day. With more time spent indoors by humans, investigations into the communities of microbes inhabiting occupied spaces have become important to deduce the impacts of these microbes on human health and building health. Studies so far have given considerable insight into the communities of the indoor microbiota humans interact with, but mainly focus on sampling surfaces or indoor dust from filters. Beneath the surfaces though, building envelopes have the potential to contain environments that would support the growth of microbial communities. But due to design choices and distance from ground moisture, for example, the temperature and humidity across a building will vary and cause environmental gradients. These microenvironments could then influence the composition of the microbial communities within the walls. Here we present a case study designed to quantify any patterns in the compositions of fungal and bacterial communities existing in a building envelope and determine some of the key variables, such as cardinal direction, distance from floor or distance from wall joinings, that may influence any microbial community composition variation. By drilling small holes across walls of a house, we extracted microbes onto air filters and conducted amplicon sequencing. We found sampling height (distance from the floor) and cardinal direction the wall was facing caused differences in the diversity of the microbial communities, showing that patterns in the microbial composition will be dependent on sampling location within the building. By sampling beneath the surfaces, our approach provides a more complete picture of the microbial condition of a building environment, with the significant variation in community composition demonstrating a potential sampling bias if multiple sampling locations across a building are not considered. By identifying features of the built environment that promote/retard microbial growth, improvements to building designs can be made to achieve overall healthier occupied spaces. creator: Lucy R. Davies creator: Aitor Barbero-López creator: Veli-Matti Lähteenmäki creator: Antti Salonen creator: Filip Fedorik creator: Antti Haapala creator: Phillip C. Watts uri: https://doi.org/10.7717/peerj.16355 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Davies et al. title: Chicago sky blue gel for better visualization of Demodex in patients with Demodex blepharitis link: https://peerj.com/articles/16378 last-modified: 2023-11-17 description: BackgroundDemodex blepharitis is a common chronic disease. The number of mites is associated with ocular discomfort. The accurate number derived from well-stained specimens is, hence, in favor of diagnosing, monitoring, and determining treatment responses.MethodsA cross-sectional study was conducted between April and July 2022 at the dermatology and ophthalmology clinic, Walailak University, Thailand. Adult participants with clinical suspicion of Demodex blepharitis were recruited. We examined eyelashes under light microscopy to quantify the number of Demodex mites before and after adding CSB gel. The mite counts, evaluated by an untrained investigator and an experienced investigator, were recorded and compared.ResultsA total of 30 participants were included for final analysis, among which 25 (83.3%) were female. The median age was 64.0 years (IQR, 61.0–68.0). The median Demodex counts evaluated by the experienced investigator before and after adding CSB gel were 1.0 (IQR, 0.0–1.0) and 2.5 (IQR, 2.0–3.0), respectively (p < 0.001). Moreover, the median Demodex counts evaluated by the untrained investigator before and after adding CSB gel were 1.0 (IQR, 0.0–1.0) and 2.0 (IQR, 1.0–3.0), respectively (p < 0.001). The correlation coefficient between Demodex counts after the addition of CSB counted by the experienced investigator and those counted by the untrained investigator was 0.92 (p < 0.001). CSB gel is a promising product to identify and quantify the number of Demodex mites. The findings supported the consideration of CSB gel as one of the diagnostic stains. creator: Lunla Udomwech creator: Weeratian Tawanwongsri creator: Auemphon Mordmuang uri: https://doi.org/10.7717/peerj.16378 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Udomwech et al. title: Comparative chloroplast genome analyses provide insights into evolutionary history of Rhizophoraceae mangroves link: https://peerj.com/articles/16400 last-modified: 2023-11-17 description: BackgroundThe Rhizophoraceae family comprises crucial mangrove plants that inhabit intertidal environments. In China, eight Rhizophoraceae mangrove species exist. Although complete chloroplast (Cp) genomes of four Rhizophoraceae mangrove plants have been reported, the Cp genomes of the remaining four species remain unclear, impeding a comprehensive understanding of the evolutionary history of this family.MethodsIllumina high-throughput sequencing was employed to obtain the DNA sequences of Rhizophoraceae species. Cp genomes were assembled by NOVOPlasty and annotated using CpGAVAS software. Phylogenetic and divergence time analyses were conducted using MEGA and BEAST 2 software.ResultsFour novel Cp genomes of Rhizophoraceae mangrove species (Bruguiera sexangula, Bruguiera gymnorrhiza, Bruguiera × rhynchopetala and Rhizophora apiculata) were successfully assembled. The four Cp genomes ranged in length from 163,310 to 164,560 bp, with gene numbers varying from 124 to 128. The average nucleotide diversity (Pi) value of the eight Rhizophoraceae Cp genomes was 0.00596. Phylogenetic trees constructed based on the complete Cp genomes supported the monophyletic origin of Rhizophoraceae. Divergence time estimation based on the Cp genomes of representative species from Malpighiales showed that the origin of Rhizophoraceae occurred at approximately 58.54–50.02 million years ago (Mya). The divergence time within the genus Rhizophora (∼4.51 Mya) was much earlier than the divergence time within the genus Bruguiera (∼1.41 Mya), suggesting recent speciation processes in these genera. Our data provides new insights into phylogenetic relationship and evolutionary history of Rhizophoraceae mangrove plants. creator: Ying Zhang creator: Yuchen Yang creator: Meng He creator: Ziqi Wei creator: Xi Qin creator: Yuanhao Wu creator: Qingxing Jiang creator: Yufeng Xiao creator: Yong Yang creator: Wei Wang creator: Xiang Jin uri: https://doi.org/10.7717/peerj.16400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Genome-wide analysis of sugar transporter genes in maize (Zea mays L.): identification, characterization and their expression profiles during kernel development link: https://peerj.com/articles/16423 last-modified: 2023-11-17 description: Sugar transporters (STs) play a crucial role in the development of maize kernels. However, very limited information about STs in maize is known. In this study, sixty-eight ZmST genes were identified from the maize genome and classified into eight major groups based on phylogenetic relationship. Gene structure analysis revealed that members within the same group shared similar exon numbers. Synteny analysis indicated that ZmSTs underwent 15 segmental duplication events under purifying selection. Three-dimensional structure of ZmSTs demonstrated the formation of a compact helix bundle composed of 8–13 trans-membrane domains. Various development-related cis-acting elements, enriched in promoter regions, were correlated with the transcriptional response of ZmSTs during kernel development. Transcriptional expression profiles exhibited expression diversity of various ZmST genes in roots, stems, leaves, tassels, cobs, embryos, endosperms and seeds tissues. During kernel development, the expression of 24 ZmST genes was significantly upregulated in the early stage of grain filling. This upregulation coincided with the sharply increased grain-filling rate observed in the early stage. Overall, our findings shed light on the characteristics of ZmST genes in maize and provide a foundation for further functional studies. creator: Nan Sun creator: Yanfeng Liu creator: Tao Xu creator: Xiaoyan Zhou creator: Heyang Xu creator: Hongxia Zhang creator: Renhui Zhan creator: Limin Wang uri: https://doi.org/10.7717/peerj.16423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sun et al. title: Assessing the link between hygienic material use during menstruation and self-reported reproductive tract infections among women in India: a propensity score matching approach link: https://peerj.com/articles/16430 last-modified: 2023-11-17 description: BackgroundReproductive tract infections (RTIs) present a substantial health concern for women, especially in developing nations such as India, where inadequate access to proper sanitation and hygiene facilities frequently results in suboptimal menstrual health and hygiene (MHH), exacerbating the risk of RTIs. In this study, we analysed the self-reported prevalence of RTIs among young women in India and evaluated the impact of hygienic menstrual material usage on these RTIs.MethodsThe study used information on 27,983 women aged 15–24 years, from the National Family Health Survey (NFHS-5) (2019-21). The prevalence of RTIs was calculated for all the states and UTs of India, and propensity score matching (PSM) technique was used to evaluate the impact of hygienic material use on RTIs among women in India.ResultsEvery four out of 100 women reported RTIs in India in 2019–21. Notably, RTI prevalence displayed substantial state-level disparities. West Bengal exhibited the highest RTI prevalence at 9.3%, followed by Meghalaya, Arunachal Pradesh, and Himachal Pradesh, all surpassing 6%. In contrast, the lowest RTI rates were recorded in Puducherry at 0.9%, succeeded by Andaman and Nicobar Islands, Odisha, and Jammu & Kashmir, all registering rates below 2%. The PSM analysis revealed that women who utilized hygienic materials during menstruation exhibited a reduced prevalence of RTIs (referred to as the “treated group” with an Average Treatment Effect on the Treated (ATT) of 0.0315) compared to those who did not utilize such materials (referred to as the “control group” with an ATT of 0.0416).ConclusionsThe study underscores the critical significance of using hygienic materials during menstruation as a preventive measure against RTIs among women in India. The findings suggest the need for targeted interventions focused at promoting hygienic menstrual materials to reduce the prevalence of RTIs among women in India. creator: Mahashweta Chakrabarty creator: Aditya Singh uri: https://doi.org/10.7717/peerj.16430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chakrabarty and Singh title: The load capacity of maxillary central incisor with simulated flared root canal restored with different fiber-reinforced composite post and cementation protocols link: https://peerj.com/articles/16469 last-modified: 2023-11-17 description: BackgroundThis study aimed to evaluate the load capacity of maxillary central incisors with simulated flared root canal restored with different fiber-reinforced composite (FRC) post cemented with either self-adhesive or self-etch resin cement and its mode of fracture.MethodsSixty-five extracted maxillary incisors were decoronated, its canal was artificially flared and randomly categorized into group tFRC (tapered FRC post) (n = 22), mFRC (multi-FRC post) (n = 21), and DIS-FRC (direct individually shaped-FRC (DIS-FRC) post) (n = 22), which were further subdivided based on cementation resin. The posts were cemented and a standardized resin core was constructed. After thermocycling, the samples were loaded statically and the maximum load was recorded.ResultsThe load capacity of the maxillary central incisor was influenced by the different FRC post system and not the resin cement (p = 0.289), and no significant interaction was found between them. Group mFRC (522.9N) yielded a significantly higher load capacity compared to DIS-FRC (421.1N). Overall, a 55% favorable fracture pattern was observed, and this was not statistically significant.ConclusionWithin the limitation of the study, it can be concluded that prefabricated FRC posts outperform DIS-FRC posts in terms of the load capacity of a maxillary central incisor with a simulated flared root canal. The cementation methods whether a self-adhesive or self-etch resin cement, was not demonstrated to influence the load capacity of a maxillary central incisor with a flared root canal. There were no significant differences between the favorable and non-favorable fracture when FRC post systems were used to restored a maxillary central incisor with a flared root canal. creator: Yew Hin Beh creator: Mohamad Syahrizal Halim creator: Zaihan Ariffin uri: https://doi.org/10.7717/peerj.16469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Beh et al. title: FTH1 indicates poor prognosis and promotes metastasis in head and neck squamous cell carcinoma link: https://peerj.com/articles/16493 last-modified: 2023-11-17 description: BackgroundCurrently, ferritin heavy chain (FTH1) has been increasingly found to play a crucial role in cancer as a core regulator of ferroptosis, while its role of non-ferroptosis in head and neck squamous cell carcinoma (HNSCC) is still unclear.MethodsHerein, we analyzed the expression level of FTH1 in HNSCC using TCGA database, and FTH1 protein in HNSCC tissues and cell lines was determined by immunohistochemistry (IHC) and western blotting, respectively. Then, its prognostic value and relationship with clinical parameters were investigated in HNSCC patients. Additionally, the biological function of FTH1 in HNSCC was explored.ResultsThe current study showed that FTH1 is significantly overexpressed in HNSCC tissues and related to poor prognosis and lymph node metastasis of HNSCC. FTH1 knockdown could suppress the metastasis and epithelial-mesenchymal transition (EMT) process of HNSCC.ConclusionOur findings indicate that FTH1 plays a critical role in the progression and metastasis of HNSCC and can serve as a promising prognostic factor and therapeutic target in HNSCC. creator: Qingyun Liao creator: Jing Yang creator: Zhaoyi Lu creator: Qingshan Jiang creator: Yongqian Gong creator: Lijun Liu creator: Hong Peng creator: Qin Wang creator: Xin Zhang creator: Zhifeng Liu uri: https://doi.org/10.7717/peerj.16493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liao et al. title: Miocene sponge assemblages in the face of the Messinian Salinity Crisis—new data from the Atlanto-Mediterranean seaway link: https://peerj.com/articles/16277 last-modified: 2023-11-16 description: The Messinian Salinity Crisis is considered as one of the most influential Cenozoic events that impacted negatively on the benthic fauna of the Mediterranean area. Changing environmental conditions, including a sharp reduction of water exchange between the Mediterranean Sea and the Atlantic Ocean, altered the geographical ranges of many organisms, including sponges (Porifera). Here, we report a unique assemblage of isolated sponge spicules from the upper Miocene of southwestern Spain. The newly recognized sponge fauna was inhabiting the Guadalquivir Basin—the corridor between the Mediterranean and the Atlantic Ocean at that time. It represents a taxonomically rich sponge community that consisted of members of “soft” and “lithistid” demosponges and hexactinellids. Demosponges are represented by at least thirty-four taxa, while hexactinellids are significantly rarer; only six taxa have been identified. From among eighteen taxa recognized to the species level, at least eight seem to be inhabiting this area to these days; six are recorded from adjacent areas, such as the Western Mediterranean, South European Atlantic Shelf, and the Azores, and three are present in the Red Sea and/or the Northern Atlantic. Intriguingly, some taxa seem to have their closest relatives in distant areas, such as the Indo-Pacific and Japanese waters which suggests that the range of some once widely-distributed populations shrunk after the isolation of the Mediterranean and the Messinian Salinity Crisis, surviving to the present day only in refugia. creator: Magdalena Łukowiak creator: Gerardo Meiro creator: Beltrán Peña creator: Perfecto Villanueva Guimerans creator: Hugo Corbí uri: https://doi.org/10.7717/peerj.16277 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Łukowiak et al. title: Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors link: https://peerj.com/articles/16342 last-modified: 2023-11-16 description: Protein kinase activity forms the backbone of cellular information transfer, acting both individually and as part of a broader network, the kinome. Their central role in signaling leads to kinome dysfunction being a common driver of disease, and in particular cancer, where numerous kinases have been identified as having a causal or modulating role in tumor development and progression. As a result, the development of therapies targeting kinases has rapidly grown, with over 70 kinase inhibitors approved for use in the clinic and over double this number currently in clinical trials. Understanding the relationship between kinase inhibitor treatment and their effects on downstream cellular phenotype is thus of clear importance for understanding treatment mechanisms and streamlining compound screening in therapy development. In this work, we combine two large-scale kinome profiling data sets and use them to link inhibitor-kinome interactions with cell line treatment responses (AUC/IC50). We then built computational models on this data set that achieve a high degree of prediction accuracy (R2 of 0.7 and RMSE of 0.9) and were able to identify a set of well-characterized and understudied kinases that significantly affect cell responses. We further validated these models experimentally by testing predicted effects in breast cancer cell lines and extended the model scope by performing additional validation in patient-derived pancreatic cancer cell lines. Overall, these results demonstrate that broad quantification of kinome inhibition state is highly predictive of downstream cellular phenotypes. creator: Chinmaya U. Joisa creator: Kevin A. Chen creator: Matthew E. Berginski creator: Brian T. Golitz creator: Madison R. Jenner creator: Gabriela Herrera Loeza creator: Jen Jen Yeh creator: Shawn M. Gomez uri: https://doi.org/10.7717/peerj.16342 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Joisa et al. title: Thinking about it: the impact of COVID-19-related stimuli on prospective memory link: https://peerj.com/articles/16389 last-modified: 2023-11-16 description: BackgroundSince 2020, information regarding COVID-19 has been a constant presence in the news, in our conversations and thoughts. Continuous exposure to this type of stimuli could have an impact on cognitive processes essential for our everyday activities, such as prospective memory (PM). PM is the ability to remember to perform an intention at a specific point in the future, like remembering to take prescribed medicines at a specific time or to turn off the stove after cooking. Do COVID-related stimuli affect our ability to perform a PM task?MethodsTo answer this question, we proposed a novel version of the classical paradigm used to investigate PM. Namely, this paradigm includes a baseline condition, in which an ongoing task is presented alone, and a PM condition in which the same task is proposed again together with a second (prospective) task. In this study, a short video clip was presented between the baseline and the PM condition. The video clip displayed either neutral, negative, or COVID-related content. Additionally, participants were asked to respond to two questionnaires and a series of questions regarding their well-being and experience with the pandemic. Namely, the DASS-21 scale (evaluating depression, anxiety, and stress), and the COVID-19-PTSD questionnaire (a questionnaire evaluating post-traumatic stress disorder symptoms related to the pandemic experience) were administered. Participants’ performance and responses were analyzed using a linear mixed effect (LME) model approach, and correlation analyses were run to highlight possible correlations between participants’ scores in the DASS-21, the COVID-19-PTSD, and the additional questions on their personal experience with the pandemic.ResultsThe LME models revealed significant effects of the displayed video on performance: in line with previous studies, the clip displaying standard negative contents led to impaired accuracy in the ongoing task in the PM condition, compared to the Baseline. In contrast, participants who saw the COVID-related clip showed improved accuracy in the ongoing task compared to the other participants, selectively in the block performed after the video clip was displayed (PM condition). Furthermore, the explanatory power of the LME model calculated on accuracy to the ongoing trials was enhanced by the inclusion of the scores in the anxiety subscale of the DASS-21, suggesting a detrimental role of anxiety. Altogether, these results indicate a different effect of the exposure to classical negative contents (associated with a cost in terms of accuracy in the ongoing task between the baseline and the PM condition) and the pandemic-related one, which was instead characterized by a higher accuracy to ongoing trials compared to the other video clips. This counterintuitive finding seems to suggest that COVID-related stimuli are processed as “acute stressors” rather than negative stimuli, thus inducing a state of increased alertness and responsivity. creator: Stefano Vicentin creator: Giovanni Cantarella creator: Giorgia Cona creator: Patrizia Bisiacchi uri: https://doi.org/10.7717/peerj.16389 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Vicentin et al. title: Sensitivity analysis of selection bias: a graphical display by bias-correction index link: https://peerj.com/articles/16411 last-modified: 2023-11-16 description: BackgroundIn observational studies, how the magnitude of potential selection bias in a sensitivity analysis can be quantified is rarely discussed. The purpose of this study was to develop a sensitivity analysis strategy by using the bias-correction index (BCI) approach for quantifying the influence and direction of selection bias.MethodsWe used a BCI, a function of selection probabilities conditional on outcome and covariates, with different selection bias scenarios in a logistic regression setting. A bias-correction sensitivity plot was illustrated to analyze the associations between proctoscopy examination and sociodemographic variables obtained using the data from the Taiwan National Health Interview Survey (NHIS) and of a subset of individuals who consented to having their health insurance data further linked.ResultsWe included 15,247 people aged ≥20 years, and 87.74% of whom signed the informed consent. When the entire sample was considered, smokers were less likely to undergo proctoscopic examination (odds ratio (OR): 0.69, 95% CI [0.57–0.84]), than nonsmokers were. When the data of only the people who provided consent were considered, the OR was 0.76 (95% CI [0.62–0.94]). The bias-correction sensitivity plot indicated varying ORs under different degrees of selection bias.ConclusionsWhen data are only available in a subsample of a population, a bias-correction sensitivity plot can be used to easily visualize varying ORs under different selection bias scenarios. The similar strategy can be applied to models other than logistic regression if an appropriate BCI is derived. creator: Ping-Chen Chung creator: I-Feng Lin uri: https://doi.org/10.7717/peerj.16411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chung and Lin title: Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics link: https://peerj.com/articles/16416 last-modified: 2023-11-16 description: Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2–10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species. creator: Wendy Y. Wang creator: Aiki Yamada uri: https://doi.org/10.7717/peerj.16416 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang and Yamada title: High variability of perezone content in rhizomes of Acourtia cordata wild plants, environmental factors related, and proteomic analysis link: https://peerj.com/articles/16136 last-modified: 2023-11-15 description: With the aim of exploring the source of the high variability observed in the production of perezone, in Acourtia cordata wild plants, we analyze the influence of soil parameters and phenotypic characteristics on its perezone content. Perezone is a sesquiterpene quinone responsible for several pharmacological effects and the A. cordata plants are the natural source of this metabolite. The chemistry of perezone has been widely studied, however, no studies exist related to its production under natural conditions, nor to its biosynthesis and the environmental factors that affect the yield of this compound in wild plants. We also used a proteomic approach to detect differentially expressed proteins in wild plant rhizomes and compare the profiles of high vs. low perezone-producing plants. Our results show that in perezone-producing rhizomes, the presence of high concentrations of this compound could result from a positive response to the effects of some edaphic factors, such as total phosphorus (Pt), total nitrogen (Nt), ammonium (NH4), and organic matter (O. M.), but could also be due to a negative response to the soil pH value. Additionally, we identified 616 differentially expressed proteins between high and low perezone producers. According to the functional annotation of this comparison, the upregulated proteins were grouped in valine biosynthesis, breakdown of leucine and isoleucine, and secondary metabolism such as terpenoid biosynthesis. Downregulated proteins were grouped in basal metabolism processes, such as pyruvate and purine metabolism and glycolysis/gluconeogenesis. Our results suggest that soil parameters can impact the content of perezone in wild plants. Furthermore, we used proteomic resources to obtain data on the pathways expressed when A. cordata plants produce high and low concentrations of perezone. These data may be useful to further explore the possible relationship between perezone production and abiotic or biotic factors and the molecular mechanisms related to high and low perezone production. creator: Ma del Carmen García Méndez creator: Sergio Encarnación-Guevara creator: Ángel Gabriel Martínez Batallar creator: Leopoldo Gómez-Caudillo creator: Roque Bru-Martínez creator: Ascensión Martínez Márquez creator: Susana Selles Marchart creator: Efraín Tovar-Sánchez creator: Laura Álvarez-Berber creator: Silvia Marquina Bahena creator: Irene Perea-Arango creator: José de Jesús Arellano-García uri: https://doi.org/10.7717/peerj.16136 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Garcia Mendez et al. title: Determining Minnesota bee species’ distributions and phenologies with the help of participatory science link: https://peerj.com/articles/16146 last-modified: 2023-11-15 description: The Minnesota Bee Atlas project contributed new information about bee distributions, phenologies, and community structure by mobilizing participatory science volunteers to document bees statewide. Volunteers submitted iNaturalist (©2016 California Academy of Sciences) photograph observations, monitored nest-traps for tunnel-nesting bees, and conducted roadside observational bumble bee surveys. By pairing research scientists and participatory science volunteers, we overcame geographic and temporal challenges to document the presence, phenologies, and abundances of species. Minnesota Bee Atlas project observations included new state records for Megachile inimica, Megachile frugalis, Megachile sculpturalis, Osmia georgica, Stelis permaculata, and Bombus nevadensis, nesting phenology for 17 species, a new documentation of bivoltinism for Megachile relativa in Minnesota, and over 500 observations of the endangered species Bombus affinis. We also expanded known ranges for 16 bee species compared with specimens available from the University of Minnesota (UMN) Insect Collection. Surveys with standardized effort across the state found ecological province associations for six tunnel-nesting species and lower bumble bee abundance in the Prairie Parkland ecological province than the Laurentian Mixed Forest or Eastern Broadleaf Forest ecological provinces, indicating potential benefit of a focus on bumble bee habitat management in the Prairie Parkland. Landcover analysis found associations for four tunnel-nesting species, as well as a possible association of B. affinis with developed areas. These data can inform management decisions affecting pollinator conservation and recovery of endangered species. By engaging over 2,500 project volunteers and other iNaturalist users, we also promoted conservation action for pollinators through our educational programs and interactions. creator: Colleen D. Satyshur creator: Elaine C. Evans creator: Britt M. Forsberg creator: Thea A. Evans creator: Robert Blair uri: https://doi.org/10.7717/peerj.16146 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Satyshur et al. title: Pharmacokinetic and pharmacodynamic herb-drug interactions—part I. Herbal medicines of the central nervous system link: https://peerj.com/articles/16149 last-modified: 2023-11-15 description: Unlike conventional drug substances, herbal medicines are composed of a complex of biologically active compounds. Therefore, the potential occurrence of herb-drug interactions is even more probable than for drug-drug interactions. Interactions can occur on both the pharmacokinetic and pharmacodynamic level. Herbal medicines may affect the resulting efficacy of the concomitantly used (synthetic) drugs, mainly on the pharmacokinetic level, by changing their absorption, distribution, metabolism, and excretion. Studies on the pharmacodynamic interactions of herbal medicines and conventional drugs are still very limited. This interaction level is related to the mechanism of action of different plant constituents. Herb-drug interactions can cause changes in drug levels and activities and lead to therapeutic failure and/or side effects (sometimes toxicities, even fatal). This review aims to provide a summary of recent information on the potential drug interactions involving commonly used herbal medicines that affect the central nervous system (Camellia, Valeriana, Ginkgo, Hypericum, Humulus, Cannabis) and conventional drugs. The survey databases were used to identify primary scientific publications, case reports, and secondary databases on interactions were used later on as well. Search keywords were based on plant names (botanical genera), officinal herbal drugs, herbal drug preparations, herbal drug extracts. creator: Szilvia Czigle creator: Milan Nagy creator: Přemysl Mladěnka creator: Jaroslav Tóth uri: https://doi.org/10.7717/peerj.16149 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Czigle et al. title: Comparison of feeding preferences of herbivorous fishes and the sea urchin Diadema antillarum in Little Cayman link: https://peerj.com/articles/16264 last-modified: 2023-11-15 description: On Caribbean coral reefs, losses of two key groups of grazers, herbivorous fishes and Diadema antillarum, coincided with dramatic increases in macroalgae, which have contributed to decreases in the resilience of these coral reefs and continued low coral cover. In some locations, herbivorous reef fishes and D. antillarum populations have begun to recover, and reductions in macroalgal cover and abundance have followed. Harder to determine, and perhaps more important, are the combined grazing effects of herbivorous fishes and D. antillarum on the structure of macroalgal communities. Surprisingly few studies have examined the feeding preferences of D. antillarum for different macroalgal species, and there have been even fewer comparative studies between these different herbivore types. Accordingly, a series of in-situ and ex-situ feeding assays involving herbivorous fishes and D. antillarum were used to examine feeding preferences. Ten macrophytes representing palatable and chemically and/or structurally defended species were used in these assays, including nine macroalgae, and one seagrass. All species were eaten by at least one of the herbivores tested, although consumption varied greatly. All herbivores consumed significant portions of two red algae species while avoiding Halimeda tuna, which has both chemical and structural defenses. Herbivorous fishes mostly avoided chemically defended species while D. antillarum consumed less of the structurally defended algae. These results suggest complementarity and redundancy in feeding by these different types of herbivores indicating the most effective macroalgal control and subsequent restoration of degraded coral reefs may depend on the recovery of both herbivorous fishes and D. antillarum. creator: Lindsay Spiers creator: Thomas K. Frazer uri: https://doi.org/10.7717/peerj.16264 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Spiers and Frazer title: In-silico study of antisense oligonucleotide antibiotics link: https://peerj.com/articles/16343 last-modified: 2023-11-15 description: BackgroundThe rapid emergence of antibiotic-resistant bacteria directly contributes to a wave of untreatable infections. The lack of new drug development is an important driver of this crisis. Most antibiotics today are small molecules that block vital processes in bacteria. To optimize such effects, the three-dimensional structure of targeted bacterial proteins is imperative, although such a task is time-consuming and tedious, impeding the development of antibiotics. The development of RNA-based therapeutics has catalyzed a new platform of antibiotics—antisense oligonucleotides (ASOs). These molecules hybridize with their target mRNAs with high specificity, knocking down or interfering with protein translation. This study aims to develop a bioinformatics pipeline to identify potent ASO targets in essential bacterial genes.MethodsThree bacterial species (P. gingivalis, H. influenzae, and S. aureus) were used to demonstrate the utility of the pipeline. Open reading frames of bacterial essential genes were downloaded from the Database of Essential Genes (DEG). After filtering for specificity and accessibility, ASO candidates were ranked based on their self-hybridization score, predicted melting temperature, and the position on the gene in an operon. Enrichment analysis was conducted on genes associated with putative potent ASOs.ResultsA total of 45,628 ASOs were generated from 348 unique essential genes in P. gingivalis. A total of 1,117 of them were considered putative. A total of 27,273 ASOs were generated from 191 unique essential genes in H. influenzae. A total of 847 of them were considered putative. A total of 175,606 ASOs were generated from 346 essential genes in S. aureus. A total of 7,061 of them were considered putative. Critical biological processes associated with these genes include translation, regulation of cell shape, cell division, and peptidoglycan biosynthetic process. Putative ASO targets generated for each bacterial species are publicly available here: https://github.com/EricSHo/AOA. The results demonstrate that our bioinformatics pipeline is useful in identifying unique and accessible ASO targets in bacterial species that post major public health issues. creator: Erica S. Chen creator: Eric S. Ho uri: https://doi.org/10.7717/peerj.16343 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chen and Ho title: Seq2science: an end-to-end workflow for functional genomics analysis link: https://peerj.com/articles/16380 last-modified: 2023-11-15 description: Sequencing databases contain enormous amounts of functional genomics data, making them an extensive resource for genome-scale analysis. Reanalyzing publicly available data, and integrating it with new, project-specific data sets, can be invaluable. With current technologies, genomic experiments have become feasible for virtually any species of interest. However, using and integrating this data comes with its challenges, such as standardized and reproducible analysis. Seq2science is a multi-purpose workflow that covers preprocessing, quality control, visualization, and analysis of functional genomics sequencing data. It facilitates the downloading of sequencing data from all major databases, including NCBI SRA, EBI ENA, DDBJ, GSA, and ENCODE. Furthermore, it automates the retrieval of any genome assembly available from Ensembl, NCBI, and UCSC. It has been tested on a variety of species, and includes diverse workflows such as ATAC-, RNA-, and ChIP-seq. It consists of both generic as well as advanced steps, such as differential gene expression or peak accessibility analysis and differential motif analysis. Seq2science is built on the Snakemake workflow language and thus can be run on a range of computing infrastructures. It is available at https://github.com/vanheeringen-lab/seq2science. creator: Maarten van der Sande creator: Siebren Frölich creator: Tilman Schäfers creator: Jos G.A. Smits creator: Rebecca R. Snabel creator: Sybren Rinzema creator: Simon J. van Heeringen uri: https://doi.org/10.7717/peerj.16380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 van der Sande et al. title: Impact of nitrogen application and crop stage on epiphytic microbial communities on silage maize leaf surfaces link: https://peerj.com/articles/16386 last-modified: 2023-11-15 description: This study aimed to examine the impact of nitrogen (N) fertilization on phyllosphere microorganisms in silage maize (Zea mays) to enhance the production of high-quality silage. The effects of different N application rates (160, 240, and 320 kg ha−1) and maturity stages (flowering and dough stages) on microbial diversity, abundance and physiochemical properties of the leaf surfaces were evaluated in a field experiment. The results showed that N application rates did not significantly impact the abundance of lactic acid bacteria (LAB), aerobic bacteria (AB), yeasts, or molds on the leaf surfaces. However, these microbes were more abundant during the flowering stage compared to the dough stage. Furthermore, the N application rate had no significant impact on inorganic phosphorus, soluble sugar, free amino acids, total phenolic content, and soluble protein concentrations, or pH levels on the leaf surfaces. Notably, these chemical indices were lower during the dough stage. The abundance of Pantoea decreased with higher N application rates, while that of other microorganisms did not changes significantly. The abundance of AB, LAB, yeasts, and molds were positively correlated with soluble sugar, soluble protein, inorganic phosphorus, free amino acids, and total phenolic concentrations on leaf surfaces. Moreover, water loss was negatively correlated with the abundance of AB, LAB, yeasts, and molds, whereas water retention capacity and stomatal density were positively correlated with microbial abundance. We recommend applying an optimal N rate of 160 kg ha−1 to silage maize and harvesting at the flowering stage is recommended. creator: Dan Wu creator: Xueling Ma creator: Yuanyan Meng creator: Rongjin Cai creator: Xiaolong Zhang creator: Li Liu creator: Lianping Deng creator: Changjing Chen creator: Fang Wang creator: Qingbiao Xu creator: Bin He creator: Mingzhu He creator: Rensheng Hu creator: Jinjing Zhen creator: Yan Han creator: Shaoshen He creator: Liuxing Xu uri: https://doi.org/10.7717/peerj.16386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wu et al. title: Genetic divergences and hybridization within the Sebastes inermis complex link: https://peerj.com/articles/16391 last-modified: 2023-11-15 description: The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and “Kumano” (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the “Kumano” morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow. creator: Diego Deville creator: Kentaro Kawai creator: Hiroki Fujita creator: Tetsuya Umino uri: https://doi.org/10.7717/peerj.16391 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Deville et al. title: Profile of the bile acid FXR-FGF15 pathway in the glucolipid metabolism disorder of diabetic mice suffering from chronic stress link: https://peerj.com/articles/16407 last-modified: 2023-11-15 description: BackgroundImbalances in bile acid (BA) synthesis and metabolism are involved in the onset of diabetes and depression in humans and rodents. However, the role of BAs and the farnesoid X receptor (FXR)/fibroblast growth factor (FGF) 15 signaling pathway in the development of diabetes and depression is still largely unknown. Therefore, we investigated the potential molecular mechanisms of BAs that may be associated with glucolipid metabolism disorders in diabetic mice subjected to chronic stress.MethodsThe type 2 diabetes mellitus (T2DM) mouse model was induced by feeding mice a high-fat diet and administering an intraperitoneal injection of streptozotocin (STZ). The chronic unpredictable mild stress (CUMS) procedure was performed by introducing a series of mild stressors. Forty mice were randomly divided into the regular chow feeding group and the high-fat diet feeding group. After two weeks of feeding, the mice were randomly divided into four groups: the Control group, CUMS group, T2DM group, and T2DM+CUMS group. The T2DM group and T2DM+CUMS group received an intraperitoneal injection of STZ to induce the T2DM model. The CUMS and T2DM+CUMS groups were exposed to CUMS to induce depressive-like phenotypes. Blood and tissue samples were obtained for pertinent analysis and detection.ResultsCompared with the T2DM mice, T2DM+CUMS mice had higher blood glucose and lipid levels, insulin resistance, inflammation of the liver and pancreas, impaired liver function, and increased total bile acids. These changes were accompanied by attenuated FXR signaling. Chronic stress was found to attenuate FXR expression and its downstream target, FGF15, in the ileum when compared with the T2DM group.ConclusionFXR may play a role in the diabetic disorder of glucolipid metabolism when aggravated by chronic stress. FXR and its downstream target, FGF15, may be therapeutic targets for treating comorbid T2DM and depression. creator: Weijia Cai creator: Canye Li creator: Zuanjun Su creator: Jinming Cao creator: Zhicong Chen creator: Yitian Chen creator: Zhijun Guo creator: Jian Cai creator: Feng Xu uri: https://doi.org/10.7717/peerj.16407 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cai et al. title: VGGish-based detection of biological sound components and their spatio-temporal variations in a subtropical forest in eastern China link: https://peerj.com/articles/16462 last-modified: 2023-11-15 description: Passive acoustic monitoring technology is widely used to monitor the diversity of vocal animals, but the question of how to quickly extract effective sound patterns remains a challenge due to the difficulty of distinguishing biological sounds within multiple sound sources in a soundscape. In this study, we address the potential application of the VGGish model, pre-trained on Google’s AudioSet dataset, for the extraction of acoustic features, together with an unsupervised clustering method based on the Gaussian mixture model, to identify various sound sources from a soundscape of a subtropical forest in China. The results show that different biotic and abiotic components can be distinguished from various confounding sound sources. Birds and insects were the two primary biophony sound sources, and their sounds displayed distinct temporal patterns across both diurnal and monthly time frames and distinct spatial patterns in the landscape. Using the clustering and modeling method of the general sound feature set, we quickly depicted the soundscape in a subtropical forest ecosystem, which could be used to track dynamic changes in the acoustic environment and provide help for biodiversity and ecological environment monitoring. creator: Mei Wang creator: Jinjuan Mei creator: Kevin FA Darras creator: Fanglin Liu uri: https://doi.org/10.7717/peerj.16462 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Assessing the ecological risk of heavy metal sediment contamination from Port Everglades Florida USA link: https://peerj.com/articles/16152 last-modified: 2023-11-14 description: Port sediments are often contaminated with metals and organic compounds from anthropogenic sources. Remobilization of sediment during a planned expansion of Port Everglades near Fort Lauderdale, Florida (USA) has the potential to harm adjacent benthic communities, including coral reefs. Twelve sediment cores were collected from four Port Everglades sites and a control site; surface sediment was collected at two nearby coral reef sites. Sediment cores, sampled every 5 cm, were analyzed for 14 heavy metals using inductively coupled plasma-mass spectrometry. Results for all three locations yielded concentration ranges (µg/g): As (0.607–223), Cd (n/d–0.916), Cr (0.155–56.8), Co (0.0238–7.40), Cu (0.004–215), Pb (0.0169–73.8), Mn (1.61–204), Hg (n/d–0.736), Mn (1.61–204), Ni (0.232–29.3), Se (n/d–4.79), Sn (n/d–140), V (0.160–176), and Zn (0.112–603), where n/d = non-detected. The geo-accumulation index shows moderate-to-strong contamination of As and Mo in port sediments, and potential ecological risk indicates moderate-to-significantly high overall metal contamination. All four port sites have sediment core subsamples with As concentrations above both threshold effect level (TEL, 7.24 µg/g) and probable effect level (PEL, 41.6 µg/g), while Mo geometric mean concentrations exceed the background continental crust level (1.5 µg/g) threshold. Control site sediments exceed TEL for As, while the reef sites has low to no overall heavy metal contamination. Results of this study indicate there is a moderate to high overall ecological risk from remobilized sediment due to metal contamination. Due to an imminent dredging at Port Everglades, this could have the potential to harm the threatened adjacent coral communities and surrounding protected habitats. creator: Dimitrios G. Giarikos creator: Laura White creator: Andre M. Daniels creator: Radleigh G. Santos creator: Paul E. Baldauf creator: Amy C. Hirons uri: https://doi.org/10.7717/peerj.16152 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Giarikos et al. title: Seasonal benthic species composition linked to coastal defense structures (CDS) in Kuala Nerus, Terengganu, Malaysia link: https://peerj.com/articles/16203 last-modified: 2023-11-14 description: BackgroundThe natural hydrodynamic process of Kuala Nerus, Terengganu, has changed since the extension of Sultan Mahmud Airport runway in 2008. Consequently, severe coastal erosion has occurred in the area, particularly during the northeast monsoon season (NEM). Numerous types of coastal defense structures (CDS) have been constructed to protect the coastline. Despite the loss of esthetic values, the effect of CDS construction on marine organisms in the area remains unknown. Hence, this study aims to assess the ecological aspects of macrobenthic compositions at the CDS area of Kuala Nerus, Terengganu, based on the differences between the southwest (SWM) and northeast (NEM) monsoon seasons.MethodsMacrobenthos were collected from the sediment in July (SWM) and December 2021 (NEM) using the Ponar grab at 12 substations from five sampling stations.ResultsThe density of macrobenthos was higher in SWM (48,190.82 ind./m2) than in NEM (24,504.83 ind./m2), with phylum Mollusca recording the highest species composition (60–99.3%). The macrobenthos species had a low to moderate level of diversity (H’ = 1.4–3.1) with the species were almost evenly distributed (J’ = 0.2–0.8). Windward substations exhibited coarser grain sizes (38.56%–86.84%), whereas landward substations exhibited very fine grain sizes (44.26%–86.70%). The SWM season recorded a higher organic matter content (1.6%–6.33%) than the NEM season (0.4%–3.1%). However, metal concentrations in the surface sediment were within the safe range and permissible limits for both seasons, inferring that the macrobenthos composition was unaffected.DiscussionThis study demonstrated that the CDS associated with the monsoon system has controlled the hydrodynamics and nearshore sedimentary processes in the Kuala Nerus coastal zone, thereby affecting the macrobenthos population, in terms of richness and density. The ecological and energetic effects of the coastal structures in different seasons have resulted in a more significant result, with the SWM exhibiting a higher macrobenthos composition than the NEM. creator: Nur Fazne Ibrahim creator: Muzzalifah Abd Hamid creator: Mohd Fadzil Mohd Akhir creator: Meng Chuan Ong creator: Wan Izatul Asma Wan Talaat creator: Izwandy Idris uri: https://doi.org/10.7717/peerj.16203 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ibrahim et al. title: Osteology of the axial skeleton of Aucasaurus garridoi: phylogenetic and paleobiological inferences link: https://peerj.com/articles/16236 last-modified: 2023-11-14 description: Aucasaurus garridoi is an abelisaurid theropod from the Anacleto Formation (lower Campanian, Upper Cretaceous) of Patagonia, Argentina. The holotype of Aucasaurus garridoi includes cranial material, axial elements, and almost complete fore- and hind limbs. Here we present a detailed description of the axial skeleton of this taxon, along with some paleobiological and phylogenetic inferences. The presacral elements are somewhat fragmentary, although these show features shared with other abelisaurids. The caudal series, to date the most complete among brachyrostran abelisaurids, shows several autapomorphic features including the presence of pneumatic recesses on the dorsal surface of the anterior caudal neural arches, a tubercle lateral to the prezygapophysis of mid caudal vertebrae, a marked protuberance on the lateral rim of the transverse process of the caudal vertebrae, and the presence of a small ligamentous scar near the anterior edge of the dorsal surface in the anteriormost caudal transverse process. The detailed study of the axial skeleton of Aucasaurus garridoi has also allowed us to identify characters that could be useful for future studies attempting to resolve the internal phylogenetic relationships of Abelisauridae. Computed tomography scans of some caudal vertebrae show pneumatic traits in neural arches and centra, and thus the first reported case for an abelisaurid taxon. Moreover, some osteological correlates of soft tissues present in Aucasaurus and other abelisaurids, especially derived brachyrostrans, underscore a previously proposed increase in axial rigidity within Abelisauridae. creator: Mattia Antonio Baiano creator: Rodolfo Coria creator: Luis M. Chiappe creator: Virginia Zurriaguz creator: Ludmila Coria uri: https://doi.org/10.7717/peerj.16236 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Baiano et al. title: Characteristic of persistent human papillomavirus infection in women worldwide: a meta–analysis link: https://peerj.com/articles/16247 last-modified: 2023-11-14 description: ObjectivesWe aimed to estimate the genotype distribution of persistent human papillomavirus (HPV) infection in females worldwide, and provided a scientific basis for the prevention strategies of cervical cancer (CC) and the development of HPV vaccines.MethodsBoth English and Chinese databases were researched from the inception to July 2023. The pooled persistent HPV infection prevalence was calculated using a random effects model. The subgroup analysis was performed to explore the heterogeneity. Publication bias was evaluated using funnel plot, Egger’s and Begg’s test.ResultsTwenty-eight studies with 27,335 participants were included. The pooled prevalence of persistent HPV infection was 29.37% (95% CI [24.05%∼35.31%]), and the genotypes with the persistent infection prevalence were HPV16 (35.01%), HPV52 (28.19%), HPV58 (27.06%), HPV18 (25.99%), HPV33 (24.37%), HPV31 (23.35%), HPV59 (21.87%), HPV39 (19.54%), HPV68 (16.61%) and HPV45 (15.05%). The prevalence of multiple and single HPV persistent infection were 48.66% and 36.71%, respectively; the prevalence of persistent HPV infection in different age groups (<30, 30∼39, 40∼49, >50) were 29.83%, 28.39%, 22.24% and 30.22%, respectively. The follow-up time was significantly associated with heterogeneity by subgroup analysis (P < 0.05), and the prevalence of persistent infection decreased with longer follow-up time.ConclusionsMultiple infections were more likely to occur persistent HPV infection than single infection. In addition to HPV vaccination, we should emphasize the follow-up management for women under 30 and over 50 years old, those with high-risk HPV infection (HPV59, 39, 68) and multiple infections. creator: Ming Zhao creator: Dan Zhou creator: Min Zhang creator: Peipei Kang creator: Meimei Cui creator: Liling Zhu creator: Limei Luo uri: https://doi.org/10.7717/peerj.16247 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: Immune activity score to assess the prognosis, immunotherapy and chemotherapy response in gastric cancer and experimental validation link: https://peerj.com/articles/16317 last-modified: 2023-11-14 description: BackgroundGastric cancer (GC) is an extremely heterogeneous malignancy with a complex tumor microenvironment (TME) that contributes to unsatisfactory prognosis.MethodsThe overall activity score for assessing the immune activity of GC patients was developed based on cancer immune cycle activity index in the Tracking Tumor Immunophenotype (TIP). Genes potentially affected by the overall activity score were screened using weighted gene co-expression network analysis (WGCNA). Based on the expression profile data of GC in The Cancer Genome Atlas (TCGA) database, COX analysis was applied to create an immune activity score (IAS). Differences in TME activity in the IAS groups were analyzed. We also evaluated the value of IAS in estimating immunotherapy and chemotherapy response based on immunotherapy cohort. Gene expression in IAS model and cell viability were determined by real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) and Cell Counting Kit-8 (CCK-8) assay, respectively.ResultsWGCAN analysis screened 629 overall activity score-related genes, which were mainly associated with T cell response and B cell response. COX analysis identified AKAP5, CTLA4, LRRC8C, AOAH-IT1, NPC2, RGS1 and SLC2A3 as critical genes affecting the prognosis of GC, based on which the IAS was developed. Further RT-qPCR analysis data showed that the expression of AKAP5 and CTLA4 was downregulated, while that of LRRC8C, AOAH-IT1, NPC2, RGS1 and SLC2A3 was significantly elevated in GC cell lines. Inhibition of AKAP5 increased cell viability but siAOAH-IT1 promoted viability of GC cells. IAS demonstrated excellent robustness in predicting immunotherapy outcome and GC prognosis, with low-IAS patients having better prognosis and immunotherapy. In addition, resistance to Erlotinib, Rapamycin, MG-132, Cyclopamine, AZ628, and Sorafenib was reduced in patients with low IAS.ConclusionIAS was a reliable prognostic indicator. For GC patients, IAS showed excellent robustness in predicting GC prognosis, immune activity status, immunotherapy response, and chemotherapeutic drug resistance. Our study provided novel insights into the prognostic assessment in GC. creator: Xuan Wu creator: Fengrui Zhou creator: Boran Cheng creator: Gangling Tong creator: Minhua Chen creator: Lirui He creator: Zhu Li creator: Shaokang Yu creator: Shubin Wang creator: Liping Lin uri: https://doi.org/10.7717/peerj.16317 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wu et al. title: Bite and tooth marks on sauropod dinosaurs from the Morrison Formation link: https://peerj.com/articles/16327 last-modified: 2023-11-14 description: Tooth-marked bones provide important evidence for feeding choices made by extinct carnivorous animals. In the case of the dinosaurs, most bite traces are attributed to the large and robust osteophagous tyrannosaurs, but those of other large carnivores remain underreported. Here we report on an extensive survey of the literature and some fossil collections cataloging a large number of sauropod bones (68) from the Upper Jurassic Morrison Formation of the USA that bear bite traces that can be attributed to theropods. We find that such bites on large sauropods, although less common than in tyrannosaur-dominated faunas, are known in large numbers from the Morrison Formation, and that none of the observed traces showed evidence of healing. The presence of tooth wear in non-tyrannosaur theropods further shows that they were biting into bone, but it remains difficult to assign individual bite traces to theropod taxa in the presence of multiple credible candidate biters. The widespread occurrence of bite traces without evidence of perimortem bites or healed bite traces, and of theropod tooth wear in Morrison Formation taxa suggests preferential feeding by theropods on juvenile sauropods, and likely scavenging of large-sized sauropod carcasses. creator: Roberto Lei creator: Emanuel Tschopp creator: Christophe Hendrickx creator: Mathew J. Wedel creator: Mark Norell creator: David W.E. Hone uri: https://doi.org/10.7717/peerj.16327 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lei et al. title: Tricks of the puppet masters: morphological adaptations to the interaction with nervous system underlying host manipulation by rhizocephalan barnacle Polyascus polygeneus link: https://peerj.com/articles/16348 last-modified: 2023-11-14 description: BackgroundRhizocephalan interaction with their decapod hosts is a superb example of host manipulation. These parasites are able to alter the host’s physiology and behavior. Host-parasite interaction is performed, presumably, via special modified rootlets invading the ventral ganglions.MethodsIn this study, we focus on the morphology and ultrastructure of these special rootlets in Polyascus polygeneus (Lützen & Takahashi, 1997), family Polyascidae, invading the neuropil of the host’s nervous tissue. The ventral ganglionic mass of the infected crabs were fixed, and the observed sites of the host-parasite interplay were studied using transmission electron microscopy, immunolabeling and confocal microscopy.ResultsThe goblet-shaped organs present in the basal families of parasitic barnacles were presumably lost in a common ancestor of Polyascidae and crown “Akentrogonida”, but the observed invasive rootlets appear to perform similar functions, including the synthesis of various substances which are transferred to the host’s nervous tissue. Invasive rootlets significantly differ from trophic ones in cell layer composition and cuticle thickness. Numerous multilamellar bodies are present in the rootlets indicating the intrinsic cell rearrangement. The invasive rootlets of P. polygeneus are enlaced by the thin projections of glial cells. Thus, glial cells can be both the first hosts’ respondents to the nervous tissue damage and the mediator of the rhizocephalan interaction with the nervous cells. One of the potential molecules engaged in the relationships of P. polygeneus and its host is serotonin, a neurotransmitter which is found exclusively in the invasive rootlets but not in trophic ones. Serotonin participates in different biological pathways in metazoans including the regulation of aggression in crustaceans, which is reduced in infected crabs. We conclude that rootlets associated with the host’s nervous tissue are crucial for the regulation of host-parasite interplay and for evolution of the Rhizocephala. creator: Anastasia Lianguzova creator: Natalia Arbuzova creator: Ekaterina Laskova creator: Elizaveta Gafarova creator: Egor Repkin creator: Dzmitry Matach creator: Irina Enshina creator: Aleksei Miroliubov uri: https://doi.org/10.7717/peerj.16348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lianguzova et al. title: Plasma thrombin-activatable fibrinolysis inhibitor and the 1040C/T polymorphism are risk factors for diabetic kidney disease in Chinese patients with type 2 diabetes link: https://peerj.com/articles/16352 last-modified: 2023-11-14 description: BackgroundInflammatory and hemostatic disorders in diabetic microangiopathy (DMA) can be linked to thrombin-activatable fibrinolysis inhibitor (TAFI) and its own gene polymorphisms. Thus, the study aimed to investigate the associations of plasma TAFI and gene polymorphisms with DMA in Chinese patients with type 2 diabetes (T2D).MethodsPlasma TAFI of 223 patients with T2D was measured, and the genotypes and alleles of the 1040C/T, 438G/A, and 505G/A polymorphisms of the TAFI gene were analyzed. A ROC curve was constructed to evaluate the identifying power of TAFI between patients with T2D and DMA, and logistic regression analysis was used to observe the correlation of plasma TAFI and gene polymorphisms with the risk for DMA.ResultsPlasma TAFI was higher in patients with DMA than in patients with only T2D (p < 0.05). TAFI exhibited the largest area under ROC in identifying diabetic kidney disease (DKD) from only T2D (0.763, 95% CI [0.674–0.853], p < 0.01), and adjusted multivariate analysis showed a high odds ratio (OR: 15.72, 95% CI [4.573–53.987], p < 0.001) for DKD. Higher frequencies of the CT genotype and T allele of the 1040C/T polymorphism were found in DKD compared with only T2D (respectively p < 0.05), and the CT genotype exhibited a high OR (1.623, 95% CI [1.173–2.710], p < 0.05) for DKD. DKD patients with the CT genotype had higher plasma TAFI levels, while T2D and DKD patients with CC/TT genotypes had lower plasma TAFI levels.ConclusionPlasma TAFI and the CT genotype and T allele of the 1040C/T polymorphism are independent risk factors for DKD in Chinese T2D patients. creator: Qinghua Huang creator: Dujin Feng creator: Lianlian Pan creator: Huan Wang creator: Yan Wu creator: Bin Zhong creator: Jianguang Gong creator: Huijun Lin creator: Xianming Fei uri: https://doi.org/10.7717/peerj.16352 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Huang et al. title: Psychometric properties of the Mexican version of the opening minds stigma scale for health care providers (OMS-HC) link: https://peerj.com/articles/16375 last-modified: 2023-11-14 description: BackgroundHealthcare providers are one of the main groups that contribute to the stigmatization of people with mental disorders. Apathy, accusation, fatalism, and morbid curiosity are the most common forms of stigmatization encountered, and these are associated with inadequate treatment, reduced treatment adherence, decreased help-seeking behavior, an increased risk of relapse, and complications with other medical conditions. The aim of this study was to examine the psychometric properties of an adapted Spanish version of the Opening Minds Stigma Scale (OMS-HC) for healthcare providers in Mexico and identify certain stigmatizing attitudes within this group.MethodsAn ex-post facto cross-sectional observational study was conducted with 556 healthcare providers in Mexico, with an average age of 29.7 years, who were mostly women (80.4%). Validity was examined through confirmatory factor analysis. Differences according to gender, discipline, occupation, and educational level were analyzed using multivariate methods.ResultsThe factor structure of the OMS-HC, consisting of three subscales identified by the original authors of the instrument (attitudes of healthcare providers towards people with mental illness, secrecy/help-seeking, and social distance), was confirmed. The model demonstrated good fit (x2/df = 2.36, RMSEA = 0.050, CFI = 0.970, TLI = 0.962, SRMR = 0.054, NFI = 0.950, PNFI = 0.742). Internal consistency was found to be adequate (α = 0.73, ω = 0.76) for the scale itself and slightly lower than acceptable for the subscales. Significant differences were found by discipline, educational level, and, for student providers, by academic semester. Higher scores were observed on the OMS-HC scale among nursing and medical professionals, undergraduate students, and those in early semesters.ConclusionsThe Spanish version of the OMS-HC has demonstrated adequate psychometric properties and could be a useful tool to facilitate research on this topic in Mexico, and to carry out comparative studies with healthcare personnel in other Spanish-speaking countries. creator: Hugo Noel Valdivia Ramos creator: Jazmín Mora-Rios creator: Guillermina Natera creator: Liliana Mondragón uri: https://doi.org/10.7717/peerj.16375 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Valdivia Ramos et al. title: Endoplasmic reticulum stress in the pathogenesis of alcoholic liver disease link: https://peerj.com/articles/16398 last-modified: 2023-11-14 description: The endoplasmic reticulum (ER) plays a pivotal role in protein synthesis, folding, and modification. Under stress conditions such as oxidative stress and inflammation, the ER can become overwhelmed, leading to an accumulation of misfolded proteins and ensuing ER stress. This triggers the unfolded protein response (UPR) designed to restore ER homeostasis. Alcoholic liver disease (ALD), a spectrum disorder resulting from chronic alcohol consumption, encompasses conditions from fatty liver and alcoholic hepatitis to cirrhosis. Metabolites of alcohol can incite oxidative stress and inflammation in hepatic cells, instigating ER stress. Prolonged alcohol exposure further disrupts protein homeostasis, exacerbating ER stress which can lead to irreversible hepatocellular damage and ALD progression. Elucidating the contribution of ER stress to ALD pathogenesis may pave the way for innovative therapeutic interventions. This review delves into ER stress, its basic signaling pathways, and its role in the alcoholic liver injury. creator: Man Na creator: Xingbiao Yang creator: Yongkun Deng creator: Zhaoheng Yin creator: Mingwei Li uri: https://doi.org/10.7717/peerj.16398 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Na et al. title: Temporal bright light at low frequency retards lens-induced myopia in guinea pigs link: https://peerj.com/articles/16425 last-modified: 2023-11-14 description: PurposeBright light conditions are supposed to curb eye growth in animals with experimental myopia. Here we investigated the effects of temporal bright light at very low frequencies exposures on lens-induced myopia (LIM) progression.MethodsMyopia was induced by application of −6.00 D lenses over the right eye of guinea pigs. They were randomly divided into four groups based on exposure to different lighting conditions: constant low illumination (CLI; 300 lux), constant high illumination (CHI; 8,000 lux), very low frequency light (vLFL; 300/8,000 lux, 10 min/c), and low frequency light (LFL; 300/8,000 lux, 20 s/c). Refraction and ocular dimensions were measured per week. Changes in ocular dimensions and refractions were analyzed by paired t-tests, and differences among the groups were analyzed by one-way ANOVA.ResultsSignificant myopic shifts in refractive error were induced in lens-treated eyes compared with contralateral eyes in all groups after 3 weeks (all P < 0.05). Both CHI and LFL conditions exhibited a significantly less refractive shift of LIM eyes than CLI and vLFL conditions (P < 0.05). However, only LFL conditions showed significantly less overall myopic shift and axial elongation than CLI and vLFL conditions (both P < 0.05). The decrease in refractive error of both eyes correlated significantly with axial elongation in all groups (P < 0.001), except contralateral eyes in the CHI group (P = 0.231). LFL condition significantly slacked lens thickening in the contralateral eyes.ConclusionsTemporal bright light at low temporal frequency (0.05 Hz) appears to effectively inhibit LIM progression. Further research is needed to determine the safety and the potential mechanism of temporal bright light in myopic progression. creator: Baodi Deng creator: Wentao Li creator: Ziping Chen creator: Junwen Zeng creator: Feng Zhao uri: https://doi.org/10.7717/peerj.16425 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Deng et al. title: Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus link: https://peerj.com/articles/16455 last-modified: 2023-11-14 description: BackgroundApis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues.MethodsShort-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly.ResultsAt least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with ‘Africanized’ honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1–100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species.DiscussionCollectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage. creator: Robert S. Cornman uri: https://doi.org/10.7717/peerj.16455 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Epidemiology and transmission of hepatitis A in Shaanxi (western China) after more than ten years of universal vaccination link: https://peerj.com/articles/16305 last-modified: 2023-11-13 description: BackgroundHepatitis A (HepA) vaccination and economic factors can change the epidemiology of HepA. In China, the implementation of free vaccination for children under 1.5 years of age in 2008 has resulted in a decline in the overall incidence of HepA. Nevertheless, further investigation is required to comprehensively understand the epidemiological patterns of HepA in economically disadvantaged regions of China.MethodIn this study, we evaluated the incidence, seroprevalence, and transmission characteristics of HepA in Shaanxi with less economically developed. We obtained data on reported cases of HepA from 2005 to 2020. Blood samples from 1,559 individuals aged 0 to 60 years were tested for anti-hepatitis A (HAV) antibodies. A questionnaire survey and blood sample collection were conducted in two sentinel sites from 2019 to 2021.ResultBetween 2008 to 2020, the number of reported cases of HepA decreased from 3.44/100,000 person-years to 0.65/100,000 person-years, indicating an 81.1% decrease, which was particularly pronounced among younger age groups (0–19 years). From 2015–2020, infections were more likely to occur in people in their 40s and those over the age of 60. Farmers were still the most common occupation of HepA in the last decade. The results of the serological investigation showed the highest anti-HAV seroprevalence was observed in adults aged 39–60 years (94.6%) and those aged 28–38 years (87.8%). The 10–15 years group had the lowest seroprevalence at 49.3%. During the study period, a total of 22 cases were reported by sentinel sites, but the common risk factors (like raw food exposure, travel history, and closed contact with patients) were not identified.ConclusionGiven the greater severity of illness in the adult population and the ambiguous transmission routine, enhanced surveillance for HepA and evaluations that identify feasible approaches to mitigate the risk of HAV transmission are urgent priorities. creator: Xiaotong Hu creator: Weijun Hu creator: Yuanyuan Dong creator: Xuan Lu creator: Fujie Xu creator: Shaobai Zhang uri: https://doi.org/10.7717/peerj.16305 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hu et al. title: Prognostic value of high-sensitivity cardiac troponin for major adverse cardiovascular events in patients with diabetes: a systematic review and meta-analysis link: https://peerj.com/articles/16376 last-modified: 2023-11-13 description: BackgroundHigh-sensitivity cardiac troponin (hs-cTn) is associated with cardiovascular outcomes in the general population, but the prognostic value of hs-cTn in the diabetic population remains inconclusive. This study aimed to systematically review current evidence regarding the association between hs-cTn and the prognosis of diabetic patients.MethodsMEDLINE, Embase, and the Cochrane Database were searched from inception to May, 2023. Observational studies that investigated the prognostic value of hs-cTn in diabetic patients were included in this meta-analysis. Studies were excluded if they did not report outcomes of interest, or urine hs-cTn were measured. Two independent investigators extracted and analyzed the data according to the PRISMA guidelines. The primary outcome was long-term major adverse cardiovascular events (MACE).ResultsWe included 30 cohort studies of 62,419 diabetic patients. After a median follow-up of 5 (4.1–9.5) years, the pooled results suggested elevation of hs-cTn was associated with a significantly increased risk of MACE (adjusted hazard ratio (HR) per standard deviation (SD) change 1.15, 95% CI [1.06–1.25], I2 = 0%) and heart failure (adjusted HR per SD change 1.33, 95% CI [1.08–1.63], I2 = 0%) in patients with diabetes. No significant association was found regarding the association between elevation of hs-cTn and risk of all-cause mortality (adjusted HR per SD change 1.24, 95% CI [0.98–1.57], I2 = 0%). The results of sensitivity analyses were similar in prospective cohort studies, high-quality studies, or population without major cardiovascular comorbidities at baseline. hs-cTn may represent a strong and independent predictor of MACE and heart failure in diabetic patients. Future research is warranted to determine the appropriate cutoff value for hs-cTn with different comorbidities, for instance, diabetic nephropathy, peripheral artery diseases, etc. creator: Tiange Song creator: Yu Lan creator: Kecheng Li creator: Honglang Huang creator: Li Jiang uri: https://doi.org/10.7717/peerj.16376 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Song et al. title: The correlation between heart rate variability index and vulnerability prognosis in patients with acute decompensated heart failure link: https://peerj.com/articles/16377 last-modified: 2023-11-13 description: ObjectiveTo explore the correlation between Heart Rate Variability Index (HRV) and poor prognosis in patients with acute decompensated heart failure (ADHF).MethodsA retrospective compilation of clinical data encompassed 128 cases of patients afflicted with acute decompensated heart failure (ADHF) who were admitted to and discharged from our hospital between April 2019 and July 2022. Subsequent to assessing their follow-up progress during the tracking period, the subjects were categorized into two cohorts: the poor prognosis group (n = 31) and the good prognosis group (n = 97). Comparative analysis of clinical data and Heart Rate Variability (HRV) parameters was executed between these two groups. Moreover, a multiple linear regression analysis was employed to identify the contributing factors associated with adverse prognoses in ADHF patients. Furthermore, the receiver operating characteristic (ROC) curve was employed to evaluate the prognostic predictive capability of HRV parameters among ADHF patients.ResultsThe levels of SDNN (t = 3.924, P < 0.001), SDANN (t = 4.520, P < 0.001) and LF (t = 2.676, P = 0.018) in the poor prognosis group were significantly higher than those in the good prognosis group, and the differences were statistically significant (P < 0.05). The levels of PNN50 (t = 2.132, P = 0.035), HF (t = 11.781, P < 0.001) and LF/HF (t = 11.056, P < 0.001) in the poor prognosis group were significantly lower than those in the good prognosis group (P < 0.05). The results of multiple linear regression analysis indicated that SDNN, SDANN, LF, PNN50, and HF were factors influencing poor prognosis in ADHF patients (P < 0.05). The results of the ROC curve analysis indicate that the area under the curve (AUC) for predicting poor prognosis in ADHF patients using HRV parameters were as follows: SDNN (AUC = 0.818, 95% CI [0.722–0.914]), SDANN (AUC = 0.684, 95% CI [0.551–0.816]), PNN50 (AUC = 0.754, 95% CI [0.611–0.841]), LF/HF (AUC = 0.787, 95% CI [0.679–0.896]), and combined diagnosis (AUC = 0.901, 95% CI [0.832–0.970]). Among these, the combined diagnosis exhibited the highest AUC, sensitivity, and specificity for predicting poor prognosis in ADHF patients (P < 0.001).ConclusionThe HRV parameters of SDNN, SDANN, PNN50 and LF/HF are closely related to the prognosis of ADHF patients. The combined detection of the above HRV parameters can improve the efficacy of predicting the poor prognosis of ADHF patients. This suggests that clinical staff can identify ADHF patients at risk of poor prognosis by long-term monitoring of HRV in the future. creator: Hongbo Liu creator: Xiaotong Wang creator: Xiaowei Wang uri: https://doi.org/10.7717/peerj.16377 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liu et al. title: The impact of vestibular dysfunction on falls and postural instability in individuals with type 2 diabetes with and without diabetic polyneuropathy link: https://peerj.com/articles/16382 last-modified: 2023-11-13 description: AimThis study aimed to determine the association between vestibular dysfunction, falls, and postural instability in individuals with type 2 diabetes (T2D) compared to healthy control individuals and to examine the impact of diabetic polyneuropathy (DPN).MethodsThis cross-sectional study included individuals with T2D with DPN (n = 43), without DPN (n = 32), and healthy controls (n = 32). Cervical and ocular vestibular evoked myogenic potentials (VEMP) were recorded, and latencies and amplitudes were determined. DPN was diagnosed based on nerve conduction studies and clinical scores. Postural instability was examined using a static posturographic balance system and calculated as an instability index (ST). Falls were recorded retrospectively during the past year. Group comparisons were conducted by using univariate and bivariate statistics.ResultsIndividuals with T2D experienced more falls than healthy controls (T2D with DPN n = 12[38%], T2D without DPN n = 15[35%], controls n = 5[16%], p = 0.04). Individuals with T2D had decreased postural stability, T2D with DPN, ST (median of 52[iqi = 33; 77]), T2D without DPN, ST (median of 31[iqi = 24; 39]), controls ST (median of 26[iqi = 19; 33], p = 0.01), when comparing all three groups. Individuals with T2D had a greater number of no-responses in oVEMP compared to controls (T2D with DPN, n = 15[46.9%] T2D without DPN n = 25[58.1%], controls n = 9[28.1%], p = 0.04). No difference was found in cVEMP and oVEMP amplitudes in any of the groups. Irrespectively of DPN, fallers with T2D had decreased oVEMP and cVEMP latencies on the right ears, when comparing to non-fallers, respectively, n10 (fallers [median of 16, iqi=15;19 ms.] vs. non-fallers [median of 25 iqi=16;35 ms]); p13 (fallers [median of 16, iqi=15;17 ms.] vs. non-fallers [median of 15, iqi=8;16 ms.], p < 0.05).ConclusionFalls and postural instability were more frequent in individuals with T2D compared to healthy controls. Fallers with T2D had vestibular end-organ impairments based on the oVEMP and cVEMP latencies on the right but not the left ears, irrespective of DPN. Individuals with T2D had more frequent no-response of the oVEMP, indicating impaired vestibular nerve function. creator: Ina Ejsing Hunnerup Jørgensen creator: Louise Devantier creator: Hatice Tankisi creator: Henning Andersen creator: Karolina Snopek Khan uri: https://doi.org/10.7717/peerj.16382 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jørgensen et al. title: Identification and characterization of cold-responsive aquaporins from the larvae of a crambid pest Agriphila aeneociliella (Eversmann) (Lepidoptera: Crambidae) link: https://peerj.com/articles/16403 last-modified: 2023-11-13 description: As small ectotherms, insects need to cope with the challenges of winter cold by regulating the water content through water transport. Aquaporins (AQPs) are key players to enhance the cold resistance by mediating essential homeostatic processes in many animals but remain poorly characterized in insects. Agriphila aeneociliella is a newly discovered winter wheat pest in China, and its early-stage larvae have strong tolerance to low temperature stress. Six AQP genes were identified, which belong to five AQP subfamilies (RPIP, Eglp, AQP12L, PRIP, DRIP). All of them contained six hydrophobic transmembrane helices (TMHs) and two relatively conservative Asparagine-Proline-Alanine motifs. The three-dimensional homology modeling showed that the six TMHs folded into an hourglass-like shape, and the imperceptible replace of four ar/R residues in contraction region had critical effects on changing the pore size of channels. Moreover, the transcript levels of AaAQP 1, 3, and 6 increased significantly with the treatment time below 0 °C. Combined with the results of pore radius variation, it is suggested that AaAQP1 and AaAQP3 may be considered to be the key anti-hypothermia proteins in A. aeneociliella by regulating rapid cell dehydration and allowing the influx of extracellular cold resistance molecules, thus avoiding death in winter. creator: Chunqing Zhao creator: Zhen Liu creator: Yong Liu creator: Yidi Zhan uri: https://doi.org/10.7717/peerj.16403 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhao et al. title: Comparison of nutritional supplements in improving glycolipid metabolism and endocrine function in polycystic ovary syndrome: a systematic review and network meta-analysis link: https://peerj.com/articles/16410 last-modified: 2023-11-13 description: ObjectiveTo explore the comparative effectiveness of nutritional supplements in improving glycolipid metabolism and endocrine function in patients with polycystic ovary syndrome (PCOS).MethodRandomized controlled clinical trials on the effects of nutritional supplements in PCOS patients were searched in PubMed, Embase, Cochrane Library, and Web of Science from their establishments to March 15, 2023. Then, literature screening, data extraction, and network meta-analysis were performed. This study was registered at PROSPERO (registration number CRD 42023441257).ResultForty-one articles involving 2,362 patients were included in this study. The network meta-analysis showed that carnitine, inositol, and probiotics reduced body weight and body mass index (BMI) compared to placebo, and carnitine outperformed the other supplements (SUCRAs: 96.04%, 97.73%, respectively). Omega-3 lowered fasting blood glucose (FBG) (SUCRAs: 93.53%), and chromium reduced fasting insulin (FINS) (SUCRAs: 72.90%); both were superior to placebo in improving insulin resistance index (HOMA-IR), and chromium was more effective than Omega-3 (SUCRAs: 79.99%). Selenium was potent in raising the quantitative insulin sensitivity index (QUICKI) (SUCRAs: 87.92%). Coenzyme Q10 was the most effective in reducing triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C) levels (SUCRAs: 87.71%, 98.78%, and 98.70%, respectively). Chromium and probiotics decreased TG levels, while chromium and vitamin D decreased TC levels. No significant differences were observed in high-density lipoprotein cholesterol (HDL-C), total testosterone (TT), sex-hormone binding globulin (SHBG), and C-reactive protein (CRP) between nutritional supplements and placebo.ConclusionCarnitine was relatively effective in reducing body mass, while chromium, Omega-3, and selenium were beneficial for improving glucose metabolism. Meanwhile, coenzyme Q10 was more efficacious for improving lipid metabolism. However, publication bias may exist, and more high-quality clinical randomized controlled trials are needed. creator: Xinyin Hu creator: Wanyi Wang creator: Xuhan Su creator: Haoye Peng creator: Zuolin Tan creator: Yunqing Li creator: Yuhua Huang uri: https://doi.org/10.7717/peerj.16410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hu et al. title: A pyroptosis gene-based prognostic model for predicting survival in low-grade glioma link: https://peerj.com/articles/16412 last-modified: 2023-11-13 description: BackgroundPyroptosis, a lytic form of programmed cell death initiated by inflammasomes, has been reported to be closely associated with tumor proliferation, invasion and metastasis. However, the roles of pyroptosis genes (PGs) in low-grade glioma (LGG) remain unclear.MethodsWe obtained information for 1,681 samples, including the mRNA expression profiles of LGGs and normal brain tissues and the relevant corresponding clinical information from two public datasets, TCGA and GTEx, and identified 45 differentially expressed pyroptosis genes (DEPGs). Among these DEPGs, nine hub pyroptosis genes (HPGs) were identified and used to construct a genetic risk scoring model. A total of 476 patients, selected as the training group, were divided into low-risk and high-risk groups according to the risk score. The area under the curve (AUC) values of the receiver operating characteristic (ROC) curves verified the accuracy of the model, and a nomogram combining the risk score and clinicopathological characteristics was used to predict the overall survival (OS) of LGG patients. In addition, a cohort from the Gene Expression Omnibus (GEO) database was selected as a validation group to verify the stability of the model. qRT-PCR was used to analyze the gene expression levels of nine HPGs in paracancerous and tumor tissues from 10 LGG patients.ResultsSurvival analysis showed that, compared with patients in the low-risk group, patients in the high-risk group had a poorer prognosis. A risk score model combining PG expression levels with clinical features was considered an independent risk factor. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that immune-related genes were enriched among the DEPGs and that immune activity was increased in the high-risk group.ConclusionIn summary, we successfully constructed a model to predict the prognosis of LGG patients, which will help to promote individualized treatment and provide potential new targets for immunotherapy. creator: Hua Wang creator: Lin Yan creator: Lixiao Liu creator: Xianghe Lu creator: Yingyu Chen creator: Qian Zhang creator: Mengyu Chen creator: Lin Cai creator: Zhang’an Dai uri: https://doi.org/10.7717/peerj.16412 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Critical re-examination of known purported fossil Bombycoidea (Lepidoptera) link: https://peerj.com/articles/16049 last-modified: 2023-11-10 description: We critically re-examine 17 records of fossils currently assigned to the lepidopteran superfamily Bombycoidea, which includes the silk moths, emperor moths and hawk moths. These records include subfossils, compression and impression fossils, permineralizations and ichnofossils. We assess whether observable morphological features warrant their confident assignment to the superfamily. None of the examined fossils displays characters that allow unequivocal identification as Sphingidae, but three fossils and a subfossil (Mioclanis shanwangiana Zhang, Sun and Zhang, 1994, two fossil larvae, and a proboscis in asphaltum) have combinations of diagnostic features that support placement in the family. The identification of a fossil pupa as Bunaeini (Saturniidae) is well supported. The other fossils that we evaluate lack definitive bombycoid and, in several cases, even lepidopteran characters. Some of these dubious fossils have been used as calibration points in earlier studies casting doubt on the resulting age estimates. All fossil specimens reliably assigned to Bombycoidea are relatively young, the earliest fossil evidence of the superfamily dating to the middle Miocene. creator: Maria Heikkilä creator: Joël Minet creator: Andreas Zwick creator: Anna Hundsdoerfer creator: Rodolphe Rougerie creator: Ian J. Kitching uri: https://doi.org/10.7717/peerj.16049 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Heikkilä et al. title: Efficacy and safety of veliparib combined with traditional chemotherapy for treating patients with lung cancer: a comprehensive review and meta-analysis link: https://peerj.com/articles/16402 last-modified: 2023-11-10 description: ObjectiveLung cancer, originating from bronchial mucosa or lung glands, poses significant health risks due to its rising incidence and mortality. This study aimed to assess the efficacy and safety of Veliparib combined with chemotherapy versus pharmacotherapy alone for lung cancer treatment, guiding clinical approaches for this severe disease.MethodsComprehensive searches in PubMed, EMBASE, Cochrane, and Web of Science were conducted to identify randomized controlled trials (RCTs) comparing Veliparib combined with standard chemotherapy to chemotherapy alone in lung cancer treatment, up until December 28, 2022. Two reviewers meticulously selected literature based on inclusion and exclusion criteria. The Cochrane tool was used to assess the bias risk of the included studies, and meta-analysis was performed using Stata 15.0.ResultsFive RCTs (1,010 participants) were included. The analysis results showed that only Veliparib combinedwith chemotherapy prolonged the progression-free survival (PFS) in small cell lung cancer (SCLC) patients [HR = 0.72, 95% CI = (0.57, 0.90)]. No significant differences were observed in overall survival (OS) and objective response rate (ORR). Veliparib and combined chemotherapy caused some side effects in patients with lung cancer, including leukopenia [RR = 2.12, 95% CI = (1.27, 3.55)], neutropenia [RR = 1.51, 95% CI = (1.01, 2.26)], anemia [RR = 1.71, 95% CI = (1.07, 3.07)], and thrombocytopenia [RR = 3.33, 95% CI = (1.19, 9.30)]. For non-small cell lung cancer (NSCLC) patients, there were no statistically significant differences in PFS, OS, or ORR between the experimental and control groups [HR = 0.97, 95% CI = (0.75, 1.27)].ConclusionThe strategy of combining Veliparib with chemotherapy may, to some extent, prolong the PFS in lung cancer patients. However, this benefit is not observed in OS or ORR. Additionally, there are evident adverse reactions. Due to a limited number of the included studies, additional extensive multicenter RCTs are required to validate these results. PROSPERO registration number: CRD42023411510. creator: Guanhua Zhao creator: Enzhi Feng creator: Yalu Liu uri: https://doi.org/10.7717/peerj.16402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: Effects of a single bout of mobile action video game play on attentional networks link: https://peerj.com/articles/16409 last-modified: 2023-11-10 description: BackgroundVideo game play has been linked to a range of cognitive advantages, and investigations in this domain have predominantly utilized cross-sectional designs or long-term training paradigms. Nevertheless, the specific effects of engaging in a single bout of video game play remain poorly understood. Consequently, the objective of this study is to examine the influence of a single session of mobile action video game (MAVG) play on attentional networks among college students.MethodsSeventy-two nonvideo game players were assigned randomly into an MAVG and a control game group. Participants in the MAVG group engaged in a 60-minute session of an action video game played on mobile phones, while the control group played a mobile card game for the same duration. All participants completed the attentional network test (ANT), which assesses alerting, orienting, and executive control network efficiencies, before and after the intervention.ResultsThe MAVG group had significantly improved alerting network efficiency following the intervention, compared to before (p < 0.05); the control game group did not. Neither executive control network efficiency nor orienting network efficiency were found to be improved by the intervention.ConclusionThe present data demonstrated that a single bout of MAVG play can improve alerting network efficiency selectively in young-adult college students. MAVGs may be useful for promoting attentional function with the advantages of being accessible virtually any time and anywhere. creator: Biye Wang creator: Jiahui Jiang creator: Wei Guo uri: https://doi.org/10.7717/peerj.16409 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Participation in youth sports influences sarcopenia parameters in older adults link: https://peerj.com/articles/16432 last-modified: 2023-11-10 description: BackgroundThe degree of deterioration in sarcopenia parameters may be affected by a person’s level of physical activity (PA) and sedentary behavior (SB). Our study focused on examining the PA and SB of active older adults including those with and without history of sports in youth.MethodsForty-four participants (20 men and 24 women, mean age of total sample 76.1 ± 5.2 years) were included in analysis of PA, SB habits and sarcopenia parameters, determined by skeletal muscle index, hand-grip strength, gait speed, Timed Up and Go tests (TUG). PA and SB were recorded with accelerometers. Our primary aim was to compare participants with (AH) or without a sport history in youth (NAH), in their sarcopenia parameters and PA and SB habits.ResultsWhen divided participants in two groups (AH and NAH) and adjusting for age, we have detected the differences for skeletal muscle index (p = 0.007) and hand-grip strength (p = 0.004) in favor of participants who were engaged in sports in youth. We did not find any differences in PA and SB habits between the AH and NAH groups. After adjusting for age, participants with a higher number of daily steps, longer moderate to vigorous physical activity (MVPA) bouts, a higher number of MVPA bouts in a day and higher overall MVPA engagement achieved better results in hand-grip strength and TUG. Participants with lower SB had better TUG and gait speed results.ConclusionsOur findings suggest that engaging in sports activities in youth can make a difference with sarcopenia parameters. Although we found no differences in PA and SB habits between participants with AH and NAH, participants with an athlete history performed better results in sarcopenia parameters. creator: Kaja Teraž creator: Miloš Kalc creator: Boštjan Šimunič creator: Uros Marusic creator: Primož Pori creator: Saša Pišot creator: Rado Pišot uri: https://doi.org/10.7717/peerj.16432 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Teraž et al. title: Recent and rapid reef recovery around Koh Phangan Island, Gulf of Thailand, driven by plate-like hard corals link: https://peerj.com/articles/16115 last-modified: 2023-11-09 description: Mass bleaching events and local anthropogenic influences have changed the benthic communities of many coral reefs with pronounced spatial differences that are linked to resilience patterns. The Gulf of Thailand is an under-investigated region with only few existing datasets containing long-term developments of coral reef communities using the same method at fixed sites. We thus analyzed benthic community data from seven reefs surrounding the island of Koh Phangan collected between 2014 and 2022. Findings revealed that the average live hard coral cover around Koh Phangan increased from 37% to 55% over the observation period, while turf algae cover decreased from 52% to 29%, indicating some recovery of local reefs. This corresponds to a mean increased rate of coral cover by 2.2% per year. The increase in live hard coral cover was mainly driven by plate-like corals, which quadrupled in proportion over the last decade from 7% to 28% while branching corals decreased in proportion from 9% to 2%. Furthermore, the hard coral genus richness increased, indicating an increased hard coral diversity. While in other reefs, increasing live hard coral cover is often attributed to fast-growing, branching coral species, considered more susceptible to bleaching and other disturbances, the reefs around Koh Phangan recovered mainly via growth of plate-like corals, particularly of the genus Montipora. Although plate-like morphologies are not necessarily more bleaching tolerant, they are important for supporting reef fish abundance and structural complexity on reefs, aiding reef recovery and sturdiness. Hence, our findings indicate that the intensity of local stressors around Kho Phangan allows reef recovery driven by some hard coral species. creator: Florian Stahl creator: Selma D. Mezger creator: Valentina Migani creator: Marko Rohlfs creator: Victoria J. Fahey creator: Eike Schoenig creator: Christian Wild uri: https://doi.org/10.7717/peerj.16115 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Stahl et al. title: Unraveling plant-pollinator interactions from a south-west Andean forest in Colombia link: https://peerj.com/articles/16133 last-modified: 2023-11-09 description: BackgroundLoss of biological connectivity increases the vulnerability of ecological dynamics, thereby affecting processes such as pollination. Therefore, it is important to understand the roles of the actors that participate in these interaction networks. Nonetheless, there is a significant oversight regarding the main actors in the pollination networks within the highly biodiverse forests of Colombia. Hence, the present study aims to evaluate the interaction patterns of a network of potential pollinators that inhabit an Andean Forest in Totoró, Cauca, Colombia.MethodsThe interactions between plants and potential pollinators were recorded through direct observation in 10 transects during six field trips conducted over the course of one year. Subsequently, an interaction matrix was developed, and network metrics such as connectance, specialization, nestedness, and asymmetry of interaction strength were evaluated by applying null models. An interpolation/extrapolation curve was calculated in order to assess the representativeness of the sample. Finally, the key species of the network were identified by considering degree (k), centrality, and betweenness centrality.ResultsA total of 53 plant species and 52 potential pollinator species (including insects and birds) were recorded, with a sample coverage of 88.5%. Connectance (C = 0.19) and specialization (H2’ = 0.19) were low, indicating a generalist network. Freziera canescens, Gaiadendron punctatum, Persea mutisii, Bombus rubicundus, Heliangelus exortis, Chironomus sp., and Metallura tyrianthina were identified as the key species that contribute to a more cohesive network structure.DiscussionThe present study characterized the structure of the plant-pollinator network in a highly diverse Andean forest in Colombia. It is evident that insects are the largest group of pollinators; however, it is interesting to note that birds form a different module that specializes in pollinating a specific group of plants. On the other hand, the diversity and generality of the species found suggest that the network may be robust against chains of extinction. Nevertheless, the presence of certain introduced species, such as Apis mellifera, and the rapid changes in vegetation cover may affect the dynamics of this mutualistic network. So, it is imperative to apply restoration and conservation strategies to these ecosystems in order to enhance plant-animal interactions and prevent the loss of taxonomical and functional diversity. creator: Jorge Mario Becoche-Mosquera creator: Luis German Gomez-Bernal creator: Giselle Zambrano-Gonzalez creator: David Angulo-Ortiz uri: https://doi.org/10.7717/peerj.16133 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Becoche-Mosquera et al. title: Glomeromycota associations with bamboos (Bambusoideae) worldwide, a qualitative systematic review of a promising symbiosis link: https://peerj.com/articles/16151 last-modified: 2023-11-09 description: BackgroundAround the world, bamboos are ecologically, economically, and culturally important plants, particularly in tropical regions of Asia, America, and Africa. The association of this plant group with arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota is still a poorly studied field, which limits understanding of the reported ecological and physiological benefits for the plant, fungus, soil, and ecosystems under this symbiosis relationship.MethodsThrough a qualitative systematic review following the PRISMA framework for the collection, synthesis, and reporting of evidence, this paper presents a compilation of the research conducted on the biology and ecology of the symbiotic relationship between Glomeromycota and Bambusoideae from around the world. This review is based on academic databases enriched with documents retrieved using different online databases and the Google Scholar search engine.ResultsThe literature search yielded over 6,000 publications, from which 18 studies were included in the present review after a process of selection and validation. The information gathered from the publications included over 25 bamboo species and nine Glomeromycota genera from eight families, distributed across five countries on two continents.ConclusionThis review presents the current state of knowledge regarding the symbiosis between Glomeromycota and Bambusoideae, while reflecting on the challenges and scarcity of research on this promising association found across the world. creator: Juan José Sánchez-Matiz creator: Lucia Ana Díaz-Ariza uri: https://doi.org/10.7717/peerj.16151 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sánchez-Matiz and Díaz-Ariza title: Manipulating network connectance by altering plant attractiveness link: https://peerj.com/articles/16319 last-modified: 2023-11-09 description: BackgroundMutualistic interactions between plants and their pollinating insects are critical to the maintenance of biodiversity. However, we have yet to demonstrate that we are able to manage the structural properties of these networks for the purposes of pollinator conservation and preserving functional outcomes, such as pollination services. Our objective was to explore the extent of our ability to experimentally increase, decrease, and maintain connectance, a structural attribute that reflects patterns of insect visitation and foraging preferences. Patterns of connectance relate to the stability and function of ecological networks.MethodsWe implemented a 2-year field experiment across eight sites in urban Dublin, Ireland, applying four agrochemical treatments to fixed communities of seven flowering plant species in a randomized block design. We spent ~117 h collecting 1,908 flower-visiting insects of 92 species or morphospecies with standardized sampling methods across the 2 years. We hypothesized that the fertilizer treatment would increase, herbicide decrease, and a combination of both maintain the connectance of the network, relative to a control treatment of just water.ResultsOur results showed that we were able to successfully increase network connectance with a fertilizer treatment, and maintain network connectance with a combination of fertilizer and herbicide. However, we were not successful in decreasing network connectance with the herbicide treatment. The increase in connectance in the fertilized treatment was due to an increased species richness of visiting insects, rather than changes to their abundance. We also demonstrated that this change was due to an increase in the realized proportion of insect visitor species rather than increased visitation by common, generalist species of floral visitors. Overall, this work suggests that connectance is an attribute of network structure that can be manipulated, with implications for management goals or conservation efforts in these mutualistic communities. creator: Laura Russo creator: Jane C. Stout uri: https://doi.org/10.7717/peerj.16319 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Russo and Stout title: Impact analysis of moisture stress on growth and yield of cotton using DSSAT-CROPGRO-cotton model under semi-arid climate link: https://peerj.com/articles/16329 last-modified: 2023-11-09 description: Adequate soil moisture around the root zone of the crops is essential for optimal plant growth and productivity throughout the crop season, whereas excessive as well as deficient moisture is usually detrimental. A field experiment was conducted on cotton (Gossipium hirsuttum) with three water regimes (viz. well-watered (control); rainfed after one post-sowing irrigation (1-POSI) and rainfed after two post-sowing irrigations (2-POSI)) in main plots and application of eight osmoprotectants in sub plots of Split plot design to quantify the loss of seed cotton yield (SCY) under high and mild moisture stress. The DSSAT-CROPGRO-cotton model was calibrated to validate the response of cotton crop to water stress. Results elucidated that in comparison of well watered (control) crop, 1-POSI and 2-POSI reduced plant height by 13.5–28.4% and lower leaf area index (LAI) by 21.6–37.6%. Pooled analysis revealed that SCY under control was higher by 1,127 kg ha−1 over 1-POSI and 597 kg ha−1 than 2-POSI. The DSSAT-CROPGRO-cotton model fairly simulated the cotton yield as evidenced by good accuracy (d-stat ≥ 0.92) along with lower root mean square error (RMSE) of ≤183.2 kg ha−1; mean absolute percent error (MAPE) ≤6.5% under different irrigation levels. Similarly, simulated and observed biomass also exhibited good agreement with ≥0.98 d-stat; ≤533.7 kg ha−1 RMSE; and ≤4.6% MAPE. The model accurately simulated the periodical LAI, biomass and soil water dynamics as affected by varying water regimes in conformity with periodical observations. Both the experimental and the simulated results confirmed the decline of SCY with any degree of water stress. Thus, a well calibrated DSSAT-CROPGRO-cotton model may be successfully used for estimating the crop performance under varying hydro-climatic conditions. creator: Rotash Kumar creator: Sudhir Kumar Mishra creator: Kulvir Singh creator: Ibrahim Al-Ashkar creator: Muhammad Aamir Iqbal creator: Muhammad Noor Muzamil creator: Muhammad Habib ur Rahman creator: Ayman El Sabagh uri: https://doi.org/10.7717/peerj.16329 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kumar et al. title: A novel metabolism-related gene signature in patients with hepatocellular carcinoma link: https://peerj.com/articles/16335 last-modified: 2023-11-09 description: Hepatocellular carcinoma (HCC) remains a global challenge as it is the sixth most common neoplasm worldwide and the third leading cause of cancer-related death. A key feature of HCC is abnormal metabolism, which promotes cancer cell proliferation, survival, invasion, and metastasis. However, the significance of metabolism-related genes (MRGs) in HCC remains to be elucidated. Here, we aim to establish a novel metabolism-related prognostic signature for the prediction of patient outcomes and to investigate the value of MRG expression in the prognostic prediction of HCC. In our research, a Metabolism-Related Risk Score (MRRS) model was constructed using 14 MRGs (DLAT, SEPHS1, ACADS, UCK2, GOT2, ADH4, LDHA, ME1, TXNRD1, B4GALT2, AK2, PTDSS2, CSAD, and AMD1). The Kaplan-Meier curve confirmed that the MRRS has a high accuracy in predicting the prognosis of HCC patients (p < 0.001). According to the MRRS model, the area under the curve (AUC) values for predicting the prognosis of patients with hepatocellular carcinoma at 1, 3, and 5 years reached 0.829, 0.760, and 0.739, respectively. Functional analyses revealed that signaling pathways associated with the cell cycle were largely enriched by differential genes between high and low-risk groups. In addition, dendritic cells (DCs) (p < 0.001), CD4+ T cells (p < 0.01), CD8+ T cells (p < 0.001), B cells (p < 0.001), neutrophils (p < 0.001), macrophages (p < 0.001) had a higher proportion of infiltrates in high-risk populations. Low GOT2 expression is associated with poor prognosis in patients with hepatocellular carcinoma. Knockdown of GOT2 significantly increased the migration capacity of the Huh7 and MHCC97H hepatocellular carcinoma lines. Our research reveals that GOT2 is negatively related to the survival of patients with hepatocellular carcinoma and GOT2 may contribute to tumor progression by inhibiting the ability of tumor cells to migrate. creator: Bin Ru creator: Jiaqi Hu creator: Nannan Zhang creator: Quan Wan uri: https://doi.org/10.7717/peerj.16335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ru et al. title: Comparative study of the efficacy of intra-arterial and intravenous transplantation of human induced pluripotent stem cells-derived neural progenitor cells in experimental stroke link: https://peerj.com/articles/16358 last-modified: 2023-11-09 description: BackgroundCell therapy using neural progenitor cells (NPCs) is a promising approach for ischemic stroke treatment according to the results of multiple preclinical studies in animal stroke models. In the vast majority of conducted animal studies, the therapeutic efficacy of NPCs was estimated after intracerebral transplantation, while the information of the effectiveness of systemic administration is limited. Nowadays, several clinical trials aimed to estimate the safety and efficacy of NPCs transplantation in stroke patients were also conducted. In these studies, NPCs were transplanted intracerebrally in the subacute/chronic phase of stroke. The results of clinical trials confirmed the safety of the approach, however, the degree of functional improvement (the primary efficacy endpoint) was not sufficient in the majority of the studies. Therefore, more studies are needed in order to investigate the optimal transplantation parameters, especially the timing of cell transplantation after the stroke onset. This study aimed to evaluate the therapeutic effects of intra-arterial (IA) and intravenous (IV) administration of NPCs derived from induced pluripotent stem cells (iNPCs) in the acute phase of experimental stroke in rats. Induced pluripotent stem cells were chosen as the source of NPCs as this technology is perspective, has no ethical concerns and provides the access to personalized medicine.MethodsHuman iNPCs were transplanted IA or IV into male Wistar rats 24 h after the middle cerebral artery occlusion stroke modeling. Therapeutic efficacy was monitored for 14 days and evaluated in comparison with the cell transplantation-free control group. Additionally, cell distribution in the brain was assessed.ResultsThe obtained results show that both routes of systemic transplantation (IV and IA) significantly reduced the mortality and improved the neurological deficit of experimental animals compared to the control group. At the same time, according to the MRI data, only IA administration led to faster and prominent reduction of the stroke volume. After IA administration, iNPCs transiently trapped in the brain and were not detected on day 7 after the transplantation. In case of IV injection, transplanted cells were not visualized in the brain. The obtained data demonstrated that the systemic transplantation of human iNPCs in the acute phase of ischemic stroke can be a promising therapeutic strategy. creator: Elvira Cherkashova creator: Daria Namestnikova creator: Georgiy Leonov creator: Ilya Gubskiy creator: Kirill Sukhinich creator: Pavel Melnikov creator: Vladimir Chekhonin creator: Konstantin Yarygin creator: Dmitry Goldshtein creator: Diana Salikhova uri: https://doi.org/10.7717/peerj.16358 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cherkashova et al. title: Bone marrow mesenchymal stem cell-derived exosomal microRNA regulates microglial polarization link: https://peerj.com/articles/16359 last-modified: 2023-11-09 description: ObjectiveThis study aimed to explore the effects of bone marrow mesenchymal stem cell (BMSC)-derived exosomal miR-146a-5p on microglial polarization and the potential underlying mechanisms in oxygen-glucose deprivation (OGD)-exposed microglial cells.MethodsExosomes were isolated from BMSCs, and their characteristics were examined. The effects of BMSC-derived exosomes on microglial polarization were investigated in OGD-exposed BV-2 cells. Differentially expressed miRNAs were identified and their biological function was explored using enrichment analyses. The regulatory role of miR-146a-5p in microglial polarization was studied via flow cytometry. Finally, the downstream target gene Traf6 was validated, and the role of the miR-146a-5p/Traf6 axis in modulating microglial polarization was investigated in OGD-exposed BV-2 cells.ResultsBMSC-derived exosomes were successfully isolated and characterized. A total of 10 upregulated and 33 downregulated miRNAs were identified. Exosomal treatment resulted in significant changes in microglial polarization markers. miR-146a-5p was found to be significantly downregulated in OGD-exposed microglial cells treated with exosomes. Manipulation of miR-146a-5p expression modulated microglial polarization. Moreover, the miR-146a-5p/Traf6 axis regulated microglial polarization.ConclusionOur findings demonstrate that BMSC-derived exosomal via miR-146a-5p modulates microglial polarization by targeting Traf6, providing a potential thermal target for the treatment of neurological diseases involving microglial activation. creator: Xianwei Huang creator: Xiong Liu creator: Jiaqi Zeng creator: Penghui Du creator: Xiaodong Huang creator: Jiyan Lin uri: https://doi.org/10.7717/peerj.16359 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Confidence intervals for ratio of means of delta-lognormal distributions based on left-censored data with application to rainfall data in Thailand link: https://peerj.com/articles/16397 last-modified: 2023-11-09 description: Thailand is a country that is prone to both floods and droughts, and these natural disasters have significant impacts on the country’s people, economy, and environment. Estimating rainfall is an important part of flood and drought prevention. Rainfall data typically contains both zero and positive observations, and the distribution of rainfall often follows the delta-lognormal distribution. However, it is important to note that rainfall data can be censored, meaning that some values may be missing or truncated. The interval estimator for the ratio of means will be useful when comparing the means of two samples. The purpose of this article was to compare the performance of several approaches for statistically analyzing left-censored data. The performance of the confidence intervals was evaluated using the coverage probability and average length, which were assessed through Monte Carlo simulation. The approaches examined included several variations of the generalized confidence interval, the Bayesian, the parametric bootstrap, and the method of variance estimates recovery approaches. For (ξ1, ξ2) = (0.10,0.10), simulations showed that the Bayesian approach would be a suitable choice for constructing the credible interval for the ratio of means of delta-lognormal distributions based on left-censored data. For (ξ1, ξ2) = (0.10,0.25), the parametric bootstrap approach was a strong alternative for constructing the confidence interval. However, the generalized confidence interval approach can be considered to construct the confidence when the sample sizes are increase. Practical applications demonstrating the use of these techniques on rainfall data showed that the confidence interval based on the generalized confidence interval approach covered the ratio of population means and had the smallest length. The proposed approaches’ effectiveness was illustrated using daily rainfall datasets from the provinces of Chiang Rai and Chiang Mai in Thailand. creator: Warisa Thangjai creator: Sa-Aat Niwitpong uri: https://doi.org/10.7717/peerj.16397 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Thangjai and Niwitpong title: Investigating altered brain functional hubs and causal connectivity in coronary artery disease with cognitive impairment link: https://peerj.com/articles/16408 last-modified: 2023-11-09 description: BackgroundCoronary artery disease (CAD) and cognitive impairment (CI) have become significant global disease and medical burdens. There have been several reports documenting the alterations in regional brain function and their correlation with CI in CAD patients. However, there is limited research on the changes in brain network connectivity in CAD patients. To investigate the resting-state connectivity and further understand the effective connectivity strength and directionality in patients with CAD, we utilized degree centrality (DC) and spectral dynamic causal modeling (spDCM) to detect functional hubs in the whole brain network, followed by an analysis of directional connections. Using the aforementioned approaches, it is possible to investigate the hub regions and aberrant connections underlying the altered brain function in CAD patients, providing neuroimaging evidence for the cognitive decline in patients with coronary artery disease.Materials and MethodsThis study was prospectively conducted involving 24 patients diagnosed with CAD and 24 healthy controls (HC) who were matched in terms of age, gender, and education. Functional MRI (fMRI) scans were utilized to investigate brain activity in these individuals. Neuropsychological examinations were performed on all participants. DC analysis and spDCM were employed to investigate abnormal brain networks in patients with CAD. Additionally, the association between effective connectivity strength and cognitive function in patients with CAD was examined based on the aforementioned results.ResultsBy assessing cognitive functions, we discovered that patients with CAD exhibited notably lower cognitive function compared to the HC group. By utilizing DC analysis and spDCM, we observed significant reductions in DC values within the left parahippocampal cortex (PHC) and the left medial temporal gyrus (MTG) in CAD patients when compared to the control group. In terms of effective connectivity, we observed the absence of positive connectivity between the right superior frontal gyrus (SFG) and PHC in CAD patients. Moreover, there was an increase in negative connectivity from PHC and MTG to SFG, along with a decrease in the strength of positive connectivity between PHC and MTG. Furthermore, we identified a noteworthy positive correlation (r = 0.491, p = 0.015) between the strength of connectivity between the PHC and the MTG and cognitive function in CAD patients.ConclusionsThese research findings suggest that alterations in the connectivity of the brain networks involving SFG, PHC, and MTG in CAD patients may mediate changes in cognitive function. creator: Rui Qin creator: Tong Li creator: Cuicui Li creator: Lin Li creator: Ximing Wang creator: Li Wang uri: https://doi.org/10.7717/peerj.16408 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Qin et al. title: Arbuscular mycorrhizal fungi alter rhizosphere fungal community characteristics of Acorus calamus to improve Cr resistance link: https://peerj.com/articles/15681 last-modified: 2023-11-08 description: To investigate changes in fungal community characteristics under different Cr(VI) concentration stresses and the advantages of adding arbuscular mycorrhizal fungi (AMF), we used high throughput sequencing to characterize the fungal communities. Cr(VI) stress reduced rhizosphere soil SOM (soil organic matter) content and AMF addition improved this stress phenomenon. There were significant differences in fungal community changes under different Cr(VI) concentrations. The fungal community characteristics changed through inhibition of fungal metabolic ability, as fungal abundance increased after AMF addition, and the fungal diversity increased under high Cr(VI) concentration. The dominant phyla were members of the Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. Dominant groups relevant to Cr resistance were Ascomycota and Basidiomycota fungi. Moreover, Fungal community characteristics were analyzed using high-throughput sequencing of the cytochrome c metabolic pathway, NADH dehydrogenase, and NADH: ubiquinone reductase and all these functions were enhanced after AMF addition. Therefore, Cr(VI) stress significantly affects fungal community structure, while AMF addition could increase its SOM content, and metabolic capacity, and improve fungal community tolerance to Cr stress. This study contributed to the understanding response of rhizosphere fungal community in AMF-assisted wetland phytoremediation under Cr stress. creator: Guodong Xia creator: Sixi Zhu creator: Wei Zhao creator: Xiuqing Yang creator: Luying Sheng creator: Huan Mao uri: https://doi.org/10.7717/peerj.15681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xia et al. title: AL360181.1 promotes proliferation and invasion in colon cancer and is one of ten m6A-related lncRNAs that predict overall survival link: https://peerj.com/articles/16123 last-modified: 2023-11-08 description: BackgroundN6-methyladenosine (m6A) exerted a pivotal role in colon cancer. Nevertheless, the long non-coding RNAs (lncRNAs) associated with this process have yet to be elucidated.MethodsThe open-access data used for analysis was downloaded from The Cancer Genome Atlas (TCGA) database for analysis, employing the R software for computational evaluations. The RNA level of specific molecules was assessed using the quantitative real-time PCR. CCK8, colony formation and transwell assay were used to evaluate the proliferation, invasion and migration ability of colon cancer cells.ResultsHere, we identified the m6A regulators from TCGA data and subsequently pinpointed lncRNAs with a —Cor— > 0.3 and P < 0.05, categorizing them as m6A-associated lncRNAs. Moreover, we formulated a prognosis signature rooted in ten m6A-related lncRNAs, consisting of AL360181.1, PCAT6, SNHG26, AC016876.1, AC104667.2, AL114730.3, LINC02257, AC147067.1, AP006621.3 and AC009237.14. This signature exhibited notable predictive accuracy in gauging patient survival. Immune-related evaluations revealed varied immune cell infiltration patterns across different risk groups, with our findings suggesting superior immunotherapy response in low-risk patients. Biological enrichment analysis indicated that the high-risk patients had a higher activity of multiple carcinogenic pathways, including glycolysis. The previously unreported lncRNA, AL360181.1, displayed a connection to glycolytic activity and diminished survival rates, warranting further investigation. The result indicated that AL360181.1 was correlated with more aggressive clinical characteristics. Immune infiltration assessments found AL360181.1 to have a positive correlation with Tcm infiltration, but an inverse relationship with entities like Th2 cells, T cells, neutrophils and macrophages. Biological enrichment analysis indicated that the pathways of WNT/β-catenin, pancreas beta cells, hedgehog signaling and some metabolism pathways were upregulated in high AL360181.1 patients. In vitro experiments showed that AL360181.1 was upregulated in the colon cancer cells. Moreover, AL360181.1 significantly promotes the proliferation, invasion and migration of colon cancer cells.ConclusionsOur results can provide direction for future studies on m6A-related lncRNA in colon cancer. creator: Yi Luo creator: Yayun Xie creator: Dejun Wu creator: Bingyi Wang creator: Helei Lu creator: Zhiqiang Wang creator: Yingjun Quan creator: Bo Han uri: https://doi.org/10.7717/peerj.16123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Luo et al. title: Elucidating the role of nicotinamide N-methyltransferase-p53 axis in the progression of chronic kidney disease link: https://peerj.com/articles/16301 last-modified: 2023-11-08 description: BackgroundChronic kidney disease (CKD) is a significant global health issue characterized by progressive loss of kidney function. Renal interstitial fibrosis (TIF) is a common feature of CKD, but current treatments are seldom effective in reversing TIF. Nicotinamide N-methyltransferase (NNMT) has been found to increase in kidneys with TIF, but its role in renal fibrosis is unclear.MethodsUsing mice with unilateral ureteral obstruction (UUO) and cultured renal interstitial fibroblast cells (NRK-49F) stimulated with transforming growth factor-β1 (TGF-β1), we investigated the function of NNMT in vivo and in vitro.ResultsWe performed single-cell transcriptome sequencing (scRNA-seq) on the kidneys of mice and found that NNMT increased mainly in fibroblasts of UUO mice compared to sham mice. Additionally, NNMT was positively correlated with the expression of renal fibrosis-related genes after UUO injury. Knocking down NNMT expression reduced fibroblast activation and was accompanied by an increase in DNA methylation of p53 and a decrease in its phosphorylation.ConclusionsOur findings suggest that chronic kidney injury leads to an accumulation of NNMT, which might decrease p53 methylation, and increase the expression and activity of p53. We propose that NNMT promotes fibroblast activation and renal fibrosis, making NNMT a novel target for preventing and treating renal fibrosis. creator: Xin Zhen creator: Yuxiang Sun creator: Hongchun Lin creator: Yuebo Huang creator: Tianwei Liu creator: Yuanqing Li creator: Hui Peng uri: https://doi.org/10.7717/peerj.16301 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhen et al. title: Naringenin attenuates inflammation and apoptosis of osteoarthritic chondrocytes via the TLR4/TRAF6/NF-κB pathway link: https://peerj.com/articles/16307 last-modified: 2023-11-08 description: Naringenin is a flavonoid extracted from the seed coat of Anacardiaceae plants. Increasing evidence indicates that it has several properties of biological significance, such as anti-infection, sterilization, anti-allergy, antioxidant free radical, and anti-tumor. However, its effect on osteoarthritis has not been elucidated properly. In this study, the treatment of primary chondrocytes with interleukin (IL)-1β was found to increase the secretions of IL-6, tumor necrosis factor (TNF)-α, and cyclooxygenase-2 (COX-2). Further, the mRNA expression of matrix metalloproteinase ((MMP)3, MMP9, and MMP13), the protein expression of Recombinant A Disintegrin And Metalloproteinase With Thrombospondin 5 (ADAMTS5), and cell apoptosis increased; the protein expression of Collagen II decreased. The injury of primary chondrocytes induced by IL-1β was reversed under the intervention of naringenin; this reversal was dose-dependent. The mechanistic study showed that naringenin inhibited the toll-like receptor 4 (TLR4)/TNF receptor-associated factor 6 (TRAF6)/NF-κB pathway in IL-1β-stimulated primary cells, and LPS, a TLR4 activator, reversed this inhibitory effect. In addition, a mouse model of osteoarthritis was established and treated with naringenin. The results revealed that naringenin alleviated the pathological symptoms of osteoarthritis in mice, reduced the expression of TLR4 and TRAF6, and the phosphorylation of NF-κB in knee cartilage tissue. It also inhibited the secretion of inflammatory factors, reduced extracellular matrix degradation, and decreased the protein expression of cleaved caspase3. In conclusion, the findings of this study suggest that naringenin may be a potential option for the treatment of osteoarthritis. creator: Yan Wang creator: Zhengzhao Li creator: Bo Wang creator: Ke Li creator: Jiaxuan Zheng uri: https://doi.org/10.7717/peerj.16307 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis link: https://peerj.com/articles/16351 last-modified: 2023-11-08 description: Many tools and algorithms are available for analyzing transcriptomics data. These include algorithms for performing sequence alignment, data normalization and imputation, clustering, identifying differentially expressed genes, and performing gene set enrichment analysis. To make the best choice about which tools to use, objective benchmarks can be developed to compare the quality of different algorithms to extract biological knowledge maximally and accurately from these data. The Dexamethasone Benchmark (Dex-Benchmark) resource aims to fill this need by providing the community with datasets and code templates for benchmarking different gene expression analysis tools and algorithms. The resource provides access to a collection of curated RNA-seq, L1000, and ChIP-seq data from dexamethasone treatment as well as genetic perturbations of its known targets. In addition, the website provides Jupyter Notebooks that use these pre-processed curated datasets to demonstrate how to benchmark the different steps in gene expression analysis. By comparing two independent data sources and data types with some expected concordance, we can assess which tools and algorithms best recover such associations. To demonstrate the usefulness of the resource for discovering novel drug targets, we applied it to optimize data processing strategies for the chemical perturbations and CRISPR single gene knockouts from the L1000 transcriptomics data from the Library of Integrated Network Cellular Signatures (LINCS) program, with a focus on understudied proteins from the Illuminating the Druggable Genome (IDG) program. Overall, the Dex-Benchmark resource can be utilized to assess the quality of transcriptomics and other related bioinformatics data analysis workflows. The resource is available from: https://maayanlab.github.io/dex-benchmark. creator: Zhuorui Xie creator: Clara Chen creator: Avi Ma’ayan uri: https://doi.org/10.7717/peerj.16351 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xie et al. title: Change in demand for health-related undergraduate studies in Spain during 2015–2021: a temporal series study link: https://peerj.com/articles/16353 last-modified: 2023-11-08 description: IntroductionThe expansion of higher education is a worldwide phenomenon. To our knowledge, there are no studies analyzing the trends in demands of enrollment in health-related studies in Spain. Therefore, the objective was to analyze the change in demand (the number of requests for enrollment divided by the number of offered places) for undergraduate health-related studies in Spain during the period 2015–2021 as well as compare the change by region in the pre (2015–2019) and pandemic (2020–2021) period.MethodsThis is an observational (ecological type) study with temporal series analyses using data from public (non-for-profit) higher education institutions from the Integrated University Information System. For the analysis by region, we calculated the demand of all twelve undergraduate health-related degrees and the percentages of change between both periods using the Wilcoxon test. The Joinpoint Regression program was used to analyze the trends in demand for each degree during the 7-year period.ResultsSignificant (p < 0.001) increases in demand during the pandemic period were observed in all regions. During the pandemic, medicine, biomedicine, nursing, odontology and pharmacy presented a higher demand in comparison with data collected before the pandemic started. In contrast, this pattern was not confirmed in the following cases: physiotherapy, occupational therapy, podiatry, psychology, social work, human nutrition and dietetics. By regions, Navarra, Asturias, and La Rioja presented the most drastic changes. In regions with the biggest number of universities, such as Catalonia, Andalusia and Madrid, the change observed was smaller. creator: Javier Jerez-Roig creator: Dyego L. Bezerra de Souza creator: Irene Cambra-Badii creator: Jaume-Miquel March-Amengual creator: Agustí Comella creator: Montse Masó-Aguado creator: Anna Ramon-Aribau creator: Alejandro Luque-Suárez creator: Lydia Feito Grande creator: Núria Terribas creator: Luis Vivanco creator: Ester Busquets-Alibés uri: https://doi.org/10.7717/peerj.16353 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jerez-Roig et al. title: A multimodal prediction model for suicidal attempter in major depressive disorder link: https://peerj.com/articles/16362 last-modified: 2023-11-08 description: BackgroundSuicidal attempts in patients with major depressive disorder (MDD) have become an important challenge in global mental health affairs. To correctly distinguish MDD patients with and without suicidal attempts, a multimodal prediction model was developed in this study using multimodality data, including demographic, depressive symptoms, and brain structural imaging data. This model will be very helpful in the early intervention of MDD patients with suicidal attempts.MethodsTwo feature selection methods, support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF) algorithms, were merged for feature selection in 208 MDD patients. SVM was then used as a classification model to distinguish MDD patients with suicidal attempts or not.ResultsThe multimodal predictive model was found to correctly distinguish MDD patients with and without suicidal attempts using integrated features derived from SVM-RFE and RF, with a balanced accuracy of 77.78%, sensitivity of 83.33%, specificity of 70.37%, positive predictive value of 78.95%, and negative predictive value of 76.00%. The strategy of merging the features from two selection methods outperformed traditional methods in the prediction of suicidal attempts in MDD patients, with hippocampal volume, cerebellar vermis volume, and supracalcarine volume being the top three features in the prediction model.ConclusionsThis study not only developed a new multimodal prediction model but also found three important brain structural phenotypes for the prediction of suicidal attempters in MDD patients. This prediction model is a powerful tool for early intervention in MDD patients, which offers neuroimaging biomarker targets for treatment in MDD patients with suicidal attempts. creator: Qiaojun Li creator: Kun Liao uri: https://doi.org/10.7717/peerj.16362 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li and Liao title: Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand link: https://peerj.com/articles/16401 last-modified: 2023-11-08 description: BackgroundEscherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern.ObjectivesTo characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS.MethodsAntimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms.ResultsST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6′)-Ib (57.28%) was found and the coexistence of aac(6′)-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6′)-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene.ConclusionsThis study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism. creator: Parichart Boueroy creator: Peechanika Chopjitt creator: Rujirat Hatrongjit creator: Masatomo Morita creator: Yo Sugawara creator: Yukihiro Akeda creator: Tetsuya Iida creator: Shigeyuki Hamada creator: Anusak Kerdsin uri: https://doi.org/10.7717/peerj.16401 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Boueroy et al. title: BIBR1532 inhibits proliferation and enhances apoptosis in multiple myeloma cells by reducing telomerase activity link: https://peerj.com/articles/16404 last-modified: 2023-11-08 description: BackgroundMultiple myeloma (MM) is a rare haematological disorder with few therapeutic options. BIBR1532, a telomerase inhibitor, is widely used in cancer treatment and has promising outcomes. In this study, we investigated the efficacy and mechanism of action of BIBR1532 in MM.MethodsK562 and MEG-01 cells were cultured with BIBR1532 at different concentrations. After 24 and 48 h, cell survival was analyzed. Next, these cells were cultured with 25 and 50 µM BIBR1532 for 48 h, then, cell proliferation, apoptosis, and the expression of the telomerase activity related markers were tested by 5-Ethynyl-2′-deoxyuridine (EdU) staining, flow cytometric analysis, western blot and quantitative real-time PCR (qRT-PCR), respectively. Expression of Bcl-xL, Bad, Survivin, phosphorylation of PI3K, AKT, mTOR, ERK1/2, and MAPK were tested via western blotting. Further experiments were conducted to evaluate the synergistic effects of BIBR1532 and doxorubicin (Dox) or bortezomib (Bor).ResultsBIBR1532 inhibited K562 and MEG-01 cell survival in a dose- and time-dependent manner. In addition, BIBR1532 hindered cell proliferation while promoting apoptosis, and this effect was enhanced by increasing the BIBR1532 concentration. Moreover, BIBR1532 inhibited TERT and c-MYC expression, PI3K, AKT, mTOR phosphorylation, and facilitated ERK1/2 and MAPK phosphorylation. Additionally, BIBR1532 combined with Dox or Bor showed synergistic effects in MM treatment.ConclusionBIBR1532 inhibits proliferation and promotes apoptosis in MM cells by inhibiting telomerase activity. Additionally, BIBR1532 combined with Dox or Bor exhibited synergistic effects, indicating that BIBR1532 may be a novel medicine for the treatment of MM. creator: Yuefeng Zhang creator: Xinxin Yang creator: Hangqun Zhou creator: Guoli Yao creator: Li Zhou creator: Chunyan Qian uri: https://doi.org/10.7717/peerj.16404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Population structure of wild soybean (Glycine soja) based on SLAF-seq have implications for its conservation link: https://peerj.com/articles/16415 last-modified: 2023-11-08 description: BackgroundGlycine soja Sieb. & Zucc. is the wild ancestor from which the important crop plant soybean was bred. G. soja provides important germplasm resources for the breeding and improvement of cultivated soybean crops, however the species is threatened by habitat loss and fragmentation, and is experiencing population declines across its natural range. Understanding the patterns of genetic diversity in G. soja populations can help to inform conservation practices.MethodsIn this study, we analyzed the genetic diversity and differentiation of G. soja at different sites and investigated the gene flow within the species. We obtained 147 G. soja accessions collected from 16 locations across the natural range of the species from China, Korea and Japan. Samples were analyzed using SLAF-seq (Specific-Locus Amplified Fragment Sequencing).ResultsWe obtained a total of 56,489 highly consistent SNPs. Our results suggested that G. soja harbors relatively high diversity and that populations of this species are highly differentiated. The populations harboring high genetic diversity, especially KR, should be considered first when devising conservation plans for the protection of G. soja, and in situ protection should be adopted in KR. G. soja populations from the Yangtze River, the Korean peninsula and northeastern China have a close relationship, although these areas are geographically disconnected. Other populations from north China clustered together. Analysis of gene flow suggested that historical migrations of G. soja may have occurred from the south northwards across the East-Asia land-bridge, but not across north China. All G. soja populations could be divided into one of two lineages, and these two lineages should be treated separately when formulating protection policies. creator: Jing Meng creator: Guoqian Yang creator: Xuejiao Li creator: Yan Zhao creator: Shuilian He uri: https://doi.org/10.7717/peerj.16415 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Meng et al. title: A new pseudoscorpion genus (Garypinoidea: Garypinidae) from the Eocene supports extinction and range contraction in the European paleobiota link: https://peerj.com/articles/15989 last-modified: 2023-11-07 description: During the Paleogene, the Holarctic experienced drastic climatic oscillations, including periods of extensive glaciation. These changes had a severe impact on both the flora and fauna causing widespread extinction and range shifts with some taxa retreating to refugia in the Mediterranean Basin. Here we provide evidence for this hypothesis using fossils from the pseudoscorpion family Garypinidae Daday, 1889 (Arachnida: Pseudoscorpiones). This family comprises 21 extant genera from all continents except Antarctica but is restricted to low mid-latitudes (<44°N) in the Northern Hemisphere. We provide the second record of garypinids from the European succinite ambers of the Eocene by describing the first extinct genus in Garypinidae, Baltamblyolpium gen. nov., which includes two species: Baltamblyolpium gizmotum sp. nov. from Baltic amber and Baltamblyolpium grabenhorsti sp. nov. from Bitterfeld amber. The new genus exhibits a morphology that closely resembles Neoamblyolpium Hoff, 1956 from western North America and the genus Amblyolpium Simon, 1898, which is widespread but includes taxa restricted to Mediterranean refugia in Europe. The discovery of a new fossil genus of Garypinidae from Europe confirms that the family was found at more northerly latitudes during the Eocene, however, extinction and range contraction resulted in their present-day relictual distribution in southern Europe like many other lineages that once thrived in the European “Baltic amber forest” of the Eocene. creator: Nova Stanczak creator: Mark S. Harvey creator: Danilo Harms creator: Jörg U. Hammel creator: Ulrich Kotthoff creator: Stephanie F. Loria uri: https://doi.org/10.7717/peerj.15989 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Stanczak et al. title: Participatory ethnobotany: comparison between two quilombos in the Atlantic Forest, Ubatuba, São Paulo, Brazil link: https://peerj.com/articles/16231 last-modified: 2023-11-07 description: Ethnobotanical studies that use the participatory research approach seek to involve the residents of a community in different stages of the study, promoting the registration, dissemination and strengthening of local knowledge, as well as the empowerment of decisions related to the sustainable use and management of resources. Using the participatory methodology, this study recorded and made a comparative analysis on the use of plants in two quilombola communities (Quilombo do Cambury-QC and Quilombo da Fazenda-QF) in the State of São Paulo. After a training on anthropological and botanical methods, local researchers selected and interviewed the local experts, recording their knowledge on plant uses and collecting the indicated plants, to be identified and deposited in herbariums. In addition, participant observation and field diaries were used by the academic researchers, helping to analyze the data. To test the differences in the composition of species known to local community, a Jaccard dissimilarity matrix was created, and a Permanova test was employed. During the 178 days of fieldwork, three local researchers from the QC and two from the QF, selected nine and eight experts on the uses of the plants in each quilombo, respectively, corresponding to 214 plant species, indicated for eight ethnobotanical categories. Our hypothesis has been confirmed, since the traditional knowledge found in both quilombos, regarding plant uses and the number of plant species by category, are distinct, since each community occupies particular plant areas and different phytophysiognomies. Most of the indicated species are native to the Atlantic forest, and no significant differences were observed in the proportion of native species vs. introduced among quilombos for any of the categories of use studied. Furthermore, the innovative methodology used, participatory ethnobotany, contributed to the empowerment of community members with regard to the use of their available resources in the environment in which they live, while retaining the intellectual property rights over their own knowledge. creator: Thamara Sauini creator: Paulo Henrique Gonçalves Santos creator: Ulysses Paulino Albuquerque creator: Priscila Yazbek creator: Cremilda da Cruz creator: Eduardo Hortal Pereira Barretto creator: Maria Alice dos Santos creator: Maria Angélica Silva Gomes creator: Ginacil dos Santos creator: Silvestre Braga creator: Ricardo José Francischetti Garcia creator: Sumiko Honda creator: Priscila Matta creator: Sonia Aragaki creator: Anderson Ueno creator: Eliana Rodrigues uri: https://doi.org/10.7717/peerj.16231 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sauini et al. title: circMSH3 is a potential biomarker for the diagnosis of colorectal cancer and affects the distant metastasis of colorectal cancer link: https://peerj.com/articles/16297 last-modified: 2023-11-07 description: ObjectivesTo identify the most significantly differentially expressed circular RNAs (circRNAs) in colorectal cancer (CRC) tissues in terms of their expression levels and circularity, and to analyze the relationship between their expression levels and the clinical characteristics of patients.MethodscircRNA RNA-seq technology was used to screen differentially expressed circRNAs in CRC. Sanger sequencing was used to identify circRNA back-splice junction sites. The relative expression levels of hsa_circ_0003761 (circMSH3) in CRC tissues and cell lines were detected by quantitative real-time fluorescence PCR technology. An RNA-protein pull-down assay was used to detect protein binding to circRNAs. Dual-luciferase reporter gene vectors were constructed to verify that circRNAs bind to microRNAs.ResultsFour hundred twenty circRNAs were found to be upregulated, and 616 circRNAs were downregulated. circMSH3 was derived from the MutS homolog 3 (MSH3) gene and was formed by a loop of exons 9, 10, 11, and 12. In 110 pairs of CRC and adjacent tissues, circMSH3 expression was 4.487-fold higher in CRC tissues. circMSH3 was also highly expressed in the HT-29 and LOVO CRC cell lines. The expression level of circMSH3 was associated with distant metastasis in CRC patients (P = 0.043); the area under the curve (AUC) of circMSH3 for CRC diagnosis was 0.75, with a sensitivity and specificity of 70.9% and 66.4%, respectively. circMSH3 could bind to a variety of proteins, mainly those involved in RNA transcription, splicing, cell cycle, and cell junctions. Furthermore, circMSH3 could bind to miR-1276, miR-942-5p, and miR-409-3p.ConclusioncircMSH3 is a potential biomarker for the diagnosis of CRC and affects the distant metastasis of CRC. Multiple RNA-binding protein binds to circMSH3, and circMSH3 binds to miR-1276, miR-942-5p, and miR-409-3p, thereby affecting the expression of circMSH3. creator: Jian Shen creator: Yu Min creator: Jingen Luo creator: Xingkui Tang creator: Zeping Han creator: Wenfeng Luo creator: Fangmei Xie creator: Mingrong Cao creator: Taicheng Zhou creator: Jinhua He uri: https://doi.org/10.7717/peerj.16297 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Shen et al. title: RBM25 binds to and regulates alternative splicing levels of Slc38a9, Csf1, and Coro6 to affect immune and inflammatory processes in H9c2 cells link: https://peerj.com/articles/16312 last-modified: 2023-11-07 description: BackgroundAlternative splicing (AS) is a biological process that allows genes to be translated into diverse proteins. However, aberrant AS can predispose cells to aberrations in biological mechanisms. RNA binding proteins (RBPs), closely affiliated with AS, have gained increased attention in recent years. Among these RBPs, RBM25 has been reported to participate in the cardiac pathological mechanism through regulating AS; however, the involvement of RBM25 as a splicing factor in heart failure remains unclarified.MethodsRBM25 was overexpressed in H9c2 cells to explore the target genes bound and regulated by RBM25 during heart failure. RNA sequencing (RNA-seq) was used to scrutinize the comprehensive transcriptional level before identifying AS events influenced by RBM25. Further, improved RNA immunoprecipitation sequencing (iRIP-seq) was employed to pinpoint RBM25-binding sites, and RT-qPCR was used to validate specific genes modulated by RBM25.ResultsRBM25 was found to upregulate the expression of genes pertinent to the inflammatory response and viral processes, as well as to mediate the AS of genes associated with cellular apoptosis and inflammation. Overlap analysis between RNA-seq and iRIP-seq suggested that RBM25 bound to and manipulated the AS of genes associated with inflammation in H9c2 cells. Moreover, qRT-PCR confirmed Slc38a9, Csf1, and Coro6 as the binding and AS regulatory targets of RBM25.ConclusionOur research implies that RBM25 plays a contributory role in cardiac inflammatory responses via its ability to bind to and regulate the AS of related genes. This study offers preliminary evidence of the influence of RBM25 on inflammation in H9c2 cells. creator: Xin Tian creator: Guangli Zhou creator: Hao Li creator: Xueting Zhang creator: Lingmin Zhao creator: Keyi Zhang creator: Luqiao Wang creator: Mingwei Liu creator: Chen Liu creator: Ping Yang uri: https://doi.org/10.7717/peerj.16312 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Tian et al. title: Association of triglyceride-glucose index with the risk of prostate cancer: a retrospective study link: https://peerj.com/articles/16313 last-modified: 2023-11-07 description: BackgroundProstate cancer is the most common malignancy in men, and its incidence is increasing year by year. Some studies have shown that risk factors for prostate cancer are related to insulin resistance. The triglyceride-glucose (TyG) index is a marker of insulin resistance. We investigated the validity of TyG index for predicting prostate cancer and the dose-response relationship in prostate cancer in relation to it.ObjectiveTo investigate the risk factors of TyG index and prostate cancer prevalence.MethodsThis study was screened from the First Affiliated Hospital of Xinjiang Medical University and included 767 people, including 136 prostate cancer patients in the case group and 631 healthy people in the control group. The relationship between TyG index and the risk of prostate cancer was analyzed by one-way logistic regression, adjusted for relevant factors, and multi-factor logistic regression analysis was performed to further investigate the risk factors affecting the prevalence of prostate cancer. ROC curves and Restricted Cubic Spline were established to determine the predictive value and dose-response relationship of TyG index in prostate cancer.ResultsBlood potassium (OR = 0.056, 95% CI [0.021–0.148]), total cholesterol (OR = 1.07, 95% CI [0.792–1.444]) and education level (OR = 0.842, 95% CI [0.418–1.697]) were protective factors for prostate cancer, alkaline phosphatase, age, LDL, increased the risk of prostate cancer (OR = 1.016, 95% CI [1.006–1.026]) (OR = 139.253, 95% CI [18.523–1,046.893] (OR = 0.318, 95% CI [0.169–0.596]); TyG index also was a risk factor for prostate cancer, the risk increased with TyG levels,and persons in the TyGQ3 group (8.373–8.854 mg/dL) was 6.918 times (95% CI [2.275–21.043]) higher than in the Q1 group,in the TyGQ4 group (≥8.854) was 28.867 times of those in the Q1 group (95% CI [9.499–87.727]).ConclusionTyG index may be a more accurate and efficient predictor of prostate cancer. creator: Tianqi Li creator: Yijie Zhou creator: Jinru Wang creator: Songtao Xiao creator: Yajun Duan creator: Caihong Li creator: Yi Gao creator: Hengqing An creator: Ning Tao uri: https://doi.org/10.7717/peerj.16313 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Assessment of intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on omega, gamma and alpha-gliadin profiles link: https://peerj.com/articles/16330 last-modified: 2023-11-07 description: Durum and bread wheat are well adapted to the Mediterranean Basin. Twenty-three genotypes of each species were grown to evaluate the intra- and inter-genetic diversity based on omega (ω), gamma (γ) and alpha (α)-gliadin profiles. To achieve this purpose, the endosperm storage proteins (both gliadins and glutenins) were extracted from wheat grains and electrophoresed on sodium dodecyl sulfate (SDS)–polyacrylamide gels. The results of SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) revealed nine polymorphic loci out of 16 loci with durum wheat genotypes and nine polymorphic loci out of 18 loci with bead wheat genotypes. The polymorphisms revealed by the SDS-PAGE were 56% and 50% in durum and bread wheat genotypes, respectively. Using the cluster analysis, the durum wheat genotypes were clustered into five groups, while the bread wheat genotypes were grouped into six clusters using un-weighed pair group mean analyses based on ω, γ, and α-gliadins profiles. The 46 durum and bread wheat genotypes were grouped into seven clusters based on the combined ω, γ, and α-gliadins profiles revealed by the SDS-PAGE. The in silico analysis determined the intra-genetic diversity between bread and durum wheat based on the sequences of ω, γ, and α-gliadins. The alignment of ω-gliadin revealed the highest polymorphism (52.1%) between bread and durum wheat, meanwhile, the alignment of γ and α-gliadins revealed very low polymorphism 6.6% and 15.4%, respectively. According to computational studies, all gliadins contain a lot of glutamine and proline residues. The analysis revealed that the bread wheat possessed ω and γ -gliadins with a lower content of proline and a higher content of glutamine than durum wheat. In contrast, durum wheat possessed α-gliadin with a lower content of proline and a higher content of glutamine than bread wheat. In conclusion, the SDS-PAGE, in silico and computational analyses are effective tools to determine the intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on ω, γ, and α-gliadins profiles. creator: Jameel M. Al-Khayri creator: Khairiah M. Alwutayd creator: Fatmah A. Safhi creator: Mesfer M. Alqahtani creator: Rana M. Alshegaihi creator: Diaa Abd El-Moneim creator: Shri Mohan Jain creator: Ahmed S. Eldomiaty creator: Rahma Alshamrani creator: Amani Omar Abuzaid creator: Abdallah A. Hassanin uri: https://doi.org/10.7717/peerj.16330 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Al-Khayri et al. title: Identification of potential molecular mimicry in pathogen-host interactions link: https://peerj.com/articles/16339 last-modified: 2023-11-07 description: Pathogens have evolved sophisticated strategies to manipulate host signaling pathways, including the phenomenon of molecular mimicry, where pathogen-derived biomolecules imitate host biomolecules. In this study, we resurrected, updated, and optimized a sequence-based bioinformatics pipeline to identify potential molecular mimicry candidates between humans and 32 pathogenic species whose proteomes’ 3D structure predictions were available at the start of this study. We observed considerable variation in the number of mimicry candidates across pathogenic species, with pathogenic bacteria exhibiting fewer candidates compared to fungi and protozoans. Further analysis revealed that the candidate mimicry regions were enriched in solvent-accessible regions, highlighting their potential functional relevance. We identified a total of 1,878 mimicked regions in 1,439 human proteins, and clustering analysis indicated diverse target proteins across pathogen species. The human proteins containing mimicked regions revealed significant associations between these proteins and various biological processes, with an emphasis on host extracellular matrix organization and cytoskeletal processes. However, immune-related proteins were underrepresented as targets of mimicry. Our findings provide insights into the broad range of host-pathogen interactions mediated by molecular mimicry and highlight potential targets for further investigation. This comprehensive analysis contributes to our understanding of the complex mechanisms employed by pathogens to subvert host defenses and we provide a resource to assist researchers in the development of novel therapeutic strategies. creator: Kaylee D. Rich creator: Shruti Srivastava creator: Viraj R. Muthye creator: James D. Wasmuth uri: https://doi.org/10.7717/peerj.16339 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rich et al. title: Molecular signature of the ontogenic development of the prawn Macrobrachium tenellum link: https://peerj.com/articles/16344 last-modified: 2023-11-07 description: The prawn Macrobrachium tenellum shows aquaculture potential due to its well-defined reproductive cycle linked to female nutritional requirements. Significant changes occur in egg composition during the 16 to 17-day embryo development. Understanding the ontogenic proteins is crucial for developmental insights and controlled reproduction. We employed free-label quantitative proteomics to analyze egg peptides at the initial and final stages of wild females. Using the emPAI protocol and Proteome Discoverer 2.0, we identified 89 differentially expressed proteins in M. tenellum eggs. Of these, 27 were exclusive to early-stage development and three to late-stage. Abundant proteins included Vitellogenin, glyceraldehyde-3-phosphate dehydrogenase, histone 4, beta-actin, and hemocyanin. Gene Ontology analysis revealed 518 terms across molecular functions, biological processes, and cellular components using the GoRetriever tool of AgBase and the CateGOrizer tool of the Animal Genome Research Program. Carbohydrate metabolism was significant in early-stage development, with glyceraldehyde-3-phosphate dehydrogenase being the second most abundant protein. Proteins involved in ATP synthesis and cytoplasmic proteins associated with catalytic and binding activities related to primary metabolism were also detected. Our study elucidates the role of Vitellogenin in lipid transport activity and its potential involvement in the juvenile hormone feedback pathway. This pathway includes farnesoic acid O-methyltransferase and juvenile hormone epoxide oxidase, regulating protein biosynthesis, molt cycles (including chitinase activity), and potentially influencing controlled reproduction. Our proteomic analysis provides insights into the molecular mechanisms driving Ontogenic development in Macrobrachium tenellum, with implications for controlled reproduction strategies and advancements in aquaculture practices. creator: Dulce Mateos Guerrero creator: Margarito Martínez-Cruz creator: Eduardo Pérez-Campos creator: Marcelo García-Guerrero creator: Rodolfo de los Santos-Romero creator: Carlos Solórzano-Mata creator: José Luís Sánchez-Salgado creator: Mohamed Ali Pereyra Morales creator: Agustin Lugo-Radillo creator: Anayetzin Torres-Rivera creator: Juan Alpuche uri: https://doi.org/10.7717/peerj.16344 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mateos Guerrero et al. title: Diversity and conservation of mammals in indigenous territories of southern Mexico: proposal for an “Archipelago Reserve” link: https://peerj.com/articles/16345 last-modified: 2023-11-07 description: Southern Mexico’s tropical forests are home to the country’s highest richness of mammal species; La Chinantla region is situated within this area, its name from the indigenous group residing in the area and holding territorial ownership, namely the Chinantecos. In La Chinantla, there are no Protected Areas; instead, there are Areas Destined Voluntarily for Conservation (ADVC) and “Voluntary Conservation Areas” (VCA), that are managed by local inhabitants through social consensus. These ADVC may function as an archipelago reserve, which represents regional diversity, including the social context, through complementarity. To verify its biodiversity, we analyzed the richness, composition, distribution, and conservation of wild mammals in the region. Records were obtained from four sources—primary data collection, databases, scientific literature, and community monitoring—and were organized into four zones based on altitudinal and vegetation gradients. We compared the diversity between zones for three categories of mammals: small (<100 gr.), bats, and medium and large (>100 gr.). 134 species were identified comprising 11 orders, 26 families and 86 genera. The zone with highest elevation presented the greatest species richness for the assemblage of mammals and terrestrial mammals, while the zone with the lowest elevation had the highest richness of bats. For each mammal category, the zone with the most species also registered the highest number of exclusive species. For the assemblage of mammals and for medium and large mammals, the similarity index was highest between the two intermediate zones, while for small mammals and bats, the greatest similarity occurred between the areas of higher altitude. The study region was found to have the second highest richness of mammals in Mexico. Finally, we suggest that the conservation proposals by indigenous people could function as a set of “islands” that promote the conservation of biodiversity, possibly as an Archipelago Reserve. creator: Miguel Briones-Salas creator: Rosa E. Galindo-Aguilar creator: Graciela E. González creator: María Delfina Luna-Krauletz uri: https://doi.org/10.7717/peerj.16345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Briones-Salas et al. title: Leaf defenses of subtropical deciduous and evergreen trees to varying intensities of herbivory link: https://peerj.com/articles/16350 last-modified: 2023-11-07 description: Generally, deciduous and evergreen trees coexist in subtropical forests, and both types of leaves are attacked by numerous insect herbivores. However, trees respond and defend themselves from herbivores in different ways, and these responses may vary between evergreen and deciduous species. We examined both the percentage of leaf area removed by herbivores as well as the percentage of leaves attacked by herbivores to evaluate leaf herbivore damage across 14 subtropical deciduous and evergreen tree species, and quantified plant defenses to varying intensities of herbivory. We found that there was no significant difference in mean percentage of leaf area removed between deciduous and evergreen species, yet a higher mean percentage of deciduous leaves were damaged compared to evergreen leaves (73.7% versus 60.2%). Although percent leaf area removed was mainly influenced by hemicellulose concentrations, there was some evidence that the ratio of non-structural carbohydrates:lignin and the concentration of tannins contribute to herbivory. We also highlight that leaf defenses to varying intensities of herbivory varied greatly among subtropical plant species and there was a stronger response for deciduous trees to leaf herbivore (e.g., increased nitrogen or lignin) attack than that of evergreen trees. This work elucidates how leaves respond to varying intensities of herbivory, and explores some of the underlying relationships between leaf traits and herbivore attack in subtropical forests. creator: Xiaoyu Liu creator: Carri J. LeRoy creator: Guobing Wang creator: Yuan Guo creator: Shuwang Song creator: Zhipei Wang creator: Jingfang Wu creator: Fenggang Luan creator: Qingni Song creator: Xiong Fang creator: Qingpei Yang creator: Dongmei Huang creator: Jun Liu uri: https://doi.org/10.7717/peerj.16350 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Herpetogaster collinsi from the Cambrian of China elucidates the dispersal and palaeogeographic distribution of early deuterostomes and the origin of the ambulacrarian larva link: https://peerj.com/articles/16385 last-modified: 2023-11-07 description: The Cambrian Radiation represents one of the largest diversification events in Earth history. While the resulting taxonomic diversity is exceptional, relatively few of these novel species can be traced outside the boundaries of a single palaeocontinent. Many of those species with cosmopolitan distributions were likely active swimmers, presenting opportunity and means to conquer new areas, but this would not have been the case for sessile organisms. Herpetogaster is a lower to middle Cambrian (Series 2–Miaolingian, Stage 3–Wuliuan) genus of sessile, stalked, filter-feeding deuterostomes with two species, H. collinsi and H. haiyanensis, known respectively from Laurentia and Gondwana. Here, we expand the distribution of H. collinsi to Gondwana with newly discovered specimens from the Balang Formation of Hunan, China. This discovery raises questions on the origin of the genus and how sessile organisms were able to disperse over such a broad distance in the lower Cambrian. As Herpetogaster has been recovered at the base of the Ambulacrarian tree in recent phylogenies, a planktonic larval stage is suggested, which implies, that the last common ancestor of the Ambulacraria might have already had planktonic larvae or that such larvae developed multiple times within the Ambulacraria. creator: Xianfeng Yang creator: Julien Kimmig creator: James D. Schiffbauer creator: Shanchi Peng uri: https://doi.org/10.7717/peerj.16385 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yang et al. title: Estimate of lysine nutritional requirements for Japanese quail breeders link: https://peerj.com/articles/15637 last-modified: 2023-11-06 description: BackgroundJapanese quail breeders are the basis for genetic improvement and multiplication for commercial layers, however, there have been no known studies on the optimal lysine level for these birds. Thus, study the egg output response to the lysine (Lys) supply using different e-functions and evaluate the that best fit, have allowed the partition the lysine requirements for maintenance, both weight and egg output maximum.MethodsThe objectives of this study were to identify the responses to various Lys levels, identify the functions related to these responses and determine the ideal Lys intake amount for Japanese quail breeders. A completely randomized design of seven treatments with seven replicated was used. Treatments consisted of diet supplementation by Lys in concentrations of 16.8, 11.8, 8.4, 6.7, 5.0, 3.4, and 1.7 g/kg. Six exponential models were adjusted.ResultsThe level of Lys was found to affect bird responses (P < 0.001). The birds responded to the levels provided, allowing for the creation of a lysine response curve. A monomolecular function with four parameters was balanced against the statistics of adjustment and selection of models. It was possible to estimate the level of lysine required for maintenance as 133 ± 2 mg/kg BW0.67, and based an average of 41% efficiency, 22 mg Lys produced 1 g of egg output (EO). The daily intake calculated by the monomolecular factorial model was 284 mg Lys for a bird with 0.170 kg body weight and production of 10 g EO/day. The four-parameter monomolecular function proposed in this study is adequate for interpreting the animal response and calculating lysine intake for breeders. creator: Lizia Cordeiro de Carvalho creator: Manoela Garcia Borgi Lino de Sousa creator: Jaqueline Aparecida Pavanini creator: Tadia Emanuele Stivanin creator: Nelson José Peruzzi creator: Alan Rodrigo Panosso creator: Michele Bernardino de Lima creator: Edney Pereira da Silva uri: https://doi.org/10.7717/peerj.15637 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Carvalho et al. title: PCMT1 knockdown attenuates malignant properties by globally regulating transcriptome profiles in triple-negative breast cancer cells link: https://peerj.com/articles/16006 last-modified: 2023-11-06 description: BackgroundAs the most frequently diagnosed cancer in women, Breast cancer has high mortality and metastasis rate, especially triple-negative breast cancer (TNBC). As an oncogene, protein-L-isoaspartate (D-aspartate) O-methyltransferase (PCMT1) is a prognostic biomarker in breast cancer and is highly expressed, while its underlying functions remain unknown.MethodsIn this study, we silenced PCTM1 in TNBC MDA-MB-231 cells by short hairpin RNA (shPCMT1) to investigate its cellular functions using cell proliferation, apoptosis, migration, and invasion experiments. Following this, the transcriptome sequencing (RNA-seq) experiment was conducted to explore the molecular targets of PCMT1, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs).ResultsThe results showed that shPCMT1 inhibited the proliferation, migration, and invasion of MDA-MB-231 cells. We obtained 1,084 DEGs and 2,287 RASEs between shPCMT1 and negative control (NC) groups through RNA-seq. The DEGs were significantly enriched in immune or inflammation response and cell adhesion-associated pathways, pathways associated with PCMT1 cellular function in cell migration. The RASE genes were enriched in cell cycle-associated pathways and were associated with the altered cell proliferation rate. We finally validated the changed expression and splicing levels of DEGs and RASEs. We found that 34 RNA binding protein (RBP) genes were dysregulated by shPCMT1, including NQO1, S100A4, EEF1A2, and RBMS2. The dysregulated RBP genes could partially explain how PCMT1 regulates the global transcriptome profiles.ConclusionIn conclusion, our study identified the molecular targets of PCMT1 in the TNBC cell line, expands our understanding of the regulatory mechanisms of PCMT1 in cancer progression, and provides novel insights into the progression of TNBC. The identified molecular targets are potential therapeutic targets for future TNBC treatment. creator: Aili Saiding creator: Dilinuer Maimaitiyiming creator: Minglan Chen creator: Futian Yan creator: Dong Chen creator: Xinyu Hu creator: Ping Shi uri: https://doi.org/10.7717/peerj.16006 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Saiding et al. title: Isolation of soil bacteria able to degrade the anthelminthic compound albendazole link: https://peerj.com/articles/16127 last-modified: 2023-11-06 description: Anthelmintic (AHs) veterinary drugs constitute major environmental contaminants. The use of AH-contaminated fecal material as manures in agricultural settings constitutes their main route of environmental dispersal. Once in soils, these compounds induce toxic effects to soil fauna and soil microbiota, both having a pivotal role in soil ecosystem functioning. Therefore, it is necessary to identify mitigation strategies to restrict the environmental dispersal of AHs. Bioaugmentation of AH-contaminated manures or soils with specialized microbial inocula constitutes a promising remediation strategy. In the present study, we aimed to isolate microorganisms able to actively transform the most widely used benzimidazole anthelminthic albendazole (ABZ). Enrichment cultures in minimal growth media inoculated with a soil known to exhibit rapid degradation of ABZ led to the isolation of two bacterial cultures able to actively degrade ABZ. Two oxidative products of ABZ, ABZSO and ABZSO2, were detected at low amounts along its degradation. This suggested that the oxidation of ABZ is not a major transformation process in the isolated bacteria which most probably use other biotic pathways to degrade ABZ leading to the formation of products not monitored in this study. Full length sequencing of their 16S rRNA gene and phylogenetic analysis assigned both strains to the genus Acinetobacter. The sequences were submitted in GeneBank NCBI, database with the accession numbers OP604271 to OP604273. Further studies will employ omic tools to identify the full transformation pathway and the associated genetic network of Acinetobacter isolates, information that will unlock the potential use of these isolates in the bioaugmentation of contaminated manures. creator: Stathis Lagos creator: Kalliopi Koutroutsiou creator: Dimitrios G. Karpouzas uri: https://doi.org/10.7717/peerj.16127 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lagos et al. title: #DeOlhoNosCorais: a polygonal annotated dataset to optimize coral monitoring link: https://peerj.com/articles/16219 last-modified: 2023-11-06 description: Corals are colonial animals within the Phylum Cnidaria that form coral reefs, playing a significant role in marine environments by providing habitat for fish, mollusks, crustaceans, sponges, algae, and other organisms. Global climate changes are causing more intense and frequent thermal stress events, leading to corals losing their color due to the disruption of a symbiotic relationship with photosynthetic endosymbionts. Given the importance of corals to the marine environment, monitoring coral reefs is critical to understanding their response to anthropogenic impacts. Most coral monitoring activities involve underwater photographs, which can be costly to generate on large spatial scales and require processing and analysis that may be time-consuming. The Marine Ecology Laboratory (LECOM) at the Federal University of Rio Grande do Norte (UFRN) developed the project “#DeOlhoNosCorais” which encourages users to post photos of coral reefs on their social media (Instagram) using this hashtag, enabling people without previous scientific training to contribute to coral monitoring. The laboratory team identifies the species and gathers information on coral health along the Brazilian coast by analyzing each picture posted on social media. To optimize this process, we conducted baseline experiments for image classification and semantic segmentation. We analyzed the classification results of three different machine learning models using the Local Interpretable Model-agnostic Explanations (LIME) algorithm. The best results were achieved by combining EfficientNet for feature extraction and Logistic Regression for classification. Regarding semantic segmentation, the U-Net Pix2Pix model produced a pixel-level accuracy of 86%. Our results indicate that this tool can enhance image selection for coral monitoring purposes and open several perspectives for improving classification performance. Furthermore, our findings can be expanded by incorporating other datasets to create a tool that streamlines the time and cost associated with analyzing coral reef images across various regions. creator: Daniel P. Furtado creator: Edson A. Vieira creator: Wildna Fernandes Nascimento creator: Kelly Y. Inagaki creator: Jessica Bleuel creator: Marco Antonio Zanata Alves creator: Guilherme O. Longo creator: Luiz S. Oliveira uri: https://doi.org/10.7717/peerj.16219 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Furtado et al. title: Network analysis of depression and anxiety symptoms in Chinese rheumatoid arthritis patients link: https://peerj.com/articles/16356 last-modified: 2023-11-06 description: BackgroundRheumatoid arthritis (RA) patients are susceptible to comorbid anxiety and depression. From the network model perspective, comorbidity is due to direct interactions between depression and anxiety symptoms. The objective of this study was to assess the network structure of depression and anxiety symptoms in Chinese RA patients and identify the central and bridge symptoms as well as how depression and anxiety symptoms are related to quality of life (QoL) in the network.MethodsA total of 402 Chinese RA patients were included in this study. Depression and anxiety symptoms were measured by the Hospital Anxiety and Depression Scale (HADS). R software was used to estimate the network. Specifically, we computed the predictability, expected influence (EI) and bridge expected influence (BEI) for each symptom and showed a flow network of “QoL”.ResultsOur network revealed that the strongest edge was D2 “See the bad side of things” and D3 “Not feeling cheerful” across the whole network. For centrality indices, D3 “Not feeling cheerful” and D6 “Feeling down” had the highest EI values in the network, while A4 “Trouble relaxing” and D6 “Feeling down” had the highest BEI values of their respective community. As to “QoL”, the strongest direct edge related to it was A1 “Nervousness”.Conclusions“Feeling down” and “Not feeling cheerful” emerged as the strongest central symptoms, while “Trouble relaxing” and “Feeling down” were bridge symptoms in the anxiety-depression network of RA patients. Intervention on depression and anxiety symptoms in nurses should prioritize these symptoms. creator: Lijuan Zhang creator: Weiyi Zhu creator: Beiwen Wu uri: https://doi.org/10.7717/peerj.16356 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Different gut microbial types were found in captive striped hamsters link: https://peerj.com/articles/16365 last-modified: 2023-11-06 description: BackgroundTyping analysis has become a popular approach to categorize individual differences in studies of animal gut microbial communities. However, previous definitions of gut microbial types were more understood as a passive reaction process to different external interferences, as most studies involve diverse environmental variables. We wondered whether distinct gut microbial types can also occur in animals under the same external environment. Moreover, the role of host sex in shaping gut microbiota has been widely reported; thus, the current study preliminarily explores the effects of sex on potential different microbial types.MethodsHere, adult striped hamsters Cricetulus barabensis of different sexes were housed under the same controlled laboratory conditions, and their fecal samples were collected after two months to assess the gut microbiota by 16S rRNA sequencing.ResultsThe gut microbiota of captive striped hamsters naturally separated into two types at the amplicon sequence variant (ASV) level. There was a significant difference in the Shannon index among these two types. A receiver operating characteristic (ROC) curve showed that the top 30 ASVs could effectively distinguish each type. Linear discriminant analysis of effect size (LEfSe) showed enrichment of the genera Lactobacillus, Treponema and Pygmaiobacter in one gut microbial type and enrichment of the genera Turicibacter and Ruminiclostridium in the other. The former type had higher carbohydrate metabolism ability, while the latter harbored a more complex co-occurrence network and higher amino acid metabolism ability. The gut microbial types were not associated with sex; however, we did find sex differences in the relative abundances of certain bacterial taxa, including some type-specific sex variations.ConclusionsAlthough captive animals live in a unified environment, their gut bacteria can still differentiate into distinct types, but the sex of the hosts may not play an important role in the typing process of small-scale captive animal communities. The relevant driving factors as well as other potential types need to be further investigated to better understand host-microbe interactions. creator: Chao Fan creator: Yunjiao Zheng creator: Huiliang Xue creator: Jinhui Xu creator: Ming Wu creator: Lei Chen creator: Laixiang Xu uri: https://doi.org/10.7717/peerj.16365 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Fan et al. title: MiR-525-5p inhibits diffuse large B cell lymphoma progression via the Myd88/NF-κB signaling pathway link: https://peerj.com/articles/16388 last-modified: 2023-11-06 description: Diffuse large B-cell lymphoma (DLBCL) is a B-cell lymphoma with a high degree of aggressiveness. Recently, evidence has shown that miR-525-5p is decreased in DLBCL, suggesting its possible involvement in tumor progression. In this study, miR-525-5p suppressed proliferation, invasion and clonogenicity, and increased apoptosis of U2932 cells, whereas miR-525-5p silencing enhanced tumor cell growth. Next, miR-525-5p targets the 3′-UTR of Myd88, and Myd88 protein was increased in lymphoma tissues. Similar to the miR-525-5p mimic, Myd88 siRNA suppressed proliferation, invasion, and clonogenicity, and enhanced apoptosis of U2932 cells. We observed that Myd88 reversed the inhibitory effect of miR-525-5p on tumor cell growth by transfecting cells with miR-525-5p mimics alone or together with Myd88 overexpression vector. In addition, in vivo studies have shown that compared to the control group, U2932 cells with upregulated miR-525-5p expression have a reduced ability to induce tumor formation. In conclusion, our results demonstrate that miR-525-5p inhibits the progression of DLBCL through the Myd88/NF-κB pathway, which largely fills the gap of previous studies, and our results may provide a new reference for the targeted treatment of DLBCL. creator: Xiuchen Guo creator: Jingbo Zhang creator: Jingya Zeng creator: Yiwei Guo creator: Lina Zhao uri: https://doi.org/10.7717/peerj.16388 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Guo et al. title: Sperm specificity and potential paternal effects in gynogenesis in the Amazon Molly (Poecilia formosa) link: https://peerj.com/articles/16118 last-modified: 2023-11-03 description: The Amazon Molly (Poecilia formosa) reproduces by gynogenesis, a relatively rare form of asexual reproduction where sperm is required to trigger embryogenesis, but male genes are not incorporated into the genome of the embryo. Studying gynogenesis could isolate paternal non-genetic effects on reproduction. This study explored which of eleven related species can produce sperm to trigger gynogenesis through natural mating in P. formosa, and whether sympatry affects reproductive success in P. formosa. Reproductive outcomes measured were relative reproductive output (number of offspring in the first brood divided by female standard length), relative embryo output (number of embryos in the first brood divided by female standard length) and combined relative reproductive output (sum of relative reproductive output and relative embryo output). For large (>4 cm) P. formosa, combined relative reproductive output was higher with sympatric Atlantic Molly (Poecilia mexicana) males than with allopatric P. mexicana males. P. formosa produced live offspring or late-stage embryos with all species tested in the genera Poecilia and Limia but did not produce offspring or embryos with males from the genera Gambusia, Girardinus, Heterandria, Poeciliopsis, or Xiphophorus. This information, as well as the limitations characterized in this study, will set a foundation for use of P. formosa as a model for paternal effects and the species specificity of sperm on fertilization, embryogenesis, and reproductive success. creator: Clarissa Cerepaka creator: Ingo Schlupp uri: https://doi.org/10.7717/peerj.16118 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cerepaka and Schlupp title: Enhancing wheat production and quality in alkaline soil: a study on the effectiveness of foliar and soil applied zinc link: https://peerj.com/articles/16179 last-modified: 2023-11-03 description: Cultivation of high-yield varieties and unbalanced fertilization have induced micronutrient deficiency in soils worldwide. Zinc (Zn) is an essential nutrient for plant growth and its deficiency is most common in alkaline and calcareous soils. Therefore, this study aimed to evaluate the effect of Zn applied either alone or in combination with foliar application on the quality and production of wheat grown in alkaline soils. Zn was applied in the form of zinc sulfate (ZnSo4) to the soil and as a foliar spray during the sowing and tillering stages, respectively. Results showed that Zn fertilization of wheat, irrespective of modes of application, significantly increased grain and biological yield, grain per spike, and 1,000 grains weight over control; however, its effect was more noticeable when applied as 7.5 kg ha−1 of soil Zn combined with foliar Zn at 2.5 kg ha−1. Zn application significantly increased the grain protein content from 9.40% in the control to a maximum of 11.83% at soil Zn of 10 kg ha−1. Similarly, Zn application improved Zn, phosphorus (P), and potassium (K) concentrations in wheat grains. Moreover, correlation analysis showed that the grain Zn concentration was positively correlated with the grain P concentration. The correlation between P concentration in wheat grains and 1,000 grain weight was not significant. A total of 1,000 grains weight was positively correlated with tillers per plant, grain yield, and biological yield. There were positive correlations between protein content, biological yield, grain yield, and tillers per plant. Therefore, soil-applied Zn + foliar application in alkaline soils with limited Zn availability is crucial for improving wheat yield and grain quality. creator: Farhat Ullah Khan creator: Adnan Anwar Khan creator: Yuanyuan Qu creator: Qi Zhang creator: Muhammad Adnan creator: Shah Fahad creator: Fatima Gul creator: Muhammad Ismail creator: Shah Saud creator: Shah Hassan creator: Xuexuan Xu uri: https://doi.org/10.7717/peerj.16179 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Khan et al. title: Drone images afford more detections of marine wildlife than real-time observers during simultaneous large-scale surveys link: https://peerj.com/articles/16186 last-modified: 2023-11-03 description: There are many advantages to transitioning from conducting marine wildlife surveys via human observers onboard light-aircraft, to capturing aerial imagery using drones. However, it is important to maintain the validity of long-term data series whilst transitioning from observer to imagery surveys. We need to understand how the detection rates of target species in images compare to those collected from observers in piloted aircraft, and the factors influencing detection rates from each platform. We conducted trial ScanEagle drone surveys of dugongs in Shark Bay, Western Australia, covering the full extent of the drone’s range (∼100 km), concurrently with observer surveys, with the drone flying above or just behind the piloted aircraft. We aimed to test the assumption that drone imagery could provide comparable detection rates of dugongs to human observers when influenced by same environmental conditions. Overall, the dugong sighting rate (i.e., count of individual dugongs) was 1.3 (95% CI [0.98–1.84]) times higher from the drone images than from the observers. The group sighting rate was similar for the two platforms, however the group sizes detected within the drone images were significantly larger than those recorded by the observers, which explained the overall difference in sighting rates. Cloud cover appeared to be the only covariate affecting the two platforms differently; the incidence of cloud cover resulted in smaller group sizes being detected by both platforms, but the observer group sizes dropped much more dramatically (by 71% (95% CI [31–88]) compared to no cloud) than the group sizes detected in the drone images (14% (95% CI [−28–57])). Water visibility and the Beaufort sea state also affected dugong counts and group sizes, but in the same way for both platforms. This is the first direct simultaneous comparison between sightings from observers in piloted aircraft and a drone and demonstrates the potential for drone surveys over a large spatial-scale. creator: Amanda J. Hodgson creator: Nat Kelly creator: David Peel uri: https://doi.org/10.7717/peerj.16186 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hodgson et al. title: Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole link: https://peerj.com/articles/16257 last-modified: 2023-11-03 description: Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming. creator: Hongxi Zhang creator: Taoshu Wei creator: Qingmei Li creator: Liang Fu creator: Lisheng He creator: Yong Wang uri: https://doi.org/10.7717/peerj.16257 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Hidden shifts in allometry scaling between sound production and perception in anurans link: https://peerj.com/articles/16322 last-modified: 2023-11-03 description: BackgroundAnimal communication consists of signal production and perception, which are crucial for social interactions. The main form used by anurans is auditory communication, in most cases produced as advertisement calls. Furthermore, sound perception happens mainly through an external tympanic membrane, and plays an important role in social behavior. In this study, we evaluated the influence of body and tympanic membrane sizes on call frequency across the phylogeny of anurans.MethodsWe use data on snout-vent length, tympanic membrane diameter, and dominant frequency of the advertisement call from the literature and from natural history museum collections. We mapped these traits across the anuran phylogeny and tested different models of diversification. Our final dataset includes data on body size, tympanic membrane size, and call dominant frequency of 735 anuran species.ResultsThe best explanatory model includes body and tympanum size with no interaction term. Although our results show that call frequency is strongly constrained by body and tympanum size, we identify five evolutionary shifts in allometry from that ancestral constraint. We relate these evolutionary shifts to the background noise experienced by populations. Body size is important for myriad ecological interactions and tympanum size is strongly associated with female call frequency preferences. Thus, allometric escape in frog calls might arise through environmental selection such as breeding in fast flowing or soundscape competition, as well as sexual selection linked to tympanum size. creator: Bruna Maria creator: João F.R. Tonini creator: Raoni Rebouças creator: Luís Felipe Toledo uri: https://doi.org/10.7717/peerj.16322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Maria et al. title: Bacterial communities of the psyllid pest Bactericera cockerelli (Hemiptera: Triozidae) Central haplotype of tomato crops cultivated at different locations of Mexico link: https://peerj.com/articles/16347 last-modified: 2023-11-03 description: BackgroundThe psyllid, Bactericera cockerelli, is an insect vector of ‘Candidatus Liberibacter’ causing “Zebra chip” disease that affects potato and other Solanaceae crops worldwide. In the present study, we analyzed the bacterial communities associated with the insect vector Bactericera cockerelli central haplotype of tomato crop fields in four regions from Mexico.MethodsPCR was used to amplify the mitochondrial cytochrome oxidase I gene (mtCOI) and then analyze the single nucleotide polymorphisms (SNP) and phylogenetic analysis for haplotype identification of the isolated B. cockerelli. Moreover, we carried out the microbial diversity analysis of several B. cockerelli collected from four regions of Mexico through the NGS sequencing of 16S rRNA V3 region. Finally, Wolbachia was detected by the wsp gene PCR amplification, which is the B. cockerelli facultative symbiont. Also we were able to confirm the relationship with several Wolbachia strains by phylogenetic analysis.ResultsOur results pointed that B. cockerelli collected in the four locations from Mexico (Central Mexico: Queretaro, and Northern Mexico: Sinaloa, Coahuila, and Nuevo Leon) were identified, such as the central haplotype. Analyses of the parameters of the composition, relative abundance, and diversity (Shannon index: 1.328 ± 0.472; Simpson index 0.582 ± 0.167), showing a notably relatively few microbial species in B. cockerelli. Analyses identified various facultative symbionts, particularly the Wolbachia (Rickettsiales: Anaplasmataceae) with a relative abundance higher. In contrast, the genera of Sodalis and ‘Candidatus Carsonella’ (Gammaproteobacteria: Oceanospirillales: Halomonadaceae) were identified with a relatively low abundance. On the other hand, the relative abundance for the genus ‘Candidatus Liberibacter’ was higher only for some of the locations analyzed. PCR amplification of a fragment of the gene encoding a surface protein (wsp) of Wolbachia and phylogenetic analysis corroborated the presence of this bacterium in the central haplotype. Beta-diversity analysis revealed that the presence of the genus ‘Candidatus Liberibacter’ influences the microbiota structure of this psyllid species.ConclusionsOur data support that the members with the highest representation in microbial community of B. cockerelli central haplotype, comprise their obligate symbiont, Carsonella, and facultative symbionts. We also found evidence that among the factors analyzed, the presence of the plant pathogen affects the structure and composition of the bacterial community associated with B. cockerelli. creator: Maria Goretty Caamal-Chan creator: Aarón Barraza creator: Abraham Loera-Muro creator: Juan J. Montes-Sánchez creator: Thelma Castellanos creator: Yolanda Rodríguez-Pagaza uri: https://doi.org/10.7717/peerj.16347 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Caamal-Chan et al. title: Increased academic stress is associated with decreased plasma BDNF in Chilean college students link: https://peerj.com/articles/16357 last-modified: 2023-11-03 description: IntroductionAcademic stress (AS) is a prevalent challenge faced by university students, potentially affecting molecular indicators such as brain-derived neurotrophic factor (BDNF) and global DNA methylation (G-DNA-M). These indicators could illuminate the physiological ramifications of academic stress.Study Design and MethodsThis research followed a quantitative, non-experimental, longitudinal panel design spanning two academic semesters, observing phenomena in their natural context. Students from the Medical Technology program at Universidad de Concepción, Chile were involved, with assessments at the beginning and during heightened academic stress periods.SampleOf the total participants, 63.0% were females, with an average age of 21.14 years at baseline, and 36.92% were males, averaging 21.36 years. By the study’s conclusion, female participants averaged 21.95 years, and males 22.13 years.ResultsSignificant differences were observed between initial and final assessments for the SISCO-II Inventory of Academic Stress and Beck Depression Inventory-II, notably in stressor scores, and physical, and psychological reactions. Gender differences emerged in the final physical and psychological reactions. No significant changes were detected between the two assessments in plasma BDNF or G-DNA-M values. A refined predictive model showcased that, on average, there was a 3.56% decrease in females’ plasma BDNF at the final assessment and a 17.14% decrease in males. In the sample, the G-DNA-M percentage at the final assessment increased by 15.06% from the baseline for females and 18.96% for males.ConclusionsThe study underscores the physiological impact of academic stress on university students, evidenced by changes in markers like BDNF and G-DNA-M. These findings offer an in-depth understanding of the intricate mechanisms regulating academic stress responses and highlight the need for interventions tailored to mitigate its physiological and psychological effects. creator: Juan-Luis Castillo-Navarrete creator: Claudio Bustos creator: Alejandra Guzman-Castillo creator: Benjamin Vicente uri: https://doi.org/10.7717/peerj.16357 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Castillo-Navarrete et al. title: Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls link: https://peerj.com/articles/16394 last-modified: 2023-11-03 description: BackgroundShotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods.MethodsTo continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal.ResultsThe number of bacterial species detected by metagenomics gradually increased from the phylum to species level, consistent with 16S rDNA sequencing. Several taxa were commonly shared by both sequencing methods. However, Escherichia, Shigella, Erwinia, Klebsiella, Salmonella, Escherichia albertii, Shigella sonnei, Salmonella enterica, and Shigella flexneri were unique taxa for the metagenome compared with Escherichia-Shigella, Hafnia-Obesumbacterium, Catellicoccus marimammalium, Lactococcus garvieae, and Streptococcus gallolyticus for 16S rDNA sequencing. The largest differences in relative abundance between the two methods were identified at the species level, which identified many pathogenic bacteria to humans using metagenomic sequencing. Pearson correlation analysis indicated that the correlation coefficient for the two methods gradually decreased with the refinement of the taxonomic levels. The high consistency of the correlation coefficient was identified at the genus level for the beta diversity of the two methods.ConclusionsIn general, relatively consistent patterns and reliability could be identified by both sequencing methods, but the results varied following the refinement of taxonomic levels. Metagenomic sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls. Although there were large differences in the numbers and abundance of bacterial species of the two methods in terms of taxonomic levels, the patterns and reliability results of the samples were consistent. creator: Feng Liao creator: Yilan Xia creator: Wenpeng Gu creator: Xiaoqing Fu creator: Bing Yuan uri: https://doi.org/10.7717/peerj.16394 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Liao et al. title: Genetic analysis of two species of Mnomen in the Kalamazoo Watershed reveal panmixia in Z. Aquatica, structure among Z. Palustris, and hybridization in areas of sympatry link: https://peerj.com/articles/15971 last-modified: 2023-11-02 description: Mnomen or wild rice of the genus Zizania is an important part of Native American culture, especially in Michigan for the Ojibwe nation. An oil spill in 2010 along the Kalamazoo River and the subsequent clean-up lead to renewed interest in management of Mnomen within the Kalamazoo watershed. The affected water bodies were surveyed for Zizania species to map existing populations, determine the existing genetic diversity and species present, and to identify potential hybridization. Using Traditional Ecological Knowledge of rice beds and opportunistic sampling of encountered plants, 28 rice beds were sampled. Two species of Zizania were identified Z. palustris and Z. aquatica. Genetic diversity was measured using 11 microsatellite loci and was moderately high for both species (Z. aquatica HE = 0.669, H0 = 0.672, n = 26 and Z. palustris HE = 0.697, H0 = 0.636, n = 57). No evidence of population bottle-necking was found. Z. palustris was found to have k = 3 populations on the landscape, while Z. aquatica was found to be a single panmictic population. Several individual hybrids were confirmed using genotyping and they were all found in areas where the two species co-occurred. Additionally, Z. aquatica was found to have expanded into areas historically with only Z. palustris downstream of the oil spill, potentially due to dredging and sediment relocation as part of the clean-up effort. creator: Katarina A. Kieleczawa creator: Kaylee Luke creator: Andrew Gregory uri: https://doi.org/10.7717/peerj.15971 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kieleczawa et al. title: Higher physical activity level and perceived social support is associated with less psychological distress in people with anxiety link: https://peerj.com/articles/16000 last-modified: 2023-11-02 description: IntroductionAnxiety is one of the most prevalent mental illnesses in first world societies, generating discomfort in the people who suffer from it, and high expenses and economic losses in the society. The physical activity (PA) performed, together with the perceived social support (PSS) by people with anxiety could be related to the psychological distress of people with anxiety.ObjectivesTo study the relationships between mental health and its dimensions, through Golberg’s General Health Questionnaire (GHQ12), and the level of PA (PAL) and the PSS in the Spanish adult population with anxiety.HypothesisA higher PAL, and a higher PSS, is related to a lower psychological distress in this population.Design and MethodologyThis study included 1,661 adults with anxiety, residents in Spain. It was a cross-sectional study with data obtained from the Spanish National Health Survey. A Kolmogorov–Smirnov test was applied to examine the data distribution of the variables. The median and interquartile range were used to characterize the sample for continuous variables, and absolute and relative frequencies were used for categorical variables. The Mann–Whitney U test was used to examine the differences between sexes. Dependence between PAL and sex was studied using the chi-square statistic. A Krustal–Wallis test was used to evaluate the existence of differences in the baseline medians on the GHQ-12, according to PAL level. Finally, the correlations between mental health and its dimensions with PAL and the Duke-UNC-11 scores were analysed, obtaining Spearman’s rho and Pearson’s correlation coefficient.ResultsModerate inverse correlations were found between the GHQ-12 and: PAL (rho: −0.219); PSS (r: −0.347). PAL and PSS presented moderate inverse correlations with successful coping (rho: −0.206 and r: −0.325), self-esteem (rho: −0.222 and r: −0.333) and stress (rho: −0.158 and r: −0.288).ConclusionsGreater PAL and social support are associated with reduced psychological distress in people with anxiety. creator: Damián Pereira-Payo creator: Ángel Denche-Zamorano creator: Noelia Mayordomo-Pinilla creator: Juan Manuel Franco-García creator: Antonio Castillo-Paredes creator: Miguel Angel Garcia-Gordillo creator: Jorge Rojo-Ramos creator: Sabina Barrios-Fernández uri: https://doi.org/10.7717/peerj.16000 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pereira-Payo et al. title: Genome-wide association and RNA-seq analyses reveal a potential gene related to linolenic acid in soybean seeds link: https://peerj.com/articles/16138 last-modified: 2023-11-02 description: Linolenic acid (LA) has poor oxidative stability since it is a polyunsaturated fatty acid. Soybean oil has a high LA content and thus has poor oxidative stability. To identify candidate genes that affect the linolenic acid (LA) content in soybean seeds, a genome-wide association study (GWAS) was performed with 1,060 soybean cultivars collected in China between 2019–2021 and which LA content was measured using matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS). A candidate gene, GmWRI14, encoding an APETALA2 (AP2)-type transcription factor, was detected by GWAS in cultivars from all three study years. Multiple sequence alignments showed that GmWRI14 belongs to the plant WRI1 family. The fatty acid contents of different soybean lines were evaluated in transgenic lines with a copy of GmWRI14, control lines without GmWRI14, and the gmwri14 mutant. MALDI-TOF IMS revealed that GmWRI14 transgenic soybeans had a lower LA content with a significant effect on seed size and shape, whereas gmwri14 mutants had a higher LA content. compared to control. The RNA-seq results showed that GmWRI14 suppresses GmFAD3s (GmFAD3B and GmFAD3C) and GmbZIP54 expression in soybean seeds, leading to decreased LA content. Based on the RNA-seq data, yeast one-hybrid (Y1H) and qRT-PCR were performed to confirm the transcriptional regulation of FAD3s by GmWRI14. Our results suggest that FAD3 is indirectly regulated by GmWRI14, representing a new molecular mechanism of fatty acid biosynthesis, in which GmWRI14 regulates LA content in soybean seeds. creator: Di Qin creator: Jiehua Xing creator: Ping Cheng creator: Guohui Yu uri: https://doi.org/10.7717/peerj.16138 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Qin et al. title: Discovering the fish fauna of a lagoon from the southeast of the Yucatan Peninsula, Mexico, using DNA barcodes link: https://peerj.com/articles/16285 last-modified: 2023-11-02 description: BackgroundAquatic ecosystems in the tropics are typically environments with a high species richness of fishes. These systems are also among the most vulnerable in the world, threatening the overall biodiversity of tropical regions. As a first step, it is important to enumerate the species in any ecosystem to promote its conservation. This study aims to inventory the ichthyofauna in the Chile Verde Lagoon, Quintana Roo, on the Yucatan Peninsula, a system fortunately well protected in Mexico, based on faunal surveys backed up with mtDNA barcodes.MethodsWe collected larvae, juveniles, and adults of fishes in the lagoon with a variety of sampling gear targeting various life stages. Species were identified using both morphology and DNA barcodes. The abundance of species and ichthyoplankton biomass (wet weight, suction technique) were calculated from 43 samples.ResultsWe collected 197 adult and juvenile fishes and 3,722 larvae, of which 306 specimens were DNA-sequenced with a success rate of 96.7%. We identified 13 families, 24 genera, and 27 species in our inventory. The species number was estimated to comprise 75% of the potential total richness using the Chao 1 richness estimator. Clupeids and gobiids accounted for 87.9% of the total abundance of fishes, and, together with cyprinodontids, also accounted for the highest ichthyoplankton biomass.ConclusionAdult and juvenile fishes were identified by morphology and meristic values, however larvae required DNA barcoding to identify species. The high biomass and abundance of larvae of clupeids, gobiids and cyprinodontids suggests that the Chile Verde Lagoon may be important for reproduction of these species in the region. Microgobius microlepis, a marine goby species, is reported for the first time in an inland oligohaline system. This study provides a basis for future environmental assessment and biomonitoring of the Chile Verde Lagoon in the Yucatan Peninsula of Mexico. creator: Adrian Emmanuel Uh-Navarrete creator: Martha Valdez-Moreno creator: Mariana E. Callejas-Jiménez creator: Lourdes Vásquez-Yeomans uri: https://doi.org/10.7717/peerj.16285 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Uh-Navarrete et al. title: Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns link: https://peerj.com/articles/16290 last-modified: 2023-11-02 description: Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health. creator: Manuel Ochoa-Sánchez creator: Eliana Paola Acuña Gomez creator: Lucila Moreno creator: Claudio A. Moraga creator: Katherine Gaete creator: Luis E. Eguiarte creator: Valeria Souza uri: https://doi.org/10.7717/peerj.16290 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ochoa-Sánchez et al. title: The influence of media narratives on microplastics risk perception link: https://peerj.com/articles/16338 last-modified: 2023-11-02 description: BackgroundMedia are the interface between scientists and citizens, communicating and interpreting the risk message and powerfully influencing individual awareness, public debate, and, hence, people’s behavior. Pollution by microplastics (MPs), a threat to public health and terrestrial and marine ecosystems, has received research, media, and public interest. However, how MPs environmental and health risks are reflected in the media and assessed in the scientific literature does not find consensus over time. To date, few studies have examined social aspects around MPs, such as, for example, factors that influence awareness and perception of the risk of MPs. In this context, the objective of this study is twofold. First, we determined if media narratives influenced Romanians’ awareness of MPs, and second, we investigated if media narratives influenced Romanians’ perceptions of MPs health and environmental risk.MethodAn online survey was conducted among 417 Romanian respondents. The questionnaire had 21 questions. The questions were related to the awareness of MPs, the perceived health risk of MPs, the perceived environmental risk of MPs, the intensity of exposure to media narratives about the MPs impact on health and the environment, and the demographics. Binary logistic regression was run to identify what media narratives influenced MPs awareness and risk perception. In recent times, mass media has shaped perceptions of health and environmental risks, driven by events like COVID-19 and global climate change. Our study relies on media narratives as its foundation.ResultsBinary logistic regression showed that the awareness of MPs is influenced by the media narrative “Microplastics in the sea threaten fish stocks” (p = 0.001). When the frequency of exposure to this media narrative increases, the probability of reporting awareness of MPs increases. Likewise, an increase in age represents a higher probability of reporting awareness of MPs. The perceived health risk of MPs, with the highest weighting, was related to the dependent variable “Leakage of harmful chemicals from MPs affects the soil” (p = 0.014).ConclusionsMedia narratives about plastic and MPs pollution have increased over time, influencing the perception of this risk. The study argues the need for accurate and balanced media reporting on MPs to prevent the spread of misinformation and ensure that people clearly understand MPs risks. Furthermore, a closer examination of people’s perceptions supports the design of appropriate interventions to reduce plastic consumption, thereby decreasing the risks of MPs pollution with benefits for human health and the environment. creator: Valeria Pop creator: Alexandru Ozunu creator: Dacinia Crina Petrescu creator: Adrian-Daniel Stan creator: Ruxandra Malina Petrescu-Mag uri: https://doi.org/10.7717/peerj.16338 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pop et al. title: Pilot study of locomotor asymmetry in horses walking in circles with and without a rider link: https://peerj.com/articles/16373 last-modified: 2023-11-02 description: BackgroundHorses commonly show asymmetries that manifest as left (L)-right (R) differences in vertical excursion of axial body segments. Moving on a circle confounds inherent individual asymmetries. Our goals were to evaluate individual and group asymmetry patterns and compare objective data with subjective impressions of side preference/laterality in horses walking on L and R circles.MethodsFifteen horses walked on L and R circles unridden and ridden on long and short reins. Optical motion capture (150 Hz) tracked skin-fixed markers. Variables were trunk horizontal angle; neck-to-trunk angle; vertical range of motion (ROM) for the head, withers and sacrum; ROM for pelvic roll, pitch, and yaw; mean pelvic pitch; and ROM for hip, stifle and tarsal joints. Differences between inside and outside hind steps were determined for vertical minima and maxima of the head (HMinDiff/HMaxDiff), withers (WMinDiff/WMaxDiff) and sacrum (PMinDiff/PMaxDiff). Subjective laterality was provided by owners. Data analysis used mixed models, first without and then with subjective laterality. Iterative k-means cluster analysis was used to associate biomechanical variables with subjective laterality.ResultsPMaxDiff, PMinDiff and WMaxDiff indicated R limb asymmetry in both directions. WMinDiff indicated L (inside) fore asymmetry for L direction but was close to zero for R direction. Hip ROM was significantly smaller for the inside limb in both directions (L inside/outside: 16.7° vs. 20.6°; R: 17.8° vs. 19.4°). Stifle ROM was significantly larger for the inside limb in both directions (L: 43.1° vs. 39.0°; R: 41.9° vs. 40.4°). Taking the general direction effect into account the R hip and L stifle had larger ROM. Adding laterality to the models (seven horses L- vs. six horses R-hollow), PMaxDiff R hind asymmetry was more obvious for L-hollow horses than for R-hollow horses. L-hollow horses had greater pelvic roll ROM moving in L vs. R direction. L-hollow horses had smaller inside and greater outside hip joint ROM in L vs. R direction. R-hollow horses had a significant difference in HMinDiff between L (0 mm) and R (−14 mm) directions, indicating less head lowering at outside forelimb midstance in R direction, and larger outside tarsal ROM in R (38.6°) vs. L (37.4°) direction (p ≤ 0.05). The variables that agreed most frequently with subjective laterality in cluster analysis were pelvic roll ROM, followed by HMinDiff and PMaxDiff.ConclusionDifferences between horses walking in L and R directions were found both at group and individual levels, as well as evidence of associations with subjective laterality. Horses maintained more symmetric hip and stifle ROM and withers vertical motion when walking on the R circle. Findings suggest that left and right lateralised horses may not be perfect mirror images. Pelvic roll ROM emerged as a promising variable to determine laterality in walk as perceived by the rider, especially when considered together with other variables. creator: Agneta Egenvall creator: Hilary M. Clayton creator: Anna Byström uri: https://doi.org/10.7717/peerj.16373 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Egenvall et al. title: Progress in overactive bladder: novel avenues from psychology to clinical opinions link: https://peerj.com/articles/16112 last-modified: 2023-11-01 description: RationaleOveractive bladder (OAB) is a common, distressing condition that worsens with age and impacts quality of life significantly. As a results of its clinical symptoms, patients suffer from serious physical and mental health issues, have a poor quality of life, and participate in a serious economic burden. The key social-psychological factors include living habits, eating habits, and personality characteristics on this disease, even though the pathogenesis of OAB is complex. However, there is few cognitions and research on OAB in the field of psychology.Methods/Search StrategyBetween 2000 and 2022, two electronic databases were systematically searched in accordance with Cochrane library guidelines (PubMed/Medline, Web of Science). An analysis of the remaining articles with relevant information was conducted using a data extraction sheet. An itemized flow diagram was adopted and used to report systematic reviews and meta-analysis. A systematic review of studies published from 2000 to 2022 in English language were conducted and included in the review.The intended audienceUrological surgeon and psychologists majoring in urinary diseases.ImplicationAs a result of this information, we are able to develop a better understanding of the role of psychological factors in the development of OAB and suggest potential therapeutic directions for OAB patients. This may benefit the recovery of OAB patients. creator: Zhaofeng Jin creator: Qiumin Zhang creator: Yanlan Yu creator: Ruilin Zhang creator: Guoqing Ding creator: Tian Li creator: Yuping Song uri: https://doi.org/10.7717/peerj.16112 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jin et al. title: Mechanism of LEF1-AS1 regulating HUVEC cells by targeting miR-489-3p/S100A11 axis link: https://peerj.com/articles/16128 last-modified: 2023-11-01 description: BackgroundThe venous malformation is the most common congenital vascular malformation and exhibits the characteristics of local invasion and lifelong progressive development. Long noncoding RNA (lncRNA) regulates endothelial cells, vascular smooth muscle cells, macrophages, vascular inflammation, and metabolism and also affects the development of venous malformations. This study aimed to elucidate the role of the lncRNA LEF1-AS1 in the development of venous malformations and examine the interaction among LEF1-AS1, miR-489-3p, and S100A11 in HUVEC cells.MethodsVenous malformation tissues, corresponding normal venous tissues, and HUVEC cells were used. Agilent human lncRNA microarray gene chip was used to screen differential genes, RNA expression was detected using quantitative reverse transcription PCR, and protein expression was detected using Western blotting. The proliferation, migration, and angiogenesis of HUVEC cells were assessed using CCK8, transwell, and in vitro angiogenesis tests.ResultsA total of 1,651 lncRNAs were screened using gene chip analysis, of which 1015 were upregulated and 636 were downregulated. The lncRNA LEF1-AS1 was upregulated with an obvious difference multiple, and the fold-change value was 11.03273. The results of the analysis performed using the StarBase bioinformatics prediction website showed that LEF1-AS1 and miR-489-3p possessed complementary binding sites and that miR-489-3p and S100A11 also had complementary binding sites. The findings of tissue experiments revealed that the expressions of LEF1-AS1 and S100A11 were higher in tissues with venous malformations than in normal tissues, whereas the expression of miR-489-3p was lower in venous malformations than in normal tissues. Cell culture experiments indicated that LEF1-AS1 promoted the proliferation, migration, and angiogenesis of HUVEC cells. In these cells, LEF1-AS1 targeted miR-489-3p, which in turn targeted S100A11. LEF1-AS1 acted as a competitive endogenous RNA and promoted the expression of S100A11 by competitively binding to miR-489-3p and enhancing the proliferation, migration, and angiogenesis of HUVEC cells. Thus, LEF1-AS1 participated in the occurrence and development of venous malformation.ConclusionsThe expression of LEF1-AS1 was upregulated in venous malformations, and the expression of S100A11 was increased by the adsorption of miR-489-3p to venous endothelial cells, thus enhancing the proliferation, migration, and angiogenesis of HUVEC cells. In conclusion, LEF1-AS1 is involved in the occurrence and development of venous malformations by regulating the miR-489-3p/S100A11 axis, which provides valuable insights into the pathogenesis of this disease and opens new avenues for its treatment. creator: Haoran Zhang creator: Wenqiu Wang creator: Junjie Lin creator: Junbo Qiao creator: Xinjun Wang creator: Bin Fang creator: Changkuan Chen creator: Yujiao Wang creator: Gaozan Zhu creator: Wenbo Liu uri: https://doi.org/10.7717/peerj.16128 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Conservation tillage and fertiliser management strategies impact on basmati rice (Oryza sativa L): crop performance, crop water productivity, nutrient uptake and fertility status of the soil under rice-wheat cropping system link: https://peerj.com/articles/16271 last-modified: 2023-11-01 description: BackgroundThe sustainability of paddy production systems in South Asia has recently been affected by a decline in soil health and excessive water usage. As a response to the global energy crisis, escalating costs of synthetic fertilisers, and growing environmental concerns, the utilization of organic plant-nutrient sources has gained considerable attention. Emerging adaptation technologies, including conservation tillage and innovative approaches to fertilizer management, present practical choices that can significantly contribute to the long-term preservation of soil fertility.MethodsThe two year-long field experiment was completed in sandy loam soil during rainy (Kharif) seasons in 2019 and 2020 at the crop research centre farm of Sardar Vallabhbhai Patel University of Agricultural & Technology, Meerut, Uttar Pradesh to analyze the impacts of different tillage establishment of the crop and its methodologies as well as integrated nutritional management approaches on rice growth, yield, productivity of water, nutrient uptake, and fertility status of soil under a rice-wheat rotation system. The experiment was set up in a factorial randomized block design and replicated three times in a semi-arid subtropical environment.ResultsThe conventionally transplanted rice puddled (CT-TPR) grew substantially better taller plants, and higher dry matter buildup leads to increased yields than transplanted rice under raised wide bed (WBed-TPR). WBed-TPR plots had more tillers, LAI, CGR, RGR, and yield characteristics of the rice in two year study. CT-TPR increased grain yield by 4.39 and 4.03% over WBed-TPR in 2019 and 2020, while WBed-TPR produced the highest water productivity (0.44 kg m−3) than CT-TPR, respectively. The 100% RDF+ ZnSO4 25 kg ha−1 + FYM (5 t ha−1) + PSB (5 kg ha−1) + Azotobacter 20 kg ha−1 (N6) treatment outperformed the other fertiliser management practices in terms of crop growth parameters, yields of grain (4,903 and 5,018 kg ha−1), nutrient uptake and NPK availability, organic soil carbon. Among the fertilizer management practices, with the direct applications of the recommended dose of fertilizer (RDF), farm yard manure (FYM), phosphate solubilizing bacteria (PSB), Azatobactor and zinc worked synergistically and increased grain yields by 53.4, 51.3, 47.9 and 46.2% over their respective control treatment.ConclusionsTo enhance rice productivity and promote soil health, the study suggests that adopting conservation tillage-based establishment practices and implementing effective fertilizer management techniques could serve as practical alternatives. It is concluded that the rice yield was improved by the inclusive use of inorganic fertiliser and organic manure (FYM). Additionally, the study observed that the combination of conventional puddled transplanted rice (CT-TPR) and N6 nitrogen application resulted in enhanced rice crop productivity and improved soil health. creator: Mandapelli Sharath Chandra creator: R.K. Naresh creator: Rajan Bhatt creator: Praveen V. Kadam creator: Manzer H. Siddiqui creator: Abdel-Rhman Z. Gaafar creator: Md Atikur Rahman uri: https://doi.org/10.7717/peerj.16271 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chandra et al. title: Bacterial diversity of herbal rhizospheric soils in Ordos desert steppes under different degradation gradients link: https://peerj.com/articles/16289 last-modified: 2023-11-01 description: ObjectivesThis study explored the effects of different degradation gradients on bacterial diversity in the rhizospheric soils of herb plants.MethodsThe alpha diversity, species composition and correlations of bacterial communities in the rhizospheric soils of herb plants were studied using metagenomics 16SrDNA gene high-throughput sequencing.ResultsThe diversity of bacterial communities in the rhizospheric soils of herb plants differed during the degradation of desert steppes. An analysis of bacterial community alpha diversity indices showed the bacterial diversity and species evenness of rhizospheric soils were best in moderately degraded desert steppes. Among all samples, a total of 43 phyla, 133 classes, 261 orders, 421 families, 802 genera and 1,129 species were detected. At the phylum level, the predominant bacterial phyla were: Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Bacteroidetes. At the genus level, the predominant bacterial genera were: RB41, Sphingomonas, WD2101_soil_group_unclassified, Pseudomonas and Actinomyces. The relative abundance of unknown genera was very large, which deserves further research. At the phylum and genus levels, the species abundance levels under slight and moderate degradation were significantly higher than those under extreme degradation. Correlation network diagrams showed there were many nodes in both slightly deteriorated and moderately deteriorated soils, and the node proportions were large and mostly positively correlated. These results indicate the bacterial communities in rhizospheric soils under slight or moderate deterioration are relatively stable. The rhizospheric soil microbes of desert steppes can form a stable network structure, allowing them to adequately respond to environmental conditions.ConclusionsThe bacterial communities in the rhizospheric soils of herb plants differ between different degradation gradients. The species number, abundance and diversity of bacterial communities in rhizospheric soils are not directly correlated with degree of degradation. The abundance, species diversity and species abundance of bacterial communities in the rhizospheric soils of moderately degraded desert steppes are the highest and most stable. The soil bacterial diversity is lowest in severely degraded desert steppes. creator: Yuefeng Guo creator: Dan Zhang creator: Wei Qi uri: https://doi.org/10.7717/peerj.16289 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: A benzochalcone derivative synchronously induces apoptosis and ferroptosis in pancreatic cancer cells link: https://peerj.com/articles/16291 last-modified: 2023-11-01 description: BackgroundPancreatic cancer is a highly aggressive and lethal disease with limited treatment options. In this study, we investigated the potential therapeutic effects of compound KL-6 on pancreatic cancer cells.MethodsThe study involved assessing the inhibitory effects of KL-6 on cell proliferation, clonogenic potential, cell cycle progression, apoptosis, migration, and invasion. Additionally, we examined the action mechanism of KL-6 by RNA-seq and bioinformatic analysis and validated by qRT-PCR and western blot in pancreatic cancer cells.ResultsOur results demonstrated that KL-6 effectively inhibited the growth of pancreatic cancer cells in a dose-dependent manner. It induced G2/M phase cell cycle arrest and apoptosis, disrupting the cell cycle progression and promoting cell death. KL-6 also exhibited inhibitory effects on cell migration and invasion, suggesting its potential to suppress the metastatic properties of pancreatic cancer cells. Furthermore, KL-6 modulated the expression of genes involved in various cancer-related pathways including apoptosis and ferroptosis.ConclusionThese findings collectively support the potential of KL-6 as a promising therapeutic option for pancreatic cancer treatment. Further research is needed to fully understand the underlying mechanisms and evaluate the clinical efficacy of KL-6 in pancreatic cancer patients. creator: Xiaoqing Guan creator: Bing Zhao creator: Xiaodan Guan creator: Jinyun Dong creator: Jieer Ying uri: https://doi.org/10.7717/peerj.16291 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guan et al. title: Genome-wide identification of CaARR-Bs transcription factor gene family in pepper and their expression patterns under salinity stress link: https://peerj.com/articles/16332 last-modified: 2023-11-01 description: In plants, ARRs-B transcription factors play a crucial role in regulating cytokinin signal transduction, abiotic stress resistance, and plant development. A number of adverse environmental conditions have caused severe losses for the pepper (Capsicum annuum L.)—a significant and economically important vegetable. Among the transcription factors of the type B-ARRs family, multiple members have different functions. In pepper, only a few members of the ARRs-B family have been reported and characterized. The current study aimed to characterize ARRs-B transcription factors in C. annuum, including phylogenetic relationships, gene structures, protein motif arrangement, and RT-qPCR expression analyses and their role in salinity stress. In total, ten genes encode CaARRs-B transcription factors (CaARR1 to CaARR10) from the largest subfamily of type-B ARRs were identified in C. annum. The genome-wide analyses of the CaARRs-B family in C. annuum were performed based on the reported ARRs-B genes in Arabidopsis. An analysis of homologous alignments of candidate genes, including their phylogenetic relationships, gene structures, conserved domains, and qPCR expression profiles, was conducted. In comparison with other plant ARRs-B proteins, CaARRs-B proteins showed gene conservation and potentially specialized functions. In addition, tissue-specific expression profiles showed that CaARRs-B genes were differentially expressed, suggesting functionally divergent. CaARRs-B proteins had a typical conserved domain, including AAR-like (pfam: PF00072) and Myb DNA binding (pfam: PF00249) domains. Ten of the CaARRs-B genes were asymmetrically mapped on seven chromosomes in Pepper. Additionally, the phylogenetic tree of CaARRs-B genes from C. annuum and other plant species revealed that CaARRs-B genes were classified into four clusters, which may have evolved conservatively. Further, using quantitative real-time qRT-PCR, the study assessed the expression patterns of CaARRs-B genes in Capsicum annuum seedlings subjected to salt stress. The study used quantitative real-time qRT-PCR to examine CaARRs-B gene expression in Capsicum annuum seedlings under salt stress. Roots exhibited elevated expression of CaARR2 and CaARR9, while leaves showed decreased expression for CaARR3, CaARR4, CaARR7, and CaARR8. Notably, no amplification was observed for CaARR10. This research sheds light on the roles of CaARRs-B genes in pepper’s response to salinity stress. These findings enrich our comprehension of the functional implications of CaARRs-B genes in pepper, especially in responding to salinity stress, laying a solid groundwork for subsequent in-depth studies and applications in the growth and development of Capsicum annuum. creator: Rana M. Alshegaihi creator: Salha Mesfer Alshamrani uri: https://doi.org/10.7717/peerj.16332 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Alshegaihi and Alshamrani title: Trends in soil organic matter and topsoil thickness under regenerative practices at the University of Washington student farm link: https://peerj.com/articles/16336 last-modified: 2023-11-01 description: Conventional methods of agriculture, especially tillage, are often accompanied by soil degradation in the form of erosion and organic matter depletion. Regenerative agricultural methods seek to repair soil ecosystems by building topsoil and soil organic matter (SOM), decreasing reliance on chemical fertilizers and increasing both water retention capacity and the diversity and quantity of soil microbial and fungal communities. The University of Washington (UW) student farm is an organic and regeneratively managed site on the UW Seattle campus. Over the past 20 years the farm gradually expanded so locations on the farm encompass both unimproved topsoil and soils managed regeneratively for periods of 5 to 20 years. This arrangement allows a time-trend analysis of soil development under regenerative methods. Measurements of topsoil thickness (defined as the distance from the ground surface to the base of the soil A horizon) and organic matter content were collected across 14 distinct plots on the farm to quantify trends over time and estimate net change in SOM (and soil organic carbon, or SOC). While SOM content weakly increased by 0.5% per year, topsoil thickness exhibited a significant linear increase of 0.86 cm per year. Over a twenty-year period under the management practices of the UW Farm total organic carbon storage in soils, determined using topsoil thickness, density, and SOC content, increased by between 4 and 14 t ha−1 yr−1. The general increases in topsoil thickness, SOM content, and total soil carbon demonstrate the potential of soil-health-focused practices to help maintain a productive and efficient urban growing space. creator: Julia E. Macray creator: David R. Montgomery uri: https://doi.org/10.7717/peerj.16336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Macray and Montgomery title: Two new species of Parahesione (Annelida: Hesionidae) associated with ghost shrimps (Crustacea: Decapoda) and their phylogenetic relationships link: https://peerj.com/articles/16346 last-modified: 2023-11-01 description: Two new species of Hesionidae, Parahesione pulvinata sp. nov. and Parahesione apiculata sp. nov. are described based on materials collected at tidal flats in Okinawa (Japan) from burrows of the ghost shrimps Neocallichirus jousseaumei and Glypturus armatus. The two new species are characterized by having eight enlarged cirri, dorsal cirrophores with dorsal foliose lobe and biramous parapodia, and by lacking median antenna. Parahesione apiculata sp. nov. has digitate lobes on the posterior margin of the dorsal foliose lobe (absent in P. pulvinata sp. nov.). The two new species were never found outside the ghost shrimp burrows, suggesting they are obligate symbionts. Phylogenetic analyses based on four concatenated genes suggest that the symbiotic lifestyle has evolved several times in Hesionidae. creator: Naoto Jimi creator: Hiroki Nakajima creator: Taigi Sato creator: Brett C. Gonzalez creator: Sau Pinn Woo creator: Greg W. Rouse creator: Temir Britayev uri: https://doi.org/10.7717/peerj.16346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jimi et al. title: Shining a light on duckweed: exploring the effects of artificial light at night (ALAN) on growth and pigmentation link: https://peerj.com/articles/16371 last-modified: 2023-11-01 description: BackgroundArtificial light at night (ALAN) is a novel environmental stressor of global concern. Various sources of artificial light are now common in urbanized areas and have diverse negative effects on many species of animals and plants. However, ALAN has also been shown to have no effect or a positive effect on some organisms. This study investigates the impact of ALAN on the growth and leaf pigmentation of a common floating freshwater plant species.MethodsWe exposed wild-derived dotted duckweed (Landoltia punctata) to either darkness during the night (Control group) or to artificial light at night (ALAN group) for 49 days. We set up two large boxes of eighty samples each with 2–3 leaves of duckweed in each sample at the start of the experiment. The ALAN box had an opaque lid with a small lamp that was turned on at night. The Control box was also covered at night with an opaque lid but without a lamp. During the day, plants in both boxes were exposed to natural light. We counted the number of leaves in each sample weekly. We took photos of the samples on day 28 to measure the total leaf surface area per sample. On day 49, we took photos of the underside of the leaves for analyses of the relative levels of dark pigmentation across all samples.ResultsWe found that ALAN-exposed plant samples had, on average, more leaves than control plants after a few weeks of exposure. They also had a more variable number of leaves per sample. The total leaf area per sample on day 28 was larger in the ALAN samples. The underside of the leaves on day 49 was, on average, darker in the ALAN plants than in the control plants.ConclusionThere is a significant growth-enhancing effect from exposure to artificial light at night on Landolita punctata. However, higher variability induced by ALAN exposure indicates that ALAN is also a stressful condition for these plants. This is in line with our finding of the presence of larger amounts of dark pigments in the leaves of ALAN-exposed plants. Dark pigmentation in duckweed species could be a defence mechanism protecting tissues from stress-induced oxidative damage. Overall, both positive and negative effects of ALAN can be observed simultaneously in different traits of the same organism. Increased individual variation can facilitate population-level adaptation to stressful conditions. As such, this work contributes to our knowledge of the effects of light pollution in urban environments on common plants. creator: Totoro Nakagawa-Lagisz creator: Malgorzata Lagisz uri: https://doi.org/10.7717/peerj.16371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nakagawa-Lagisz and Lagisz