title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2024-06 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Doubling the known diversity of a remote island fauna: marine bivalves of the Juan Fernández and Desventuradas oceanic archipelagos (Southeastern Pacific Ocean) link: https://peerj.com/articles/17305 last-modified: 2024-06-28 description: Juan Fernández and Desventuradas are two oceanic archipelagos located in the southeastern Pacific Ocean far off the Chilean coast that received protected status as marine parks in 2016. Remoteness and access difficulty contributed to historically poor biodiversity sampling and limited associated research. This is particularly noticeable for bivalves, with most prior regional publications focused on single taxa or un-illustrated checklists. This study investigates marine bivalves collected between the intertidal and 415 m depth during (1) the 1997 IOC97 expedition aboard the M/V Carlos Porter, with special focus on scuba-collected micro-mollusks of both archipelagos, (2) two expeditions by the R/V Anton Bruun (Cruise 12/1965 and Cruise 17/1966), and (3) Cruise 21 of USNS Eltanin under the United States Antarctic Program, which sampled at Juan Fernández in 1965. Also, relevant historical material of the British H.M.S. Challenger Expedition (1873–1876), the Swedish Pacific Expedition (1916–1917), and by German zoologist Ludwig H. Plate (1893–1895) is critically revised. A total of 48 species are recognized and illustrated, including 19 new species (described herein) and six other potentially new species. The presence of two species mentioned in the literature for the region (Aulacomya atra and Saccella cuneata) could not be confirmed. The genera Verticipronus and Halonympha are reported for the first time from the Eastern Pacific, as are Anadara and Condylocardia from Chilean waters. Lectotypes are designated for Arca (Barbatia) platei and Mytilus algosus. These findings double the number of extant bivalve species known from the Juan Fernández and Desventuradas archipelagos, highlighting the lack of attention these islands groups have received in the past. A high percentage of species endemic to one or both archipelagos are recognized herein, accounting for almost 78% of the total. The newly recognized level of bivalve endemism supports the consideration of Juan Fernández and Desventuradas as two different biogeographic units (Provinces or Ecoregions) of the Eastern Pacific Ocean. creator: Diego Gabriel Zelaya creator: Marina Güller creator: Rüdiger Bieler uri: https://doi.org/10.7717/peerj.17305 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zelaya et al. title: Labeled-free quantitative proteomic analysis of cervical squamous cell carcinoma identifies potential protein biomarkers link: https://peerj.com/articles/17444 last-modified: 2024-06-28 description: BackgroundCervical cancer remains a prevalent cancer among women, and reliance on surgical and radio-chemical therapies can irreversibly affect patients’ life span and quality of life. Thus, early diagnosis and further exploration into the pathogenesis of cervical cancer are crucial. Mass spectrometry technology is widely applied in clinical practice and can be used to further investigate the protein alterations during the onset of cervical cancer.MethodsEmploying labeled-free quantitative proteomics technology and bioinformatics tools, we analyzed and compared the differential protein expression profiles between normal cervical squamous cell tissues and cervical squamous cell cancer tissues. GEPIA is an online website for analyzing the RNA sequencing expression data of tumor and normal tissue data from the TCGA and the GTEx databases. This approach aided in identifying qualitative and quantitative changes in key proteins related to the progression of cervical cancer.ResultsCompared to normal samples, a total of 562 differentially expressed proteins were identified in cervical cancer samples, including 340 up-regulated and 222 down-regulated proteins. Gene ontology functional annotation, and KEGG pathway, and enrichment analysis revealed that the differentially expressed proteins mainly participated in metabolic pathways, spliceosomes, regulation of the actin cytoskeleton, and focal adhesion signaling pathways. Specifically, desmoplakin (DSP), protein phosphatase 1, regulatory (inhibitor) subunit 13 like (PPP1R13L) and ANXA8 may be involved in cervical tumorigenesis by inhibiting apoptotic signal transmission. Moreover, we used GEPIA database to validate the expression of DSP, PPP1R13L and ANXA8 in human cancers and normal cervix.ConclusionIn this study, we identified 562 differentially expressed proteins, and there were three proteins expressed higher in the cervical cancer tissues. The functions and signaling pathways of these differentially expressed proteins lay a theoretical foundation for elucidating the molecular mechanisms of cervical cancer. creator: Hua Bai creator: Hongyun Zheng uri: https://doi.org/10.7717/peerj.17444 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bai and Zheng title: A taxonomic revision of Rhizophora L. (Rhizophoraceae) in Thailand link: https://peerj.com/articles/17460 last-modified: 2024-06-28 description: A taxonomic revision of Rhizophora L. (Rhizophoraceae) in Thailand is presented. Two species, R. apiculata Blume and R. mucronata Poir., are enumerated with updated morphological descriptions, illustrations and a taxonomic identification key, together with notes on distributions, habitats and ecology, phenology, conservation assessments, etymology, vernacular names, uses, and specimens examined. Three names in Rhizophora, are lectotypified: R. apiculata and two associated synonyms of R. mucronata (i.e., R. latifolia Miq. and R. macrorrhiza Griff.). R. longissima Blanco, a synonym of R. mucronata, is neotypified. All two Rhizophora species have a conservation assessment of Least Concern (LC). Based on the morphological identification, these two species can be distinguished from one another by the shape and width of the leaf laminae and the length of a terminal stiff point of the leaf laminae; the type and position of the inflorescences and the number of flowers per inflorescence; the character and color of the bracteoles; the presence or absence of the flower pedicels; the shape of the mature flower buds; the shape, color, and texture of the sepals; the shape, character, and the presence or absence of hairs of the petals; the number of stamens per flower; the size of the fruits; the color and size of the hypocotyls; the color and diameter of the cotyledonous cylindrical tubes; and the color of the colleters and exudate. The thick cuticles, sunken stomata, large hypodermal cells, and cork warts are adaptive anatomical features of leaves in Rhizophora that live in the mangrove environments. The pollen grains of Thai Rhizophora species are tricolporate, prolate spheroidal or oblate spheroidal shapes, small-sized, and reticulate exine sculpturing. creator: Chatchai Ngernsaengsaruay creator: Pichet Chanton creator: Nisa Leksungnoen creator: Suwimon Uthairatsamee creator: Nittaya Mianmit uri: https://doi.org/10.7717/peerj.17460 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ngernsaengsaruay et al. title: Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress link: https://peerj.com/articles/17461 last-modified: 2024-06-28 description: Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety ‘Jingu 21’ (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1). creator: Pengyu Zhao creator: Yujing Li creator: Xue Bai creator: Xiuqing Jing creator: Dongao Huo creator: Xiaodong Zhao creator: Yuqin Ding creator: Yuxuan Shi uri: https://doi.org/10.7717/peerj.17461 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al. title: Restoring South African subtropical succulent thicket using Portulacaria afra: root growth of cuttings differs depending on the harvest site during a drought link: https://peerj.com/articles/17471 last-modified: 2024-06-28 description: The restoration of succulent thicket (the semi-arid components of the Albany Subtropical Thicket biome endemic to South Africa) has largely focused on the reintroduction of Portulacaria afra L. Jacq—a leaf- and stem-succulent shrub—through the planting of unrooted cuttings directly into field sites. However, there has been inconsistent establishment and survival rates, with low rates potentially due to a range of factors (e.g., post-planting drought, frost or herbivory), including the poor condition of source material used. Here we test the effect of parent-plant and harvesting site on the root development of P. afra cuttings in a common garden experiment. Ten sites were selected along a ∼110 km transect, with cuttings harvested from five parent-plants per site. Leaf moisture content was determined for each parent-plant at the time of harvesting as a proxy for plant condition. Root development—percentage of rooted cuttings and mean root dry weight—was recorded for a subset of cuttings from each parent-plant after 35, 42, 48, 56, and 103 days after planting in a common garden setting. We found evidence for cutting root development (rooting percentage and root dry mass) to be strongly associated with harvesting site across all sampling days (p < 0.005 for all tests). These differences are likely a consequence of underlying physiological factors; this was supported by the significant but weak correlation (r2 = 0.10–0.26) between the leaf moisture content of the parent-plant (at the time of harvesting) and dry root mass of the cuttings (at each of the sampling days). Our findings demonstrate that varying plant condition across sites can significantly influence root development during dry phases (i.e., intra- and inter-annual droughts) and that this may be a critical component that needs to be understood as part of any restoration programme. Further work is required to identify the environmental conditions that promote or impede root development in P. afra cuttings. creator: Alastair J. Potts creator: Robbert Duker creator: Kristen L. Hunt creator: Anize Tempel creator: Nicholas C. Galuszynski uri: https://doi.org/10.7717/peerj.17471 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Potts et al. title: Combined uranium-series and electron spin resonance dating from the Pliocene fossil sites of Aves and Milo’s palaeocaves, Bolt’s Farm, Cradle of Humankind, South Africa link: https://peerj.com/articles/17478 last-modified: 2024-06-28 description: Bolt’s Farm is the name given to a series of non-hominin bearing fossil sites that have often been suggested to be some of the oldest Pliocene sites in the Cradle of Humankind, South Africa. This article reports the results of the first combined Uranium-Series and Electron Spin Resonance (US-ESR) dating of bovid teeth at Milo’s Cave and Aves Cave at Bolt’s Farm. Both tooth enamel fragments and tooth enamel powder ages were presented for comparison. US-ESR, EU and LU models are calculated. Overall, the powder ages are consistent with previous uranium-lead and palaeomagnetic age estimates for the Aves Cave deposit, which suggest an age between ~3.15 and 2.61 Ma and provide the first ages for Milo’s Cave dates to between ~3.1 and 2.7 Ma. The final ages were not overly dependent on the models used (US-ESR, LU or EU), which all overlap within error. These ages are all consistent with the biochronological age estimate (<3.4–>2.6 Ma) based on the occurrence of Stage I Metridiochoerus andrewsi. Preliminary palaeomagnetic analysis from Milo’s Cave indicates a reversal takes place at the site with predominantly intermediate directions, suggesting the deposit may date to the period between ~3.03 and 3.11 Ma within error of the ESR ages. This further suggests that there are no definitive examples of palaeocave deposits at Bolt’s Farm older than 3.2 Ma. This research indicates that US-ESR dating has the potential to date fossil sites in the Cradle of Humankind to over 3 Ma. However, bulk sample analysis for US-ESR dating is recommended for sites over 3 Ma. creator: Wenjing Yu creator: Andy I. R. Herries creator: Tara Edwards creator: Brian Armstrong creator: Renaud Joannes-Boyau uri: https://doi.org/10.7717/peerj.17478 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu et al. title: Internet addiction among adolescents during the COVID-19 pandemic: Associations with sociodemographic and psychological distress link: https://peerj.com/articles/17489 last-modified: 2024-06-28 description: BackgroundThe COVID-19 pandemic has had tremendous implications for billions of adolescents worldwide due to school closures, forcing students to embrace internet usage for daily tasks. Uncontrolled use of the internet among adolescents makes them vulnerable to internet addiction (IA). This study aims to determine the prevalence of IA among adolescents and assess its association with sociodemographic factors, smartphone use, and psychological distress during the pandemic.MethodA cross-sectional self-administered online survey was conducted among students aged 13–17 from May 15th, 2021, until May 30th, 2021, using the Malay version of the Internet Addiction Test (MVIAT), the Depression, Anxiety, and Stress Scale (DASS-21), and the Coronavirus Impacts Questionnaires, as well as a sociodemographic information form. The data was analyzed with IBM SPSS Statistics version 23.ResultsA total of 420 adolescents participated in the survey. The majority of them (70.7%) were female, with a mean age of 15.47 years (±1.49 years old). About 45.5% of the respondents were classified as internet addicted users. The Chi-square test analysis showed that age (p = 0.002), smartphone usage (p = 0.010), rate of midnight use (p < 0.001), frequency (p < 0.001), duration (p < 0.001) of device usage, and presence of depression, anxiety, and stress (p < 0.001) were all significantly associated with IA. Multiple logistic regression showed age (aOR = 1.16, 95% CI [1.00–1.35], p = 0.048), smartphone usage (aOR =3.52, 95% CI [1.43–8.67], p = 0.006), mild or moderate depression (aOR = 2.43, 95% CI [1.36–4.34], p = 0.003), severe or extremely severe stress (aOR = 6.41, 95% CI [2.18–18.82], p = 0.001) were significantly related to IA.ConclusionsLate adolescence, the use of smartphones, and the presence of psychological distress like depression, and stress were potentially associated with IA. Wise use of smartphones and early identification of any psychological distress among adolescents are warranted, especially during the pandemic. creator: AyuZeity Bistari Md Bukhori creator: Mohd Hasni Ja’afar uri: https://doi.org/10.7717/peerj.17489 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Md Bukhori and Ja’afar title: Impact of white blood cell count on the development of contrast-induced acute kidney injury in patients receiving percutaneous coronary intervention link: https://peerj.com/articles/17493 last-modified: 2024-06-28 description: This study aimed to investigate the efficacy of a pre-procedural white blood cell (WBC) count in the prediction of contrast-induced acute kidney injury (CI-AKI) risk in coronary artery disease patients receiving a percutaneous coronary intervention (PCI). This observational study comprises a sample of 1,013 coronary artery disease patients (including ACS and stable angina) receiving PCI, gathered from September 2015 to July 2017. CI-AKI incidence in the study population was 4.8% (49/1013). Patients in the CI-AKI group had significantly higher WBC counts than those in the non-CI-AKI group (10.41 ± 5.37 vs. 8.09 ± 3.10, p = 0.004). Logistic analysis showed that WBC count (odds ratio [OR]: 1.12, 95% CI [1.03–1.21], P = 0.006) was a significant and independent predictor of CI-AKI risk in patients receiving PCI, Receiver-operating characteristic (ROC) curve analysis found that pre-procedural WBC count ≥11.03*109/L was the optimal cut-off value in the prediction of CI-AKI risk with a sensitivity of 41.0% and a specificity of 86.5%. Patients with CI-AKI had a significantly worse 1-year survival rate than patients without CI-AKI (91.8% vs. 97.6%, P = 0.012). In summary, increased pre-procedural WBC count is associated with an increased risk of developing CI-AKI in patients receiving PCI. creator: Chengxiao Fu creator: Chenxi Ouyang creator: Guoping Yang creator: Jingle Li creator: Guiyang Chen creator: Yu Cao creator: Liying Gong uri: https://doi.org/10.7717/peerj.17493 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Fu et al. title: Wing mechanics and acoustic communication of a new genus of sylvan katydid (Orthoptera: Tettigoniidae: Pseudophyllinae) from the Central Cordillera cloud forest of Colombia link: https://peerj.com/articles/17501 last-modified: 2024-06-28 description: Stridulation is used by male katydids to produce sound via the rubbing together of their specialised forewings, either by sustained or interrupted sweeps of the file producing different tones and call structures. There are many species of Orthoptera that remain undescribed and their acoustic signals are unknown. This study aims to measure and quantify the mechanics of wing vibration, sound production and acoustic properties of the hearing system in a new genus of Pseudophyllinae with taxonomic descriptions of two new species. The calling behaviour and wing mechanics of males were measured using micro-scanning laser Doppler vibrometry, microscopy, and ultrasound sensitive equipment. The resonant properties of the acoustic pinnae of the ears were obtained via μ-CT scanning and 3D printed experimentation, and numerical modelling was used to validate the results. Analysis of sound recordings and wing vibrations revealed that the stridulatory areas of the right tegmen exhibit relatively narrow frequency responses and produce narrowband calls between 12 and 20 kHz. As in most Pseudophyllinae, only the right mirror is activated for sound production. The acoustic pinnae of all species were found to provide a broadband increased acoustic gain from ~40–120 kHz by up to 25 dB, peaking at almost 90 kHz which coincides with the echolocation frequency of sympatric bats. The new genus, named Satizabalus n. gen., is here derived as a new polytypic genus from the existing genus Gnathoclita, based on morphological and acoustic evidence from one described (S. sodalis n. comb.) and two new species (S. jorgevargasi n. sp. and S. hauca n. sp.). Unlike most Tettigoniidae, Satizabalus exhibits a particular form of sexual dimorphism whereby the heads and mandibles of the males are greatly enlarged compared to the females. We suggest that Satizabalus is related to the genus Trichotettix, also found in cloud forests in Colombia, and not to Gnathoclita. creator: Lewis B. Holmes creator: Charlie Woodrow creator: Fabio A. Sarria-S creator: Emine Celiker creator: Fernando Montealegre-Z uri: https://doi.org/10.7717/peerj.17501 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Holmes et al. title: Utilization of ripe coconut water in the development of probiotic gelatin link: https://peerj.com/articles/17502 last-modified: 2024-06-28 description: BackgroundDesserts with vegetable ingredients are a constantly expanding global market due to the search for alternatives to cow’s milk. Fermentation of these matrices by lactic acid bacteria can add greater functionality to the product, improving its nutritional, sensory, and food safety characteristics, as well as creating bioactive components with beneficial effects on health. Concern for health and well-being has aroused interest in byproducts of the industry that have functional properties for the body, such as mature coconut water, a normally discarded residue that is rich in nutrients. This study aimed to develop a probiotic gelatin based on pulp and water from mature coconuts and evaluate the physicochemical characteristics, viability of the Lacticaseibacillus rhamnosus LR32 strain in the medium, as well as the texture properties of the product.MethodsAfter collection and cleaning, the physicochemical characterization, mineral analysis, analysis of the total phenolic content and antioxidant activity of mature coconut water were carried out, as well as the centesimal composition of its pulp. Afterwards, the gelling was developed with the addition of modified corn starch, gelatin, sucrose, and probiotic culture, being subjected to acidity analysis, texture profile and cell count, on the first day and every 7 days during 21 days of storage, under refrigeration at 5 °C. An analysis of the centesimal composition was also carried out.ResultsThe main minerals in coconut water were potassium (1,932.57 mg L−1), sodium (19.57 mg L−1), magnesium (85.13 mg L−1) calcium (279.93 mg L−1) and phosphorus (11.17 mg L−1), while the pulp had potassium (35.96 g kg−1), sodium (0.97 g kg−1), magnesium (2.18 g kg−1), 37 calcium (1.64 g kg−1), and phosphorus (3.32 g kg−1). The phenolic content of the water and pulp was 5.72 and 9.77 mg gallic acid equivalent (GAE) 100 g−1, respectively, and the antioxidant capacity was 1.67 and 0.98 39 g of 2, 2-diphenyl-1-picrylhydrazyl (DPPH) mg−1, respectively. The coconut pulp had 2.81 g 100 g−1of protein, 1.11 g 100 g−1 of 40 ash, 53% moisture, and 5.81 g 100 g−1 of carbohydrates. The gelatin produced during the storage period presented firmness parameters ranging from 145.82 to 206.81 grams-force (gf), adhesiveness from 692.85 to 1,028.63 gf sec, cohesiveness from 0.604 to 0.473, elasticity from 0.901 to 0.881, gumminess from 86.27 to 97.87 gf, and chewiness from 77.72 to 91.98 gf. Regarding the viability of the probiotic microorganism, the dessert had 7.49 log CFU g−1 that remained viable during the 21-day storage, reaching 8.51 CFU g−1. Acidity ranged from 0.15 to 0.64 g of lactic acid 100 g−1. The centesimal composition of the product showed 4.88 g 100 g−1 of protein, 0.54 g 100 g−1 of ash, 85.21% moisture, and 5.37g 100 g−1 of carbohydrates. The development of the gelatin made it possible to obtain a differentiated product, contributing to diversification in the food sector, providing a viable alternative for maintaining consumer health and reducing costs compared to desserts already available on the market. creator: Beatriz Patricio Rocha creator: Pedro Luan de Brito Lopes creator: Miqueas Oliveira Morais da Silva creator: Ana Catarina Guimarães Gomes creator: Flávia Carolina Alonso Buriti creator: Isanna Menezes Florêncio creator: Eliane Rolim Florentino uri: https://doi.org/10.7717/peerj.17502 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Patricio Rocha et al. title: Response of the subalpine bunchgrasses to wildfires and its effects in the relative abundance of the volcano rabbit in the Ajusco-Chichinautzin Mountain Range link: https://peerj.com/articles/17510 last-modified: 2024-06-28 description: The volcano rabbit (Romerolagus diazi) is a lagomorph endemic to the central mountains of the Trans-Mexican Volcanic Belt and is classified as threatened at extinction risk. It is a habitat specialist in bunchgrass communities. The annual wildfires that occur throughout its distribution range are a vulnerability factor for the species. However, the effects of wildfires on volcano rabbit populations are not fully understood. We evaluated the occupancy and change in the volcano rabbit relative abundance index in the burned bunchgrass communities of the Ajusco-Chichinautzin Mountain Range during an annual cycle of wildfire events. Additionally, we assessed the factors that favor and limit occupation and reoccupation by the volcano rabbit using the relative abundance index in burned plots as an indicator of these processes. The explanatory factors for the response of the volcano rabbit were its presence in the nearby unburned bunchgrasses, the height of three species of bunchgrass communities, the proportion of different types of vegetation cover within a 500 m radius around the burned plots, heterogeneity of the vegetation cover, and the extent of the wildfire. Statistical analyses indicated possible reoccupation in less than a year in burned bunchgrass communities adjacent to unburned bunchgrass communities with volcano rabbits. The relative abundance index of volcano rabbits was not favored when the maximum height of the Muhlenbergia macroura bunchgrass community was less than 0.77 m. When the vegetation around the burned plots was dominated by forest (cover >30% of the buffer) and the fire was extensive, the number of latrines decreased per month but increased when the bunchgrass and shrub cover was greater around the burned plots. While the statistical results are not conclusive, our findings indicate a direction for future projects, considering extensive monitoring to obtain a greater number of samples that contribute to consolidating the models presented. creator: Juan M. Uriostegui-Velarde creator: Alberto González-Romero creator: Areli Rizo-Aguilar creator: Dennia Brito-González creator: José Antonio Guerrero uri: https://doi.org/10.7717/peerj.17510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Uriostegui-Velarde et al. title: Molecular characterization of Pectobacterium atrosepticum infecting potato and its management through chemicals link: https://peerj.com/articles/17518 last-modified: 2024-06-28 description: Potato farming is a vital component of food security and the economic stability especially in the under developing countries but it faces many challenges in production, blackleg disease caused by Pectobacterium atrosepticum (Pa) is one of the main reason for damaging crop yield of the potato. Effective management strategies are essential to control these losses and to get sustainable potato crop yield. This study was focused on characterizing the Pa and the investigating new chemical options for its management. The research was involved a systematic survey across the three district of Punjab, Pakistan (Khanewal, Okara, and Multan) to collect samples exhibiting the black leg symptoms. These samples were analyzed in the laboratory where gram-negative bacteria were isolated and identified through biochemical and pathogenicity tests for Pa. DNA sequencing further confirmed these isolates of Pa strains. Six different chemicals were tested to control blackleg problem in both vitro and vivo at different concentrations. In vitro experiment, Cordate demonstrated the highest efficacy with a maximum inhibition zones of 17.139 mm, followed by Air One (13.778 mm), Profiler (10.167 mm), Blue Copper (7.7778 mm), Spot Fix (7.6689 mm), and Strider (7.0667 mm). In vivo, Cordate maintained its effectiveness with the lowest disease incidence of 14.76%, followed by Blue Copper (17.49%), Air One (16.98%), Spot Fix (20.67%), Profiler (21.45%), Strider (24.99%), and the control group (43.00%). The results highlight Cordate’s potential as a most effective chemical against Pa, offering promising role for managing blackleg disease in potato and to improve overall productivity. creator: Akhtar Hameed creator: Muhammad Zeeshan creator: Rana Binyamin creator: Muhammad Waqar Alam creator: Subhan Ali creator: Muhammad Saqlain Zaheer creator: Habib Ali creator: Muhammad Waheed Riaz creator: Hafiz Haider Ali creator: Mohamed Soliman Elshikh creator: Khaloud Mohammed Alarjani uri: https://doi.org/10.7717/peerj.17518 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hameed et al. title: Effect of glucocorticoid blockade on inflammatory responses to acute sleep fragmentation in male mice link: https://peerj.com/articles/17539 last-modified: 2024-06-28 description: The association between sleep and the immune-endocrine system is well recognized, but the nature of that relationship is not well understood. Sleep fragmentation induces a pro-inflammatory response in peripheral tissues and brain, but it also activates the hypothalamic-pituitary-adrenal (HPA) axis, releasing glucocorticoids (GCs) (cortisol in humans and corticosterone in mice). It is unclear whether this rapid release of glucocorticoids acts to potentiate or dampen the inflammatory response in the short term. The purpose of this study was to determine whether blocking or suppressing glucocorticoid activity will affect the inflammatory response from acute sleep fragmentation (ASF). Male C57BL/6J mice were injected i.p. with either 0.9% NaCl (vehicle 1), metyrapone (a glucocorticoid synthesis inhibitor, dissolved in vehicle 1), 2% ethanol in polyethylene glycol (vehicle 2), or mifepristone (a glucocorticoid receptor antagonist, dissolved in vehicle 2) 10 min before the start of ASF or no sleep fragmentation (NSF). After 24 h, samples were collected from brain (prefrontal cortex, hypothalamus, hippocampus) and periphery (liver, spleen, heart, and epididymal white adipose tissue (EWAT)). Proinflammatory gene expression (TNF-α and IL-1β) was measured, followed by gene expression analysis. Metyrapone treatment affected pro-inflammatory cytokine gene expression during ASF in some peripheral tissues, but not in the brain. More specifically, metyrapone treatment suppressed IL-1β expression in EWAT during ASF, which implies a pro-inflammatory effect of GCs. However, in cardiac tissue, metyrapone treatment increased TNF-α expression in ASF mice, suggesting an anti-inflammatory effect of GCs. Mifepristone treatment yielded more significant results than metyrapone, reducing TNF-α expression in liver (only NSF mice) and cardiac tissue during ASF, indicating a pro-inflammatory role. Conversely, in the spleen of ASF-mice, mifepristone increased pro-inflammatory cytokines (TNF-α and IL-1β), demonstrating an anti-inflammatory role. Furthermore, irrespective of sleep fragmentation, mifepristone increased pro-inflammatory cytokine gene expression in heart (IL-1β), pre-frontal cortex (IL-1β), and hypothalamus (IL-1β). The results provide mixed evidence for pro- and anti-inflammatory functions of corticosterone to regulate inflammatory responses to acute sleep loss. creator: Zim Warda Hasan creator: Van Thuan Nguyen creator: Noah T. Ashley uri: https://doi.org/10.7717/peerj.17539 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hasan et al. title: The best of two worlds: reprojecting 2D image annotations onto 3D models link: https://peerj.com/articles/17557 last-modified: 2024-06-28 description: Imagery has become one of the main data sources for investigating seascape spatial patterns. This is particularly true in deep-sea environments, which are only accessible with underwater vehicles. On the one hand, using collaborative web-based tools and machine learning algorithms, biological and geological features can now be massively annotated on 2D images with the support of experts. On the other hand, geomorphometrics such as slope or rugosity derived from 3D models built with structure from motion (sfm) methodology can then be used to answer spatial distribution questions. However, precise georeferencing of 2D annotations on 3D models has proven challenging for deep-sea images, due to a large mismatch between navigation obtained from underwater vehicles and the reprojected navigation computed in the process of building 3D models. In addition, although 3D models can be directly annotated, the process becomes challenging due to the low resolution of textures and the large size of the models. In this article, we propose a streamlined, open-access processing pipeline to reproject 2D image annotations onto 3D models using ray tracing. Using four underwater image datasets, we assessed the accuracy of annotation reprojection on 3D models and achieved successful georeferencing to centimetric accuracy. The combination of photogrammetric 3D models and accurate 2D annotations would allow the construction of a 3D representation of the landscape and could provide new insights into understanding species microdistribution and biotic interactions. creator: Marin Marcillat creator: Loic Van Audenhaege creator: Catherine Borremans creator: Aurélien Arnaubec creator: Lenaick Menot uri: https://doi.org/10.7717/peerj.17557 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Marcillat et al. title: Bioaccessibility of condensed tannins and their effect on the physico-chemical characteristics of lamb meat link: https://peerj.com/articles/17572 last-modified: 2024-06-28 description: The bioaccessibility of tannins as antioxidants in meat is essential to maximise their effectiveness in protecting the product. This property determines the amount of tannins available to interact with meat components, inhibiting lipid and protein oxidation and, consequently, prolonging shelf life and preserving the sensory quality of the product. The objective of this study was to evaluate the bioaccessibility of condensed tannins (CT) from Acacia mearnsii extract (AME) and their effect on the physico-chemical characteristics of fattened lamb meat. Thirty-six Dorset × Hampshire lambs (3 months old and 20.8 ± 3.3 kg live weight) were used. The lambs were distributed equally (n = 9) into four treatments: T1, T2, T3 and T4, which included a basal diet plus 0%, 0.25%, 0.5% and 0.75% of CT from AME, respectively. At the end of the fattening period, bioaccessibility was evaluated, the animals were slaughtered and a sample of the longissimus dorsi (LD) muscle was collected to assess colour, lipid oxidation, cooking weight loss and shear force on days 1, 4, 7 and 14 of shelf-life, in samples preserved at −20 °C. In addition, the long chain fatty acid profile was analysed. A completely randomised design was used, and the means were compared with Tukey’s test (P < 0.05). The mean lightness (L*), yellowness (b*) and hue (H*) values were higher for T3 and T4. The addition of CT did not affect (P > 0.05) redness (a*), cooking weight loss (CWL) or shear force (SF). T4 decreased (P < 0.05) stearic acid and increased cis-9 trans-12 conjugated linoleic acid (CLA). Bioaccessibility was higher in the supplemented groups (T1 < T2, T3 and T4). In conclusion, supplementing CT from AME in the diet of lambs did not reduce lipid oxidation, but T3 or T4 improved some aspects of meat colour and CLA deposition. creator: Alejandro García Salas creator: Jose Ricardo Bárcena-Gama creator: Joel Ventura creator: Canuto Muñoz-García creator: José Carlos Escobar-España creator: Maria Magdalena Crosby creator: David Hernandez uri: https://doi.org/10.7717/peerj.17572 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 García Salas et al. title: Effects of wheat intercropping on growth and occurrence of Fusarium wilt in watermelon link: https://peerj.com/articles/17587 last-modified: 2024-06-28 description: Watermelon is commonly affected by Fusarium wilt in a monoculture cropping system. Wheat intercropping alleviates the affection of Fusarium wilt of watermelon. The objective of this study was to determine the effects of wheat and watermelon intercropping on watermelon growth and Fusarium wilt. Our results showed that wheat and watermelon intercropping promoted growth, increased chlorophyll content, and photosynthesis of watermelon. Meanwhile, wheat and watermelon intercropping inhibited watermelon Fusarium wilt occurrence, decreased spore numbers, increased root vigor, increased antioxidant enzyme activities, and decreased malondialdehyde (MDA) content in watermelon roots. Additionally, wheat and watermelon intercropping enhanced the bacterial colonies and total microbes growth in soil, decreased fungi and Fusarium oxysporum f. sp. niveum (FON) colonies, and increased soil enzyme activities in watermelon rhizosphere soil. Our results indicated that wheat and watermelon intercropping enhanced watermelon growth and decreased the incidence of Fusarium wilt in watermelon. These effects could be due to intercropping inducing physiological changes, regulating soil enzyme activities, and/or modulating soil microbial communities. creator: HuiFang Lv creator: CongSheng Yan uri: https://doi.org/10.7717/peerj.17587 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lv and Yan title: Positive peritoneal lavage fluid cytology based on isolation by size of epithelial tumor cells indicates a high risk of peritoneal metastasis link: https://peerj.com/articles/17602 last-modified: 2024-06-28 description: BackgroundPeritoneal metastasis (PM) is the most prevalent type of metastasis in patients with gastric cancer (GC) and has an extremely poor prognosis. The detection of free cancer cells (FCCs) in the peritoneal cavity has been demonstrated to be one of the worst prognostic factors for GC. However, there is a lack of sensitive detection methods for FCCs in the peritoneal cavity. This study aimed to use a new peritoneal lavage fluid cytology examination to detect FCCs in patients with GC, and to explore its clinical significance on diagnosing of occult peritoneal metastasis (OPM) and prognosis.MethodsPeritoneal lavage fluid from 50 patients with GC was obtained and processed via the isolation by size of epithelial tumor cells (ISET) method. Immunofluorescence and fluorescence in situ hybridization (FISH) were used to identify FCCs expressing chromosome 8 (CEP8), chromosome 17 (CEP17), and epithelial cell adhesion molecule (EpCAM).ResultsUsing a combination of the ISET platform and immunofluorescence-FISH, the detection of FCCs was higher than that by light microscopy (24.0% vs. 2.0%). Samples were categorized into positive and negative groups, based on the expressions of CEP8, CEP17, and EpCAM. Statistically significant relationships were demonstrated between age (P = 0.029), sex (P = 0.002), lymphatic invasion (P = 0.001), pTNM stage (P = 0.001), and positivity for FCCs. After adjusting for covariates, patients with positive FCCs had lower progression-free survival than patients with negative FCCs.ConclusionThe ISET platform highly enriched nucleated cells from peritoneal lavage fluid, and indicators comprising EpCAM, CEP8, and CEP17 confirmed the diagnosis of FCCs. As a potential detection method, it offers an opportunity for early intervention of OPM and an extension of patient survival. creator: Ying Xuan creator: Qizhong Gao creator: Chenhu Wang creator: Dongyan Cai uri: https://doi.org/10.7717/peerj.17602 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xuan et al. title: Effects of weight-bearing dance aerobics on lower limb muscle morphology, strength and functional fitness in older women link: https://peerj.com/articles/17606 last-modified: 2024-06-28 description: ObjectiveTo investigate the effects of 12-week weight-bearing dance aerobics (WBDA) on muscle morphology, strength and functional fitness in older women.MethodsThis controlled study recruited 37 female participants (66.31y ± 3.83) and divided them into intervention and control groups according to willingness. The intervention group received 90-min WBDA thrice a week for 12 weeks, while the control group maintained normal activities. The groups were then compared by measuring muscle thickness, fiber length and pennation angle by ultrasound, muscle strength using an isokinetic multi-joint module and functional fitness, such as 2-min step test, 30-s chair stand, chair sit-and-reach, TUG and single-legged closed-eyed standing test. The morphology, strength, and functional fitness were compared using ANCOVA or Mann-Whitney U test to study the effects of 12 weeks WBDA.ResultsAmong all recruited participants, 33 completed all tests. After 12 weeks, the thickness of the vastus intermedius (F = 17.85, P < 0.01) and quadriceps (F = 15.62, P < 0.01) was significantly increased in the intervention group compared to the control group, along with a significant increase in the torque/weight of the knee flexor muscles (F = 4.47, P = 0.04). Similarly, the intervention group revealed a significant improvement in the single-legged closed-eyed standing test (z = −2.16, P = 0.03) compared to the control group.ConclusionThe study concluded that compared to the non-exercising control group, 12-week WBDA was shown to thicken vastus intermedius, increase muscle strength, and improve physical function in older women. In addition, this study provides a reference exercise program for older women. creator: Xiaoying Peng creator: Tang Zhou creator: Hua Wu creator: Yiyan Li creator: Jiajia Liu creator: Huan Huang creator: Changshuang He creator: Shaoyu Guo creator: Muyang Huan creator: Lei Shi creator: Peijie Chen creator: Minghui Quan uri: https://doi.org/10.7717/peerj.17606 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Peng et al. title: Response of soil arbuscular mycorrhizal fungal community to chemical fertilization in sugarcane link: https://peerj.com/articles/17610 last-modified: 2024-06-28 description: Most sugarcane cultivation areas in China have undergone over 30 years of continuous monocropping, and long-term chemical fertilizer application has led to severe soil degradation. Arbuscular mycorrhizal fungi (AMF) play a crucial role in promoting plant nutrient uptake, enhancing plant stress tolerance, and improving soil quality and restoration. However, in agroecosystems, AMF are susceptible to the effects of cultivation, fertilization, and other factors. The goal of this study was to investigate the influence of chemical fertilization on the AMF community in the rhizosphere soil of plant crop of sugarcane. In this study, sugarcane varieties GT58 and GT29 were selected for experiment. Four different chemical fertilization rates were established using controlled-release compound chemical fertilizer (N: P: K = 17:7:17): T1 (0.0 kg/ha), T2 (562.5 kg/ha), T3 (1,125.0 kg/ha), and T4 (2,250.0 kg/ha). The results showed that different fertilization rates significantly affected the cane yield in GT58. T3 and T4 increased the cane yield by 12.67% and 11.11%, respectively, compared to the control T1 (P < 0.05). The impact on the cane yield in GT29 was not significant. The diversity indices of root-associated AMF in GT58 (Chao index and Shannon index) varied significantly in different fertilization rates. T3 had the highest diversity, showing no significant difference from T1 and T2 but significantly higher than T4. For GT29, there were no significant differences in the diversity indices of root-associated AMF among different fertilization rates. Analyzing the differential species in root-associated soil with different fertilization rates in GT58 at the OTU level revealed that T3 had significantly higher abundances for 5 OTUs compared to the other treatments, and all the differentially abundant species belonged to Glomus. The Mantel analysis revealed that the genus Acaulospora was significantly and positively correlated with millable stalks (P < 0.001), and significantly and positively correlated with tiller number (P < 0.05). The genus Scutellospora showed a significant positive correlation with sprouting rate (P < 0.05). However, the other AMF genera did not show significant correlations with the agronomic traits of sugarcane. In summary, different chemical fertilization rates significantly affected the cane yield in GT58 and the AMF community in the rhizosphere soil, but not in GT29, which suggests that sugarcane chemical fertilization should consider different sugarcane varieties and the diversity of AMF communities in soil. creator: Yi-Hao Kang creator: Shang-Tao Jiang creator: Qian Wang creator: Ying-Jie Nong creator: Juan Song creator: Dong-Ping Li creator: Yun-Ying Wen creator: Jie Xu creator: Ting-Su Chen creator: Jin-Lian Zhang creator: Yang-Rui Li uri: https://doi.org/10.7717/peerj.17610 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Kang et al. title: Functional variation among mesenchymal stem cells derived from different tissue sources link: https://peerj.com/articles/17616 last-modified: 2024-06-28 description: BackgroundMesenchymal stem cells (MSCs) are increasingly recognized for their regenerative potential. However, their clinical application is hindered by their inherent variability, which is influenced by various factors, such as the tissue source, culture conditions, and passage number.MethodsMSCs were sourced from clinically relevant tissues, including adipose tissue-derived MSCs (ADMSCs, n = 2), chorionic villi-derived MSCs (CMMSCs, n = 2), amniotic membrane-derived MSCs (AMMSCs, n = 3), and umbilical cord-derived MSCs (UCMSCs, n = 3). Passages included the umbilical cord at P0 (UCMSCP0, n = 2), P3 (UCMSCP3, n = 2), and P5 (UCMSCP5, n = 2) as well as the umbilical cord at P5 cultured under low-oxygen conditions (UCMSCP5L, n = 2).ResultsWe observed that MSCs from different tissue origins clustered into six distinct functional subpopulations, each with varying proportions. Notably, ADMSCs exhibited a higher proportion of subpopulations associated with vascular regeneration, suggesting that they are beneficial for applications in vascular regeneration. Additionally, CMMSCs had a high proportion of subpopulations associated with reproductive processes. UCMSCP5 and UCMSCP5L had higher proportions of subpopulations related to female reproductive function than those for earlier passages. Furthermore, UCMSCP5L, cultured under low-oxygen (hypoxic) conditions, had a high proportion of subpopulations associated with pro-angiogenic characteristics, with implications for optimizing vascular regeneration.ConclusionsThis study revealed variation in the distribution of MSC subpopulations among different tissue sources, passages, and culture conditions, including differences in functions related to vascular and reproductive system regeneration. These findings hold promise for personalized regenerative medicine and may lead to more effective clinical treatments across a spectrum of medical conditions. creator: Ning Yi creator: Qiao Zeng creator: Chunbing Zheng creator: Shiping Li creator: Bo Lv creator: Cheng Wang creator: Chanyi Li creator: Wenjiao Jiang creator: Yun Liu creator: Yuan Yang creator: Tenglong Yan creator: Jinfeng Xue creator: Zhigang Xue uri: https://doi.org/10.7717/peerj.17616 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Yi et al. title: Andrographolide induces protective autophagy and targeting DJ-1 triggers reactive oxygen species-induced cell death in pancreatic cancer link: https://peerj.com/articles/17619 last-modified: 2024-06-28 description: BackgroundAndrographolide (Andro), an extract of Andrographis paniculate (Burm.f.) Wall. ex Nees (Acanthaceae), possesses diverse biologically active properties. However, the precise mechanisms and effects of Andro on pancreatic cancer (PC) remain unclear.MethodsThe cytotoxic potential of Andro and underlying mechanism towards PC cells was investigated through in vitro experiments and a xenograft mouse model. PC cells were first subjected to varying concentrations of Andro. The reactive oxygen species (ROS) was assessed using flow cytometry and DCFH-DA staining. The apoptosis rate was detected by flow cytometry. Additionally, western blot was applied to evaluate the expression levels of cleaved-caspase-3, DJ-1, LC3-I, LC3-II, and p62. To further elucidate the involvement of ROS accumulation and autophagy, we employed N-acetylcysteine as a scavenger of ROS and 3-Methyladenine as an inhibitor of autophagy.ResultsAndro demonstrated potent anti-proliferative effects on PC cells and induced apoptosis, both in vitro and in vivo. The cytotoxicity of Andro on PC cells was counteracted by DJ-1 overexpression. The reduction in DJ-1 expression caused by Andro led to ROS accumulation, subsequently inhibiting the growth of PC cells. Furthermore, Andro stimulated cytoprotective autophagy, thus weakening the antitumor effect. Pharmacological blockade of autophagy further enhanced the antitumor efficacy of Andro.ConclusionOur study indicated that ROS accumulation induced by the DJ-1 reduction played a key role in Andro-mediated PC cell inhibition. Furthermore, the protective autophagy induced by the Andro in PC cells is a mechanism that needs to be addressed in future studies. creator: Zhaohong Wang creator: Hui Chen creator: Xufan Cai creator: Heqi Bu creator: Shengzhang Lin uri: https://doi.org/10.7717/peerj.17619 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Microbial fungicides can positively affect aubergine photosynthetic properties, soil enzyme activity and microbial community structure link: https://peerj.com/articles/17620 last-modified: 2024-06-28 description: BackgroundThis study examined the effects of microbial agents on the enzyme activity, microbial community construction and potential functions of inter-root soil of aubergine (Fragaria × ananassa Duch.). This study also sought to clarify the adaptability of inter-root microorganisms to environmental factors to provide a theoretical basis for the stability of the microbiology of inter-root soil of aubergine and for the ecological preservation of farmland soil.MethodsEggplant inter-root soils treated with Bacillus subtilis (QZ_T1), Bacillus subtilis (QZ_T2), Bacillus amyloliquefaciens (QZ_T3), Verticillium thuringiensis (QZ_T4) and Verticillium purpureum (QZ_T5) were used to analyse the effects of different microbial agents on the inter-root soils of aubergine compared to the untreated control group (QZ_CK). The effects of different microbial agents on the characteristics and functions of inter-root soil microbial communities were analysed using 16S rRNA and ITS (internal transcribed spacer region) high-throughput sequencing techniques.ResultsThe bacterial diversity index and fungal diversity index of the aubergine inter-root soil increased significantly with the application of microbial fungicides; gas exchange parameters and soil enzyme activities also increased. The structural and functional composition of the bacterial and fungal communities in the aubergine inter-root soil changed after fungicide treatment compared to the control, with a decrease in the abundance of phytopathogenic fungi and an increase in the abundance of beneficial fungi in the soil. Enhancement of key community functions, reduction of pathogenic fungi, modulation of environmental factors and improved functional stability of microbial communities were important factors contributing to the microbial stability of fungicide-treated aubergine inter-root soils. creator: Longxue Wei creator: Jinying Zhu creator: Dongbo Zhao creator: Yanting Pei creator: Lianghai Guo creator: Jianjun Guo creator: Zhihui Guo creator: Huini Cui creator: Yongjun Li creator: Jiansheng Gao uri: https://doi.org/10.7717/peerj.17620 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wei et al. title: The effect of a spinal thrust manipulation’s audible pop on brain wave activity: a quasi-experimental repeated measure design link: https://peerj.com/articles/17622 last-modified: 2024-06-28 description: IntroductionHigh velocity thrust manipulation is commonly used when managing joint dysfunctions. Often, these thrust maneuvers will elicit an audible pop. It has been unclear what conclusively causes this audible sound and its clinical meaningfulness. This study sought to identify the effect of the audible pop on brainwave activity directly following a prone T7 thrust manipulation in asymptomatic/healthy subjects.MethodsThis was a quasi-experimental repeated measure study design in which 57 subjects completed the study protocol. Brain wave activity was measured with the Emotiv EPOC+, which collects data with a frequency of 128 HZ and has 14 electrodes. Testing was performed in a controlled environment with minimal electrical interference (as measured with a Gauss meter), temperature variance, lighting variance, sound pollution, and other variable changes that could have influenced or interfered with pure EEG data acquisition. After accommodation each subject underwent a prone T7 posterior-anterior thrust manipulation. Immediately after the thrust manipulation the brainwave activity was measured for 10 seconds.ResultsThe non-audible group (N = 20) consisted of 55% males, and the audible group (N = 37) consisted of 43% males. The non-audible group EEG data revealed a significant change in brain wave activity under some of the electrodes in the frontal, parietal, and the occipital lobes. In the audible group, there was a significant change in brain wave activity under all electrodes in the frontal lobes, the parietal lobe, and the occipital lobes but not the temporal lobes.ConclusionThe audible sounds caused by a thoracic high velocity thrust manipulation did not affect the activity in the audible centers in the temporal brain region. The results support the hypothesis that thrust manipulation with or without audible sound results in a generalized relaxation immediately following the manipulation. The absence of a significant difference in brainwave activity in the frontal lobe in this study might indicate that the audible pop does not produce a “placebo” mechanism. creator: Rob Sillevis creator: Joshua Unum creator: Valerie Weiss creator: Eric Shamus creator: Francisco Selva-Sarzo uri: https://doi.org/10.7717/peerj.17622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sillevis et al. title: Dragon boat exercise reshapes the temporal-spatial dynamics of the brain link: https://peerj.com/articles/17623 last-modified: 2024-06-28 description: Although exercise training has been shown to enhance neurological function, there is a shortage of research on how exercise training affects the temporal-spatial synchronization properties of functional networks, which are crucial to the neurological system. This study recruited 23 professional and 24 amateur dragon boat racers to perform simulated paddling on ergometers while recording EEG. The spatiotemporal dynamics of the brain were analyzed using microstates and omega complexity. Temporal dynamics results showed that microstate D, which is associated with attentional networks, appeared significantly altered, with significantly higher duration, occurrence, and coverage in the professional group than in the amateur group. The transition probabilities of microstate D exhibited a similar pattern. The spatial dynamics results showed the professional group had lower brain complexity than the amateur group, with a significant decrease in omega complexity in the α (8–12 Hz) and β (13–30 Hz) bands. Dragon boat training may strengthen the attentive network and reduce the complexity of the brain. This study provides evidence that dragon boat exercise improves the efficiency of the cerebral functional networks on a spatiotemporal scale. creator: Hongke Jiang creator: Shanguang Zhao creator: Qianqian Wu creator: Yingying Cao creator: Wu Zhou creator: Youwu Gong creator: Changzhuan Shao creator: Aiping Chi uri: https://doi.org/10.7717/peerj.17623 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jiang et al. title: ULK2 suppresses ovarian cancer cell migration and invasion by elevating IGFBP3 link: https://peerj.com/articles/17628 last-modified: 2024-06-28 description: BackgroundOvarian cancer is an aggressive malignancy with high mortality known for its considerable metastatic potential. This study aimed to explore the expression and functional role of Unc-51 like autophagy activating kinase 2 (ULK2) in the progression of ovarian cancer.MethodsULK2 expression patterns in ovarian cancer tissues as well as benign tumor control samples obtained from our institution were evaluated using immunohistochemistry. Cell counting kit 8 and Transwell assays were applied to assess the effects of ULK2 overexpression on cell proliferation, migration and invasion, respectively. RNA sequencing was performed to explore potential mechanisms of action of ULK2 beyond its classical autophagy modulation.ResultsOur experiments showed significant downregulation of ULK2 in ovarian cancer tissues. Importantly, low expression of ULK2 was markedly correlated with decreased overall survival. In vitro functional studies further demonstrated that overexpression of ULK2 significantly suppressed tumor cell proliferation, migration, and invasion. RNA sequencing analysis revealed a potential regulatory role of ULK2 in the insulin signaling pathway through upregulation of insulin-like growth factor binding protein-3 (IGFBP3) in ovarian cancer cells.ConclusionsIn summary, the collective data indicated that ULK2 acted as a tumor suppressor in ovarian cancer by upregulating the expression of IGFBP3. Our study underscores the potential utility of ULK2 as a valuable prognostic marker for ovarian cancer. creator: Xiaoxi Chen creator: Changxiang Shao creator: Jing Liu creator: Huizhen Sun creator: Bingyi Yao creator: Chengbin Ma creator: Han Xu creator: Weipei Zhu uri: https://doi.org/10.7717/peerj.17628 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Prevalence of type 2 diabetes mellitus and hypertension in patient’s visiting the conservative dentistry and endodontics department: a cross-sectional study in Surabaya City link: https://peerj.com/articles/17638 last-modified: 2024-06-28 description: BackgroundThis descriptive cross-sectional study focuses on the prevalence of hypertension (HTN) and type 2 diabetes mellitus (T2DM) amongst patients who visited the Conservative Dentistry and Endodontics department. Recognizing these incidence statistics is critical for improving endodontic therapy delivery and assuring high-quality dental care with positive treatment outcomes.MethodsIn advance of getting dental care, all patients visiting the department were advised to get their blood sugar and blood pressure levels checked at random. Measurements were taken with digital equipment, and individuals with high levels were encouraged to seek medical advice before undergoing dental procedures. The obtained data was imported into Excel and analyzed with IBM SPSS software (version 21).ResultsThe investigation had 1,100 participants (55.8% female and 44.2% male), with an average age of 44.58 ± 12.77 years. Of the individuals, 40.6% were referred for type 2 diabetes, 12.6% for hypertension, and 24.0% for both diseases. There was a significant correlation (p < 0.05) between referral status and gender. The average blood pressure and random blood sugar readings were 141.02 mmHg ± 56.28 mmHg (systolic), 79.83 mmHg ± 10.68 mmHg (diastolic), and 126.68 mg/dL ± 15.36 mg/dL, respectively. There was a substantial (p < 0.05) difference in mean systolic blood pressure between men and women. Furthermore, age was strongly connected with random blood sugar levels (p < 0.05) and systolic and diastolic blood pressure (p < 0.05). There were significant (p < 0.05) variations in mean blood pressure and blood sugar levels between referred and non-referred individuals.ConclusionAge had a relationship with higher random blood sugar levels, systolic blood pressure, and diastolic blood pressure. Dentists should consider patient age while planning treatment, as type 2 diabetes mellitus and hypertension require unique techniques to emphasize patient safety and produce excellent outcomes. creator: Meet Manihar creator: Dian Agustin Wahjuningrum creator: Shreya Manihar creator: Ajinkya M. Pawar creator: Jatin Atram creator: Kulvinder Banga creator: Alexander Maniangat Luke creator: Firas Elmsmari uri: https://doi.org/10.7717/peerj.17638 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Manihar et al. title: Food addiction and the physical and mental health status of adults with overweight and obesity link: https://peerj.com/articles/17639 last-modified: 2024-06-28 description: BackgroundOverweight and obesity now affect more than a third of the world’s population. They are strongly associated with somatic diseases, in particular increasing the risk of many metabolic and cardiovascular diseases, but also with mental disorders. In particular, there is a strong association between obesity and depression. As a result, more attention is paid to the neurobiological, behavioural, and psychological mechanisms involved in eating. One of these is food addiction (FA). Research comparing lifestyle elements, physical and mental health problems of excess body weight and individuals with FA is limited and has focused on younger people, mainly students. There is also a lack of studies that relate actual metabolic parameters to FA. To better understand the problem of FA also in older adults, it is important to understand the specific relationships between these variables.MethodsA cross-sectional survey was conducted with 172 adults with overweight and obesity (82% female) aged 23–85 years. The mean age of all subjects was M = 59.97 years (SD = 11.93), the mean BMI was M = 32.05 kg/m2 (SD = 4.84), and the mean body fat was M = 39.12% (SD = 6.48). The following questionnaires were used: Food Frequency Questionnaire-6 (FFQ-6), Global Physical Activity Questionnaire (GPAQ), Three Factor Eating Questionnaire-R18 (TFEQ-R18), Yale Food Addiction Scale 2. 0 (YFAS 2.0), Zung Self-Rating Depression Scale (SDS). Body composition, anthropometry, fasting glucose, lipid profile, and blood pressure were measured.ResultsA total of 22.7% of participants with overweight and obesity had symptoms of depression according to the SDS, and 18.6% met the criteria for FA according to YFAS 2.0. FA was statistically significantly more common among people up to 50 years. BMI, body fat mass, diastolic blood pressure and sedentary behaviour were statistically significantly higher in people with FA symptoms. Those who were sedentary for 301–450 min per day were significantly more likely to have depressive symptoms, and those who were sedentary for more than 450 min per day were significantly more likely to have FA symptoms.ConclusionsOur findings complement the current literature on FA, particularly in older adults and metabolic parameters, and suggest further research directions. Although our cross-sectional study design does not allow causal interpretations, increasing physical activity appears to be particularly important in the management of people with overweight or obesity and FA. This may be even more important than for people with depression alone, but future research is needed to explore these relationships further. creator: Magdalena Zielińska creator: Edyta Łuszczki creator: Anna Szymańska creator: Katarzyna Dereń uri: https://doi.org/10.7717/peerj.17639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zielińska et al. title: Comparative in-vivo bond failure rate of orthodontic brackets when bracket base is treated with micro-abrasive blasting vs. acid etching: eighteen month randomized control trial and scanning electron microscope study link: https://peerj.com/articles/17645 last-modified: 2024-06-28 description: BackgroundThe aim of this study was threefold. Firstly, it aimed to introduce and detail a novel method for chemically etching the bases of stainless-steel orthodontic brackets. Secondly, the study sought to investigate the structural alterations within the brackets’ microstructure following chemical etching compared to those with sandblasted bases, using electron microscopy analysis. Lastly, the study aimed to evaluate and compare the long-term durability and survivability of orthodontic brackets with chemically etched bases versus those with sandblasted bases, both bonded using the conventional acid etch technique with Transbond XT adhesive, over an 18-month follow-up period.MethodsThe study was a randomized clinical control trial with triple blinding and split-mouth study design and consisted of two groups. The brackets in the sandblasted group were prepared by sandblasting the intaglio surface of the base of the bracket with 50 µm SiO2 particles. Hydrofluoric acid was used to roughen the base in the acid-etched group. The bases of the brackets were viewed under an electron microscope to analyze the topographical changes.ResultsA total of 5,803 brackets (3,006 acid-etch, 2,797 sandblasted) in 310 patients were bonded, in a split-mouth design by the same operator. The patients were followed for 18 months. The failure rate of 2.59% and 2.7% was noted in an acid-etched and sandblasted group, respectively. There was a close approximation of curves in the Kaplan-Meier plot, and the survival distribution of the two groups in the log-rank (Mantel-Cox) test was insignificant; x2 = 0.062 (P value = 0.804).ConclusionAcid etching if the bases of the brackets can be used as an alternative to sandblasting furthermore acid etching can be performed on the chair side. creator: Owais Khalid Durrani creator: Ulfat Bashir Raja creator: Farooq Ahmad Chaudhary creator: Umar Hamid creator: Muhammad Qasim Javed creator: Sundus Atique creator: Syed Rashid Habib uri: https://doi.org/10.7717/peerj.17645 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Durrani et al. title: Enhancing small-scale acetification processes using adsorbed Acetobacter pasteurianus UMCC 2951 on κ-carrageenan-coated luffa sponge link: https://peerj.com/articles/17650 last-modified: 2024-06-28 description: BackgroundThis study explored the utilization of luffa sponge (LS) in enhancing acetification processes. LS is known for having high porosity and specific surface area, and can provide a novel means of supporting the growth of acetic acid bacteria (AAB) to improve biomass yield and acetification rate, and thereby promote more efficient and sustainable vinegar production. Moreover, the promising potential of LS and luffa sponge coated with κ-carrageenan (LSK) means they may represent effective alternatives for the co-production of industrially valuable bioproducts, for example bacterial cellulose (BC) and acetic acid.MethodsLS and LSK were employed as adsorbents for Acetobacter pasteurianus UMCC 2951 in a submerged semi-continuous acetification process. Experiments were conducted under reciprocal shaking at 1 Hz and a temperature of 32 °C. The performance of the two systems (LS-AAB and LSK-AAB respectively) was evaluated based on cell dry weight (CDW), acetification rate, and BC biofilm formation.ResultsThe use of LS significantly increased the biomass yield during acetification, achieving a CDW of 3.34 mg/L versus the 0.91 mg/L obtained with planktonic cells. Coating LS with κ-carrageenan further enhanced yield, with a CDW of 4.45 mg/L. Acetification rates were also higher in the LSK-AAB system, reaching 3.33 ± 0.05 g/L d as opposed to 2.45 ± 0.05 g/L d for LS-AAB and 1.13 ± 0.05 g/L d for planktonic cells. Additionally, BC biofilm formation during the second operational cycle was more pronounced in the LSK-AAB system (37.0 ± 3.0 mg/L, as opposed to 25.0 ± 2.0 mg/L in LS-AAB).ConclusionsThis study demonstrates that LS significantly improves the efficiency of the acetification process, particularly when enhanced with κ-carrageenan. The increased biomass yield, accelerated acetification, and enhanced BC biofilm formation highlight the potential of the LS-AAB system, and especially the LSK-AAB variant, in sustainable and effective vinegar production. These systems offer a promising approach for small-scale, semi-continuous acetification processes that aligns with eco-friendly practices and caters to specialized market needs. Finally, this innovative method facilitates the dual production of acetic acid and bacterial cellulose, with potential applications in biotechnological fields. creator: Wiramsri Sriphochanart creator: Warawut Krusong creator: Nialmas Samuela creator: Pichayada Somboon creator: Panmanas Sirisomboon creator: Jiraporn Onmankhong creator: Soisuda Pornpukdeewattana creator: Theppanya Charoenrat uri: https://doi.org/10.7717/peerj.17650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sriphochanart et al. title: The effects of meliponicultural use of Tetragonula laeviceps on other bee pollinators and pollination efficacy of lemon link: https://peerj.com/articles/17655 last-modified: 2024-06-28 description: The augmentation of pollination success in lemon (Citrus limon Eureka) flowers remains contingent on the involvement of bee pollinators. With wild bee pollinator populations declining in agroecosystems, meliponiculture has emerged as a potential option in Indonesia. This study aimed to investigate the effects of meliponicultural use of Tetragonula laeviceps on diversity, foraging behavior, and monthly population of bee pollinators, as well as lemon pollination efficacy with and without meliponiculture treatment during two periods. Using scan and focal sampling methods in first and second periods, the study found that the diversity of wild bee pollinators was six species (Apis cerana, Lasioglossum albescens, Megachile laticeps, Xylocopa confusa, Xylocopa latipes, and Xylocopa caerulea), and T. laeviceps when using meliponiculture. The relative abundance and daily foraging activity of wild bee pollinators were initially reduced in the first period (March–June) and then maintained in the second period (July–October). T. laeviceps foraged on the flowers, involving specific sequences for 72 s with highest visitation rate of 0.25 flowers/h from 10:00–13:00. Light intensity was observed to be the most influential factor for bee pollinator density. Pollination efficacy results showed that meliponiculture usage has greater benefit compared to meliponiculture absence across various parameters, including fruit sets, fruit weight, yield, and estimated productivity. The effects of meliponicultural use of T. laeviceps can enhance lemon pollination efficacy while preserving the diversity of wild insect pollinators. This suggests that meliponiculture stingless bees could be a beneficial practice in agroecosystems, especially in tropical regions where wild bee populations and diversity are declining. creator: Muhamad Aldi Nurdiansyah creator: Muhammad Yusuf Abduh creator: Aos Aos creator: Asep Hidayat creator: Agus Dana Permana uri: https://doi.org/10.7717/peerj.17655 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Nurdiansyah et al. title: Creatine kinase mitochondrial 2 promotes the growth and progression of colorectal cancer via enhancing Warburg effect through lactate dehydrogenase B link: https://peerj.com/articles/17672 last-modified: 2024-06-28 description: BackgroundMitochondrial creatine kinase (MtCK) plays a pivotal role in cellular energy metabolism, exhibiting enhanced expression in various tumors, including colorectal cancer (CRC). Creatine kinase mitochondrial 2 (CKMT2) is a subtype of MtCK; however, its clinical significance, biological functions, and underlying molecular mechanisms in CRC remain elusive.MethodsWe employed immunohistochemical staining to discern the expression of CKMT2 in CRC and adjacent nontumor tissues of patients. The correlation between CKMT2 levels and clinical pathological factors was assessed. Additionally, we evaluated the association between CKMT2 and the prognosis of CRC patients using Kaplan-Meier survival curves and Cox regression analysis. Meanwhile, quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to detect the expression levels of CKMT2 in different CRC cell lines. Finally, we explored the biological functions and potential molecular mechanisms of CKMT2 in CRC cells through various techniques, including qRT-PCR, cell culture, cell transfection, western blot, Transwell chamber assays, flow cytometry, and co-immunoprecipitation.ResultsWe found that CKMT2 was significantly overexpressed in CRC tissues compared with adjacent nontumor tissues. The expression of CKMT2 is correlated with pathological types, tumor size, distant metastasis, and survival in CRC patients. Importantly, CKMT2 emerged as an independent prognostic factor through Cox regression analysis. Experimental downregulation of CKMT2 expression in CRC cell lines inhibited the migration and promoted apoptosis of these cells. Furthermore, we identified a novel role for CKMT2 in promoting aerobic glycolysis in CRC cells through interaction with lactate dehydrogenase B (LDHB).ConclusionIn this study, we found the elevated expression of CKMT2 in CRC, and it was a robust prognostic indicator in CRC patients. CKMT2 regulates glucose metabolism via amplifying the Warburg effect through interaction with LDHB, which promotes the growth and progression of CRC. These insights unveil a novel regulatory mechanism by which CKMT2 influences CRC and provide promising targets for future CRC therapeutic interventions. creator: Shasha Cai creator: Qingqing Xia creator: Darong Duan creator: Junhui Fu creator: Zhenxing Wu creator: Zaixing Yang creator: Changfa Yu uri: https://doi.org/10.7717/peerj.17672 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cai et al. title: Comprehensive identification and expression analysis of FAR1/FHY3 genes under drought stress in maize (Zea mays L.) link: https://peerj.com/articles/17684 last-modified: 2024-06-28 description: BackgroundFAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the FAR1/FHY3 genes in maize are not well characterized and their function in drought are unknown.MethodThe FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR).ResultsA total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of ZmFARs contain abundant abiotic stress-responsive and hormone-respovensive cis-elements. Among them, drought-responsive cis-elements are quite abundant. ZmFARs were expressed in all tissues detected, but the expression level varies widely. The expression of ZmFARs were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most ZmFARs were down-regulated in root after PEG-simulated drought stress.ConclusionsWe performed a genome-wide and systematic identification of FAR1/FHY3 genes in maize. And most ZmFARs were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of ZmFARs in response to drought stress. creator: Dongbo Zhao creator: Peiyan Guan creator: Longxue Wei creator: Jiansheng Gao creator: Lianghai Guo creator: Dianbin Tian creator: Qingfang Li creator: Zhihui Guo creator: Huini Cui creator: Yongjun Li creator: Jianjun Guo uri: https://doi.org/10.7717/peerj.17684 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhao et al. title: A review of predator exclusion fencing to create mainland islands in Hawaiʻi link: https://peerj.com/articles/17694 last-modified: 2024-06-28 description: BackgroundInvasive species are the primary threat to island ecosystems globally and are responsible for approximately two-thirds of all island species extinctions in the past 400 years. Non-native mammals—primarily rats, cats, mongooses, goats, sheep, and pigs—have had devastating impacts on at-risk species and are major factors in population declines and extinctions in Hawaiʻi. With the development of fencing technology that can exclude all mammalian predators, the focus for some locations in Hawaiʻi shifted from predator control to local eradication.MethodsThis article describes all existing and planned full predator exclusion fences in Hawaiʻi by documenting the size and design of each fence, the outcomes the predator eradications, maintenance issues at each fence, and the resulting native species responses.ResultsTwelve predator exclusion fences were constructed in the Hawaiian Islands from 2011–2023 and six more were planned or under construction; all were for the protection of native seabirds and waterbirds. Fences ranged in length from 304–4,877 m and enclosed 1.2–640 ha. One-third of the 18 fences were peninsula-style with open ends; the remaining two-thirds of the fences were complete enclosures. The purpose of twelve of the fences (67%) was to protect existing bird populations, and six (33%) were initiated for mitigation required under the U.S. Endangered Species Act. Of the six mitigation fences, 83% were for the social attraction of seabirds and one fence was for translocation of seabirds; none of the mitigation fences protected existing bird populations. Rats and mice were present in every predator exclusion fence site; mice were eradicated from five of six sites (83%) where they were targeted and rats (three species) were eradicated from eight of 11 sites (72%). Mongoose, cats, pigs, and deer were eradicated from every site where they were targeted. Predator incursions occurred in every fence. Rat and mouse incursions were in many cases chronic or complete reinvasions, but cat and mongoose incursions were occasional and depended on fence type (i.e., enclosed vs. peninsula). The advent of predator exclusion fencing has resulted in great gains for protecting existing seabirds and waterbirds, which demonstrated dramatic increases in reproductive success and colony growth. With threats from invasive species expected to increase in the future, predator exclusion fencing will become an increasingly important tool in protecting island species. creator: Lindsay Young creator: Eric VanderWerf uri: https://doi.org/10.7717/peerj.17694 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Young and VanderWerf title: Geographic disparities and temporal changes of diabetes-related mortality risks in Florida: a retrospective study link: https://peerj.com/articles/17408 last-modified: 2024-06-27 description: BackgroundOver the last few decades, diabetes-related mortality risks (DRMR) have increased in Florida. Although there is evidence of geographic disparities in pre-diabetes and diabetes prevalence, little is known about disparities of DRMR in Florida. Understanding these disparities is important for guiding control programs and allocating health resources to communities most at need. Therefore, the objective of this study was to investigate geographic disparities and temporal changes of DRMR in Florida.MethodsRetrospective mortality data for deaths that occurred from 2010 to 2019 were obtained from the Florida Department of Health. Tenth International Classification of Disease codes E10–E14 were used to identify diabetes-related deaths. County-level mortality risks were computed and presented as number of deaths per 100,000 persons. Spatial Empirical Bayesian (SEB) smoothing was performed to adjust for spatial autocorrelation and the small number problem. High-risk spatial clusters of DRMR were identified using Tango’s flexible spatial scan statistics. Geographic distribution and high-risk mortality clusters were displayed using ArcGIS, whereas seasonal patterns were visually represented in Excel.ResultsA total of 54,684 deaths were reported during the study period. There was an increasing temporal trend as well as seasonal patterns in diabetes mortality risks with high risks occurring during the winter. The highest mortality risk (8.1 per 100,000 persons) was recorded during the winter of 2018, while the lowest (6.1 per 100,000 persons) was in the fall of 2010. County-level SEB smoothed mortality risks varied by geographic location, ranging from 12.6 to 81.1 deaths per 100,000 persons. Counties in the northern and central parts of the state tended to have high mortality risks, whereas southern counties consistently showed low mortality risks. Similar to the geographic distribution of DRMR, significant high-risk spatial clusters were also identified in the central and northern parts of Florida.ConclusionGeographic disparities of DRMR exist in Florida, with high-risk spatial clusters being observed in rural central and northern areas of the state. There is also evidence of both increasing temporal trends and Winter peaks of DRMR. These findings are helpful for guiding allocation of resources to control the disease, reduce disparities, and improve population health. creator: Nirmalendu Deb Nath creator: Agricola Odoi uri: https://doi.org/10.7717/peerj.17408 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Deb Nath and Odoi title: Factors associated with poor sleep quality among dental students in Malaysia link: https://peerj.com/articles/17522 last-modified: 2024-06-27 description: BackgroundGood sleep quality is crucial for dental students as they must have optimal cognitive function, memory, and decision-making to accomplish their learning requirements. This study aims to determine sleep quality, its associated factors, and the association between sleep quality and academic performance among dental students in Malaysia.MethodsThis cross-sectional study involved dental students at four public universities in Malaysia. A validated Pittsburgh Sleep Quality Index (PSQI) questionnaire was used to assess their sleep quality. An additional self-administered questionnaire was employed to obtain the students’ sociodemographic profile, lifestyle, and academic performance. The data were analysed using descriptive, chi-square, and multiple logistic regression.ResultsThree hundred eighty-four dental students participated in this study. About half of the dental students (51.6%) have poor sleep quality. The mean of sleep hours per night was 5.72 (SD 1.06). The sleep quality was significantly poor among Malay students (P = 0.023), students who stayed at hostel (P = 0.002), and those who consumed caffeinated drinks (P = 0.028). Multiple logistic regression analysis revealed that the poor sleep quality was significantly associated with self-perceived poor academic performance (Adjusted Odds Ratio (AOR) 2.95, 95% CI [1.25–6.96], P-value = 0.013) and students skipping class (AOR 1.70, 95% CI [1.00–2.91], P-value = 0.046).ConclusionsMost of the dental students in Malaysia have poor sleep quality. Ethnicity, accommodation, and caffeine consumption were significantly associated with sleep quality. Awareness to sleep quality among dental students is needed to ensure they are able to cope with the challenging dental school learning environment. creator: Khor Yong Jie creator: Noraini Mohamad creator: Munirah Mohd Adnan creator: Nor Azlida Mohd Nor creator: Nor Faharina Abdul Hamid creator: Zurainie Abllah uri: https://doi.org/10.7717/peerj.17522 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jie et al. title: β-asarone induces viability and angiogenesis and suppresses apoptosis of human vascular endothelial cells after ischemic stroke by upregulating vascular endothelial growth factor A link: https://peerj.com/articles/17534 last-modified: 2024-06-27 description: Ischemic stroke (IS) is a disease with a high mortality and disability rate worldwide, and its incidence is increasing per year. Angiogenesis after IS improves blood supply to ischemic areas, accelerating neurological recovery. β-asarone has been reported to exhibit a significant protective effect against hypoxia injury. The ability of β-asarone to improve IS injury by inducing angiogenesis has not been distinctly clarified. The experimental rats were induced with middle cerebral artery occlusion (MCAO), and oxygen-glucose deprivation (OGD) model cells were constructed using human microvascular endothelial cell line (HMEC-1) cells. Cerebral infarction and pathological damage were first determined via triphenyl tetrazolium chloride (TTC) and hematoxylin and eosin (H&E) staining. Then, cell viability, apoptosis, and angiogenesis were assessed by utilizing cell counting kit-8 (CCK-8), flow cytometry, spheroid-based angiogenesis, and tube formation assays in OGD HMEC-1 cells. Besides, angiogenesis and other related proteins were identified with western blot. The study confirms that β-asarone, like nimodipine, can ameliorate cerebral infarction and pathological damage. β-asarone can also upregulate vascular endothelial growth factor A (VEGFA) and endothelial nitric oxide synthase (eNOS) and induce phosphorylation of p38. Besides, the study proves that β-asarone can protect against IS injury by increasing the expression of VEGFA. In vitro experiments affirmed that β-asarone can induce viability and suppress apoptosis in OGD-mediated HMEC-1 cells and promote angiogenesis of OGD HMEC-1 cells by upregulating VEGFA. This establishes the potential for β-asarone to be a latent drug for IS therapy. creator: Dazhong Sun creator: Lulu Wu creator: Siyuan Lan creator: Xiangfeng Chi creator: Zhibing Wu uri: https://doi.org/10.7717/peerj.17534 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sun et al. title: Genetic characterization of the prion protein gene in camels (Camelus) with comments on the evolutionary history of prion disease in Cetartiodactyla link: https://peerj.com/articles/17552 last-modified: 2024-06-27 description: Transmissible spongiform encephalopathies (TSEs) are a fatal neurogenerative disease that include Creutzfeldt–Jakob disease in humans, scrapie in sheep and goats, bovine spongiform encephalopathy (BSE), and several others as well as the recently described camel prion disease (CPD). CPD originally was documented in 3.1% of camels examined during an antemortem slaughterhouse inspection in the Ouargla region of Algeria. Of three individuals confirmed for CPD, two were sequenced for the exon 3 of the prion protein gene (PRNP) and were identical to sequences previously reported for Camelus dromedarius. Given that other TSEs, such as BSE, are known to be capable of cross–species transmission and that there is household consumption of meat and milk from Camelus, regulations to ensure camel and human health should be a One Health priority in exporting countries. Although the interspecies transmissibility of CPD currently is unknown, genotypic characterization of Camelus PRNP may be used for predictability of predisposition and potential susceptibility to CPD. Herein, eight breeds of dromedary camels from a previous genetic (mitochondrial DNA and microsatellites) and morphological study were genotyped for PRNP and compared to genotypes from CPD–positive Algerian camels. Sequence data from PRNP indicated that Ethiopian camels possessed 100% sequence identity to CPD–positive camels from Algeria. In addition, the camel PRNP genotype is unique compared to other members of the Orders Cetartiodactyla and Perissodactyla and provides an in–depth phylogenetic analysis of families within Cetartiodactyla and Perissodactyla that was used to infer the evolutionary history of the PRNP gene. creator: Emily A. Wright creator: Madison B. Reddock creator: Emma K. Roberts creator: Yoseph W. Legesse creator: Gad Perry creator: Robert D. Bradley uri: https://doi.org/10.7717/peerj.17552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wright et al. title: PLAUR facilitates the progression of clear cell renal cell carcinoma by activating the PI3K/AKT/mTOR signaling pathway link: https://peerj.com/articles/17555 last-modified: 2024-06-27 description: BackgroundPLAUR has been found upregulated in various tumors and closely correlated with the malignant phenotype of tumor cells. The aim of this study was to investigate the relationship between PLAUR and clear cell renal cell carcinoma (ccRCC) and its potential mechanism of promoting tumor progression.MethodsThe expression levels and clinical significance of PLAUR, along with the associated signaling pathways, were extensively investigated in ccRCC samples obtained from The Cancer Genome Atlas (TCGA). PLAUR expression in 20 pairs of ccRCC tumor tissues and the adjacent tissues was assessed using qRT-PCR and IHC staining. Additionally, a series of in vitro experiments were conducted to investigate the impact of PLAUR suppression on cellular proliferation, migration, invasion, cell cycle progression, and apoptosis in ccRCC. The Western blot analysis was employed to investigate the expression levels of pivotal genes associated with the PI3K/AKT/mTOR signaling pathway.ResultsThe expression of PLAUR was significantly upregulated in ccRCC compared to normal renal tissues, and higher PLAUR expression in ccRCC was associated with a poorer prognosis than low expression. The in-vitro functional investigations demonstrated that knockdown of PLAUR significantly attenuated the proliferation, migration, and invasion capabilities of ccRCC cells. Concurrently, PLAUR knockdown effectively induced cellular apoptosis, modulated the cell cycle, inhibited the EMT process, and attenuated the activation of the PI3K/AKT/mTOR signaling pathway. PLAUR may represent a key mechanism underlying ccRCC progression.ConclusionsThe involvement of PLAUR in ccRCC progression may be achieved through the activation of the PI3K/AKT/mTOR signaling pathway, making it a reliable biomarker for the identification and prediction of ccRCC. creator: Tianzi Qin creator: Minyu Huang creator: Wenjuan Wei creator: Wei Zhou creator: Qianli Tang creator: Qun Huang creator: Ning Tang creator: Shasha Gai uri: https://doi.org/10.7717/peerj.17555 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Qin et al. title: Continuous training in young athletes decreases hepcidin secretion and is positively correlated with serum 25(OH)D and ferritin link: https://peerj.com/articles/17566 last-modified: 2024-06-27 description: BackgroundIron deficiency is known to impair muscle function and reduce athletic performance, while vitamin D has been reported to induce iron deficiency. However, the mechanism underlying exercise-induced changes in iron metabolism and the involvement of vitamins in this mechanism are unclear. The present study examined changes in biological iron metabolism induced by continuous training and the effects of vitamin D on these changes.MethodsDiet, physical characteristics, and blood test data were collected from 23 female high school students in a dance club on the last day of each of a 2-month continuous training period and a 2-week complete rest periods.ResultsSerum hepcidin-25 levels were significantly lower during the training period than the rest period (p = 0.013), as were the red blood cell count, hemoglobin, and hematocrit (all p < 0.001). Serum erythropoietin was significantly higher (p = 0.001) during the training period. Significant positive correlations were observed between 25(OH)D levels and serum iron, serum ferritin, and transferrin saturation during the training period. Multiple regression analysis with serum 25(OH)D level as the dependent variable and serum ferritin and iron levels as independent variables during the training period revealed a significant association with serum ferritin.ConclusionContinuous training may promote hemolysis and erythropoiesis, contributing to the suppression of hepcidin expression. The relationship between serum 25(OH)D and iron in vivo may be closely related to metabolic changes induced by the exercise load. creator: Yukiko Kobayashi creator: Rikako Taniguchi creator: Emiko Shirasaki creator: Yuko Segawa Yoshimoto creator: Wataru Aoi creator: Masashi Kuwahata uri: https://doi.org/10.7717/peerj.17566 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kobayashi et al. title: The mechanism of static postural control in the impact of lower limb muscle strength asymmetry on gait performance in the elderly link: https://peerj.com/articles/17626 last-modified: 2024-06-27 description: BackgroundAbnormal gait is prevalent among the elderly population, leading to reduced physical activity, increased risk of falls, and the potential development of dementia and disabilities, thus degrading the quality of life in later years. Numerous studies have highlighted the crucial roles of lower limb muscle strength asymmetry and static postural control in gait, and the reciprocal influence of lower limb muscle strength asymmetry on static postural control. However, research exploring the interrelationship between lower limb muscle strength asymmetry, static postural control, and gait performance has been limited.MethodsA total of 55 elderly participants aged 60 to 75 years were recruited. Isokinetic muscle strength testing was used to assess bilateral knee extension strength, and asymmetry values were calculated. Participants with asymmetry greater than 15% were categorized as the Asymmetry Group (AG), while those with asymmetry less than 15% were classified in the Symmetry Group (SG). Gait parameters were measured using a plantar pressure gait analysis system to evaluate gait performance, and static postural control was assessed through comfortable and narrow stance tests.ResultsFirst, participants in the AG demonstrated inferior gait performance, characterized by slower gait speed, longer stance time and percentage of stance time in gait, and smaller swing time and percentage of swing time in gait. Spatial-temporal gait parameters of the weaker limb tended to be abnormal. Second, static postural control indices were higher in AG compared to SG in all aspects except for the area of ellipse during the comfortable stance with eyes open test. Third, abnormal gait parameters were associated with static postural control.ConclusionFirstly, elderly individuals with lower limb muscle strength asymmetry are prone to abnormal gait, with the weaker limb exhibiting poorer gait performance. Secondly, lower limb muscle strength asymmetry contributes to diminished static postural control in the elderly. Thirdly, the mechanism underlying abnormal gait in the elderly due to lower limb muscle strength asymmetry may be linked to a decline in static postural control. creator: Beili Si creator: Hao Zhu creator: Xinmei Wei creator: Shun Li creator: Xueping Wu uri: https://doi.org/10.7717/peerj.17626 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Si et al. title: Investigating the eye movement characteristics of basketball players executing 3-point shot at varied intensities and their correlation with shot accuracy link: https://peerj.com/articles/17634 last-modified: 2024-06-27 description: BackgroundThe 3-point shot plays a significant and pivotal role in the historical context of basketball competitions. Visual attention exerts a crucial influence on the shooting performance of basketball players. This study aims to investigate the eye movement characteristics exhibited by high-level basketball players while executing 3-point shot at varying exercise intensities, as well as explore the correlation between these eye movement characteristics and 3-point field goal percentage.MethodsA total of twenty highly skilled female basketball players were recruited as participants for this study. During the experiment, the participants wore an eye tracker to record their eye movement data while executing 3-point shot at varying exercise intensities (low, moderate, and high). The collected eye movement data was analyzed using Tobii Pro Lab software. Additionally, the participants’ exercise intensity was monitored by wearing Polar Team Pro sensors.ResultsThe average number of fixations during the execution of a 3-point shot at three exercise intensities exhibited statistically significant differences in the front, bottom, top left, and bottom right. Moreover, notable disparities were observed in the average fixation duration for the front, bottom, and bottom right. The average total number of fixations and fixation duration in the moderate intensity shot were comparatively lower than those observed in the low and high intensity shots, while the average number of fixations and percentage of fixation duration on the front were relatively higher compared to those in the low and high intensity shots. Under varying intensities, there were no significant differences observed in the average number of fixations and the 3-point field goal percentage each AOI; however, a significantly positive correlation was found between the front average fixation duration and the 3-point field goal percentage.ConclusionDuring the execution of a moderate intensity 3-point shot, the player’s fixation is focused and stable, their information search strategy is efficient, and their information processing is precise. Variations in exercise intensity result in changes to both the information search strategy and degree of processing. Fixating on the front has a positive impact on 3-point field goal percentage. creator: Xuetong Zhao creator: Chunzhou Zhao creator: Na Liu creator: Sunnan Li uri: https://doi.org/10.7717/peerj.17634 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al. title: The human touch: a meta-analysis of anthropogenic effects on plant-pollinator interaction networks link: https://peerj.com/articles/17647 last-modified: 2024-06-27 description: BackgroundAnthropogenic activities significantly impact natural ecosystems, leading to alterations in plant and pollinator diversity and abundance. These changes often result in shifts within interacting communities, potentially reshaping the structure of plant-pollinator interaction networks. Given the escalating human footprint on habitats, evaluating the response of these networks to anthropization is critical for devising effective conservation and management strategies.MethodsWe conducted a comprehensive review of the plant-pollinator network literature to assess the impact of anthropization on network structure. We assessed network metrics such as nestedness measure based on overlap and decreasing fills (NODF), network specialization (H2’), connectance (C), and modularity (Q) to understand structural changes. Employing a meta-analytical approach, we examined how anthropization activities, such as deforestation, urbanization, habitat fragmentation, agriculture, intentional fires and livestock farming, affect both plant and pollinator richness.ResultsWe generated a dataset for various metrics of network structure and 36 effect sizes for the meta-analysis, from 38 articles published between 2010 and 2023. Studies assessing the impact of agriculture and fragmentation were well-represented, comprising 68.4% of all studies, with networks involving interacting insects being the most studied taxa. Agriculture and fragmentation reduce nestedness and increase specialization in plant-pollinator networks, while modularity and connectance are mostly not affected. Although our meta-analysis suggests that anthropization decreases richness for both plants and pollinators, there was substantial heterogeneity in this regard among the evaluated studies. The meta-regression analyses helped us determine that the habitat fragment size where the studies were conducted was the primary variable contributing to such heterogeneity.ConclusionsThe analysis of human impacts on plant-pollinator networks showed varied effects worldwide. Responses differed among network metrics, signaling nuanced impacts on structure. Activities like agriculture and fragmentation significantly changed ecosystems, reducing species richness in both pollinators and plants, highlighting network vulnerability. Regional differences stressed the need for tailored conservation. Despite insights, more research is crucial for a complete understanding of these ecological relationships. creator: Karla López-Vázquez creator: Carlos Lara creator: Pablo Corcuera creator: Citlalli Castillo-Guevara creator: Mariana Cuautle uri: https://doi.org/10.7717/peerj.17647 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 López-Vázquez et al. title: Development and application of multiplex PCR for the rapid identification of four Fusarium spp. associated with Fusarium crown rot in wheat link: https://peerj.com/articles/17656 last-modified: 2024-06-27 description: Fusarium crown rot (FCR), caused by Fusarium spp., is a devastating disease in wheat growing areas. Previous studies have shown that FCR is caused by co-infection of F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides in Hubei Province, China. In this study, a method was developed to simultaneously detected DNAs of F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides that can efficiently differentiate them. Whole genome sequence comparison of these four Fusarium spp. was performed and a 20 bp sequence was designed as an universal upstream primer. Specific downstream primers of each pathogen was also designed, which resulted in a 206, 482, 680, and 963 bp amplicon for each pathogen, respectively. Multiplex PCR specifically identified F. graminearum, F. pseudograminearum, F. proliferatum and F. verticillioides but not from other 46 pathogens, and the detection limit of target pathogens is about 100 pg/μl. Moreover, we accurately determined the FCR pathogen species in wheat samples using the optimized multiplex PCR method. These results demonstrate that the multiplex PCR method established in this study can efficiently and rapidly identify F. graminearum, F. pseudograminearum, F. proliferatum, and F. verticillioides, which should provide technical support for timely and targeted prevention and control of FCR. creator: Siyi Deng creator: Wei Chang creator: Quanke Liu creator: Youfu Zhao creator: Jun Liu creator: Hua Wang uri: https://doi.org/10.7717/peerj.17656 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Deng et al. title: Acute warming tolerance (CTmax) in zebrafish (Danio rerio) appears unaffected by changes in water salinity link: https://peerj.com/articles/17343 last-modified: 2024-06-26 description: Tolerance against acute warming is an essential trait that can determine how organisms cope during heat waves, yet the mechanisms underlying it remain elusive. Water salinity has previously been suggested to modulate warming tolerance in fish and may therefore provide clues towards these limiting mechanisms. Here, using the critical thermal maximum (CTmax) test, we investigated whether short (2 hours) and long (10 days) term exposure to different water salinities (2 hours: 0–5 ppt, 10 days: 0–3 ppt) affected acute warming tolerance in zebrafish (N = 263). We found that water salinity did not affect the warming tolerance of zebrafish at either time point, indicating that salinity does not affect the mechanism limiting acute warming tolerance in zebrafish at these salinity ranges, and that natural fluctuations in salinity levels might not have a large impact on acute warming tolerance in wild zebrafish. creator: Eirik R. Åsheim creator: Anna H. Andreassen creator: Rachael Morgan creator: Mireia Silvestre creator: Fredrik Jutfelt uri: https://doi.org/10.7717/peerj.17343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Åsheim et al. title: Neurological phenotypes and treatment outcomes in Eagle syndrome: systematic review and meta-analysis link: https://peerj.com/articles/17423 last-modified: 2024-06-26 description: BackgroundEagle syndrome is caused by an elongated styloid process affecting carotid arteries and cranial nerves. Pain, dysphagia, tinnitus, paresthesia (classic subtype), and neurovascular events (vascular subtype) may be triggered by head movements or arise spontaneously. However, Eagle syndrome remains underappreciated in the neurological community. We aimed to determine the most common neurological and non-neurological clinical presentations in patients with Eagle syndrome and to assess the clinical outcome post-surgical resection in comparison to non-surgical therapies.MethodologyWe conducted a systematic review of patient-level data on adults with Eagle syndrome, following PRISMA guidelines. We extracted data on demographics, presenting symptoms, neurological deficits, radiological findings, and treatments, including outcomes and complications, from studies in multiple indexing databases published between 2000 and 2023. The study protocol is registered with PROSPERO.ResultsIn total, 285 studies met inclusion criteria, including 497 patients with Eagle syndrome (mean age 47.3 years; 49.8% female). Classical Eagle (370 patients, 74.5%) was more frequent than vascular Eagle syndrome (117 patients, 23.5%, p < 0.0001). Six patients (1.2%) presented with both variants and the subvariant for four patients (0.8%) was unknown. There was a male preponderance (70.1% male) in the vascular subtype. A history of tonsillectomy was more frequent in classic (48/153 cases) than in vascular (2/33 cases) Eagle syndrome (Odds Ratio 5.2, 95% CI [1.2–22.4]; p = 0.028). By contrast, cervical movements as trigger factors were more prevalent in vascular (12/33 cases) than in classic (7/153 cases) Eagle syndrome (Odds Ratio 7.95, 95% CI [2.9–21.7]; p = 0.0001). Headache and Horner syndrome were more frequent in vascular Eagle syndrome and dysphagia and neck pain more prominent in classic Eagle syndrome (all p < 0.01). Surgically treated patients achieved overall better outcomes than medically treated ones: Eighty-one (65.9%) of 123 medically treated patients experienced improvement or complete resolution, while the same applied to 313 (97.8%) of 320 surgical patients (Odds Ratio 1.49, 95% CI [1.1–2.0]; p = 0.016).ConclusionsEagle syndrome is underdiagnosed with potentially serious neurovascular complications, including ischemic stroke. Surgical treatment achieves better outcomes than conservative management. Although traditionally the domain of otorhinolaryngologist, neurologist should include this syndrome in differential diagnostic considerations because of the varied neurological presentations that are amenable to effective treatment. creator: Melika Hassani creator: Elisabeth Waldemar Grønlund creator: Simon Sander Albrechtsen creator: Daniel Kondziella uri: https://doi.org/10.7717/peerj.17423 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Hassani et al. title: State of the art and future directions for measuring event-related potentials during cycling exercise: a systematic review link: https://peerj.com/articles/17448 last-modified: 2024-06-26 description: IntroElectroencephalography (EEG) is a technique for measuring brain activity that is widely used in neuroscience research. Event-related potentials (ERPs) in the EEG make it possible to study sensory and cognitive processes in the brain. Previous reports have shown that aerobic exercise can have an impact on components of ERPs such as amplitude and latency. However, they focused on the measurement of ERPs after exercise.ObjectivesThe aim of this systematic review was to investigate the feasibility of measuring ERPs during cycling, and to assess the impact of cycling on ERPs during cycling.MethodsWe followed the PRISMA guidelines for new systematic reviews. To be eligible, studies had to include healthy adults and measure ERPs during cycling. All articles were found using Google Scholar and by searching references. Data extracted from the studies included: objectives of ERP studies, ERP paradigm, EEG system, study population data, exercise characteristics (duration, intensity, pedaling cadence), and ERP and behavioral outcomes. The Cochrane Risk of Bias 2 tool was used to assess study bias.ResultsTwenty studies were selected. The effect of cycling on ERPs was mainly based on a comparison of P3 wave amplitude between cycling and resting states, using an attentional task. The ERP paradigm most often used was the auditory oddball task. Exercise characteristics and study methods varied considerably.DiscussionIt is possible to measure ERPs during cycling under conditions that are likely to introduce more artifacts, including a 3-h athletic exercise session and cycling outdoors. Secondly, no assessment of the effect of cycling on ERPs was possible, because the methods differed too widely between studies. In addition, the theories proposed to explain the results sometimes seemed to contradict each other. Although most studies reported significant results, the direction of the effects was inconsistent. Finally, we suggest some areas for improvement for future studies on the subject. creator: Rémi Renoud-Grappin creator: Lionel Pazart creator: Julie Giustiniani creator: Damien Gabriel uri: https://doi.org/10.7717/peerj.17448 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Cropping with Vicia villosa and native grass improves soil’s bacterial structure and ecological network in a jujube orchard link: https://peerj.com/articles/17458 last-modified: 2024-06-26 description: In a jujube orchard, cropping withgrass may influence bacterial diversity and ecological networks due to changes of physicochemical properties in soil, which has a serious effect on the stability of soil ecosystems. The aim of this study was to analyze the effects of different cultivation methods (CK: cleaning tillage; NG: cropping with native grass; VV: cropping with Vicia villosa) on the soil’s bacterial structure and its co-occurrence network in a jujube orchard. The results showed that the highest moisture content, total nitrogen, and organic matter in the rhizosphere soil of a jujube orchard was found in the VV group. The soil’s moisture content, total nitrogen, and organic matter in the VV group were 2.66%, 0.87 g kg−1, and 5.55 mg kg−1 higher than that found in the CK group. Compared to the CK group, the number of unique species in the rhizosphere soil in the NG and the VV groups increased by 7.33% and 21.44%. The PICRUSt and FAPROTAX analysis showed that sown grass had a greater influence on the ecological function of the soil’s bacteria. Cropping with Vicia villosa and native grass significantly increased aerobic chemoheterotrophy, nitrogen respiration, nitrate reduction related to biochemical cycles, and the relative abundance of genes related to carbohydrate metabolism and the biodegradation of xenobiotics. The bacterial network complexity in the NG group was higher than that in the CK and VV groups and was greatest in the hub nodes (OTU42, Bacteroidota; OTU541, Nitrospiraceae). In this study, the ecological benefit seen in the soil’s microbial function provides support to the theory that cropping with grass (Vicia villosa) increases the sustainable development of a jujube orchard. creator: Shoule Wang creator: Zhongtang Wang creator: Qing Hao creator: Bin Peng creator: Pan Li creator: Xuelong Qi creator: Qiong Zhang uri: https://doi.org/10.7717/peerj.17458 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: First fossil species of family Hyidae (Arachnida: Pseudoscorpiones) confirms 99 million years of ecological stasis in a Gondwanan lineage link: https://peerj.com/articles/17515 last-modified: 2024-06-26 description: Burmese amber preserves a diverse assemblage of Cretaceous arachnids, and among pseudoscorpions (Arachnida: Pseudoscorpiones), ten species in five families have already been named. Here, we describe a new fossil species from Burmese amber in the pseudoscorpion family Hyidae, providing detailed measurements, photographs and 3D-models from synchrotron scanning. Based on morphology, the new fossil, Hya fynni sp. nov. is placed in the genus Hya, and is nearly identical to extant species in the genus, except for the position of trichobothrium est on the pedipalpal chela, thereby indicating extreme morphological stasis in this invertebrate lineage over the last 99 million years. Hya fynni represents the first described fossil species in Hyidae, and the third described Burmese fossil in the superfamily Neobisioidea. It also joins the garypinid, Amblyolpium burmiticum, in representing the oldest fossil records for extant pseudoscorpion genera. Considering proposed divergence dates, the newly described fossil species bolsters a Gondwanan origin for Hyidae, and provides evidence for the “Late Jurassic Rifting” hypothesis for the Burma Terrane, in which this landmass rifted from Gondwana in the Late Jurassic and collided with Eurasia by the Cretaceous/Eocene. Like Hya species today, H. fynni likely inhabited humicolous microhabitats in tropical forests on the Burma Terrane, supporting ecological niche stasis for this family since the Mesozoic. creator: Liza M. Röschmann creator: Mark S. Harvey creator: Yanmeng Hou creator: Danilo Harms creator: Ulrich Kotthoff creator: Jörg U. Hammel creator: Dong Ren creator: Stephanie F. Loria uri: https://doi.org/10.7717/peerj.17515 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Röschmann et al. title: Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study link: https://peerj.com/articles/17583 last-modified: 2024-06-26 description: BackgroundRecent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated.MethodsA total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study.ResultsThe test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74–8.85]) to 6.67 (95% CI [6.2–7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The intervention led to a minimum two-fold (Log2 fold change increase in species like Phascolarctobacterium succinatutens, Bifidobacterium angulatum, and Levilactobacillus brevis which might have a beneficial role in the current context and a similar decrease in species like Alistipes finegoldii, and Sutterella faecalis which have been earlier shown to have some negative effects in the host. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters. creator: Gopalakrishna Kallapura creator: Anthony Surya Prakash creator: Kumar Sankaran creator: Prabhath Manjappa creator: Prayagraj Chaudhary creator: Sanjay Ambhore creator: Debojyoti Dhar uri: https://doi.org/10.7717/peerj.17583 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kallapura et al. title: Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah link: https://peerj.com/articles/17591 last-modified: 2024-06-26 description: Eight fossil tetrapod footprints from lake-shore deposits in the Lower Jurassic Moenave Formation at the St. George Dinosaur Discovery Site (SGDS) in southwestern Utah cannot be assigned to the prevalent dinosaurian (Anomoepus, Eubrontes, Gigandipus, Grallator, Kayentapus) or crocodyliform (Batrachopus) ichnotaxa at the site. The tridactyl and tetradactyl footprints are incomplete, consisting of digit- and digit-tip-only imprints. Seven of the eight are likely pes prints; the remaining specimen is a possible manus print. The pes prints have digit imprint morphologies and similar anterior projections and divarication angles to those of Brasilichnium, an ichnotaxon found primarily in eolian paleoenvironments attributed to eucynodont synapsids. Although their incompleteness prevents clear referral to Brasilichnium, the SGDS tracks nevertheless suggest a eucynodont track maker and thus represent a rare, Early Mesozoic occurrence of such tracks outside of an eolian paleoenvironment. creator: Holly Hurtado creator: Jerald D. Harris creator: Andrew R.C. Milner uri: https://doi.org/10.7717/peerj.17591 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hurtado et al. title: The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study link: https://peerj.com/articles/17594 last-modified: 2024-06-26 description: The disruption in daily activity performance during COVID-19 lockdowns is widely understood to have impacted health, but a better understanding of how restricted performance of specific activities are associated with health is needed. This cross-sectional study answers the following question: How were changes in the performance of 16 daily activities associated with health during COVID-19 lockdowns? A total of 116 participants completed an online survey rating their health before and during COVID-19 lockdowns and comparing their recollection of the performance of 16 activities before COVID-19 with their performance during lockdowns. Multiple stepwise linear regression analysis was used to estimate the relationship between self-reported changes in activities during lockdowns and concurrent (during-lockdown) health status, while controlling for pre-COVID-19 health status. Only changes in activities that were uniquely and significantly associated with lockdown health status were retained in the final model. Health before COVID-19 accounted for 3.7% (P = 0.039) of the variance in health during COVID-19 lockdowns. After controlling for health before COVID-19, five types of activity were significantly and uniquely predictive of health during lockdowns, together accounting for 48.3% of the variance. These activities and the variances they accounted for were rest and sleep (29.5%, P < 0.001), play and recreational activities (8%, P < 0.001), work (4.8%, P = 0.002), personal hygiene (3.2%, P = 0.01), and healthy eating (2.8%, P = 0.013). The study suggests that these five types of activity should be prioritized in policy or interventions when participation in activity is constrained by lockdowns or comparable factors. creator: Bernard Austin Kigunda Muriithi creator: R. Curtis Bay uri: https://doi.org/10.7717/peerj.17594 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Muriithi and Bay title: Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis link: https://peerj.com/articles/17604 last-modified: 2024-06-26 description: BackgroundThe methods previously proposed in the literature to assess patients with rotator cuff related shoulder pain, based on special orthopedic tests to precisely identify the structure causing the shoulder symptoms have been recently challenged. This opens the possibility of a different way of physical examination.ObjectiveTo analyze the differences in shoulder range of motion, strength and thoracic kyphosis between rotator cuff related shoulder pain patients and an asymptomatic group.MethodThe protocol of the present research was registered in the International Prospective Register of Systematic Review (PROSPERO) (registration number CRD42021258924). Database search of observational studies was conducted in MEDLINE, EMBASE, WOS and CINHAL until July 2023, which assessed shoulder or neck neuro-musculoskeletal non-invasive physical examination compared to an asymptomatic group. Two investigators assessed eligibility and study quality. The Newcastle Ottawa Scale was used to evaluate the methodology quality.ResultsEight studies (N = 604) were selected for the quantitative analysis. Meta-analysis showed statistical differences with large effect for shoulder flexion (I2 = 91.7%, p < 0.01, HG = −1.30), external rotation (I2 = 83.2%, p < 0.01, HG = −1.16) and internal rotation range of motion (I2 = 0%, p < 0.01, HG = −1.32). Regarding to shoulder strength; only internal rotation strength showed statistical differences with small effect (I2 = 42.8%, p < 0.05, HG = −0.3).ConclusionsThere is moderate to strong evidence that patients with rotator cuff related shoulder pain present less shoulder flexion, internal and external rotation range of motion and less internal rotation strength than asymptomatic individuals. creator: Daniel Manoso-Hernando creator: Javier Bailón-Cerezo creator: Santiago Angulo-Díaz-Parreño creator: Álvaro Reina-Varona creator: Ignacio Elizagaray-García creator: Alfonso Gil-Martínez uri: https://doi.org/10.7717/peerj.17604 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Manoso-Hernando et al. title: The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study link: https://peerj.com/articles/17617 last-modified: 2024-06-26 description: Antiphospholipid syndrome (APS) is a systemic autoimmune syndrome characterized by arterial or venous thrombosis, pregnancy complications and thrombocytopenia. The aim of this study is to investigate the association between APS and atrial fibrillation (AF) among patients in Peking University People’s Hospital. A single center retrospective study was conducted. Cases were hospitalized patients diagnosed with AF by a cardiologist while the control group patients did not exhibit cardiac diseases. The results of the study revealed that in multivariable logistic regression, APS, anticardiolipin antibody (aCL) positivity and anti-beta-2-glycoprotein antibody (anti-β2GPI) positivity are independent risk factors of AF. APS, aCL positivity and anti-β2GPI positivity are statistically different between AF patients and non-AF patients. Forthcoming studies are needed to clarify the potential link between APS and AF. creator: Zechuan Zhou creator: Yuansheng Liu uri: https://doi.org/10.7717/peerj.17617 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhou and Liu title: Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length link: https://peerj.com/articles/17625 last-modified: 2024-06-26 description: Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the Gossypium. hirsutum genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of GhPDCB9 peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43–4.77 mm. The results indicated that GhPDCB9 played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield. creator: Haibo Zhang creator: Xianghui Xiao creator: Ziyin Li creator: Yu Chen creator: Pengtao Li creator: Renhai Peng creator: Quanwei Lu creator: Youwu Wang uri: https://doi.org/10.7717/peerj.17625 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury link: https://peerj.com/articles/17333 last-modified: 2024-06-25 description: Acute heart attack is the primary cause of cardiovascular-related death worldwide. A common treatment is reperfusion of ischemic tissue, which can cause irreversible damage to the myocardium. The number of mitochondria in cardiomyocytes is large, which generate adenosine triphosphate (ATP) to sustain proper cardiac contractile function, and mitochondrial dysfunction plays a crucial role in cell death during myocardial ischemia-reperfusion, leading to an increasing number of studies investigating the impact of mitochondria on ischemia-reperfusion injury. The disarray of mitochondrial dynamics, excessive Ca2+ accumulation, activation of mitochondrial permeable transition pores, swelling of mitochondria, ultimately the death of cardiomyocyte are the consequences of ischemia-reperfusion injury. κ-opioid receptors can alleviate mitochondrial dysfunction, regulate mitochondrial dynamics, mitigate myocardial ischemia-reperfusion injury, exert protective effects on myocardium. The mechanism of κ-OR activation during myocardial ischemia-reperfusion to regulate mitochondrial dynamics and reduce myocardial ischemia-reperfusion injury will be discussed, so as to provide theoretical basis for the protection of ischemic myocardium. creator: Wen Zhang creator: Qi Zhang creator: Yali Liu creator: Jianming Pei creator: Na Feng uri: https://doi.org/10.7717/peerj.17333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhang et al. title: Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow link: https://peerj.com/articles/17367 last-modified: 2024-06-25 description: Turbidity flows can transport massive amounts of sediment across large distances with dramatic, long-lasting impacts on deep-sea benthic communities. The 2016 Mw 7.8 Kaikōura Earthquake triggered a canyon-flushing event in Kaikōura Canyon, New Zealand, which included significant submarine mass wasting, debris, and turbidity flows. This event provided an excellent opportunity to investigate the effects of large-scale natural disturbance on benthic ecosystems. Benthic meiofauna community structure before and after the event was analysed from a time series of sediment cores collected 10 years and 6 years before, and 10 weeks, 10 months, and 4 years after the disturbance. Immediately after the 2016 event abundances of all meiofauna dramatically decreased. Four years later the meiofauna community had recovered and was no longer distinguishable from the pre-event community. However, the nematode component of the community was similar, but not fully comparable to the pre-event community by 4 years after the disturbance. Community recovery was systematically correlated to changes in the physical characteristics of the habitat caused by the disturbance, using physical and biochemical variables derived from sediment cores, namely: sediment texture, organic matter, and pigment content. While these environmental variables explained relatively little of the overall variability in meiofauna community structure, particle size, food availability and quality were significant components. The minimum threshold time for the meiofauna community to fully recover was estimated to be between 3.9 and 4.7 years, although the predicted recovery time for the nematode community was longer, between 4.6 and 5 years. We consider the management implications of this study in comparison to the few studies of large-scale disturbances in the deep sea, in terms of their relevance to the efficacy of the marine reserve that encompasses Kaikōura Canyon, along with potential implications for our understanding of the impacts of anthropogenic seafloor disturbances, such as seabed mining. creator: Katharine T. Bigham creator: Daniel Leduc creator: Ashley A. Rowden creator: David A. Bowden creator: Scott D. Nodder creator: Alan R. Orpin uri: https://doi.org/10.7717/peerj.17367 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bigham et al. title: TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets link: https://peerj.com/articles/17470 last-modified: 2024-06-25 description: TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X’s predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user’s web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researchers can use to better illuminate understudied proteins. creator: Vincent T. Metzger creator: Daniel C. Cannon creator: Jeremy J. Yang creator: Stephen L. Mathias creator: Cristian G. Bologa creator: Anna Waller creator: Stephan C. Schürer creator: Dušica Vidović creator: Keith J. Kelleher creator: Timothy K. Sheils creator: Lars Juhl Jensen creator: Christophe G. Lambert creator: Tudor I. Oprea creator: Jeremy S. Edwards uri: https://doi.org/10.7717/peerj.17470 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Metzger et al. title: Structured peer review: pilot results from 23 Elsevier journals link: https://peerj.com/articles/17514 last-modified: 2024-06-25 description: BackgroundReviewers rarely comment on the same aspects of a manuscript, making it difficult to properly assess manuscripts’ quality and the quality of the peer review process. The goal of this pilot study was to evaluate structured peer review implementation by: 1) exploring whether and how reviewers answered structured peer review questions, 2) analysing reviewer agreement, 3) comparing that agreement to agreement before implementation of structured peer review, and 4) further enhancing the piloted set of structured peer review questions.MethodsStructured peer review consisting of nine questions was piloted in August 2022 in 220 Elsevier journals. We randomly selected 10% of these journals across all fields and IF quartiles and included manuscripts that received two review reports in the first 2 months of the pilot, leaving us with 107 manuscripts belonging to 23 journals. Eight questions had open-ended fields, while the ninth question (on language editing) had only a yes/no option. The reviews could also leave Comments-to-Author and Comments-to-Editor. Answers were independently analysed by two raters, using qualitative methods.ResultsAlmost all the reviewers (n = 196, 92%) provided answers to all questions even though these questions were not mandatory in the system. The longest answer (Md 27 words, IQR 11 to 68) was for reporting methods with sufficient details for replicability or reproducibility. The reviewers had the highest (partial) agreement (of 72%) for assessing the flow and structure of the manuscript, and the lowest (of 53%) for assessing whether interpretation of the results was supported by data, and for assessing whether the statistical analyses were appropriate and reported in sufficient detail (52%). Two thirds of the reviewers (n = 145, 68%) filled out the Comments-to-Author section, of which 105 (49%) resembled traditional peer review reports. These reports contained a Md of 4 (IQR 3 to 5) topics covered by the structured questions. Absolute agreement regarding final recommendations (exact match of recommendation choice) was 41%, which was higher than what those journals had in the period from 2019 to 2021 (31% agreement, P = 0.0275).ConclusionsOur preliminary results indicate that reviewers successfully adapted to the new review format, and that they covered more topics than in their traditional reports. Individual question analysis indicated the greatest disagreement regarding the interpretation of the results and the conducting and the reporting of statistical analyses. While structured peer review did lead to improvement in reviewer final recommendation agreements, this was not a randomized trial, and further studies should be performed to corroborate this. Further research is also needed to determine whether structured peer review leads to greater knowledge transfer or better improvement of manuscripts. creator: Mario Malički creator: Bahar Mehmani uri: https://doi.org/10.7717/peerj.17514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Malički and Mehmani title: Development and validation of a multi-parameter nomogram for venous thromboembolism in gastric cancer patients: a retrospective analysis link: https://peerj.com/articles/17527 last-modified: 2024-06-25 description: ObjectiveGastric cancer (GC), one of the highest venous thromboembolism (VTE) incidence rates in cancer, contributes to considerable morbidity, mortality, and, prominently, extra cost. However, up to now, there is not a high-quality VTE model to steadily predict the risk for VTE in China. Consequently, setting up a prediction model to predict the VTE risk is imperative.MethodsData from 3,092 patients from December 15, 2017, to December 31, 2022, were retrospectively analyzed. Multiple logistic regression analysis was performed to assess risk factors for GC, and a nomogram was constructed based on screened risk factors. A receiver operating curve (ROC) and calibration plot was created to evaluate the accuracy of the nomogram.ResultsThe risk factors of suffering from VTE were older age (OR = 1.02, 95% CI [1.00–1.04]), Karnofsky Performance Status (KPS) ≥ 70 (OR = 0.45, 95% CI [0.25–0.83]), Blood transfusion (OR = 2.37, 95% CI [1.47–3.84]), advanced clinical stage (OR = 3.98, 95% CI [1.59–9.99]), central venous catheterization (CVC) (OR = 4.27, 95% CI [2.03–8.99]), operation (OR = 2.72, 95% CI [1.55–4.77]), fibrinogen degradation product (FDP) >5 µg/mL (OR = 1.92, 95% CI [1.13–3.25]), and D-dimer > 0.5 mg/L (OR = 2.50, 95% CI [1.19–5.28]). The area under the ROC curve (AUC) was 0.82 in the training set and 0.85 in the validation set.ConclusionOur prediction model can accurately predict the risk of the appearance of VTE in gastric cancer patients and can be used as a robust and efficient tool for evaluating the possibility of VTE. creator: Hang Zhou creator: Haike Lei creator: Huai Zhao creator: Kaifeng Huang creator: Yundong Wang creator: Ruixia Hong creator: Jishun Huo creator: Li Luo creator: Fang Li uri: https://doi.org/10.7717/peerj.17527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Land-cover change in Cuba and implications for the area of distribution of a specialist’s host-plant link: https://peerj.com/articles/17563 last-modified: 2024-06-25 description: Changes in land cover directly affect biodiversity. Here, we assessed land-cover change in Cuba in the past 35 years and analyzed how this change may affect the distribution of Omphalea plants and Urania boisduvalii moths. We analyzed the vegetation cover of the Cuban archipelago for 1985 and 2020. We used Google Earth Engine to classify two satellite image compositions into seven cover types: forest and shrubs, mangrove, soil without vegetation cover, wetlands, pine forest, agriculture, and water bodies. We considered four different areas for quantifications of land-cover change: (1) Cuban archipelago, (2) protected areas, (3) areas of potential distribution of Omphalea, and (4) areas of potential distribution of the plant within the protected areas. We found that “forest and shrubs”, which is cover type in which Omphalea populations have been reported, has increased significantly in Cuba in the past 35 years, and that most of the gained forest and shrub areas were agricultural land in the past. This same pattern was observed in the areas of potential distribution of Omphalea; whereas almost all cover types were mostly stable inside the protected areas. The transformation of agricultural areas into forest and shrubs could represent an interesting opportunity for biodiversity conservation in Cuba. Other detailed studies about biodiversity composition in areas of forest and shrubs gain would greatly benefit our understanding of the value of such areas for conservation. creator: Claudia Nuñez-Penichet creator: Juan Maita creator: Jorge Soberon uri: https://doi.org/10.7717/peerj.17563 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Nuñez-Penichet et al. title: Mechanism of Brevibacillus brevis strain TR-4 against leaf disease of Photinia×fraseri Dress link: https://peerj.com/articles/17568 last-modified: 2024-06-25 description: BackgroundColletotrichum species are among the most common pathogens in agriculture and forestry, and their control is urgently needed.MethodsIn this study, a total of 68 strains of biocontrol bacteria were isolated and identified from Photinia × fraseri rhizosphere soil.ResultsThe isolates were identified as Brevibacillus brevis by 16S rRNA. The inhibitory effect of TR-4 on Colletotrichum was confirmed by an in vitro antagonistic experiment. The inhibitory effect of TR-4 was 98% at a concentration of 10 µl/ml bacterial solution, protection of the plant and inhibition of C. siamense was evident. Moreover, the secretion of cellulase and chitosan enzymes in the TR-4 fermentation liquid cultured for three days was 9.07 mol/L and 2.15 µl/mol, respectively. Scanning electron microscopy and transmission electron microscopy confirmed that TR-4 destroyed the cell wall of C. siamense, resulting in leakage of the cell contents, thus weakening the pathogenicity of the bacteria. creator: Chenxinyu Ji creator: Yun-Fei Li creator: Yao Yao creator: Zengrui Zhu creator: Shengfeng Mao uri: https://doi.org/10.7717/peerj.17568 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Not so cryptic–differences between mating calls of Hyla arborea and Hyla orientalis from Bulgaria link: https://peerj.com/articles/17574 last-modified: 2024-06-25 description: Anurans are among the most vocally active vertebrate animals and emit calls with different functions. In order to attract a mate, during the breeding season male frogs produce mating calls which have species-specific structure and parameters, and have been successfully used to resolve issues in taxonomy and phylogenetic relations. This is particularly useful when closely related taxa are concerned, as many species are morphologically almost identical, but still their status is well-supported by molecular and genetic data, suggesting the existence of mechanisms for reproductive isolation. Such is the case for treefrogs from the Hyla arborea group, which are now recognized as several distinct species. The present study aims to establish differences in call parameters between the European tree frog, Hyla arborea, and the Eastern tree frog, Hyla orientalis, which both occur on the territory of Bulgaria. Using autonomous audio loggers, calls from six sites (three in the range of H. arborea and three in the range of H. orientalis) were recorded between 7 p.m. and 12 a.m. during the breeding season in 2020–2023. The following parameters in a total of 390 mating calls were analyzed: call count, pulse count, call series duration, call period, peak (dominant) frequency, entropy. Results indicated that sites formed two distinct groups, which corresponded to the known distribution ranges of H. arborea and H. orientalis. The first two components of the PCA explained 71% of the total variance, with variables call count, call series duration, peak frequency and entropy being most important for differentiation between the sites. This study presents the first attempt to differentiate between the calls of these two sister taxa, which both fall within the “short-call treefrogs” group, and results are discussed in terms of known data for mating calls in Hyla sp., as well as limitations and future perspectives. creator: Simeon Lukanov uri: https://doi.org/10.7717/peerj.17574 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lukanov title: Applying different levels of practice variability for motor learning: More is not better link: https://peerj.com/articles/17575 last-modified: 2024-06-25 description: BackgroundVariable practice is a broadly used tool to improve motor learning processes. However, controversial results can be found in literature about the success of this type of practice compared to constant practice. This study explored one potential reason for this controversy: the manipulation of variable practice load applied during practice and its effects according to the initial performance level and the initial intrinsic variability of the learner.MethodSixty-five participants were grouped into four practice schedules to learn a serial throwing task, in which the training load of variable practice was manipulated: one constant practice group and three groups with different variable practice loads applied. After a pre-test, participants trained for 2 weeks. A post-test and three retests (96 h, 2 weeks and 1 month) were carried out after training. The participants’ throwing accuracy was assessed through error parameters and their initial intrinsic motor variability was assessed by the autocorrelation coefficient of the error.ResultsThe four groups improved their throwing performance. Pairwise comparisons and effect sizes showed larger error reduction in the low variability group. Different loads of variable practice seem to induce different performance improvements in a throwing task. The modulation of the variable practice load seems to be a step forward to clarify the controversy about its benefits, but it has to be guided by the individuals’ features, mainly by the initial intrinsic variability of the learner. creator: Carla Caballero creator: David Barbado creator: Manuel Peláez creator: Francisco J. Moreno uri: https://doi.org/10.7717/peerj.17575 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Caballero et al. title: Isolation and characterization of native antagonistic rhizobacteria against Fusarium wilt of chilli to promote plant growth link: https://peerj.com/articles/17578 last-modified: 2024-06-25 description: In the eastern coastal regions of Odisha, wilt caused by Fusarium oxysporum f. sp.capsici is an extremely damaging disease in chilli. This disease is very difficult to manage with chemical fungicides since it is soil-borne in nature. The natural rhizosphere soil of the chilli plant was used to isolate and test bacterial antagonists for their effectiveness and ability to promote plant growth. Out of the fifty-five isolates isolated from the rhizosphere of healthy chilli plants, five isolates, namely Iso 01, Iso 17, Iso 23, Iso 24, and Iso 32, showed their highly antagonistic activity against F. oxysporum f. sp. capsici under in vitro. In a dual culture, Iso 32 (73.3%) and Iso 24 (71.5%) caused the highest level of pathogen inhibition. In greenhouse trials, artificially inoculated chilli plants treated with Iso 32 (8.8%) and Iso 24 (10.2%) had decreased percent disease incidence (PDI), with percent disease reduction over control of 85.6% and 83.3%, respectively. Iso 32 and Iso 24 treated chilli seeds have shown higher seed vigor index of 973.7 and 948.8, respectively, as compared to untreated control 636.5. Furthermore, both the isolates significantly increased plant height as well as the fresh and dry weight of chilli plants under the rolled paper towel method. Morphological, biochemical, and molecular characterization identified Bacillus amyloliquefaciens (MH491049) as the key antagonist. This study demonstrates that rhizobacteria, specifically Iso 32 and Iso 24, can effectively protect chilli plants against Fusarium wilt while promoting overall plant development. These findings hold promise for sustainable and eco-friendly management of Fusarium wilt in chilli cultivation. creator: Bhanothu Shiva creator: Petikam Srinivas creator: Deepa Khulbe creator: Lellapalli Rithesh creator: Penumatsa Kishore Varma creator: Rahul Kumar Tiwari creator: Milan Kumar Lal creator: Ravinder Kumar uri: https://doi.org/10.7717/peerj.17578 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shiva et al. title: Biosynthesis of zinc oxide nanoparticles via neem extract and their anticancer and antibacterial activities link: https://peerj.com/articles/17588 last-modified: 2024-06-25 description: In the present study, zinc oxide nanoparticles (ZnO-NPs) were synthesized using neem leaf aqueous extracts and characterized using transmission electron microscopy (TEM), ultraviolet visible spectroscopy (UV-Vis), and dynamic light scattering (DLS). Then compare its efficacy as anticancer and antibacterial agents with chemically synthesized ZnO-NPs and the neem leaf extract used for the green synthesis of ZnO-NPs. The TEM, UV-vis, and particle size confirmed that the developed ZnO-NPs are nanoscale. The chemically and greenly synthesized ZnO-NPs showed their optical absorbance at 328 nm and 380 nm, respectively, and were observed as spherical particles with a size of about 85 nm and 62.5 nm, respectively. HPLC and GC-MS were utilized to identify the bioactive components in the neem leaf aqueous extract employed for the eco-friendly production of ZnO-NPs. The HPLC analysis revealed that the aqueous extract of neem leaf contains 19 phenolic component fractions. The GC-MS analysis revealed the existence of 21 bioactive compounds. The antiproliferative effect of green ZnO-NPs was observed at different concentrations (31.25 µg/mL–1000 µg/mL) on Hct 116 and A 549 cancer cells, with an IC50 value of 111 µg/mL for A 549 and 118 µg/mL for Hct 116. On the other hand, the antibacterial activity against gram-positive and gram-negative bacteria was estimated. The antibacterial result showed that the MIC of green synthesized ZnO-NPs against gram-positive and gram-negative bacteria were 5, and 1 µg/mL. Hence, they could be utilized as effective antibacterial and antiproliferative agents. creator: Hossam S. El-Beltagi creator: Marwa Ragab creator: Ali Osman creator: Ragab A. El-Masry creator: Khairiah Mubarak Alwutayd creator: Hind Althagafi creator: Leena S. Alqahtani creator: Reem S. Alazragi creator: Ahlam Saleh Alhajri creator: Mahmoud M. El-Saber uri: https://doi.org/10.7717/peerj.17588 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 El-Beltagi et al. title: Using feces to indicate plastic pollution in terrestrial vertebrate species in western Thailand link: https://peerj.com/articles/17596 last-modified: 2024-06-25 description: Plastic pollution is a widespread and growing concern due to its transformation into microplastics (MPs), which can harm organisms and ecosystems. This study, aimed to identify plastic pollution in the feces of terrestrial vertebrates using convenience sampling both inside and outside protected areas in Western Thailand. We hypothesized that MPs are likely to be detectable in the feces of all vertebrate species, primarily in the form of small black fragments. We predicted varying quantities of MPs in the feces of the same species across different protected areas. Furthermore, we expected that factors indicating human presence, landscape characteristics, scat weight, and the MP abundance in water, soils, and sediments would influence the presence of plastics in feces. Among 12 terrestrial species studied, potential MPs were found in 41.11% of 90 samples, totaling 83 pieces across eight species including the Asian elephant (Elephas maximus), Eld’s deer (Rucervus eldii), Dhole (Cuon alpinus), Gaur (Bos gaurus), Sambar deer (Rusa unicolor), Wild boar (Sus scrofa), Northern red muntjac (Muntiacus vaginalis), and Butterfly lizard (Leiolepis belliana). Specifically, 3.61% of all potential MPs (three pieces) were macroplastics, and the remaining 96.39% were considered potential MPs with the abundance of 0.92 ± 1.89 items.scat−1 or 8.69 ± 32.56 items.100 g−1 dw. There was an association between the numbers of feces with and without potential plastics and species (χ2 = 20.88, p = 0.012). Most potential plastics were fibers (95.18%), predominantly black (56.63%) or blue (26.51%), with 74.70% smaller than two millimeters. Although there were no significant associations between species and plastic morphologies, colors, and sizes, the abundance classified by these characteristics varied significantly. FTIR identified 52.38% as natural fibers, 38.10% as synthetic fibers (rayon, polyurethane (PUR), polyethylene terephthalate (PET), polypropylene (PP), and PUR blended with cotton), and 9.52% as fragments of PET and Polyvinyl Chloride (PVC). Human-related factors were linked to the occurrence of potential plastics found in the feces of land-dwelling wildlife. This study enhances the understanding of plastic pollution in tropical protected areas, revealing the widespread of MPs even in small numbers from the areas distant from human settlements. Monitoring plastics in feces offers a non-invasive method for assessing plastic pollution in threatened species, as it allows for easy collection and taxonomic identification without harming live animals. However, stringent measures to assure the quality are necessitated to prevent exogenous MP contamination. These findings underscore the importance of raising awareness about plastic pollution in terrestrial ecosystems, especially regarding plastic products from clothing and plastic materials used in agriculture and irrigation systems. creator: Jiraporn Teampanpong creator: Prateep Duengkae uri: https://doi.org/10.7717/peerj.17596 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Teampanpong and Duengkae title: Maternal effects, reciprocal differences and combining ability study for yield and its component traits in maize (Zea mays L.) through modified diallel analysis link: https://peerj.com/articles/17600 last-modified: 2024-06-25 description: Combining ability status of the inbred lines is crucial information for hybrid breeding program. Diallel or line × tester mating designs are frequently used to evaluate the combining ability. In the current study a modified diallel model was used, wherein the Griffing’s combining ability effects were further partitioned to understand the effects due to maternal and reciprocal. To do this, eight parental lines of maize were crossed in full diallel method and the generated hybrids along with parents were phenotyped. The field data on the quantitative traits was analyzed using both Griffing’s and the modified model to determine how well the parents’ and the F1 hybrids combined. For each of the traits, a sizable reciprocal and maternal variance was observed. The number of kernel rows per cob variable had a ratio of additive variance to dominance variance greater than one. All other traits including grain yield had a ratio close to zero, suggesting that non-additive gene action was primarily responsible for the genetic control of most of the traits. The narrow sense heritability was low to moderate for majority of the variables, except for number of kernel rows per cob. With the help of the improved model, it was possible to choose superior parents and cross-parent pairings with accuracy. Based on the modified general combining ability effects and maternal effects, the parental line P5 was recognized as a potential female parent and P7 as a good male parent for grain yield and yield-attributing characteristics. The cross combination of P8×P1 had the highest specific combining ability effect on grain yield. P5×P6 cross had the highest reciprocal effect. The correlation analysis implies that the Griffing’s general combining ability effects and specific combining ability effects were found to be less efficient in predicting F1 performance as compared to the modified model. creator: Bonipas Antony John creator: Rajashekhar Mahantaswami Kachapur creator: Gopalakrishna Naidu creator: Sidramappa Channappa Talekar creator: Zerka Rashid creator: Bindiganavile S. Vivek creator: Nagesh Patne creator: Shiddappa Ramappa Salakinkop creator: Prema GU uri: https://doi.org/10.7717/peerj.17600 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Antony John et al. title: Evaluation of Mac-2 binding protein glycosylation isomer (M2BPGi) as a diagnostic marker for staging liver fibrosis: a meta-analysis link: https://peerj.com/articles/17611 last-modified: 2024-06-25 description: ObjectiveThis study aimed to assess the accuracy of Mac-2 binding protein glycosylation isomer (M2BPGi) in predicting the stage of liver fibrosis.MethodsArticles published until October 10, 2023, were searched in the PubMed, Embase, Web of Science, and Cochrane Library databases. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), summary receiver–operator curves (SROC), and Spearman’s rank correlation coefficient were used to examine the accuracy of M2BPGi in predicting the stage of liver fibrosis. A 95% confidence interval (CI) was provided for each estimate.ResultsTwenty-four studies were included in this meta-analysis, including 3,839 patients with liver fibrosis, 409 of whom progressed to stage 4 or above. The pooled sensitivity, specificity, and area under the ROC (AUC) for M2BPGi predicting liver fibrosis ≥F3 were 0.74 (95% CI [0.65–0.82]), 0.84 (95% CI [0.76–0.89]), and 14.99 (95% CI [9.28–24.21]), respectively. The pooled sensitivity, specificity, and AUC for ≥F4 were 0.80 (95% CI [0.70–0.88]), 0.80 (95% CI [0.73–0.86]), and 16.43 (95% CI [0.84–0.90]), respectively.ConclusionAmong different sample partitions, M2BPGi has the best diagnostic performance for liver fibrosis stage ≥4. Furthermore, the cutoff of 1–2 is more accurate than that of 0–1 or 2–3 for fibrosis ≥ F3 and ≥ F4.RegistrationCRD42023483260. creator: Siyao Gong creator: Xin Yu creator: Qian Li creator: Ming Chen creator: Shuguang Yu creator: Sha Yang uri: https://doi.org/10.7717/peerj.17611 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Gong et al. title: The effects of exercise on FGF21 in adults: a systematic review and meta-analysis link: https://peerj.com/articles/17615 last-modified: 2024-06-25 description: BackgroundFibroblast growth factor 21 (FGF21) is a key hormone factor that regulates glucose and lipid homeostasis. Exercise may regulate its effects and affect disease states. Therefore, we sought to determine how exercise affects FGF21 concentrations in adults.MethodsThe review was registered in the International Prospective Systematic Review (PROSPERO, CRD42023471163). The Cochrane Library, PubMed, and Web of Science databases were searched for studies through July 2023. Studies that assessed the effects of exercise training on FGF21 concentration in adults were included. The random effect model, data with standardized mean difference (SMD), and 95% confidence intervals (CI) were used to evaluate the pooled effect size of exercise training on FGF21. The risk of heterogeneity and bias were evaluated. A total of 12 studies involving 401 participants were included.ResultsThe total effect size was 0.3 (95% CI [−0.3–0.89], p = 0.33) when comparing participants who exercised to those who were sedentary. However, subgroup analysis indicated that concurrent exercise and a duration ≥10 weeks significantly decreased FGF21 concentrations with an effect size of −0.38 (95% CI [−0.74–−0.01], p < 0.05) and −0.38 (95% CI [−0.63–−0.13], p < 0.01), respectively.ConclusionConcurrent exercise and longer duration may be more efficient way to decrease FGF21 concentrations in adults with metabolic disorder. creator: Chuannan Liu creator: Xujie Yan creator: Yue Zong creator: Yanan He creator: Guan Yang creator: Yue Xiao creator: Songtao Wang uri: https://doi.org/10.7717/peerj.17615 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: Influence of leaf inclination angle and tillering on population transpiration, soil evaporation, and yield in winter wheat near-isogenic lines link: https://peerj.com/articles/17618 last-modified: 2024-06-25 description: Leaf inclination angle (LIA) and tillering impact the winter wheat (Triticum aestivum L.) population canopy structure. Understanding their effects on water use (WU) parameters and yield can guide water-saving strategies through population control. In this study, six near-isogenic lines (NILs) and their parents were selected as materials. These special materials were characterized by varying tillering at the current sowing density, a similar genetic background, and, particularly, a gradient in mean flag leaf LIA. The investigation focused on the jointing to early grain-filling stage, the peak water requirement period of wheat crops. Population-scale transpiration (PT) and evaporation from the soil surface (E) were partitioned from total evapotranspiration (ET) by the means of micro-lysimeters. The results showed decreased PT, E, and ET with increased population density (PD) within a narrow density range derived from varying tillering across genotypes. Significant correlations existed between PD and ET, E, and PT, especially in the wettest 2017–2018 growing season. Within such narrow PD range, all the correlations between WU parameters and PD were negative, although some correlations were not statistically significant, thereby suggesting the population structure’s predominant impact. No significant correlation existed between LIA and both ET and PT within the LIA range of 35°–65°. However, significant correlations occurred between LIA and E in two growing seasons. Genotypes with similar LIA but different PD produced varied ET; while with similar PD, the four pairs of genotypes with different LIA each consumed similar ET, thus highlighting PD’s more crucial role in regulating ET. The yield increased with higher LIA, and showed a significant correlation, emphasizing the LIA’s significant effect on yield. However, no correlation was observed with PD, indicating the minor effect of tillering at the current sowing density. Therefore these results might offer valuable insights for breeding water-saving cultivars and optimizing population structures for effective field water conservation. creator: Guirong Huang creator: Xinying Zhang creator: Zhenzhao Wang creator: Xiaoying Liu creator: Rui Guo creator: Fengxue Gu creator: Enke Liu creator: Shuying Li creator: Xiuli Zhong creator: Qiaozhen Li creator: Xurong Mei uri: https://doi.org/10.7717/peerj.17618 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Huang et al. title: Shoulder muscle weakness and proprioceptive impairments in type 2 diabetes mellitus: exploring correlations for improved clinical management link: https://peerj.com/articles/17630 last-modified: 2024-06-25 description: BackgroundType 2 diabetes mellitus (T2DM) is a prevalent metabolic disorder with systemic implications, potentially affecting musculoskeletal health. This study aimed to assess shoulder muscle strength and joint repositioning accuracy in individuals with T2DM, exploring potential correlations and shedding light on the musculoskeletal consequences of the condition. The objectives were two-fold: (1) to assess and compare shoulder strength and joint repositioning accuracy between individuals with T2DM and asymptomatic counterparts, and (2) to examine the correlation between shoulder strength and joint repositioning accuracy in individuals with T2DM.MethodsA cross-sectional study enrolled 172 participants using the convenience sampling method, including 86 individuals with T2DM and an age-matched asymptomatic group (n = 86). Shoulder strength was assessed using a handheld dynamometer, while joint repositioning accuracy was evaluated with an electronic digital inclinometer.ResultsIndividuals with T2DM exhibited reduced shoulder muscle strength compared to asymptomatic individuals (p < 0.001). Additionally, joint repositioning accuracy was significantly lower in the T2DM group (p < 0.001). Negative correlations were observed between shoulder strength and joint repositioning accuracy in various directions (ranging from −0.29 to −0.46, p < 0.001), indicating that higher muscle strength was associated with improved joint repositioning accuracy in individuals with T2DM.ConclusionThis study highlights the significant impact of T2DM on shoulder muscle strength and joint repositioning accuracy. Reduced strength and impaired accuracy are evident in individuals with T2DM, emphasizing the importance of addressing musculoskeletal aspects in diabetes management. The negative correlations suggest that enhancing shoulder muscle strength may lead to improved joint repositioning accuracy, potentially contributing to enhanced physical functioning in this population. creator: Ravi Shankar Reddy creator: Mastour Saeed Alshahrani creator: Mohammad A. ALMohiza creator: Batool Abdulelah Alkhamis creator: Jaya Shanker Tedla creator: Venkata Nagaraj Kakaraparthi creator: Ghada Mohamed Koura creator: Debjani Mukherjee creator: Hani Hassan Alnakhli creator: Hussain Saleh H. Ghulam creator: Raee S. Alqhtani uri: https://doi.org/10.7717/peerj.17630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Reddy et al. title: Identification and serological responses to a novel Plasmodium vivax merozoite surface protein 1 (PvMSP-1) derived synthetic peptide: a putative biomarker for malaria exposure link: https://peerj.com/articles/17632 last-modified: 2024-06-25 description: BackgroundThe integration of diagnostic methods holds promise for advancing the surveillance of malaria transmission in both endemic and non-endemic regions. Serological assays emerge as valuable tools to identify and delimit malaria transmission, serving as a complementary method to rapid diagnostic tests (RDT) and thick smear microscopy. Here, we evaluate the potential of antibodies directed against peptides encompassing the entire amino acid sequence of the PvMSP-1 Sal-I strain as viable serological biomarkers for P. vivax exposure.MethodsWe screened peptides encompassing the complete amino acid sequence of the Plasmodium vivax Merozoite Surface Protein 1 (PvMSP-1) Sal-I strain as potential biomarkers for P. vivax exposure. Here, immunodominant peptides specifically recognized by antibodies from individuals infected with P. vivax were identified using the SPOT-synthesis technique followed by immunoblotting. Two 15-mer peptides were selected based on their higher and specific reactivity in immunoblotting assays. Subsequently, peptides p70 and p314 were synthesized in soluble form using SPPS (Solid Phase Peptide Synthesis) and tested by ELISA (IgG, and subclasses).ResultsThis study unveils the presence of IgG antibodies against the peptide p314 in most P. vivax-infected individuals from the Brazilian Amazon region. In silico B-cell epitope prediction further supports the utilization of p314 as a potential biomarker for evaluating malaria transmission, strengthened by its amino acid sequence being part of a conserved block of PvMSP-1. Indeed, compared to patients infected with P. falciparum and uninfected individuals never exposed to malaria, P. vivax-infected patients have a notably higher recognition of p314 by IgG1 and IgG3. creator: Aline Marzano-Miranda creator: Gustavo Pereira Cardoso-Oliveira creator: Ingrid Carla de Oliveira creator: Luiza Carvalho Mourão creator: Letícia Reis Cussat creator: Vanessa Gomes Fraga creator: Carlos Delfin Chávez Olórtegui creator: Cor Jesus Fernandes Fontes creator: Daniella Castanheira Bartholomeu creator: Erika M. Braga uri: https://doi.org/10.7717/peerj.17632 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Marzano-Miranda et al. title: Evaluation of genetic variation and host resistance to wheat stem rust pathogen (Puccinia graminis f. sp. tritici) in bread wheat (Triticum aestivum L.) varieties grown in Türkiye link: https://peerj.com/articles/17633 last-modified: 2024-06-25 description: Wheat stem rust, which is caused by Puccinia graminis f. sp. tritici (Pgt), is a highly destructive disease that affects wheat crops on a global scale. In this study, the reactions of 150 bread wheat varieties were evaluated for natural Pgt infection at the adult-plant stage in the 2019–2020 and 2020–2021 growing seasons, and they were analyzed using specific molecular markers to detect stem rust resistance genes (Sr22, Sr24, Sr25, Sr26, Sr31, Sr38, Sr50, and Sr57). Based on phenotypic data, the majority of the varieties (62%) were resistant or moderately resistant to natural Pgt infection. According to molecular results, it was identified that Sr57 was present in 103 varieties, Sr50 in nine varieties, Sr25 in six varieties, and Sr22, Sr31, and Sr38 in one variety each. Additionally, their combinations Sr25 + Sr50, Sr31 + Sr57, Sr38 + Sr50, and Sr38 + Sr57 were detected in these varieties. On the other hand, Sr24 and Sr26 were not identified. In addition, many varieties had low stem rust scores, including a large minority that lacked Sr57. These varieties must have useful resistance to stem rust and could be the basis for selecting greater, possibly durable resistance. creator: Ahmet Cat uri: https://doi.org/10.7717/peerj.17633 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cat title: The impact of the military conflict in Sudan on maternal health: a mixed qualitative and quantitative study link: https://peerj.com/articles/17484 last-modified: 2024-06-24 description: ObjectivesOngoing military conflict in Sudan has had significant repercussions on the health and well-being of the population, particularly among women of reproductive age. This study aimed to investigate the impact of conflict on maternal health by employing a mixed qualitative and quantitative research approach.MethodsThrough in-depth interviews and survey questionnaires (388 women), this study examined the experiences and challenges faced by pregnant women and new mothers and the availability and accessibility of maternal healthcare services in conflict-affected areas. Using a qualitative approach, in-depth interviews were conducted with 35 women who had recently given birth or were pregnant in regions affected by the Khartoum State–Sudan conflict. Thematic analysis was used to analyze the data collected from the interviews.ResultMost women did not have access to healthcare services (86.6%), and out of the total sample, 93 (24%) experienced adverse outcomes. The factors associated with adverse effects were parity (OR 1.78, CI [1.15–2.75], p-value 0.010), gestational age (OR 2.10, CI [1.36–3.25], p-value 0.002), access to healthcare (OR 2.35, CI [1.48–3.72], p-value 0.001), and delivery mode (OR 1.68, CI [1.05–2.69], p = 0.030). Factors significantly associated with accessibility to maternal healthcare services included age (OR, 1.28; = 0.042) and higher conflict levels (1.52 times higher odds, p = 0.021). The narratives and experiences shared by women exposed the multifaceted ways in which the conflict-affected maternal health outcomes.ConclusionThe significance of this study lies in its potential to contribute to the existing literature on maternal health in conflict-affected areas, especially in Sudan, and to help us understand how women can receive maternal health services. creator: Elhadi Miskeen uri: https://doi.org/10.7717/peerj.17484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Miskeen title: The inorganic pyrophosphatases of microorganisms: a structural and functional review link: https://peerj.com/articles/17496 last-modified: 2024-06-24 description: Pyrophosphatases (PPases) are enzymes that catalyze the hydrolysis of pyrophosphate (PPi), a byproduct of the synthesis and degradation of diverse biomolecules. The accumulation of PPi in the cell can result in cell death. Although the substrate is the same, there are variations in the catalysis and features of these enzymes. Two enzyme forms have been identified in bacteria: cytoplasmic or soluble pyrophosphatases and membrane-bound pyrophosphatases, which play major roles in cell bioenergetics. In eukaryotic cells, cytoplasmic enzymes are the predominant form of PPases (c-PPases), while membrane enzymes (m-PPases) are found only in protists and plants. The study of bacterial cytoplasmic and membrane-bound pyrophosphatases has slowed in recent years. These enzymes are central to cell metabolism and physiology since phospholipid and nucleic acid synthesis release important amounts of PPi that must be removed to allow biosynthesis to continue. In this review, two aims were pursued: first, to provide insight into the structural features of PPases known to date and that are well characterized, and to provide examples of enzymes with novel features. Second, the scientific community should continue studying these enzymes because they have many biotechnological applications. Additionally, in this review, we provide evidence that there are m-PPases present in fungi; to date, no examples have been characterized. Therefore, the diversity of PPase enzymes is still a fruitful field of research. Additionally, we focused on the roles of H+/Na+ pumps and m-PPases in cell bioenergetics. Finally, we provide some examples of the applications of these enzymes in molecular biology and biotechnology, especially in plants. This review is valuable for professionals in the biochemistry field of protein structure–function relationships and experts in other fields, such as chemistry, nanotechnology, and plant sciences. creator: Rodolfo García-Contreras creator: Javier de la Mora creator: Héctor Manuel Mora-Montes creator: José A. Martínez-Álvarez creator: Marcos Vicente-Gómez creator: Felipe Padilla-Vaca creator: Naurú Idalia Vargas-Maya creator: Bernardo Franco uri: https://doi.org/10.7717/peerj.17496 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 García-Contreras et al. title: Sedentary patterns and health outcomes in the oldest-old: a latent profile analysis link: https://peerj.com/articles/17505 last-modified: 2024-06-24 description: BackgroundSedentary behavior is most prevalent among those aged 80 years and above, referred to as the oldest-old. Current literature emphasizes the significance of sedentary behavior patterns, but further evidence is required to understand how these patterns relate to specific health outcomes and to identify at-risk profiles for tailored interventions in the oldest-old. Therefore, the aim of this study was to identify profiles of adults aged 80+ years based on their sedentary patterns and health outcomes, and to examine associations between profiles and socio-demographics.MethodsA cross-sectional study was conducted in Flanders (Belgium) from February 2021 to December 2022 recruiting 90 older adults (80+) through convenience sampling, employing word of mouth, social media and local service centers. Latent profile analysis identified device-based sedentary patterns and assessed their associations with physical and cognitive functioning, mental health-related quality of life (QoL), and social isolation. Associations of these profiles with socio-demographic factors were analyzed.ResultsThree distinct profiles were identified: (1) the ‘cognitively and physically frail’ profile, (2) the ‘healthy’ profile and (3) the ‘lower mental health-related QoL’ profile. Those in the ‘cognitively and physically frail’ profile exhibited the least favorable sedentary pattern, and had a higher likelihood of residing in a nursing home. No significant differences were found for the other socio-demographic variables, being age, sex, educational degree and family situation.ConclusionsThree distinct profiles in the oldest-old population, based on cognitive and physical functioning, mental health-related QoL, and sedentary behavior patterns, were identified. Lower physical and cognitive functioning was associated with unhealthy sedentary patterns. Further research with larger samples is crucial to uncover potential links between socio-demographics and at-risk subgroups, enhancing our understanding of sedentary behavior and geriatric health outcomes in this population. creator: Elien Lebuf creator: Delfien Van Dyck creator: Laura Van de Velde creator: Melanie Beeckman creator: Jelle Van Cauwenberg creator: Sofie Compernolle uri: https://doi.org/10.7717/peerj.17505 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lebuf et al. title: Integrated bulk and single-cell RNA sequencing identifies an aneuploidy-based gene signature to predict sensitivity of lung adenocarcinoma to traditional chemotherapy drugs and patients’ prognosis link: https://peerj.com/articles/17545 last-modified: 2024-06-24 description: BackgroundPatients with lung adenocarcinoma (LUAD) often develop a poor prognosis. Currently, researches on prognostic and immunotherapeutic capacity of aneuploidy-related genes in LUAD are limited.MethodsGenes related to aneuploidy were screened based on bulk RNA sequencing data from public databases using Spearman method. Next, univariate Cox and Lasso regression analyses were performed to establish an aneuploidy-related riskscore (ARS) model. Results derived from bioinformatics analysis were further validated using cellular experiments. In addition, typical LUAD cells were identified by subtype clustering, followed by SCENIC and intercellular communication analyses. Finally, ESTIMATE, ssGSEA and CIBERSORT algorithms were employed to analyze the potential relationship between ARS and tumor immune environment.ResultsA five-gene ARS signature was developed. These genes were abnormally high-expressed in LUAD cell lines, and in particular the high expression of CKS1B promoted the proliferative, migratory and invasive phenotypes of LUAD cell lines. Low ARS group had longer overall survival time, higher degrees of inflammatory infiltration, and could benefit more from receiving immunotherapy. Patients in low ASR group responded more actively to traditional chemotherapy drugs (Erlotinib and Roscovitine). The scRNA-seq analysis annotated 17 cell subpopulations into seven cell clusters. Core transcription factors (TFs) such as CREB3L1 and CEBPD were enriched in high ARS cell group, while TFs such as BCLAF1 and UQCRB were enriched in low ARS cell group. CellChat analysis revealed that high ARS cell groups communicated with immune cells via SPP1 (ITGA4-ITGB1) and MK (MDK-NCl) signaling pathways.ConclusionIn this research, integrative analysis based on the ARS model provided a potential direction for improving the diagnosis and treatment of LUAD. creator: Xiaobin Wang creator: Jiakuan Chen creator: Chaofan Li creator: Yufei Liu creator: Shiqun Chen creator: Feng Lv creator: Ke Lan creator: Wei He creator: Hongsheng Zhu creator: Liang Xu creator: Kaiyuan Ma creator: Haihua Guo uri: https://doi.org/10.7717/peerj.17545 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Wang et al. title: Macro and microplastic pollution in Romania: addressing knowledge gaps and potential solutions under the circular economy framework link: https://peerj.com/articles/17546 last-modified: 2024-06-24 description: BackgroundThis review reveals the role of linear economy prevalence and mismanagement practices in plastic pollution of aquatic and terrestrial environments and related knowledge gaps in Romania while outlining downstream and upstream solutions to reduce plastic pollution and adopt circular economy strategies. Thus, the major aim of this study is the investigation of the stage of scientific knowledge concerning all these demands in the Romanian context.MethodologyThis work integrates two main approaches: (i) a bibliometric analysis fed by Web of Science and Scopus databases to reveal the current coverage of peer-reviewed literature related to plastic waste in Romania and (ii) a subject-based review to underline the main themes related to plastic waste management, plastic pollution, and mitigating options in Romania in line with circular economy principles.ResultsReducing plastic pollution requires scientific knowledge, multi-sectoral cooperation, and societal awareness. Following this, the topics of plastic waste and plastic pollution appeared to be under-investigated in the literature considering Romania as a case study and concentrated around the 2020 year, emphasizing, in this way, the trendiness of plastic waste concerns and their management in the current research landscape. Our analysis points out that: (i) Romania is facing massive plastic pollution requiring solid improvements in waste management performances; (ii) few peer-reviewed research studies are performed in Romania for both macro and microplastic concerns with unknown pollution levels in most of its geographical regions; (iii) the plastic waste management is still understudied here, while waste statistics are poorly available at local levels; (iv) the perspectives of circular economy transition are still limited, feeding the plastic pollution in the coming years.ConclusionsSeveral knowledge gaps are identified and must be covered by future research such as (i) adjusting mismanaged plastic waste levels to regional waste management performances and determining littering rates in urban and rural areas to improve the plastic pollution modeling inputs; (ii) examining plastic pollution associated with landfill sites and waste imports; (iii) assessing the sectoral contributions to macro and microplastic pollution of aquatic environments related to municipalities, tourist destinations, agriculture, etc.; (iv) determining retention levels of plastic in river basins and role of riparian vegetation; (v) analyzing microplastics presence in all types of freshwater environments and interlinkage between macroplastic fragmentation and microplastic; (vi) assessing the plastic loads of transboundary rivers related to mismanagement practices; (vii) determining concentrations of microplastics in air, soil, and other land use ecosystems. creator: Florin-Constantin Mihai creator: Simona-Roxana Ulman creator: Valeria Pop uri: https://doi.org/10.7717/peerj.17546 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Mihai et al. title: Barnacle analysis as a microplastic pollution bioindicator on the East Coast of Surabaya link: https://peerj.com/articles/17548 last-modified: 2024-06-24 description: BackgroundPlastic pollution is a significant issue on the East Coast of Surabaya, emphasizing the need to develop microplastic monitoring programs. Barnacles became one of the potential microplastic bioindicator species on the East Coast of Surabaya. This study aimed to characterize the visual and polymers of microplastics found in barnacles and assess their potential as a bioindicator species for microplastic pollution on the East Coast of Surabaya.MethodsMicroplastic polymer analysis was performed using ATR-FTIR.ResultsA total of 196 microplastic particles were found in barnacles, water, and sediment. The size of microplastics in barnacles, water, and sediment varied, with the size in barnacles dominated by class 1 (1–10 µm), in water by class 2 (10–50 µm), and in sediments by class 3 (50–100 µm). Fragments dominated the shape of microplastics in barnacles, while water and sediment were dominated by fiber. The microplastic color in barnacles, water, and sediment was dominated by blue, and the microplastic polymer composition on barnacles, water, and sediments was dominated by cellophane (36%). Amphibalanus amphitrite was found to be predominant and identified as a potential microplastic bioindicator because it is a cosmopolitan species. Its population was found to correlate positively with cellophane (CP) accumulation. The Pearson’s correlation test between barnacle length and microplastic length at a = 0.05 was inversely proportional to r =  − 0.411 (p < 0.05), categorized as a strong enough correlation. These findings are essential in developing monitoring programs and mitigating the impact of microplastics on the marine environment. creator: Miftakhul Sefti Raufanda creator: Aunurohim Aunurohim creator: Romanus Edy Prabowo uri: https://doi.org/10.7717/peerj.17548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Raufanda et al. title: Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam link: https://peerj.com/articles/17553 last-modified: 2024-06-24 description: BackgroundWhite-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study.MethodIn this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay.ResultThirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests. creator: Nam-Hai Truong creator: Thi-Thu-Hong Le creator: Hong-Duong Nguyen creator: Hong-Thanh Nguyen creator: Trong-Khoa Dao creator: Thi-Minh-Nguyet Tran creator: Huyen-Linh Tran creator: Dinh-Trong Nguyen creator: Thi-Quy Nguyen creator: Thi-Hong-Thao Phan creator: Thi-Huyen Do creator: Ngoc-Han Phan creator: Thi-Cam-Nhung Ngo creator: Van-Van Vu uri: https://doi.org/10.7717/peerj.17553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Truong et al. title: Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China link: https://peerj.com/articles/17554 last-modified: 2024-06-24 description: BackgroundGymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense.MethodsA total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC.ResultsThe studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribution of G. kiangnanense and the significant genetic differentiation among its lineages, both in-situ and ex-situ conservation strategies should be implemented to protect the germplasm resources of G. kiangnanense. creator: Xiangnan Liu creator: Meizhen Wang creator: Shiqiang Song creator: Qing Ma creator: Zhaoping Yang uri: https://doi.org/10.7717/peerj.17554 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Sex difference in the association between triglyceride and intracerebral bleeding risk after intravenous thrombolysis for acute ischemic stroke, a multi-center retrospective study link: https://peerj.com/articles/17558 last-modified: 2024-06-24 description: BackgroundWhether the relationship of intracerebral bleeding risk with lipid profile may vary by sex remains unclear. This study aims to investigate potential sex differences in the association between lipid profile and the risk of symptomatic intracerebral hemorrhage (sICH) in patients with acute ischemic stroke (AIS) who received intravenous thrombolysis using recombinant tissue plasminogen activator (r-tPA).MethodsThis multicenter retrospective observational study analyzed patients with AIS treated with intravenous r-tPA. sICH was defined as a worsening of 4 or higher points in the National Institutes of Health Stroke Scale (NIHSS) score within 36 hours after intravenous thrombolysis in any hemorrhage subtype. We assessed the odds ratio (OR) with 95% confidence interval (CI) of lipid profile for sICH for each sex using logistic regression models adjusted for potential confounding factors.ResultsOf 957 participants (median age 68 (interquartile range, 59–75), men 628 (65.6%)), 56 sICH events (36 (5.7%) in men and 20 (6.1%) in women) were observed. The risk of sICH in men decreased with increasing serum levels of triglyceride after adjustment for confounding factors (vs lowest tertile, medium tertile OR 0.39, 95% CI [0.17–0.91], top tertile OR 0.33, 95% CI [0.13–0.84], overall p = 0.021; per point increase, adjusted OR 0.29, 95% CI [0.13–0.63], p = 0.002). Neither serum levels of total cholesterol nor low-density lipoprotein (LDL) was associated with sICH in men. In women, there was no association between any of the lipid levels and the risk of sICH.ConclusionsThis study indicated that the association between serum levels of triglyceride and sICH may vary by sex. In men, increased triglyceride levels decrease the risk of sICH; in women, this association was lost. Further studies on the biological mechanisms for sex differences in stroke risk associated with triglyceride are needed. creator: Qilin Yuan creator: Ying Han creator: Shuangfang Fang creator: Hanhan Lei creator: Huapin Huang creator: Huiying Lin creator: Xiaomin Wu creator: Ronghua Chen creator: Zhiting Chen creator: Jie Chen creator: Hangfeng Li creator: Nan Liu creator: Houwei Du uri: https://doi.org/10.7717/peerj.17558 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yuan et al. title: Associations between fundamental movement skills and accelerometer-measured physical activity in Chinese children: the mediating role of cardiorespiratory fitness link: https://peerj.com/articles/17564 last-modified: 2024-06-24 description: Background and purposeThe associations of fundamental motor skills (FMS), health-related physical fitness (e.g., cardiorespiratory fitness, CRF), and moderate-vigorous physical activity (MVPA) have been demonstrated in Western children, but these associations have not yet been validated in a sample of Chinese children. The aims of this study, therefore, were to examine the association between FMS subdomains and MVPA in a sample of Chinese children and to evaluate whether this association is mediated by CRF.MethodsA cross-sectional study consisting of 311 children aged 8–12 years (49.2% girls; mean age = 9.9 years) from Shanghai was conducted. FMS, CRF and MVPA were assessed using the Test of Gross Motor Development-3rd Edition, Progressive Aerobic Cardiovascular Endurance Run and ActiGraph GT3X accelerometers. Preacher & Hayes’s bootstrap method was used to test the mediating effects of CRF on the association between FMS and MVPA.ResultsCRF fully mediated the association between total FMS and MVPA in girls (indirect effects, b = 0.21, 95% CI [0.07–0.37]), while the mediation was only partial in boys (indirect effects, b = 0.12, 95% CI [0.01–0.26]). CRF fully mediated the association between locomotor skills and MVPA in girls (indirect effects, b = 0.27, 95% CI [0.09– 0.51]), whereas CRF partially mediated the association between object control skills and MVPA in boys (indirect effects, b = 0.15, 95% CI [0.18–0.35]).ConclusionIn order to better design and implement sex-specific interventions aiming to increase MVPA, it is essential to consider FMS subdomains and CRF alongside the sex differences in the association between them. creator: Dingyi Zhang creator: Sitong Chen creator: Fei Xin creator: Clemens Drenowatz creator: Xiaoqing Hu creator: Yan Tang uri: https://doi.org/10.7717/peerj.17564 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Squatting biomechanics following physiotherapist-led care or hip arthroscopy for femoroacetabular impingement syndrome: a secondary analysis from a randomised controlled trial link: https://peerj.com/articles/17567 last-modified: 2024-06-24 description: BackgroundFemoroacetabular impingement syndrome (FAIS) can cause hip pain and chondrolabral damage that may be managed non-operatively or surgically. Squatting motions require large degrees of hip flexion and underpin many daily and sporting tasks but may cause hip impingement and provoke pain. Differential effects of physiotherapist-led care and arthroscopy on biomechanics during squatting have not been examined previously. This study explored differences in 12-month changes in kinematics and moments during squatting between patients with FAIS treated with a physiotherapist-led intervention (Personalised Hip Therapy, PHT) and arthroscopy.MethodsA subsample (n = 36) of participants with FAIS enrolled in a multi-centre, pragmatic, two-arm superiority randomised controlled trial underwent three-dimensional motion analysis during squatting at baseline and 12-months following random allocation to PHT (n = 17) or arthroscopy (n = 19). Changes in time-series and peak trunk, pelvis, and hip biomechanics, and squat velocity and maximum depth were explored between treatment groups.ResultsNo significant differences in 12-month changes were detected between PHT and arthroscopy groups. Compared to baseline, the arthroscopy group squatted slower at follow-up (descent: mean difference −0.04 m∙s−1 (95%CI [−0.09 to 0.01]); ascent: −0.05 m∙s−1 [−0.11 to 0.01]%). No differences in squat depth were detected between or within groups. After adjusting for speed, trunk flexion was greater in both treatment groups at follow-up compared to baseline (descent: PHT 7.50° [−14.02 to −0.98]%; ascent: PHT 7.29° [−14.69 to 0.12]%, arthroscopy 16.32° [−32.95 to 0.30]%). Compared to baseline, both treatment groups exhibited reduced anterior pelvic tilt (descent: PHT 8.30° [0.21–16.39]%, arthroscopy −10.95° [−5.54 to 16.34]%; ascent: PHT −7.98° [−0.38 to 16.35]%, arthroscopy −10.82° [3.82–17.81]%), hip flexion (descent: PHT −11.86° [1.67–22.05]%, arthroscopy −16.78° [8.55–22.01]%; ascent: PHT −12.86° [1.30–24.42]%, arthroscopy −16.53° [6.72–26.35]%), and knee flexion (descent: PHT −6.62° [0.56– 12.67]%; ascent: PHT −8.24° [2.38–14.10]%, arthroscopy −8.00° [−0.02 to 16.03]%). Compared to baseline, the PHT group exhibited more plantarflexion during squat ascent at follow-up (−3.58° [−0.12 to 7.29]%). Compared to baseline, both groups exhibited lower external hip flexion moments at follow-up (descent: PHT −0.55 N∙m/BW∙HT[%] [0.05–1.05]%, arthroscopy −0.84 N∙m/BW∙HT[%] [0.06–1.61]%; ascent: PHT −0.464 N∙m/BW∙HT[%] [−0.002 to 0.93]%, arthroscopy −0.90 N∙m/BW∙HT[%] [0.13–1.67]%).ConclusionExploratory data suggest at 12-months follow-up, neither PHT or hip arthroscopy are superior at eliciting changes in trunk, pelvis, or lower-limb biomechanics. Both treatments may induce changes in kinematics and moments, however the implications of these changes are unknown.Trial registration detailsAustralia New Zealand Clinical Trials Registry reference: ACTRN12615001177549. Trial registered 2/11/2015. creator: Tamara M. Grant creator: David J. Saxby creator: Claudio Pizzolato creator: Trevor Savage creator: Kim Bennell creator: Edward Dickenson creator: Jillian Eyles creator: Nadine Foster creator: Michelle Hall creator: David Hunter creator: David Lloyd creator: Rob Molnar creator: Nicholas Murphy creator: John O’Donnell creator: Parminder Singh creator: Libby Spiers creator: Phong Tran creator: Laura E. Diamond uri: https://doi.org/10.7717/peerj.17567 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Grant et al. title: Optimization of polysaccharide conditions and analysis of antioxidant capacity in the co-culture of Sanghuangporus vaninii and Pleurotus sapidus link: https://peerj.com/articles/17571 last-modified: 2024-06-24 description: Fungal polysaccharides are commonly utilized in the food industry and biomedical fields as a natural and safe immune modulator. Co-culturing is a valuable method for enhancing the production of secondary metabolites. This study used intracellular polysaccharide (IPS) content as a screening index, co-culturing seven different fungi with Sanghuangporus vaninii. The seed pre-culture liquid culture time was selected through screening, and conditions were assessed using single factor experimentation, a Plackett-Burman (PB) design, and response surface methodology (RSM) optimization. RSM optimization was conducted, leading to the measurement of antioxidant capacity. Results indicated that the co-culture of S. vaninii and Pleurotus sapidus exhibited the most effective outcome. Specifically, pre-culturing S. vaninii and P. sapidus seed cultures for 2 days and 0 days, respectively, followed by co-culturing, significantly increased IPS content compared to single-strain culturing. Further optimization of co-culture conditions revealed that yeast extract concentration, liquid volume, and S. vaninii inoculum ratio notably influenced IPS content in the order of yeast extract concentration > liquid volume > S. vaninii inoculum ratio. Under the optimal conditions, IPS content reached 69.9626 mg/g, a 17.04% increase from pre-optimization co-culture conditions. Antioxidant capacity testing demonstrated that co-cultured IPS exhibited greater scavenging abilities for DPPH and ABTS free radicals compared to single strain cultures. These findings highlight the potential of co-culturing S. vaninii and P. sapidus to enhance IPS content and improve antioxidant capacity, presenting an effective strategy for increasing fungal polysaccharide production. creator: Yuantian Lu creator: Di Liu uri: https://doi.org/10.7717/peerj.17571 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lu and Liu title: Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes link: https://peerj.com/articles/17577 last-modified: 2024-06-24 description: BackgroundEnhancing detection of cryptic snakes is critical for the development of conservation and management strategies; yet, finding methods that provide adequate detection remains challenging. Issues with detecting snakes can be particularly problematic for some species, like the invasive Burmese python (Python bivittatus) in the Florida Everglades.MethodsUsing multiple survey methods, we predicted that our ability to detect pythons, larger snakes and all other snakes would be enhanced with the use of live mammalian lures (domesticated rabbits; Oryctolagus cuniculus). Specifically, we used visual surveys, python detection dogs, and time-lapse game cameras to determine if domesticated rabbits were an effective lure.ResultsTime-lapse game cameras detected almost 40 times more snakes (n = 375, treatment = 245, control = 130) than visual surveys (n = 10). We recorded 21 independent detections of pythons at treatment pens (with lures) and one detection at a control pen (without lures). In addition, we found larger snakes, and all other snakes were 165% and 74% more likely to be detected at treatment pens compared to control pens, respectively. Time-lapse cameras detected almost 40 times more snakes than visual surveys; we did not detect any pythons with python detection dogs.ConclusionsOur study presents compelling evidence that the detection of snakes is improved by coupling live mammalian lures with time-lapse game cameras. Although the identification of smaller snake species was limited, this was due to pixel resolution, which could be improved by changing the camera focal length. For larger snakes with individually distinctive patterns, this method could potentially be used to identify unique individuals and thus allow researchers to estimate population dynamics. creator: Marina McCampbell creator: McKayla Spencer creator: Kristen Hart creator: Gabrielle Link creator: Andrew Watson creator: Robert McCleery uri: https://doi.org/10.7717/peerj.17577 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches link: https://peerj.com/articles/17584 last-modified: 2024-06-24 description: Abiotic stress tolerance breeding programs present a spectrum of perspectives, yet definitive solutions remain elusive, with each approach carrying its own set of advantages and disadvantages. This study systematically evaluates extant methodologies, comparing plant performance across varied genotypes and selection traits under optimal and stress conditions. The objective is to elucidate prevailing ambiguities. Ten homozygous lines (F8 generation) were assessed using a randomized block design alongside five control varieties, with four replicates cultivated under well-watered and deficit water conditions. It is noteworthy that six of the ten homozygous lines were cultivated exclusively under well-watered conditions (F3 to F7), while four lines experienced deficit water conditions (F3 to F7). All five control varieties underwent cultivation under both conditions. These findings underscore the necessity for tailored breeding programs attuned to specific environmental exigencies, recognizing that individual traits manifest divergent responses to varying conditions. It is evident that certain traits exhibit marked disparities under well-watered conditions, while others evince heightened differentiation under water deficit conditions. Significantly, our analysis reveals a pronounced interaction between irrigation regimes and selection traits, which serves to underscore the nuanced interplay between genotype and environmental stress. creator: Hatice Kübra Gören creator: Uğur Tan uri: https://doi.org/10.7717/peerj.17584 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gören and Tan title: Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max link: https://peerj.com/articles/17590 last-modified: 2024-06-24 description: BackgroundGlutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide.MethodsIn this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions.ResultsWe identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding. creator: Hind Abdelmonim Elsanosi creator: Tiantian Zhu creator: Guisheng Zhou creator: Li Song uri: https://doi.org/10.7717/peerj.17590 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Elsanosi et al. title: Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.) link: https://peerj.com/articles/17601 last-modified: 2024-06-24 description: BackgroundTungsten (W) is an emerging heavy metal pollutant, yet research remains scarce on the biomonitor and sensitive biomarkers for W contamination.MethodsIn this study, celery and pepper were chosen as study subjects and subjected to exposure cultivation in solutions with five different levels of W. The physiological and biochemical toxicities of W on these two plants were systematically analyzed. The feasibility of utilizing celery and pepper as biomonitor organisms for W contamination was explored and indicative biomarkers were screened.ResultsThe results indicated that W could inhibit plants’ root length, shoot height, and fresh weight while concurrently promoting membrane lipid peroxidation. Additionally, W enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and total antioxidant capacity (TAOC) to counteract oxidative damage. From a physiological perspective, pepper exhibited potential as a biomonitor for W contamination. Biochemical indicators suggested that SOD could serve as a sensitive biomarker for W in celery, while TAOC and POD were more suitable for the roots and leaves of pepper. In conclusion, our study investigated the toxic effects of W on celery and pepper, contributing to the understanding of W’s environmental toxicity. Furthermore, it provided insights for selecting biomonitor organisms and sensitive biomarkers for W contamination. creator: Qi Li creator: Xiaojun Zheng creator: Ming Chen uri: https://doi.org/10.7717/peerj.17601 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: The emerging roles of circHECTD1 in human diseases and the specific underlying regulatory mechanisms link: https://peerj.com/articles/17612 last-modified: 2024-06-24 description: Circular RNAs (circRNAs) are a class of single-stranded closed-loop RNAs that have become a popular research subject in biology. Compared to linear RNAs, they are more stable, more conserved, and more widely distributed, and they play crucial biological functions in many diseases. CircHECTD1, a newly identified member of the circRNA family, is widely distributed in humans. Recent studies have shown that circHECTD1 is abnormally expressed in various human diseases, including glioma, hepatocellular carcinoma, gastric cancer, acute ischaemic stroke, silicosis, acute lung injury, ulcerative colitis, atherosclerosis, and hypertrophic scarring. In malignant tumours, circHECTD1 is thought to be an oncogene that promotes malignant tumour behaviours and influences tumour prognosis. In nontumour diseases, it plays a dual role, promoting disease in silicosis, stroke, and other diseases, while alleviating the disease process in ulcerative colitis, acute lung injury, and atherosclerosis. This article provides a review of the regulatory roles and mechanisms of action of circHECTD1 in different diseases. We also discuss and prospectively evaluate the clinical potential of circHECTD1 as a diagnostic biomarker and a therapeutic target for related diseases, providing new insights for developing new therapeutic strategies. creator: Yiran Yuan creator: Xiaomin Zhang creator: Xiaoxiao Wang creator: Lei Zhang creator: Jiefeng He uri: https://doi.org/10.7717/peerj.17612 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Yuan et al. title: Evaluation of alanine aminotransferase/aspartate aminotransferase ratio and high-density lipoprotein for predicting neonatal adverse outcomes associated with intrahepatic cholestasis of pregnancy link: https://peerj.com/articles/17613 last-modified: 2024-06-24 description: BackgroundTo determine the association between lipid metabolism and intrahepatic cholestasis of pregnancy (ICP), and explore the value of maternal alanine aminotransferase/aspartate aminotransferase (ALT/AST) and high-density lipoprotein (HDL) in predicting adverse neonatal outcomes in women with ICP.MethodsA total of 147 pregnant women with ICP admitted to The Fourth Hospital of Shijiazhuang and 120 normal pregnant women in the same period were selected in this study. The Mann-Whitney U test and Chi-square tests were used to compare the differences in clinical data. Multivariate logistic regression was used to analyze the relationship between ALT/AST and the occurrence of adverse pregnancy outcomes in patients with ICP. The combined predictive value of ALT/AST and HDL was determined by receiver operating characteristic (ROC) curve analysis.ResultsAmong 147 women with ICP, 122 women had total bile acid (TBA) levels of 10–39.9 µmol/L, and 25 had TBA ≥ 40 µmol/L. There was significantly lower gestational age in patients with severe ICP than in those with mild and control groups (all p < 0.05), and the weight of newborns in the maternal ICP group was significantly lower than in the control group (p < 0.05). Increasing TBA levels was associated with higher AST, ALT, ALT/AST, and lower HDL level (all p < 0.05). Meanwhile, higher levels of ALT/AST was positively associated with neonatal hyperbilirubinemia [adjusted odds ratio (AOR) = 4.019, 95% CI [1.757–9.194, p = 0.001] and cardiac injury [AOR = 3.500, 95% CI [1.535–7.987], p = 0.003]. HDL was a significant protective factor for neonatal hyperbilirubinemia and cardiac injury [AOR = 0.315, 95% CI [0.126–0.788], p = 0.014; AOR = 0.134 (0.039–0.461), p = 0.001]. The area under the ROC curve (AUC) for prediction of neonatal hyperbilirubinemia by ALT/AST combined with HDL was 0.668 [95% CI [56.3–77.3%], p = 0.002], and the sensitivity and specificity were 47.1% and 84.0%, respectively. To predict neonatal cardiac injury, the AUC value was 0.668 [95% CI [56.4–77.1%], p = 0.002], with sensitivity and specificity were 41.2% and 87.1%, respectively.ConclusionsThe levels of higher ALT/AST and lower HDL were significantly associated with the risk of ICP-related adverse neonatal outcomes. Moreover, ALT/AST combined with HDL has moderate clinical value in predicting the adverse outcomes of neonatal hyperbilirubinemia and cardiac injury. creator: Xizhenzi Fan creator: Xia Li creator: Tianxiao Yu creator: Ruifen Jiao creator: Wenhui Song creator: Achou Su creator: Mingwei Li creator: Qing Guo uri: https://doi.org/10.7717/peerj.17613 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Fan et al. title: Prognostic and therapeutic insights into colorectal carcinoma through immunogenic cell death gene profiling link: https://peerj.com/articles/17629 last-modified: 2024-06-24 description: While the significance of immunogenic cell death (ICD) in oncology is acknowledged, its specific impact on colorectal carcinoma remains underexplored. In this study, we delved into the role of ICD in colorectal carcinoma, a topic not yet comprehensively explored. A novel ICD quantification system was developed to forecast patient outcomes and the effectiveness of immunotherapy. Utilizing single-cell sequencing, we constructed an ICD score within the tumor immune microenvironment (TIME) and examined immunogenic cell death related genes (ICDRGs). Using data from TCGA and GEO, we discovered two separate molecular subcategories within 1,184 patients diagnosed with colon adenocarcinoma/rectum adenocarcinoma (COADREAD). The ICD score was established by principal component analysis (PCA), which classified patients into groups with low and high ICD scores. Further validation in three independent cohorts confirmed the model’s accuracy in predicting immunotherapy success. Patients with higher ICD scores exhibited a “hot” immune phenotype and showed increased responsiveness to immunotherapy. Key genes in the model, such as AKAP12, CALB2, CYR61, and MEIS2, were found to enhance COADREAD cell proliferation, invasion, and PD-L1 expression. These insights offered a new avenue for anti-tumor strategies by targeting ICD, marking advances in colorectal carcinoma treatment. creator: Jinglu Yu creator: Yabin Gong creator: Zhenye Xu creator: Lei Chen creator: Shuang Li creator: Yongkang Cui uri: https://doi.org/10.7717/peerj.17629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yu et al. title: Towards the development of cost-effective point-of-care diagnostic tools for poverty-related infectious diseases in sub-Saharan Africa link: https://peerj.com/articles/17198 last-modified: 2024-06-21 description: In this review, we examine the current landscape of point-of-care testing (POCT) diagnostic tools designed for poverty-related infectious diseases (PRIDs) in sub-Saharan Africa (sSA) while delineating key avenues for future advancements. Our analysis encompasses both established and emerging diagnostic methods for PRIDs, addressing the persistent challenges in POCT tool development and deployment, such as cost, accessibility, and reliability. We emphasize recent advancements in POCT diagnostic tools as well as platforms poised to enhance diagnostic testing in sSA. Recognizing the urgency for affordable and widely accessible POCT diagnostic tools to detect PRIDs in sSA, we advocate for a multidisciplinary approach. This approach integrates current and emerging diagnostic methods, explicitly addressing challenges hindering point-of-care (POC) tool development. Furthermore, it recognizes the profound impact of misdiagnosis on public and global health, emphasizing the need for effective tools. To facilitate the successful development and implementation of POCT diagnostic tools in sSA, we propose strategies including the creation of multi-analyte detection POCT tools, the implementation of education and training programs, community engagement initiatives, fostering public-private collaborations, and the establishment of reliable supply chains. Through these concerted efforts, we aim to accelerate the development of POCT in the sSA region, ensuring its effectiveness and accessibility in addressing the diagnostic challenges associated with PRIDs. creator: Benedict Ofori creator: Seth Twum creator: Silas Nkansah Yeboah creator: Felix Ansah creator: Kwabena Amofa Nketia Sarpong uri: https://doi.org/10.7717/peerj.17198 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ofori et al. title: Path for recovery: an ecological overview of the Jambato Harlequin Toad (Bufonidae: Atelopus ignescens) in its last known locality, Angamarca Valley, Ecuador link: https://peerj.com/articles/17344 last-modified: 2024-06-21 description: The Jambato Harlequin toad (Atelopus ignescens), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in 1988. The species was considered Extinct by the IUCN until 2016, when a fortuitous discovery of one Jambato by a local boy reignited hope. In this study, we present findings from an investigation conducted in the Angamarca parish, focusing on distribution, abundance, habitat preferences, ecology, disease susceptibility, and dietary habits of the species. In one year we identified 71 individuals at different stages of development in various habitats, with a significant presence in agricultural mosaic areas and locations near water sources used for crop irrigation, demonstrating the persistence of the species in a complex landscape, with considerable human intervention. The dietary analysis based on fecal samples indicated a diverse prey selection, primarily comprising arthropods such as Acari, Coleoptera, and ants. Amphibian declines have been associated with diseases and climate change; notably, our study confirmed the presence of the pathogen Batrachochytrium dendrobatidis (Bd), but, surprisingly, none of the infected Jambatos displayed visible signs of illness. When analyzing climatic patterns, we found that there are climatic differences between historical localities and Angamarca; the temporal analysis also exposes a generalized warming trend. Finally, in collaboration with the local community, we developed a series of management recommendations for terrestrial and aquatic environments occupied by the Jambato. creator: Mateo A. Vega-Yánez creator: Amanda B. Quezada-Riera creator: Blanca Rios-Touma creator: María del Carmen Vizcaíno-Barba creator: William Millingalli creator: Orlando Ganzino creator: Luis A. Coloma creator: Elicio E. Tapia creator: Nadine Dupérré creator: Mónica Páez-Vacas creator: David Parra-Puente creator: Daniela Franco-Mena creator: Gabriela Gavilanes creator: David Salazar-Valenzuela creator: Carlos A. Valle creator: Juan M. Guayasamin uri: https://doi.org/10.7717/peerj.17344 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vega-Yánez et al. title: Taxon-dependent diversity response along a temperate elevation gradient covered by grassland link: https://peerj.com/articles/17375 last-modified: 2024-06-21 description: Elevational gradients constitute excellent systems for understanding the mechanisms that generate and maintain global biodiversity patterns. Climatic gradients associated with elevation show strong influence on species distribution in mountains. The study of mountains covered by the same habitat type is an ideal scenario to compare alternatives to the energy hypotheses. Our aim was to investigate how changes in climatic conditions along the elevational gradient drive α- and β-diversity of four taxa in a mountain system located within a grassland biome. We sampled ants, spiders, birds and plants, and measured climatic variables at six elevational bands (with 10 sampling sites each) established between 470 and 1,000 masl on a mountain from the Ventania Mountain System, Argentina. Species richness per site and β-diversity (turnover and nestedness) between the lowest band and upper sites were estimated. For most taxa, species richness declined at high elevations and energy, through temperature, was the major driver of species richness for ants, plants and birds, prevailing over productivity and water availability. The major β-diversity component was turnover for plants, spiders and birds, and nestedness for ants. The unique environmental conditions of the upper bands could favour the occurrence of specialist and endemic species. creator: Santiago Santoandré creator: Carolina Samanta Ramos creator: Pablo Picca creator: Julieta Filloy uri: https://doi.org/10.7717/peerj.17375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Santoandré et al. title: Interlimb and trunk asymmetry in the frontal plane of table tennis female players link: https://peerj.com/articles/17526 last-modified: 2024-06-21 description: BackgroundAn interesting and little-reported problem in the literature is the scale of asymmetry in table tennis players, the magnitude of which should perhaps be treated as a risk for injury. Determining the degree of asymmetry in table tennis players can indicate the need to appropriately manage the training process, including compensatory or corrective exercises in the training program, especially since recent studies confirm that training interventions can reduce sporting asymmetries and improve performance. This study aimed to assess the amount of asymmetry in the trunk regarding the frontal plane and the difference between limb circumferences in female table tennis players compared to the control group (non-athletes).MethodsTwenty-two women took part in the study. Ten of them were table tennis professionals with an average training experience of 7 ± 4.3 years (the exclusion criterion of the study was a minimum of 3 years of training experience). As a comparison group, the study included 12 female students who did not participate in competitive sports. Body posture was assessed in all subjects using equipment for computer analysis of asymmetry in the torso using the photogrammetric method. Additionally, all the subjects had their upper and lower limb circumferences measured.ResultsThe results of the conducted research showed asymmetry in the frontal plane in the table tennis player group. As many as six parameters—regarding the pelvic rotation angle, angle of trunk inclination, the height of the angles of the lower shoulder blades and their distance from the spine, as well as the waist triangles, difference in the width and height of the waist triangles and the angle of trunk inclination—indicated asymmetry in this group but significantly differed from the control group (p ≤ 0.05) only in the first parameter given above. The calculated differences in circumference between the right and left sides in the individual groups were statistically different in several cases (p ≤ 0.05). This concerned the circumferences of the arms, forearms, elbows, and knees of table tennis players.ConclusionsThe research carried out in this study allowed us to determine the occurrence of asymmetry in the frontal plane of the trunk and between the limbs of table tennis players. According to some studies, this may be a risk factor for injury. However, despite the lack of uniform views in the literature on the importance and threats resulting from asymmetries, it appears that, if only for aesthetic reasons, table tennis would require compensatory or corrective training aimed at developing symmetry of the body structure. creator: Ziemowit Bańkosz creator: Arletta Hawrylak creator: Małgorzata Kołodziej creator: Lenka Murinova creator: Katarzyna Barczyk-Pawelec uri: https://doi.org/10.7717/peerj.17526 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bańkosz et al. title: Decrease in the usual walking speed and body fat percentage associated with a deterioration in long-term care insurance certification levels link: https://peerj.com/articles/17529 last-modified: 2024-06-21 description: BackgroundIn Japan, the number of older adults requiring long-term care insurance (LTCI) is increasing and the cost is becoming a social problem. In these fields, the role of geriatric rehabilitation includes maintaining the physical function and LTCI certification levels. The prevalence of sarcopenia is high among older adults requiring LTCI certification, and there are many opportunities to assess the handgrip strength, walking speed, and muscle mass. This study aimed to identify sarcopenia-related assessments sensitive to transitions in LTCI certification levels and determine cut-off values to predict them.MethodsThis prospective cohort study analyzed 98 daycare users (mean age ± standard error: 78.5 ± 0.8 years) between March 2019 and 2023. The participants received LTCI certification before the study, and their levels were renewed between baseline and follow-up (six months later). The measurements included handgrip strength, usual walking speed, body composition, and SARC-F score. Participants were classified into maintenance, deterioration, and improvement groups according to the changes in their LTCI certification levels. We identified factors contributing to the deterioration of LTCI certification levels using baseline and before and after comparisons, multivariate analyses, and receiver operating characteristic analyses.ResultsNo significant differences were observed in the baseline data among the groups. Only the deterioration group showed significant changes in the usual walking speed (baseline: 0.64 ± 0.25 m/s, follow-up: 0.53 ± 0.21 m/s, P = 0.008) and body fat percentage (baseline: 29.2 ± 9.9%, follow-up: 27.7 ± 10.3%, P = 0.047). Binomial logistic regression showed that changes in usual walking speed (P = 0.042) and body fat percentage (P = 0.011) were significantly associated with the deterioration of LTCI certification levels, even after adjustment. The cutoff values of change to discriminate the deterioration of LTCI certification levels were −0.14 m/s at the usual walking speed (P = 0.047) and −1.0% for body fat percentage (P = 0.029).ConclusionsDecreases in usual walking speed and body fat percentage may predict worse certification levels in older adults requiring LTCI. creator: Yohei Sawaya creator: Tamaki Hirose creator: Takahiro Shiba creator: Ryo Sato creator: Lu Yin creator: Akira Kubo creator: Tomohiko Urano uri: https://doi.org/10.7717/peerj.17529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sawaya et al. title: Construction of a nomogram for predicting catheter-related bladder discomfort in patients with end-stage renal disease after renal transplantation: a retrospective study link: https://peerj.com/articles/17530 last-modified: 2024-06-21 description: BackgroundThe incidence of catheter-related bladder discomfort (CRBD) is relatively high in the end-stage renal disease (ESRD) patients who underwent renal transplantation (RT). This study was designed to establish a nomogram for predicting CRBD after RT among ESRD patients.MethodsIn this retrospective study, we collected 269 ESRD patients who underwent RT between September 2019 and August 2023 in our hospital. The patients were divided into training set (n = 215) and test set (n = 54) based on a ratio of 8:2. Univariate and multivariate logistic regression analyses were utilized to identify the risk factors associated with CRBD after RT, and then a nomogram model was constructed. Receiver operating characteristic (ROC) and calibration curve were used to evaluate the predicting efficiency of the established nomogram.ResultsMultivariate logistic regression analysis showed that aberrant body mass index (BMI) (underweight: OR = 5.25; 95% CI [1.25–22.15], P = 0.024; overweight: OR = 2.75; 95% CI [1.17–6.49], P = 0.021), anuria (OR = 2.86; 95% CI [1.33–5.88]) and application of double J (DJ) stent with a diameter of >5Fr (OR = 15.88; 95% CI [6.47–39.01], P < 0.001) were independent risk factors for CRBD after RT. In contrast, sufentanil utilization (>100 µg) [OR = 0.39; 95% CI [0.17–0.88], P = 0.023] was associated with decreased incidence of CRBD. A nomogram was then established based on these parameters for predicting the occurrence of CRBD after RT. Area under the ROC curve (AUC) values and calibration curves confirmed the prediction efficiency of the nomogram.ConclusionA nomogram was established for predicting CRBD after RT in ESRD patients, which showed good prediction efficiency based on AUC and calibration curves. creator: Kao Liu creator: Shengli Liu creator: Zhiguo Peng creator: Na Li creator: Huaibin Sun uri: https://doi.org/10.7717/peerj.17530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: The relationship between low energy availability, injuries, and bone health in recreational female athletes link: https://peerj.com/articles/17533 last-modified: 2024-06-21 description: BackgroundLow energy availability (LEA) causes pathophysiology of the female athlete’s body affecting the bone and reproductive health and was observed to have a high prevalence in recreational female athletes previously. The aim of this study was to analyse the relationship between low energy availability in females questionnaire (LEAF-Q), bone mineral density (BMD), and postural stability in recreational athletes.MethodsRecreational female athletes (n = 24, age: 23.71 ± 2.94, Tier I) completed LEAF-Q, postural stability measurement during quiet stance (Zebris platform FDM; GmbH) and their BMD was measured using DXA (Hologic QDR Horizon A). Non-parametric statistical tests were used to analyse the relationships between LEAF-Q, BMD, and postural stability and to compare differences between participants divided by the LEAF-Q score and its subscales.ResultsRisk of LEA was observed in 50% of recreational athletes participating in this study. Up to 46% of participants perceived menstrual bleeding changes related to training and 37.50% experienced menstrual dysfunction. Body composition and body weight fluctuations were observed to affect postural stability and BMD. With the risk score for LEA, the BMD and postural stability were not negatively affected in recreational athletes. However, the high number of recreational athletes in the risk score for LEA and menstrual dysfunctions highlights the need for public health programs aimed to increase awareness of LEA and its health consequences and for open communication about the menstrual cycle. Future longitudinal studies observing LEA, BMD, menstrual function, postural stability, and their interrelationship in female athletes are needed to increase the knowledge of this topic. creator: Marta Gimunová creator: Michal Bozděch creator: Martina Bernaciková creator: Romulo Fernandes creator: Michal Kumstát creator: Ana Paludo uri: https://doi.org/10.7717/peerj.17533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Gimunová et al. title: Efficacy and safety of Brolucizumab for neovascular age-related macular degeneration: a systematic review and meta-analysis link: https://peerj.com/articles/17561 last-modified: 2024-06-21 description: BackgroundTo evaluate the efficacy and safety of Brolucizumab for neovascular age-related macular degeneration (n-AMD) through a systematic review and meta-analysis.Materials and MethodsCochrane, PubMed, Embase, and Web of Science databases were comprehensively searched for relevant studies. Stata and RevMan5.4 were applied for meta-analysis and risk of bias assessment. Data on the best-corrected visual acuity (BCVA), central subfield thickness (CSFT), presence of intraretinal fluid (IRF) and/or subretinal fluid (SRF), participants with ≥1 serious adverse events, and participants with ≥1 adverse events were analyzed.ResultsSix studies were finally included. Meta-analysis showed statistical differences in BCVA [SMD = −0.65, 95% CI [−0.17 to −0.23], P < 0.05], the presence of IRF and/or SRF [RR = 0.67, 95% CI [0.56–0.79], P < 0.05], and the safety of participants with ≥1 serious adverse events [RR = 0.57, 95% CI [0.39–0.84], P < 0.05] between the experimental group and the control group. However, no statistical differences were observed in CSFT [SMD = −1.16, 95% CI [−2.79 to 0.47], P > 0.05] or the safety of participants with ≥1 adverse events [RR = 1.07, 95% CI [0.97–1.17], P > 0.05].ConclusionsCompared to other anti-VEGF drugs such as Aflibercept and Ranibizumab, intravitreal injection of 6 mg Brolucizumab is more effective and safer for n-AMD, especially in the presence of IRF and/or SRF, and for participants with ≥1 serious adverse events. creator: Ran Dou creator: Jian Jiang uri: https://doi.org/10.7717/peerj.17561 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dou and Jiang title: Retrospective study of a novel hematological parameter for predicting the survival of patients with nasopharyngeal carcinoma link: https://peerj.com/articles/17573 last-modified: 2024-06-21 description: PurposeThis study aims to explore the prognostic values of routine pre-treatment hematological parameters in patients with nasopharyngeal carcinoma (NPC).MethodsThe hematological parameters and clinical data of patients with NPC were collected from January 2012 to December 2013 at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology. The survival statistics were obtained by regularly following-up the patients. The cut-off values for the hematological parameters were calculated using X-tile software. SPSS version 24.0 was used for the statistical analysis. The relationship between the hematological parameters and the prognosis of patients with NPC was analyzed using the Kaplan–Meier method and Cox multivariate regression. The discriminating abilities of the factors, which predict the prognosis, were evaluated by utilizing the receiver operating characteristic (ROC) area under the curve (AUC).ResultsThis study included 179 patients with NPC. Multivariate analysis shows that pretreatment platelet-to-lymphocyte ratio (PLR; hazard ratio; HR = 0.44, 95% CI [0.21–0.91], p = 0.029), serum albumin (ALB; HR = 2.49, 95% CI [1.17–5.30], p = 0.018), and globulin (GLO; HR = 0.44, 95% CI [0.21–0.90], p = 0.024) are independent predictors for 5-year overall survival (OS) in patients with NPC. In addition, pre-treatment PLR (HR = 0.47, 95% CI [0.25–0.90], p = 0.022) and pre-treatment GLO (HR = 0.37, 95% CI [0.19–0.72], p = 0.001) are associated with 5-year progression-free survival (PFS) in patients with NPC. Based on the results of the multivariate analysis, we proposed a new biomarker GLO-PLR, which is observably correlated with the T stage, N stage and clinical stage in patients with NPC. The OS resolving ability of the GLO-PLR evaluated by AUC is 0.714, which is better than those of GLO and PLR. The PFS resolving ability of the GLO-PLR evaluated by AUC was 0.696, which is also better than those of GLO and PLR.ConclusionPre-treatment PLR, ALB, and GLO are independent predictors of 5-year OS in patients with NPC, where PLR and GLO are also independent predictors of 5-year FPS. Compared with other hematological parameters, the proposed GLO-PLR is an inexpensive, effective, objective, and easy-to-measure marker for predicting the prognosis of NPC. creator: Wenhua Tang creator: Guoxian Long uri: https://doi.org/10.7717/peerj.17573 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Tang and Long title: Lokiceratops rangiformis gen. et sp. nov. (Ceratopsidae: Centrosaurinae) from the Campanian Judith River Formation of Montana reveals rapid regional radiations and extreme endemism within centrosaurine dinosaurs link: https://peerj.com/articles/17224 last-modified: 2024-06-20 description: The Late Cretaceous of western North America supported diverse dinosaur assemblages, though understanding patterns of dinosaur diversity, evolution, and extinction has been historically limited by unequal geographic and temporal sampling. In particular, the existence and extent of faunal endemism along the eastern coastal plain of Laramidia continues to generate debate, and finer scale regional patterns remain elusive. Here, we report a new centrosaurine ceratopsid, Lokiceratops rangiformis, from the lower portion of the McClelland Ferry Member of the Judith River Formation in the Kennedy Coulee region along the Canada-USA border. Dinosaurs from the same small geographic region, and from nearby, stratigraphically equivalent horizons of the lower Oldman Formation in Canada, reveal unprecedented ceratopsid richness, with four sympatric centrosaurine taxa and one chasmosaurine taxon. Phylogenetic results show that Lokiceratops, together with Albertaceratops and Medusaceratops, was part of a clade restricted to a small portion of northern Laramidia approximately 78 million years ago. This group, Albertaceratopsini, was one of multiple centrosaurine clades to undergo geographically restricted radiations, with Nasutuceratopsini restricted to the south and Centrosaurini and Pachyrostra restricted to the north. High regional endemism in centrosaurs is associated with, and may have been driven by, high speciation rates and diversity, with competition between dinosaurs limiting their geographic range. High speciation rates may in turn have been driven in part by sexual selection or latitudinally uneven climatic and floral gradients. The high endemism seen in centrosaurines and other dinosaurs implies that dinosaur diversity is underestimated and contrasts with the large geographic ranges seen in most extant mammalian megafauna. creator: Mark A. Loewen creator: Joseph J. W. Sertich creator: Scott Sampson creator: Jingmai K. O’Connor creator: Savhannah Carpenter creator: Brock Sisson creator: Anna Øhlenschlæger creator: Andrew A. Farke creator: Peter J. Makovicky creator: Nick Longrich creator: David C. Evans uri: https://doi.org/10.7717/peerj.17224 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Loewen et al. title: Gypenosides exert cardioprotective effects by promoting mitophagy and activating PI3K/Akt/GSK-3β/Mcl-1 signaling link: https://peerj.com/articles/17538 last-modified: 2024-06-20 description: BackgroundGynostemma pentaphyllum (Thunb.) Makino, a well-known edible and medicinal plant, has anti-aging properties and is used to treataging-associated conditions such as diabetes, metabolic syndrome, and cardiovascular diseases. Gypenosides (GYPs) are the primary constituents of G. pentaphyllum. Increasing evidence indicates that GYPs are effective at preserving mitochondrial homeostasis and preventing heart failure (HF). This study aimed to uncover the cardioprotective mechanisms of GYPs related to mitochondrial regulation.MethodsThe bioactive components in GYPs and the potential targets in treating HF were obtained and screened using the network pharmacology approach, followed by drug-disease target prediction and enrichment analyses. The pharmacological effects of GYPs in cardioprotection, mitochondrial function, mitochondrial quality control, and underlying mechanisms were further investigated in Doxorubicin (Dox)-stimulated H9c2 cardiomyocytes.ResultsA total of 88 bioactive compounds of GYPs and their respective 71 drug-disease targets were identified. The hub targets covered MAPK, EGFR, PI3KCA, and Mcl-1. Enrichment analysis revealed that the pathways primarily contained PI3K/Akt, MAPK, and FoxO signalings, as well as calcium regulation, protein phosphorylation, apoptosis, and mitophagy process. In Dox-stimulated H9c2 rat cardiomyocytes, pretreatment with GYPs increased cell viability, enhanced cellular ATP content, restored basal oxygen consumption rate (OCR), and improved mitochondrial membrane potential (MMP). Furthermore, GYPs improved PINK1/parkin-mediated mitophagy without influencing mitochondrial fission/fusion proteins and the autophagic LC3 levels. Mechanistically, the phosphorylation of PI3K, Akt, GSK-3β, and the protein level of Mcl-1 was upregulated by GYP treatment.ConclusionOur findings reveal that GYPs exert cardioprotective effects by rescuing the defective mitophagy, and PI3K/Akt/GSK-3β/Mcl-1 signaling is potentially involved in this process. creator: Yizhe Zheng creator: Wei Wei creator: Yukun Wang creator: Tingting Li creator: Yundong Wei creator: Si Gao uri: https://doi.org/10.7717/peerj.17538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zheng et al. title: Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population link: https://peerj.com/articles/17549 last-modified: 2024-06-20 description: Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population’s genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction. creator: Adrianna Dominika Musiał creator: Lara Radović creator: Monika Stefaniuk-Szmukier creator: Agnieszka Bieniek creator: Barbara Wallner creator: Katarzyna Ropka-Molik uri: https://doi.org/10.7717/peerj.17549 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Musiał et al. title: Identifying the source rookery of green turtles (Chelonia mydas) found in feeding grounds around the Korean Peninsula link: https://peerj.com/articles/17560 last-modified: 2024-06-20 description: Determining the genetic diversity and source rookeries of sea turtles collected from feeding grounds can facilitate effective conservation initiatives. To ascertain the genetic composition and source rookery, we examined a partial sequence of the mitochondrial control region (CR, 796 bp) of 40 green turtles (Chelonia mydas) collected from feeding grounds around the Korean Peninsula between 2014 and 2022. We conducted genetic and mixed-stock analyses (MSA) and identified 10 CR haplotypes previously reported in Japanese populations. In the haplotype network, six, three, and one haplotype(s) grouped with the Japan, Indo-Pacific, and Central South Pacific clades, respectively. The primary rookeries of the green turtles were two distantly remote sites, Ogasawara (OGA) and Central Ryukyu Island (CRI), approximately 1,300 km apart from each other. Comparing three parameters (season, maturity, and specific feeding ground), we noted that OGA was mainly associated with summer and the Jeju Sea, whereas CRI was with fall and the East (Japan) Sea ground. The maturity did not show a distinct pattern. Our results indicate that green turtles in the feeding grounds around the Korean Peninsula originate mainly from the Japan MU and have genetic origins in the Japan, Indo-Pacific, and Central South Pacific clades. Our results provide crucial insights into rookeries and MUs, which are the focus of conservation efforts of the Republic of Korea and potential parties to collaborate for green turtle conservation. creator: Min-Woo Park creator: Il-Hun Kim creator: Jaejin Park creator: Changho Yi creator: Min-Seop Kim creator: In-Young Cho creator: Il-Kook Park creator: Hee-Jin Noh creator: Sang Hee Hong creator: Daesik Park uri: https://doi.org/10.7717/peerj.17560 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Park et al. title: VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19 link: https://peerj.com/articles/17504 last-modified: 2024-06-19 description: BackgroundThe development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low.MethodsHere, we developed a “variant on epitope (VOE)” software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE.ResultsA variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%.ConclusionsTherefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges. creator: Danusorn Lee creator: Unitsa Sangket uri: https://doi.org/10.7717/peerj.17504 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lee and Sangket title: A quantitative test of the “Ecomorphotype Hypothesis” for fossil true seals (Family Phocidae) link: https://peerj.com/articles/17592 last-modified: 2024-06-19 description: The fossil record of true seals (Family Phocidae) is mostly made up of isolated bones, some of which are type specimens. Previous studies have sought to increase referral of non-overlapping and unrelated fossils to these taxa using the ‘Ecomorphotype Hypothesis’, which stipulates that certain differences in morphology between taxa represent adaptations to differing ecology. On this basis, bulk fossil material could be lumped to a specific ecomorphotype, and then referred to species in that ecomorphotype, even if they are different bones. This qualitative and subjective method has been used often to expand the taxonomy of fossil phocids, but has never been quantitatively tested. We test the proposed ecomorphotypes using morphometric analysis of fossil and extant northern true seal limb bones, specifically principal components analysis and discriminant function analysis. A large amount of morphological overlap between ecomorphotypes, and poor discrimination between them, suggests that the ‘Ecomorphotype Hypothesis’ is not a valid approach. Further, the analysis failed to assign fossils to ecomorphotypes designated in previous studies, with some fossils from the same taxa being designated as different ecomorphotypes. The failure of this approach suggests that all fossils referred using this method should be considered to have unknown taxonomic status. In light of this, and previous findings that phocid limb bones have limited utility as type specimens, we revise the status of named fossil phocid species. We conclude that the majority of named fossil phocid taxa should be considered nomina dubia. creator: James Patrick Rule creator: Gustavo Burin creator: Travis Park uri: https://doi.org/10.7717/peerj.17592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Rule et al. title: The role of monocyte chemoattractant protein-1 (MCP-1) as an immunological marker for patients with leprosy: a systematic literature review link: https://peerj.com/articles/17400 last-modified: 2024-06-18 description: Leprosy, a significant global health concern affecting primarily the peripheral nerves and integumentary system, is influenced by the host immune system’s response, affecting its pathology, disease progression, and reaction occurrence. MCP-1, integral to leprosy’s immunological processes, holds promise as a diagnostic tool and predictor of reaction occurrence. This systematic review aimed to investigate MCP-1’s involvement in leprosy. Literature search, employing specified MeSH keywords, covered databases such as PubMed, Scopus, ScienceDirect, and Wiley Online Library until September 30th, 2023, yielding seventeen relevant studies. Assessing each study’s quality with the Newcastle-Ottawa Scale (NOS) and investigating bias using the Risk of Bias Assessment tool for Non-randomized Studies (RoBANS), a narrative synthesis compiled findings. Seventeen distinct studies were included, each characterized by diverse designs, sample sizes, demographics, and outcome measures, highlighting MCP-1’s potential in diagnosing leprosy, differentiating it from control groups, and discerning leprosy types. Furthermore, MCP-1 shows promise in predicting leprosy reversal reactions. Although MCP-1 offers clinical benefits, including early diagnosis and type differentiation, further research with larger sample sizes and standardized methodologies is imperative to confirm its diagnostic utility fully. creator: Flora Ramona Sigit Prakoeswa creator: Ellen Josephine Handoko creator: Erika Diana Risanti creator: Nabila Haningtyas creator: Nasrurrofiq Risvana Bayu Pambudi creator: Muhana Fawwazy Ilyas uri: https://doi.org/10.7717/peerj.17400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Prakoeswa et al. title: Bioinformatic analysis and experimental validation of six cuproptosis-associated genes as a prognostic signature of breast cancer link: https://peerj.com/articles/17419 last-modified: 2024-06-18 description: BackgroundBreast carcinoma (BRCA) is a life-threatening malignancy in women and shows a poor prognosis. Cuproptosis is a novel mode of cell death but its relationship with BRCA is unclear. This study attempted to develop a cuproptosis-relevant prognostic gene signature for BRCA.MethodsCuproptosis-relevant subtypes of BRCA were obtained by consensus clustering. Differential expression analysis was implemented using the ‘limma’ package. Univariate Cox and multivariate Cox analyses were performed to determine a cuproptosis-relevant prognostic gene signature. The signature was constructed and validated in distinct datasets. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were also conducted using the prognostic signature to uncover the underlying molecular mechanisms. ESTIMATE and CIBERSORT algorithms were applied to probe the linkage between the gene signature and tumor microenvironment (TME). Immunotherapy responsiveness was assessed using the Tumor Immune Dysfunction and Exclusion (TIDE) web tool. Real-time quantitative PCR (RT-qPCR) was performed to detect the expressions of cuproptosis-relevant prognostic genes in breast cancer cell lines.ResultsThirty-eight cuproptosis-associated differentially expressed genes (DEGs) in BRCA were mined by consensus clustering and differential expression analysis. Based on univariate Cox and multivariate Cox analyses, six cuproptosis-relevant prognostic genes, namely SAA1, KRT17, VAV3, IGHG1, TFF1, and CLEC3A, were mined to establish a corresponding signature. The signature was validated using external validation sets. GSVA and GSEA showed that multiple cell cycle-linked and immune-related pathways along with biological processes were associated with the signature. The results ESTIMATE and CIBERSORT analyses revealed significantly different TMEs between the two Cusig score subgroups. Finally, RT-qPCR analysis of cell lines further confirmed the expressional trends of SAA1, KRT17, IGHG1, and CLEC3A.ConclusionTaken together, we constructed a signature for projecting the overall survival of BRCA patients and our findings authenticated the cuproptosis-relevant prognostic genes, which are expected to provide a basis for developing prognostic molecular biomarkers and an in-depth understanding of the relationship between cuproptosis and BRCA. creator: Xiang Chen creator: Hening Sun creator: Changcheng Yang creator: Wei Wang creator: Wenzhi Lyu creator: Kejian Zou creator: Fan Zhang creator: Zhijun Dai creator: Xionghui He creator: Huaying Dong uri: https://doi.org/10.7717/peerj.17419 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Chen et al. title: Serum proteomics study on cognitive impairment after cardiac valve replacement surgery: a prospective observational study link: https://peerj.com/articles/17536 last-modified: 2024-06-18 description: ObjectiveThe incidence of perioperative neurocognitive disorders (PND) is high, especially after cardiac surgeries, and the underlying mechanisms remain elusive. Here, we conducted a prospective observational study to observe serum proteomics differences in PND patients after cardiac valve replacement surgery.MethodsTwo hundred and twenty-six patients who underwent cardiac valve surgery were included. They were categorized based on scoring into non-PND group (group non-P) and PND group (group P’). The risk factors associated with PND were analyzed. These patients were further divided into group C and group P by propensity score matching (PSM) to investigate the serum proteome related to the PND by serum proteomics.ResultsThe postoperative 6-week incidence of PND was 16.8%. Risk factors for PND include age, chronic illness, sufentanil dosage, and time of cardiopulmonary bypass (CPB). Proteomics identified 31 down-regulated proteins and six up-regulated proteins. Finally, GSTO1, IDH1, CAT, and PFN1 were found to be associated with PND.ConclusionThe occurrence of PND can impact some oxidative stress proteins. This study provided data for future studies about PND to general anaesthesia and surgeries. creator: Huanhuan Ma creator: Yiyong Wei creator: Wei Chen creator: Song Chen creator: Yan Wang creator: Song Cao creator: Haiying Wang uri: https://doi.org/10.7717/peerj.17536 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ma et al. title: Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato link: https://peerj.com/articles/17537 last-modified: 2024-06-18 description: The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants. creator: Hui Li creator: Tingrui Zou creator: Shuisen Chen creator: Ming Zhong uri: https://doi.org/10.7717/peerj.17537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Li et al. title: Identification of key genes as potential diagnostic biomarkers in sepsis by bioinformatics analysis link: https://peerj.com/articles/17542 last-modified: 2024-06-18 description: BackgroundSepsis, an infection-triggered inflammatory syndrome, poses a global clinical challenge with limited therapeutic options. Our study is designed to identify potential diagnostic biomarkers of sepsis onset in critically ill patients by bioinformatics analysis.MethodsGene expression profiles of GSE28750 and GSE74224 were obtained from the Gene Expression Omnibus (GEO) database. These datasets were merged, normalized and de-batched. Weighted gene co-expression network analysis (WGCNA) was performed and the gene modules most associated with sepsis were identified as key modules. Functional enrichment analysis of the key module genes was then conducted. Moreover, differentially expressed gene (DEG) analysis was conducted by the “limma” R package. Protein-protein interaction (PPI) network was created using STRING and Cytoscape, and PPI hub genes were identified with the cytoHubba plugin. The PPI hub genes overlapping with the genes in key modules of WGCNA were determined to be the sepsis-related key genes. Subsequently, the key overlapping genes were validated in an external independent dataset and sepsis patients recruited in our hospital. In addition, CIBERSORT analysis evaluated immune cell infiltration and its correlation with key genes.ResultsBy WGCNA, the greenyellow module showed the highest positive correlation with sepsis (0.7, p = 2e − 19). 293 DEGs were identified in the merged datasets. The PPI network was created, and the CytoHubba was used to calculate the top 20 genes based on four algorithms (Degree, EPC, MCC, and MNC). Ultimately, LTF, LCN2, ELANE, MPO and CEACAM8 were identified as key overlapping genes as they appeared in the PPI hub genes and the key module genes of WGCNA. These sepsis-related key genes were validated in an independent external dataset (GSE131761) and sepsis patients recruited in our hospital. Additionally, the immune infiltration profiles differed significantly between sepsis and non-sepsis critical illness groups. Correlations between immune cells and these five key genes were assessed, revealing that plasma cells, macrophages M0, monocytes, T cells regulatory, eosinophils and NK cells resting were simultaneously and significantly associated with more than two key genes.ConclusionThis study suggests a critical role of LTF, LCN2, ELANE, MPO and CEACAM8 in sepsis and may provide potential diagnostic biomarkers and therapeutic targets for the treatment of sepsis. creator: Guoxin Lin creator: Nannan Li creator: Jishi Liu creator: Jian Sun creator: Hao Zhang creator: Ming Gui creator: Youjie Zeng creator: Juan Tang uri: https://doi.org/10.7717/peerj.17542 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Lin et al. title: Behavioral responses of a clonal fish to perceived predation risk link: https://peerj.com/articles/17547 last-modified: 2024-06-18 description: Predation threat is a major driver of behavior in many prey species. Animals can recognize their relative risk of predation based on cues in the environment, including visual and/or chemical cues released by a predator or from its prey. When threat of predation is high, prey often respond by altering their behavior to reduce their probability of detection and/or capture. Here, we test how a clonal fish, the Amazon molly (Poecilia formosa), behaviorally responds to predation cues. We measured aggressive and social behaviors both under ‘risk’, where chemical cues from predatory fish and injured conspecifics were present, and control contexts (no risk cues present). We predicted that mollies would exhibit reduced aggression towards a simulated intruder and increased sociability under risk contexts as aggression might increase their visibility to a predator and shoaling should decrease their chance of capture through the dilution effect. As predicted, we found that Amazon mollies spent more time with a conspecific when risk cues were present, however they did not reduce their aggression. This highlights the general result of the ‘safety in numbers’ behavioral response that many small shoaling species exhibit, including these clonal fish, which suggests that mollies may view this response as a more effective anti-predator response compared to limiting their detectability by reducing aggressive conspecific interactions. creator: Jonathan Aguiñaga creator: Sophia Jin creator: Ishita Pesati creator: Kate L. Laskowski uri: https://doi.org/10.7717/peerj.17547 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Aguiñaga et al. title: Knowledge, attitudes, and practices (KAPs) regarding tick-borne rickettsial disease among medical staff in endemic areas of China link: https://peerj.com/articles/17562 last-modified: 2024-06-18 description: Tick-borne rickettsial disease (TBRD) is a perilous acute infection that often eludes diagnosis in its early stages. The triad of knowledge, attitudes, and practices (KAPs) among medical professionals is key to reducing missed diagnosis rates. Therefore, a meticulous evaluation of KAPs is imperative. This study aimed to delve into the understanding of TBRD and explore the beliefs and practices related to personal prevention methods among individuals in Lu’an, a hotspot for TBRD. During the summer months of 2023, convenience sampling was employed by circulating a confidential questionnaire to 1,206 participants in the endemic regions of China. This questionnaire painted a comprehensive picture of the participants’ sociodemographic profiles and their KAPs levels vis-à-vis TBRD. The findings revealed that participants scored a mere 55.78% in knowledge, while their attitudes and practices garnered impressive scores of 90.09% and 90.83%, respectively. Upon further analysis using multiple linear regression, several intriguing patterns emerged. Male participants, employed in the Infectious Disease Department, held vice-senior or higher titles, or had prior medical training demonstrated superior knowledge scores. On the other hand, medical personnel who were younger than 30, possessed graduate degrees or higher qualifications, and had training excelled in attitudes and practices. Notably, when employing the Boston Consulting Group (BCG) matrix, a significant distribution of medical personnel was observed across the four quadrants. Specifically, 37.43%, 13.19%, 19.61%, and 29.77% fell into the first, second, third, and fourth quadrants. This survey underscores the commendable attitudes and practices of medical staff towards TBRD in endemic regions of China. However, their knowledge level remains wanting and demands urgent improvement. creator: Miaohui Shao creator: Peiyuan Hu creator: Pengpeng Xu creator: Jie Sun creator: Xiaqing Zhang creator: Dan Zhang creator: Yong Shen creator: Dawei Gao creator: Weigang Zhang creator: Wei Qin creator: Yong Lyu uri: https://doi.org/10.7717/peerj.17562 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shao et al. title: Hypertrophic effects of low-load blood flow restriction training with different repetition schemes: a systematic review and meta-analysis link: https://peerj.com/articles/17195 last-modified: 2024-06-17 description: ObjectiveThis systematic review and meta-analysis analyzed the effect of low-load resistance training (LL-RT) with blood flow restriction (BFR) versus high-load resistance training (HL-RT) on muscle hypertrophy focusing on the repetition scheme adopted.MethodsFour databases were searched to identify randomized controlled trials that compared the effect of LL-RT with BFR versus HL-RT on muscle hypertrophy. Standardized mean differences (SMD) were pooled in a random effects meta-analysis.ResultsThe overall analysis did not demonstrate significant differences between conditions (SMD = 0.046; p = 0.14). A similar result was observed when we separately analyzed studies that used sets to momentary muscle failure (SMD = 0.033; p = 0.520), sets of 15 repetitions (SMD = 0.005; p = 0.937) and a fixed repetition scheme composed of 75 repetitions (SMD = 0.088; p = 0.177). The analysis considering body region indicates no difference in lower limb exercise between HL-RT and LL-RT with BFR (SMD = 0.00066; p = 0.795) while upper limb exercise favors HL-RT (SMD = 0.231; p = 0.005).ConclusionLL-RT with BFR elicits muscle hypertrophy similar to HL-RT regardless of the employed repetition scheme, although there appears to be a small beneficial effect in favor of HL-RT in upper limb exercise. creator: Victor S. de Queiros creator: Nicholas Rolnick creator: Brad J. Schoenfeld creator: Ingrid Martins de França creator: João Guilherme Vieira creator: Amanda Veiga Sardeli creator: Okan Kamis creator: Gabriel Rodrigues Neto creator: Breno Guilherme de Araújo Tinôco Cabral creator: Paulo Moreira Silva Dantas uri: https://doi.org/10.7717/peerj.17195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 de Queiros et al. title: Pedagogical control scales of vertical jumping performance in untrained adolescents (13–16 years): research by strata link: https://peerj.com/articles/17298 last-modified: 2024-06-17 description: BackgroundA scale is used to establish performance ranges in different sciences, it being necessary to design specialized biological and pedagogical indicators in physical activity, sport and health.ObjectiveTo design a scale for the pedagogical control of the vertical jumping ability in untrained adolescents (13–16 years), stratifying the sample by age range, ethnicity, urban and rural area, socioeconomic level, and gender.MethodsA representative sample of the Ecuadorian population (n = 3,705) is studied, classifying it into the aforementioned strata, controlling the vertical jump by ISAK I and II level experts, applying the Sargent Test to measure vertical jumps on a multi-force wall, establishing scales with seven percentile levels, and making comparisons related to chronological age, gender, socioeconomic, and genetic indicators.ResultsSignificant differences in the vertical jumping performance were determined according to the category or age range (13–14 ≠ 15–16 years) and by gender (w = 0.000). Various levels of performance were determined, classifying the maximum level as talented in the female gender (≥40 cm; and ≥42 cm) and male gender (≥47 cm; and ≥57 cm) in the 13‒14 and 15‒16 years categories, respectively. Sampling comparisons by geographical area only determined significant differences in the male gender, with the jumping ability being higher in urban areas (13‒14 years: w = 0.046; 15‒16 years: w = 0.013). The comparison by ethnic groups showed significant differences (k = 0.030), favoring the Afro-Ecuadorian ethnic group in both genders, while there are significant differences by socioeconomic level, especially between the middle and lower classes.ConclusionsThe present research solves the lack of a tool for making correct didactic decisions related to the vertical jumping ability, taking into account various important stratified indicators. The complementary conclusions show significant differences according to the category stratum or age range, the gender stratum, and the ethnic stratum in females and males, where the best average rank favored the Afro-Ecuadorian ethnic group in both genders. There are significant differences in the geographical area stratum in the male gender, and differences in the socioeconomic stratum in favor of the upper and middle classes. creator: Santiago Calero-Morales creator: Victor Emilio Villavicencio-Alvarez creator: Elizabeth Flores-Abad creator: Antonio Jesús Monroy-Antón uri: https://doi.org/10.7717/peerj.17298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Calero-Morales et al. title: Choice-based severity scale (CSS): assessing the relative severity of procedures from a laboratory animal’s perspective link: https://peerj.com/articles/17300 last-modified: 2024-06-17 description: One primary goal of laboratory animal welfare science is to provide a comprehensive severity assessment of the experimental and husbandry procedures or conditions these animals experience. The severity, or degree of suffering, of these conditions experienced by animals are typically scored based on anthropocentric assumptions. We propose to (a) assess an animal’s subjective experience of condition severity, and (b) not only rank but scale different conditions in relation to one another using choice-based preference testing. The Choice-based Severity Scale (CSS) utilizes animals’ relative preferences for different conditions, which are compared by how much reward is needed to outweigh the perceived severity of a given condition. Thus, this animal-centric approach provides a common scale for condition severity based on the animal’s perspective. To assess and test the CSS concept, we offered three opportunistically selected male rhesus macaques (Macaca mulatta) choices between two conditions: performing a cognitive task in a typical neuroscience laboratory setup (laboratory condition) versus the monkey’s home environment (cage condition). Our data show a shift in one individual’s preference for the cage condition to the laboratory condition when we changed the type of reward provided in the task. Two additional monkeys strongly preferred the cage condition over the laboratory condition, irrespective of reward amount and type. We tested the CSS concept further by showing that monkeys’ choices between tasks varying in trial duration can be influenced by the amount of reward provided. Altogether, the CSS concept is built upon laboratory animals’ subjective experiences and has the potential to de-anthropomorphize severity assessments, refine experimental protocols, and provide a common framework to assess animal welfare across different domains. creator: Lauren Cassidy creator: Stefan Treue creator: Alexander Gail creator: Dana Pfefferle uri: https://doi.org/10.7717/peerj.17300 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cassidy et al. title: Preliminary studies of selected Lemna species on the oxygen production potential in relation to some ecological factors link: https://peerj.com/articles/17322 last-modified: 2024-06-17 description: Dissolved oxygen is fundamental for chemical and biochemical processes occurring in natural waters and critical for the life of aquatic organisms. Many organisms are responsible for altering organic matter and oxygen transfers across ecosystem or habitat boundaries and, thus, engineering the oxygen balance of the system. Due to such Lemna features as small size, simple structure, vegetative reproduction and rapid growth, as well as frequent mass occurrence in the form of thick mats, they make them very effective in oxygenating water. The research was undertaken to assess the impact of various species of duckweed (L. minor and L. trisulca) on dissolved oxygen content and detritus production in water and the role of ecological factors (light, atmospheric pressure, conductivity, and temperature) in this process. For this purpose, experiments were carried out with combinations of L. minor and L. trisulca. On this basis, the content of oxygen dissolved in water was determined depending on the growth of duckweed. Linear regression models were developed to assess the dynamics of changes in oxygen content and, consequently, organic matter produced by the Lemna. The research showed that the presence of L. trisulca causes an increase in dissolved oxygen content in water. It was also shown that an increase in atmospheric pressure had a positive effect on the ability of duckweed to produce oxygen, regardless of its type. The negative correlation between conductivity and water oxygenation, obtained in conditions of limited light access, allows us to assume that higher water conductivity limits oxygen production by all combinations of duckweeds when the light supply is low. Based on the developed models, it was shown that the highest increase in organic matter would be observed in the case of mixed duckweed and the lowest in the presence of the L. minor species, regardless of light conditions. Moreover, it was shown that pleustophytes have different heat capacities, and L. trisulca has the highest ability to accumulate heat in water for the tested duckweed combinations. The provided knowledge may help determine the good habitat conditions of duckweed, indicating its role in purifying water reservoirs as an effect of producing organic matter and shaping oxygen conditions with the participation of various Lemna species. creator: Joanna Sender creator: Monika Różańska-Boczula uri: https://doi.org/10.7717/peerj.17322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sender and Różańska-Boczula title: A comparison of the performance of bacterial biofilters and fungal–bacterial coupled biofilters in BTEp-X removal link: https://peerj.com/articles/17452 last-modified: 2024-06-17 description: BackgroundConventional biofilters, which rely on bacterial activity, face challenges in eliminating hydrophobic compounds, such as aromatic compounds. This is due to the low solubility of these compounds in water, which makes them difficult to absorb by bacterial biofilms. Furthermore, biofilter operational stability is often hampered by acidification and drying out of the filter bed.MethodsTwo bioreactors, a bacterial biofilter (B-BF) and a fungal–bacterial coupled biofilter (F&B-BF) were inoculated with activated sludge from the secondary sedimentation tank of the Sinopec Yangzi Petrochemical Company wastewater treatment plant located in Nanjing, China. For approximately 6 months of operation, a F&B-BF was more effective than a B-BF in eliminating a gas-phase mixture containing benzene, toluene, ethylbenzene, and para-xylene (BTEp-X).ResultsAfter operating for four months, the F&B-BF showed higher removal efficiencies for toluene (T), ethylbenzene (E), benzene (B), and para-X (p-Xylene), at 96.9%, 92.6%, 83.9%, and 83.8%, respectively, compared to those of the B-BF (90.1%, 78.7%, 64.8%, and 59.3%). The degradation activity order for B-BF and F&B-BF was T > E > B > p-X. Similarly, the rates of mineralization for BTEp-X in the F&B-BF were 74.9%, 66.5%, 55.3%, and 45.1%, respectively, which were higher than those in the B-BF (56.5%, 50.8%, 43.8%, and 30.5%). Additionally, the F&B-BF (2 days) exhibited faster recovery rates than the B-BF (5 days).ConclusionsIt was found that a starvation protocol was beneficial for the stable operation of both the B-BF and F&B-BF. Community structure analysis showed that the bacterial genus Pseudomonas and the fungal genus Phialophora were both important in the degradation of BTEp-X. The fungal-bacterial consortia can enhance the biofiltration removal of BTEp-X vapors. creator: Hai Wang creator: Xiaojuan Xue creator: Xujun Nan creator: Jian Zhai uri: https://doi.org/10.7717/peerj.17452 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Wang et al. title: Potential therapeutic agents of Bombyx mori silk cocoon extracts from agricultural product for inhibition of skin pathogenic bacteria and free radicals link: https://peerj.com/articles/17490 last-modified: 2024-06-17 description: BackgroundPathogenic bacteria are the cause of most skin diseases, but issues such as resistance and environmental degradation drive the need to research alternative treatments. It is reported that silk cocoon extract possesses antioxidant properties. During silk processing, the degumming of silk cocoons creates a byproduct that contains natural active substances. These substances were found to have inhibitory effects on bacterial growth, DNA synthesis, the pathogenesis of hemolysis, and biofilm formation. Thus, silk cocoon extracts can be used in therapeutic applications for the prevention and treatment of skin pathogenic bacterial infections.MethodsThe extract of silk cocoons with pupae (SCP) and silk cocoons without pupae (SCWP) were obtained by boiling with distilled water for 9 h and 12 h, and were compared to silkworm pupae (SP) extract that was boiled for 1 h. The active compounds in the extracts, including gallic acid and quercetin, were determined using high-performance liquid chromatography (HPLC). Furthermore, the total phenolic and flavonoid content in the extracts were investigated using the Folin–Ciocalteu method and the aluminum chloride colorimetric method, respectively. To assess antioxidant activity, the extracts were evaluated using the 2,2-diphenyl–1-picrylhydrazyl (DPPH) radical scavenging assay. Additionally, the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of silk extracts and phytochemical compounds were determined against skin pathogenic bacteria. This study assessed the effects of the extracts and phytochemical compounds on growth inhibition, biofilm formation, hemolysis protection, and DNA synthesis of bacteria.ResultsThe HPLC characterization of the silk extracts showed gallic acid levels to be the highest, especially in SCP (8.638–31.605 mg/g extract) and SP (64.530 mg/g extract); whereas quercetin compound was only detected in SCWP (0.021–0.031 mg/g extract). The total phenolics and flavonoids in silk extracts exhibited antioxidant and antimicrobial activity. Additionally, SCP at 9 h and 12 h revealed the highest anti-bacterial activity, with the lowest MIC and MBC of 50–100 mg/mL against skin pathogenic bacteria including Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), Cutibacterium acnes and Pseudomonas aeruginosa. Hence, SCP extract and non-sericin compounds containing gallic acid and quercetin exhibited the strongest inhibition of both growth and DNA synthesis on skin pathogenic bacteria. The suppression of bacterial pathogenesis, including preformed and matured biofilms, and hemolysis activity, were also revealed in SCP extract and non-sericin compounds. The results show that the byproduct of silk processing can serve as an alternative source of natural phenolic and flavonoid antioxidants that can be used in therapeutic applications for the prevention and treatment of pathogenic bacterial skin infections. creator: Thida Kaewkod creator: Puangphaka Kumseewai creator: Sureeporn Suriyaprom creator: Varachaya Intachaisri creator: Nitsanat Cheepchirasuk creator: Yingmanee Tragoolpua uri: https://doi.org/10.7717/peerj.17490 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Kaewkod et al. title: iTRAQ-based proteomic analysis reveals the effect of ribosomal proteins on essential-oil accumulation in Houttuynia cordata Thunb. link: https://peerj.com/articles/17519 last-modified: 2024-06-17 description: Houttuynia cordata Thunb., also known as Yuxingcao in Chinese, occupies a pivotal role in Asian traditional medicine and cuisine. The aerial parts and underground stems of H. cordata exhibit remarkable chemical diversity, particularly in essential oil. Nevertheless, the mechanisms regulating essential oil biosynthesis in H. cordata remain unclear. In this study, we present a quantitative overview of the proteomes across four tissues (flower, stem, leaf, and underground stem) of H. cordata, achieved through the application of the isobaric tag for relative and absolute quantitation (iTRAQ). Our research findings indicate that certain crucial ribosomal proteins and their interactions may significantly impact the production of essential oils in H. cordata. These results offer novel insights into the roles of ribosomal proteins and their associations in essential oil biosynthesis across various organisms of H. cordata. creator: Dandan Guo creator: Beixuan He creator: Fei Feng creator: Diya Lv creator: Ting Han creator: Xiaofei Chen uri: https://doi.org/10.7717/peerj.17519 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Guo et al. title: Incidence, mortality, and predictive factors associated with acute respiratory distress syndrome in multiple trauma patients living in high-altitude areas: a retrospective study in Shigatse link: https://peerj.com/articles/17521 last-modified: 2024-06-17 description: BackgroundAcute respiratory distress syndrome (ARDS) is a severe complication that can lead to fatalities in multiple trauma patients. Nevertheless, the incidence rate and early prediction of ARDS among multiple trauma patients residing in high-altitude areas remain unknown.MethodsThis study included a total of 168 multiple trauma patients who received treatment at Shigatse People’s Hospital Intensive Care Unit (ICU) between January 1, 2019 and December 31, 2021. The clinical characteristics of the patients and the incidence rate of ARDS were assessed. Univariable and multivariable logistic regression models were employed to identify potential risk factors for ARDS, and the predictive effects of these risk factors were analyzed.ResultsIn the high-altitude area, the incidence of ARDS among multiple trauma patients was 37.5% (63/168), with a hospital mortality rate of 16.1% (27/168). Injury Severity Score (ISS) and thoracic injuries were identified as significant predictors for ARDS using the logistic regression model, with an area under the curve (AUC) of 0.75 and 0.75, respectively. Furthermore, a novel predictive risk score combining ISS and thoracic injuries demonstrated improved predictive ability, achieving an AUC of 0.82.ConclusionsThis study presents the incidence of ARDS in multiple trauma patients residing in the Tibetan region, and identifies two critical predictive factors along with a risk score for early prediction of ARDS. These findings have the potential to enhance clinicians’ ability to accurately assess the risk of ARDS and proactively prevent its onset. creator: Dan Tu creator: Lv Ji creator: Qiang Cao creator: Tin Ley creator: Suolangpian Duo creator: Ningbo Cheng creator: Wenjing Lin creator: Jianlei Zhang creator: Weifeng Yu creator: Zhiying Pan creator: Xiaoqiang Wang uri: https://doi.org/10.7717/peerj.17521 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tu et al. title: Recognition of apnea and hypopnea by non-contact optical fiber mattress and its application in the diagnosis of obstructive sleep apnea hypopnea syndrome: a retrospective study link: https://peerj.com/articles/17570 last-modified: 2024-06-17 description: ObjectivesThis study sought to evaluate the diagnostic value of a non-contact optical fiber mattress for apnea and hypopnea and compare it with traditional polysomnography (PSG) in adult obstructive sleep apnea hypopnea syndrome (OSAHS).MethodsTo determine the value of a non-contact optical fiber mattress for apnea and hypopnea, six healthy people and six OSAHS patients were selected from Tongji Hospital to design a program to identify apnea or hypopnea. A total of 108 patients who received polysomnography for drowsiness, snoring or other suspected OSAHS symptoms. All 108 patients were monitored with both the non-contact optical fiber mattress and PSG were collected.ResultsSix healthy controls and six patients with OSAHS were included. The mean apnea of the six healthy controls was 1.22 times/h, and the mean hypopnea of the six healthy controls was 2 times/h. Of the six patients with OSAHS, the mean apnea was 12.63 times/h, and the mean hypopnea was 19.25 times/h. The non-contact optical fiber mattress results showed that the mean apnea of the control group was 3.17 times/h and the mean hypopnea of the control group was 3.83 times/h, while the mean apnea of the OSAHS group was 11.95 times/h and the mean hypopnea of the OSAHS group was 17.77 times/h. The apnea index of the non-contact optical fiber mattress was positively correlated with the apnea index of the PSG (P < 0.05, r = 0.835), and the hypopnea index of the non-contact optical fiber mattress was also positively correlated with the hypopnea index of the PSG (P < 0.05, r = 0.959). The non-contact optical fiber mattress had high accuracy (area under curve, AUC = 0.889), specificity (83.4%) and sensitivity (83.3%) for the diagnosis of apnea. The non-contact fiber-optic mattress also had high accuracy (AUC = 0.944), specificity (83.4%) and sensitivity (100%) for the diagnosis of hypopnea. Among the 108 patients enrolled, there was no significant difference between the non-contact optical fiber mattress and the polysomnography monitor in total recording time, apnea hypopnea index (AHI), average heart rate, tachycardia index, bradycardia index, longest time of apnea, average time of apnea, longest time of hypopnea, average time of hypopnea, percentage of total apnea time in total sleep time and percentage of total hypopnea time in total sleep time. The AHI value of the non-contact optical fiber mattress was positively correlated with the AHI value of the PSG (P < 0.05, r = 0.713). The specificity and sensitivity of the non-contact optical fiber mattress AHI in the diagnosis of OSAHS were 95% and 93%, with a high OSAHS diagnostic accuracy (AUC = 0.984).ConclusionThe efficacy of the non-contact optical fiber mattress for OSAHS monitoring was not significantly different than PSG monitoring. The specificity of the non-contact optical mattress for diagnosing OSAHS was 95% and its sensitivity was 93%, with a high OSAHS diagnostic accuracy. creator: Ling Zhou creator: Xiaoyan Zhu creator: Lu Liu creator: Lingling Wang creator: Pengdou Zheng creator: Fengqin Zhang creator: Zhenyu Mao creator: Guoliang Huang creator: Songlin Cheng creator: Huiguo Liu creator: Wei Liu uri: https://doi.org/10.7717/peerj.17570 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Prevalence and factors associated with Schistosoma mansoni infection among primary school children in Kersa District, Eastern Ethiopia link: https://peerj.com/articles/17439 last-modified: 2024-06-14 description: BackgroundSchistosomiasis is a neglected tropical disease and an important parasite negatively impacting socio-economic factors. Ethiopia’s Federal Ministry of Health targeted the elimination of schistosomiasis infection in school-aged children by 2020. However, Schistosoma mansoni still affects approximately 12.3 million school-aged children in Ethiopia. Although the study was conducted in some regions of the country, previous studies were conducted on urban school children and were limited to the burden of infection. Overall, there is a lack of information about schistosomiasis in eastern Ethiopia, particularly among school children. Therefore, this study aimed to assess the prevalence and factors associated with Schistosoma mansoni infection among primary school children in Kersa district, Eastern Ethiopia.MethodsA cross-sectional study was conducted among 419 school children using systematic random sampling from April 10 to May 09, 2019. The stool samples were collected and examined using the Keto-Katz method. A structured and pretested questionnaire was used to collect data from participants. Data were entered using Epi-Data version 3.1 and analysed using SPSS version 24. A bivariable and multivariable logistic regression analyses were used to identify factors associated with Schistosoma mansoni infection. P-value < 0.05 and adjusted odds ratio (AOR) (95% confidence interval (CI)) were used to identify statistically significant associations.ResultsThis study’s overall prevalence of S. mansoni was 19.4% (95% CI [16–23]). Absence of the latrines in household (AOR = 2.35, 95% CI [1.25–4.38]), swimming in the river (AOR = 2.82, 95% CI [1.33–5.88]), unprotected water sources (AOR = 3.5, 95% CI [1.72–7.10]), irregular shoe wearing habits (AOR = 2.81, 95% CI [1.51–5.23]), and water contact during cross of river (AOR = 2.192; 95% CI [1.113–4.318]) were factors independently associated with S. mansoni infection.ConclusionSchistosoma mansoni infection remains a public health problem in the study area. Using a latrine in each household, using protected water, wearing shoes regularly, and reducing water contact were necessary to control Schistosoma mansoni infection. creator: Hussen Aliyi creator: Mohammed Ahmed creator: Tesfaye Gobena creator: Bezatu Mengistie Alemu creator: Hassen Abdi Adem creator: Ahmedin Aliyi Usso uri: https://doi.org/10.7717/peerj.17439 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Aliyi et al. title: Pyrolyzed and unpyrolyzed residues enhance maize yield under varying rates of application and fertilization regimes link: https://peerj.com/articles/17513 last-modified: 2024-06-14 description: Biochar is increasingly gaining popularity due to its extensive recommendation as a potential solution for addressing the concerns of food security and climate change in agroecosystems, with biochar application for increased carbon sequestration, enhanced soil fertility, improved soil health, and increased crop yield and quality. There have been multiple studies on crop yield utilizing various biochar types and application amounts; however, none have focused on the influence of diverse biochar types at various pyrolysis temperatures with different application amounts and the integration of fertilizer regimes in maize crops. Therefore, a two-year factorial field experiment was designed in a temperate Himalayan region of India (THRI) to evaluate the residual effect of different biochar on maize yield under different pyrolysis temperatures, various application rates and fertilizer regimes. The study included three factors viz., amendment type (factor 1), rate of application (factor 2) and fertilizer regime (factor 3). Amendment type included 7 treatments: No biochar- control (A1), apple biochar @ 400 °C pyrolysis temperature (A2), apple biochar @ 600 °C pyrolysis temperature (A3), apple residue biomass (A4), dal weed biochar @ 400 °C pyrolysis temperature (A5), dal weed biochar @ 600 °C pyrolysis temperatures (A6), and dal weed residue biomass (A7). The rate of application included 3 levels: Low (L- 1 t ha−1), medium (M- 2 t ha−1), and high (H- 3 t ha−1). At the same time, the fertilizer regimes included 2 treatments: No fertilizer (N) and recommended dose of fertilizer (F). The results revealed that among the various amendment type, rate of application and fertilizer regimes, the A3 amendment, H rate of application and F fertilizer regime gave the best maize growth and productivity outcome. Results revealed that among the different pyrolyzed residues used, the A3 amendment had the highest plant height (293.87 cm), most kernels cob−1 (535.75), highest soil plant analysis development (SPAD) value (58.10), greatest cob length (27.36 cm), maximum cob girth (18.18 cm), highest grain cob yield (1.40 Mg ha−1), highest grain yield (4.78 Mg ha−1), higher test weight (305.42 gm), and highest stover yield (2.50 Mg ha−1). The maximum dry weight in maize and the number of cobs plant−1 were recorded with amendments A4 (14.11 Mg ha−1) and A6 (1.77), respectively. The comparatively 2nd year of biochar application than the 1st year, the H level of the rate of application than the L rate and the application and integration of the recommended dose of fertilizer in maize results in significantly higher values of growth and productivity in maize. Overall, these findings suggest that the apple biochar @ 600 °C pyrolysis temperature (A3) at a high application rate with the addition of the recommended dose of fertilizer is the optimal biochar for enhancing the growth and productivity of maize in the THRI. creator: Owais Ali Wani creator: Farida Akhter creator: Shamal Shasang Kumar creator: Raihana Habib Kanth creator: Zahoor Ahmed Dar creator: Subhash Babu creator: Nazir Hussain creator: Syed Sheraz Mahdi creator: Abed Alataway creator: Ahmed Z. Dewidar creator: Mohamed A. Mattar uri: https://doi.org/10.7717/peerj.17513 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wani et al. title: Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome link: https://peerj.com/articles/17520 last-modified: 2024-06-14 description: Habitual dietary changes have the potential to induce alterations in the host’s gut microbiota. Mandarin fish (Siniperca chuatsi), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals. creator: Hongyan Li creator: Shuhui Niu creator: Houjun Pan creator: Guangjun Wang creator: Jun Xie creator: Jingjing Tian creator: Kai Zhang creator: Yun Xia creator: Zhifei Li creator: Ermeng Yu creator: Wenping Xie creator: Wangbao Gong uri: https://doi.org/10.7717/peerj.17520 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Effects of combined aerobic and resistance training on glycemic control, blood pressure, inflammation, cardiorespiratory fitness and quality of life in patients with type 2 diabetes and overweight/obesity: a systematic review and meta-analysis link: https://peerj.com/articles/17525 last-modified: 2024-06-14 description: BackgroundStructured aerobic or resistance training alone seems to be a beneficial tool for improving glucose homeostasis, chronic systemic inflammation, resting cardiovascular function, and mental health in people with obesity and type 2 diabetes mellitus (T2DM). The aim of the present study was to synthesize the available data on the effectiveness of combined aerobic and resistance training (CART) on glycemic control, blood pressure, inflammation, cardiorespiratory fitness (CRF), and quality of life (QoL) in overweight and obese individuals with T2DM.MethodsA database search was carried out in PubMed, Web of Science, Scopus, Science Direct, Cochrane Library, and Google Scholar from inception up to May 2023. The Cochrane risk of bias tool was used to assess eligible studies, and the GRADE method to evaluate the reliability of evidence. A random-effects model was used, and data were analyzed using standardized mean differences and 95% confidence intervals. The study protocol was registered in the International Prospective Register of Systematic Reviews (ID: CRD42022355612).ResultsA total of 21,612 studies were retrieved; 20 studies were included, and data were extracted from 1,192 participants (mean age: 57 ± 7 years) who met the eligibility criteria. CART demonstrated significant improvements in body mass index, glycated hemoglobin, systolic and diastolic blood pressure, C-reactive protein, tumor necrosis factor-alpha, interleukin-6, CRF, and QoL compared to ST. These findings highlight the significance of exercise interventions such as CART as essential elements within comprehensive diabetes management strategies, ultimately enhancing overall health outcomes in individuals with T2DM and overweight/obesity.No differences were found in resting heart rate between CART and ST. An uncertain risk of bias and poor quality of evidence were found among the eligible studies.ConclusionThese outcomes show clear evidence considering the positive role of CART in inducing beneficial changes in various cardiometabolic and mental health-related indicators in patients with T2DM and concurrent overweight/obesity. More studies with robust methodological design are warranted to examine the dose-response relationship, training parameters configuration, and mechanisms behind these positive adaptations. creator: Sameer Badri AL-Mhanna creator: Alexios Batrakoulis creator: Wan Syaheedah Wan Ghazali creator: Mahaneem Mohamed creator: Abdulaziz Aldayel creator: Maha H. Alhussain creator: Hafeez Abiola Afolabi creator: Yusuf Wada creator: Mehmet Gülü creator: Safaa Elkholi creator: Bishir Daku Abubakar creator: Daniel Rojas-Valverde uri: https://doi.org/10.7717/peerj.17525 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 AL-Mhanna et al. title: Screening and verification of proteins that interact with the anthocyanin-related transcription factor PbrMYB114 in ‘Yuluxiang’ pear link: https://peerj.com/articles/17540 last-modified: 2024-06-14 description: Despite extensive research highlighting the pivotal role of MYB transcription factors in regulating anthocyanin biosynthesis, the interactive regulatory network involving these MYB factors in pear fruits remains inadequately characterized. In this study, the anthocyanin-regulatory gene PbrMYB114 was successfully cloned from ‘Yuluxiang’ pear (Pyrus bretschneideri) fruits, and its influence on anthocyanin accumulation was confirmed through transient expression assays. Specifically, the co-transformation of PbrMYB114 with its partner PbrbHLH3 in pears served to validate the functional role of PbrMYB114. Subsequently, PbrMYB114 was employed as bait in a yeast two-hybrid screening assay, using a ‘Yuluxiang’ pear protein library, which led to the identification of 25 interacting proteins. Further validation of the interactions between PbrMYB114 and PbrMT2/PbrMT3 was conducted. Investigations into the role of PbrMT2 and PbrMT3 in ‘Duli’ seedlings (Pyrus betulaefolia) revealed their potential to enhance anthocyanin accumulation. The outcomes of these studies provide novel insights into the protein network that regulates pear anthocyanin biosynthesis, particularly the functional interactions among PbrMYB114 and associated proteins. creator: Qingwei Liu creator: Ge Gao creator: Chen Shang creator: Tong Li creator: Yadong Wang creator: Liulin Li creator: Xinxin Feng uri: https://doi.org/10.7717/peerj.17540 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liu et al. title: Maize residue retention shapes soil microbial communities and co-occurrence networks upon freeze-thawing cycles link: https://peerj.com/articles/17543 last-modified: 2024-06-14 description: Maize residue retention is an effective agricultural practice for improving soil fertility in black soil region, where suffered from long freezing-thawing periods and intense freeze-thawing (FT) cycles. However, very few studies have examined the influence of maize residue retention on soil microbial communities under FT cycles. We investigated the response of soil microbial communities and co-occurrence networks to maize residue retention at different FT intensities over 12 cycles using a microcosm experiment conditioned in a temperature incubator. Our results indicated that maize residue retention induced dramatic shifts in soil archaeal, bacterial and fungal communities towards copiotroph-dominated communities. Maize residue retention consistently reduced soil fungal richness across all cycles, but this effect was weaker for archaea and bacteria. Normalized stochastic ratio analysis revealed that maize residue retention significantly enhanced the deterministic process of archaeal, bacterial and fungal communities. Although FT intensity significantly impacted soil respiration, it did not induce profound changes in soil microbial diversity and community composition. Co-occurrence network analysis revealed that maize residue retention simplified prokaryotic network, while did not impact fungal network complexity. The network robustness index suggested that maize residue retention enhanced the fungal network stability, but reduced prokaryotic network stability. Moreover, the fungal network in severe FT treatment harbored the most abundant keystone taxa, mainly being cold-adapted fungi. By identifying modules in networks, we observed that prokaryotic Module #1 and fungal Module #3 were enhanced by maize residue retention and contributed greatly to soil quality. Together, our results showed that maize residue retention exerted stronger influence on soil microbial communities and co-occurrence network patterns than FT intensity and highlighted the potential of microbial interactions in improving soil functionality. creator: Yang Yu creator: Quankuan Guo creator: Shuhan Zhang creator: Yupeng Guan creator: Nana Jiang creator: Yang Zhang creator: Rong Mao creator: Keyu Bai creator: Salimjan Buriyev creator: Nuriddin Samatov creator: Ximei Zhang creator: Wei Yang uri: https://doi.org/10.7717/peerj.17543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yu et al. title: Ferrostatin-1 inhibits fibroblast fibrosis in keloid by inhibiting ferroptosis link: https://peerj.com/articles/17551 last-modified: 2024-06-14 description: BackgroundKeloid is a chronic proliferative fibrotic disease caused by abnormal fibroblasts proliferation and excessive extracellular matrix (ECM) production. Numerous fibrotic disorders are significantly influenced by ferroptosis, and targeting ferroptosis can effectively mitigate fibrosis development. This study aimed to investigate the role and mechanism of ferroptosis in keloid development.MethodsKeloid tissues from keloid patients and normal skin tissues from healthy controls were collected. Iron content, lipid peroxidation (LPO) level, and the mRNA and protein expression of ferroptosis-related genes including solute carrier family 7 member 11 (SLC7A11), glutathione peroxidase 4 (GPX4), transferrin receptor (TFRC), and nuclear factor erythroid 2-related factor 2 (Nrf2) were determined. Mitochondrial morphology was observed using transmission electron microscopy (TEM). Keloid fibroblasts (KFs) were isolated from keloid tissues, and treated with ferroptosis inhibitor ferrostatin-1 (fer-1) or ferroptosis activator erastin. Iron content, ferroptosis-related marker levels, LPO level, mitochondrial membrane potential, ATP content, and mitochondrial morphology in KFs were detected. Furthermore, the protein levels of α-smooth muscle actin (α-SMA), collagen I, and collagen III were measured to investigate whether ferroptosis affect fibrosis in KFs.ResultsWe found that iron content and LPO level were substantially elevated in keloid tissues and KFs. SLC7A11, GPX4, and Nrf2 were downregulated and TFRC was upregulated in keloid tissues and KFs. Mitochondria in keloid tissues and KFs exhibited ferroptosis-related pathology. Fer-1 treatment reduced iron content, restrained ferroptosis and mitochondrial dysfunction in KFs, Moreover, ferrostatin-1 restrained the protein expression of α-SMA, collagen I, and collagen III in KFs. Whereas erastin treatment showed the opposite results.ConclusionFerroptosis exists in keloid. Ferrostatin-1 restrained ECM deposition and fibrosis in keloid through inhibiting ferroptosis, and erastin induced ECM deposition and fibrosis through intensifying ferroptosis. creator: Liu Yang creator: Xiuli Li creator: Yanli Wang uri: https://doi.org/10.7717/peerj.17551 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yang et al. title: Using linear measurements to diagnose the ecological habitat of Spinosaurus link: https://peerj.com/articles/17544 last-modified: 2024-06-13 description: Much of the ecological discourse surrounding the polarising theropod Spinosaurus has centred on qualitative discussions. Using a quantitative multivariate data analytical approach on size-adjusted linear measurements of the skull, we examine patterns in skull shape across a range of sauropsid clades and three ecological realms (terrestrial, semi-aquatic, and aquatic). We utilise cluster analyses to identify emergent properties of the data which associate properties of skull shape with ecological realm occupancy. Results revealed terrestrial ecologies to be significantly distinct from both semi- and fully aquatic ecologies, the latter two were not significantly different. Spinosaurids (including Spinosaurus) plotted away from theropods in morphospace and close to both marine taxa and wading birds. The position of nares and the degree of rostral elongation had the greatest effect on categorisation. Comparisons of supervised (k-means) and unsupervised clustering demonstrated categorising taxa into three groups (ecological realms) was inappropriate and suggested instead that cluster division is based on morphological adaptations to feeding on aquatic versus terrestrial food items. The relative position of the nares in longirostrine taxa is associated with which skull bones are elongated. Rostral elongation is observed by either elongating the maxilla and the premaxilla or by elongating the maxilla only. This results in the nares positioned towards the orbits or towards the anterior end of the rostrum respectively, with implications on available feeding methods. Spinosaurids, especially Spinosaurus, show elongation in the maxilla-premaxilla complex, achieving similar functional outcomes to elongation of the premaxilla seen in birds, particularly large-bodied piscivorous taxa. Such a skull construction would bolster “stand-and-wait” predation of aquatic prey to a greater extent than serving other proposed feeding methods. creator: Sean Smart creator: Manabu Sakamoto uri: https://doi.org/10.7717/peerj.17544 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Smart and Sakamoto title: Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies link: https://peerj.com/articles/17550 last-modified: 2024-06-13 description: The Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanusssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxa. creator: Adrián Talavera creator: Emilio Valbuena-Ureña creator: Bernat Burriel-Carranza creator: Gabriel Mochales-Riaño creator: Dean C. Adams creator: Fèlix Amat creator: Francesc Carbonell creator: Salvador Carranza uri: https://doi.org/10.7717/peerj.17550 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Talavera et al. title: When and where? Day-night alterations in wild boar space use captured by a generalized additive mixed model link: https://peerj.com/articles/17390 last-modified: 2024-06-12 description: Wild boar (Sus scrofa), an abundant species across Europe, is often subjected to management in agro-ecosystems in order to control population size, or to scare them away from agricultural fields to safeguard crop yields. Wild boar management can benefit from a better understanding on changes in its space use across the diel cycle (i.e., diel space use) in relation to variable hunting pressures or other factors. Here, we estimate wild boar diel space use in an agro-ecosystem in central Belgium during four consecutive “growing seasons” (i.e., April–September). To achieve this, we fit generalized additive mixed models (GAMMs) to camera trap data of wild boar aggregated over 1-h periods. Our results reveal that wild boar are predominantly nocturnal in all of the hunting management zones in Meerdaal, with activity peaks around sunrise and sunset. Hunting events in our study area tend to take place around sunrise and sunset, while non-lethal human activities occur during sunlight hours. Our GAMM reveals that wild boar use different areas throughout the diel cycle. During the day, wild boar utilized areas in the centre of the forest, possibly to avoid human activities during daytime. During the night, they foraged near (or in) agricultural fields. A post hoc comparison of space use maps of wild boar in Meerdaal revealed that their diurnal and nocturnal space use were uncorrelated. We did not find sufficient evidence to prove that wild boar spatiotemporally avoid hunters. Finally, our work reveals the potential of GAMMs to model variation in space across 24-h periods from camera trap data, an application that will be useful to address a range of ecological questions. However, to test the robustness of this approach we advise that it should be compared against telemetry-based methods to derive diel space use. creator: Martijn Bollen creator: Jim Casaer creator: Thomas Neyens creator: Natalie Beenaerts uri: https://doi.org/10.7717/peerj.17390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Bollen et al. title: Altered vaginal cervical microbiota diversity contributes to HPV-induced cervical cancer via inflammation regulation link: https://peerj.com/articles/17415 last-modified: 2024-06-12 description: BackgroundCancer has surpassed infectious diseases and heart ailments, taking the top spot in the disease hierarchy. Cervical cancer is a significant concern for women due to high incidence and mortality rates, linked to the human papillomavirus (HPV). HPV infection leads to precancerous lesions progressing to cervical cancer. The cervix’s external os, near the vagina, hosts various microorganisms. Evidence points to the link between vaginal microbiota and HPV-induced cervical cancer. Cervical cancer onset aligns with an imbalanced Th1/Th2 immune response, but the role of vaginal microbiota in modulating this imbalance is unclear.MethodsIn this study, we collected vaginal samples from 99 HPV-infected patients across varying degrees of lesions, alongside control groups. These samples underwent bacterial DNA sequencing. Additionally, we employed Elisa kits to quantify the protein expression levels of Th1/Th2 cytokines IL2, IL12, IL5, IL13, and TNFa within the centrifuged supernatant of vaginal-cervical secretions from diverse research subjects. Subsequently, correlation analyses were conducted between inflammatory factors and vaginal microbiota.ResultsOur findings highlighted a correlation between decreased Lactobacillus and increased Gardenerella presence with HPV-induced cervical cancer. Functionally, our predictive analysis revealed the predominant enrichment of the ABC transporter within the vaginal microbiota of cervical cancer patients. Notably, these microbiota alterations exhibited correlations with the production of Th1/Th2 cytokines, which are intimately tied to tumor immunity.ConclusionsThis study suggests the potential involvement of vaginal microbiota in the progression of HPV-induced cervical cancer through Th1/Th2 cytokine regulation. This novel insight offers a fresh perspective for early cervical cancer diagnosis and future prevention strategies. creator: Yiheng Yang creator: Jufan Zhu creator: Renqian Feng creator: Mengfei Han creator: Fenghua Chen creator: Yan Hu uri: https://doi.org/10.7717/peerj.17415 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Use of machine learning to identify protective factors for death from COVID-19 in the ICU: a retrospective study link: https://peerj.com/articles/17428 last-modified: 2024-06-12 description: BackgroundPatients in serious condition due to COVID-19 often require special care in intensive care units (ICUs). This disease has affected over 758 million people and resulted in 6.8 million deaths worldwide. Additionally, the progression of the disease may vary from individual to individual, that is, it is essential to identify the clinical parameters that indicate a good prognosis for the patient. Machine learning (ML) algorithms have been used for analyzing complex medical data and identifying prognostic indicators. However, there is still an urgent need for a model to elucidate the predictors related to patient outcomes. Therefore, this research aimed to verify, through ML, the variables involved in the discharge of patients admitted to the ICU due to COVID-19.MethodsIn this study, 126 variables were collected with information on demography, hospital length stay and outcome, chronic diseases and tumors, comorbidities and risk factors, complications and adverse events, health care, and vital indicators of patients admitted to an ICU in southern Brazil. These variables were filtered and then selected by a ML algorithm known as decision trees to identify the optimal set of variables for predicting patient discharge using logistic regression. Finally, a confusion matrix was performed to evaluate the model’s performance for the selected variables.ResultsOf the 532 patients evaluated, 180 were discharged: female (16.92%), with a central venous catheter (23.68%), with a bladder catheter (26.13%), and with an average of 8.46- and 23.65-days using bladder catheter and submitted to mechanical ventilation, respectively. In addition, the chances of discharge increase by 14% for each additional day in the hospital, by 136% for female patients, 716% when there is no bladder catheter, and 737% when no central venous catheter is used. However, the chances of discharge decrease by 3% for each additional year of age and by 9% for each other day of mechanical ventilation. The performance of the training data presented a balanced accuracy of 0.81, sensitivity of 0.74, specificity of 0.88, and the kappa value was 0.64. The test performance had a balanced accuracy of 0.85, sensitivity 0.75, specificity 0.95, and kappa value of 0.73. The McNemar test found that there were no significant differences in the error rates in the training and test data, suggesting good classification. This work showed that female, the absence of a central venous catheter and bladder catheter, shorter mechanical ventilation, and bladder catheter duration were associated with a greater chance of hospital discharge. These results may help develop measures that lead to a good prognosis for the patient. creator: Lander Dos Santos creator: Lincoln Luis Silva creator: Fernando Castilho Pelloso creator: Vinicius Maia creator: Constanza Pujals creator: Deise Helena Borghesan creator: Maria Dalva Carvalho creator: Raíssa Bocchi Pedroso creator: Sandra Marisa Pelloso uri: https://doi.org/10.7717/peerj.17428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dos Santos et al. title: Tick hazard in the South Downs National Park (UK): species, distribution, key locations for future interventions, site density, habitats link: https://peerj.com/articles/17483 last-modified: 2024-06-12 description: BackgroundSouth Downs National Park (SDNP) is UK’s most visited National Park, and a focus of tick-borne Lyme disease. The first presumed UK autochthonous cases of tick-borne encephalitis and babesiosis were recorded in 2019–20. SDNP aims to conserve wildlife and encourage recreation, so interventions are needed that reduce hazard without negatively affecting ecosystem health. To be successful these require knowledge of site hazards.MethodsBritish Deer Society members submitted ticks removed from deer. Key potential intervention sites were selected and six 50 m2 transects drag-sampled per site (mostly twice yearly for 2 years). Ticks were identified in-lab (sex, life stage, species), hazard measured as tick presence, density of ticks (all life stages, DOT), and density of nymphs (DON). Sites and habitat types were analysed for association with hazard. Distribution was mapped by combining our results with records from five other sources.ResultsA total of 87 Ixodes ricinus (all but one adults, 82% F) were removed from 14 deer (10 Dama dama; three Capreolus capreolus; one not recorded; tick burden, 1–35) at 12 locations (commonly woodland). Five key potential intervention sites were identified and drag-sampled 2015–16, collecting 623 ticks (238 on-transects): 53.8% nymphs, 42.5% larvae, 3.7% adults (13 M, 10 F). Ticks were present on-transects at all sites: I. ricinus at three (The Mens (TM); Queen Elizabeth Country Park (QECP); Cowdray Estate (CE)), Haemaphysalis punctata at two (Seven Sisters Country Park (SSCP); Ditchling Beacon Nature Reserve (DBNR)). TM had the highest DOT at 30/300 m2 (DON = 30/300 m2), followed by QECP 22/300 m2 (12/300 m2), CE 8/300 m2 (6/300 m2), and SSCP 1/300 m2 (1/300 m2). For I. ricinus, nymphs predominated in spring, larvae in the second half of summer and early autumn. The overall ranking of site hazard held for DON and DOT from both seasonal sampling periods. DBNR was sampled 2016 only (one adult H. punctata collected). Woodland had significantly greater hazard than downland, but ticks were present at all downland sites. I. ricinus has been identified in 33/37 of SDNPs 10 km2 grid squares, Ixodes hexagonus 10/37, H. punctata 7/37, Dermacentor reticulatus 1/37.ConclusionsMapping shows tick hazard broadly distributed across SDNP. I. ricinus was most common, but H. punctata’s seeming range expansion is concerning. Recommendations: management of small heavily visited high hazard plots (QECP); post-visit precaution signage (all sites); repellent impregnated clothing for deerstalkers; flock trials to control H. punctata (SSCP, DBNR). Further research at TM may contribute to knowledge on ecological dynamics underlying infection density and predator re-introduction/protection as public health interventions. Ecological research on H. punctata would aid control. SDNP Authority is ideally placed to link and champion policies to reduce hazard, whilst avoiding or reducing conflict between public health and ecosystem health. creator: Jo Middleton creator: Ian Cooper creator: Anja S. Rott uri: https://doi.org/10.7717/peerj.17483 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Middleton et al. title: Effects of wind speed and wind direction on crop yield forecasting using dynamic time warping and an ensembled learning model link: https://peerj.com/articles/16538 last-modified: 2024-06-11 description: The cultivation of cashew crops carries numerous economic advantages, and countries worldwide that produce this crop face a high demand. The effects of wind speed and wind direction on crop yield prediction using proficient deep learning algorithms are less emphasized or researched. We propose a combination of advanced deep learning techniques, specifically focusing on long short-term memory (LSTM) and random forest models. We intend to enhance this ensemble model using dynamic time warping (DTW) to assess the spatiotemporal data (wind speed and wind direction) similarities within Jaman North, Jaman South, and Wenchi with their respective production yield. In the Bono region of Ghana, these three areas are crucial for cashew production. The LSTM-DTW-RF model with wind speed and wind direction achieved an R2 score of 0.847 and the LSTM-RF model without these two key features R2 score of (0.74). Both models were evaluated using the augmented Dickey-Fuller (ADF) test, which is commonly used in time series analysis to assess stationarity, where the LSTM-DTW-RF achieved a 90% level of confidence, while LSTM-RF attained an 87.99% level. Among the three municipalities, Jaman South had the highest evaluation scores for the model, with an RMSE of 0.883, an R2 of 0.835, and an MBE of 0.212 when comparing actual and predicted values for Wenchi. In terms of the annual average wind direction, Jaman North recorded (270.5 SW°), Jaman South recorded (274.8 SW°), and Wenchi recorded (272.6 SW°). The DTW similarity distance for the annual average wind speed across these regions fell within specific ranges: Jaman North (±25.72), Jaman South (±25.89), and Wenchi (±26.04). Following the DTW similarity evaluation, Jaman North demonstrated superior performance in wind speed, while Wenchi excelled in wind direction. This underscores the potential efficiency of DTW when incorporated into the analysis of environmental factors affecting crop yields, given its invariant nature. The results obtained can guide further exploration of DTW variations in combination with other machine learning models to predict higher cashew yields. Additionally, these findings emphasize the significance of wind speed and direction in vertical farming, contributing to informed decisions for sustainable agricultural growth and development. creator: Bright Bediako-Kyeremeh creator: TingHuai Ma creator: Huan Rong creator: Benjamin Kwapong Osibo creator: Lorenzo Mamelona creator: Isaac Kofi Nti creator: Lord Amoah uri: https://doi.org/10.7717/peerj.16538 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bediako-Kyeremeh et al. title: Preeclampsia in pregnant women with COVID-19: a prospective cohort study from two tertiary hospitals in Southern Brazil link: https://peerj.com/articles/17481 last-modified: 2024-06-11 description: BackgroundCOVID-19 is an infectious pathology that shows vascular changes during pregnancy, as well as in the placentas. The main objectives of this study were to estimate the prevalence and the risk factors for preeclampsia in hospitalized pregnant women with COVID-19. As well as comparing maternal and perinatal outcomes in hospitalized pregnant women with COVID-19 and preeclampsia with those without preeclampsia.MethodsProspective cohort study of 100 hospitalized pregnant women from two tertiary hospitals, diagnosed with COVID-19, and divided into two groups: PE+ group (pregnant women with COVID-19 and preeclampsia) and PE- group (pregnant women with COVID-19 without preeclampsia). These pregnant women had prevalence, risk factors, maternal and perinatal data analyzed.ResultsThe prevalence of preeclampsia was 11%. Severe COVID-19 was the main risk factor for preeclampsia (OR = 8.18 [CI 1.53–43.52]), as well as fetal growth restriction was the main perinatal outcome (OR = 8.90 [CI 1.52–38.4]). Comorbidities were more frequent in the PE+ group (63.6% vs 31.5%, p = 0.03), as well as prematurity (81.8% vs 41.6%, p = 0.02), low birth weight (63.6% vs 24.7%, p = 0.01), and the need for neonatal intensive care admission of the newborn (63.6% vs 27.0%, p = 0.03). Pregnant women with PE had twice as long a length of stay in the intensive care unit (RR = 2.35 [CI 1.34–4.14]). Although maternal mortality was more frequent among pregnant women with PE, it was not statistically significant.ConclusionsPrevalence of preeclampsia in hospitalized pregnant women with COVID-19 was 11%. Severe COVID-19 was the main risk factor for preeclampsia and associated comorbidities increased the risk for developing preeclampsia. Long length of stay in the intensive care unit was the main maternal outcome and fetal growth restriction was the main perinatal outcome of preeclampsia. creator: Narcizo LEC Sobieray creator: Newton S. Carvalho creator: Cynthia F. Klas creator: Isabella N. Furuie creator: Jullie A. Chiste creator: Cyllian A. Fugaça creator: Jessica S. Longo creator: Juliana D. Oliveira creator: Sérgio L. Padilha uri: https://doi.org/10.7717/peerj.17481 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Sobieray et al. title: Using bioluminescence as a tool for studying diversity in marine zooplankton and dinoflagellates: an initial assessment link: https://peerj.com/articles/17516 last-modified: 2024-06-11 description: Bioluminescence is light chemically produced by an organism. It is widespread across all major marine phyla and has evolved multiple times, resulting in a high diversity of spectral properties and first flash kinetic parameters (FFKP). The bioluminescence of a system is often a good proxy for planktonic biomass. The species-specific parameters of bioluminescent displays can be measured to identify species in situ and describe planktonic biodiversity. Most bioluminescent organisms will flash when mechanically stimulated i.e., when subjected to supra-threshold levels of shear stress. Here we compare first flash kinetic parameters such as flash duration, peak intensity, rise time, decay time, first-flash mechanically stimulated light and e-folding time obtained with the commercially available Underwater Bioluminescence Assessment Tool (UBAT). We provide descriptions of the first flash kinetic parameters of several species of dinoflagellates Pyrocystis fusiformis, Pyrocystis noctiluca, Pyrodinium bahamense, Lingulodinium polyedra, Alexandrium monilatum and two zooplankton (the ctenophore Mnemiopsis leidyi and the larvacean Oikopleura sp.). FFKPs are then compared and discussed using non-parametric analyses of variance (ANOVAs), hierarchical clustering and a linear discriminant analysis to assess the ability to use bioluminescence signatures for identification. Once the first flash kinetic parameters of a bioluminescent species have been described, it is possible to detect its presence using emissions collected by in situ bathyphotometers. Assessing abundance and diversity of bioluminescent species may therefore be possible. creator: Francis Letendre creator: Abigail Blackburn creator: Ed Malkiel creator: Michael Twardowski uri: https://doi.org/10.7717/peerj.17516 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Letendre et al. title: Stress adaptive plasticity from Aegilops tauschii introgression lines improves drought and heat stress tolerance in bread wheat (Triticum aestivum L.) link: https://peerj.com/articles/17528 last-modified: 2024-06-11 description: Aegilops tauchii is a D-genome donor of hexaploid wheat and is a potential source of genes for various biotic and abiotic stresses including heat and drought. In the present study, we used multi-stage evaluation technique to understand the effects of heat and drought stresses on Ae. tauschii derived introgression lines (ILs). Preliminary evaluation (during stage-I) of 369 ILs for various agronomic traits identified 59 agronomically superior ILs. In the second stage (stage-II), selected ILs (i.e., 59 ILs) were evaluated for seedling heat (at 30 °C and 35 °C) and drought (at 20% poly-ethylene glycol; PEG) stress tolerance under growth chambers (stage-II). Heat and drought stress significantly reduced the seedling vigour by 59.29 and 60.37 percent, respectively. Genotype × treatment interaction analysis for seedling vigour stress tolerance index (STI) identified IL-50, IL-56, and IL-68 as high-performing ILs under heat stress and IL-42 and IL-44 as high-performing ILs under drought stress. It also revealed IL-44 and IL-50 as the stable ILs under heat and drought stresses. Furthermore, in the third stage (stage-III), selected ILs were evaluated for heat and drought stress tolerance under field condition over two cropping seasons (viz., 2020–21 and 2021–22), which significantly reduced the grain yield by 72.79 and 48.70 percent, respectively. Stability analysis was performed to identify IL-47, IL-51, and IL-259 as the most stable ILs in stage-III. Tolerant ILs with specific and wider adaptability identified in this study can serve as the potential resources to understand the genetic basis of heat and drought stress tolerance in wheat and they can also be utilized in developing high-yielding wheat cultivars with enhanced heat and drought stress tolerance. creator: Santosh Gudi creator: Mohit Jain creator: Satinder Singh creator: Satinder Kaur creator: Puja Srivastava creator: Gurvinder Singh Mavi creator: Parveen Chhuneja creator: Virinder Singh Sohu creator: Fatmah A. Safhi creator: Diaa Abd El-Moneim creator: Achla Sharma uri: https://doi.org/10.7717/peerj.17528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gudi et al. title: A hyaena on stilts: comparison of the limb morphology of Ictitherium ebu (Mammalia: Hyaenidae) from the Late Miocene of Lothagam, Turkana Basin, Kenya with extant Canidae and Hyaenidae link: https://peerj.com/articles/17405 last-modified: 2024-06-10 description: The long, gracile morphology of the limb bones of the Late Miocene hyaenid Ictitherium ebu has led to the hypothesis that this animal was cursorial. The forelimb and femur of the holotype were compared with specimens of extant Hyaenidae and Canidae. Two morphometric methods were used. The first used measurements to calculate indices of different morphological characters. The second method involved capturing photographs of the anterior distal humerus of each specimen, mapping six landmarks on them, and calculating truss distances. These distances represent a schematic reproduction of the elbow. Multivariate statistical analysis primarily separated the data based on taxonomy, yet locomotor and habitat categories were also considered. Ictitherium ebu has an overall morphology similar to that of the maned wolf and a distal humerus reminiscent of that of the aardwolf. The long, gracile limb bones of I. ebu are suggested to be adaptations for pouncing on prey, for locomotor efficiency, and for looking over the tall grass of the open environments the animal lived in, much like the present-day maned wolf. creator: Julien van der Hoek creator: Lars Werdelin uri: https://doi.org/10.7717/peerj.17405 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 van der Hoek and Werdelin title: Phenethyl isothiocyanate inhibits the carcinogenic properties of hepatocellular carcinoma Huh7.5.1 cells by activating MAPK/PI3K-Akt/p53 signaling pathways link: https://peerj.com/articles/17532 last-modified: 2024-06-10 description: BackgroundHepatocellular carcinoma (HCC) is an aggressive malignancy with limited effective treatment options. Phenethyl isothiocyanate (PEITC) is a bioactive substance present primarily in the cruciferous vegetables. PEITC has exhibited anti-cancer properties in various cancers, including lung, bile duct, and prostate cancers. It has been demonstrated that PEITC can inhibit the proliferation, invasion, and metastasis of SK-Hep1 cells, while effectively inducing apoptosis and cell cycle arrest in HepG2 cells. However, knowledge of its anti-carcinogenic effects on Huh7.5.1 cells and its underlying mechanism remains elusive. In the present study, we aim to evaluate the anti-carcinogenic effects of PEITC on human HCC Huh7.5.1 cells.MethodsMTT assay and colony formation assay was performed to investigate the anti-proliferative effects of PEITC against Huh7.5.1 cells. The pro-apoptosis effects of PEITC were determined by Annexin V-FITC/PI double staining assay by flow cytometry (FCM), mitochondrial transmembrane potential (MMP) measurement, and Caspase-3 activity detection. A DAPI staining and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay was conducted to estimate the DNA damage in Huh7.5.1 cells induced by PEITC. Cell cycle progression was determined by FCM. Transwell invasion assay and wound healing migration assay were performed to investigate the impact of PEITC on the migration and invasion of Huh7.5.1 cells. In addition, transcriptome sequencing and gene set enrichment analysis (GSEA) were used to explore the potential molecular mechanisms of the inhibitory effects of PEITC on HCC. Quantitative real-time PCR (qRT-PCR) analysis was performed to verify the transcriptome data.ResultsMTT assay showed that treatment of Huh7.5.1 cells with PEITC resulted in a dose-dependent decrease in viability, and colony formation assay further confirmed its anti-proliferative effect. Furthermore, we found that PEITC could induce mitochondrial-related apoptotic responses, including a decrease of mitochondrial transmembrane potential, activation of Caspase-3 activity, and generation of intracellular reactive oxygen species. It was also observed that PEITC caused DNA damage and cell cycle arrest in the S-phase in Huh7.5.1 cells. In addition, the inhibitory effect of PEITC on the migration and invasion ability of Huh7.5.1 cells was assessed. Transcriptome sequencing analysis further suggested that PEITC could activate the typical MAPK, PI3K-Akt, and p53 signaling pathways, revealing the potential mechanism of PEITC in inhibiting the carcinogenic properties of Huh7.5.1 cells.ConclusionPEITC exhibits anti-carcinogenic activities against human HCC Huh7.5.1 cells by activating MAPK/PI3K-Akt/p53 signaling pathways. Our results suggest that PEITC may be useful for the anti-HCC treatment. creator: Jiao Du creator: Yuting Zhang creator: Jiajia Chen creator: Libo Jin creator: Liying Pan creator: Pengyu Lei creator: Sue Lin uri: https://doi.org/10.7717/peerj.17532 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Du et al. title: Adoption of CRISPR-Cas for crop production: present status and future prospects link: https://peerj.com/articles/17402 last-modified: 2024-06-07 description: BackgroundGlobal food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time.MethodsThis review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security.ResultsThe review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops.ConclusionDespite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality. creator: Akinlolu Olalekan Akanmu creator: Michael Dare Asemoloye creator: Mario Andrea Marchisio creator: Olubukola Oluranti Babalola uri: https://doi.org/10.7717/peerj.17402 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Akanmu et al. title: Baseline haematological parameters in three common Australian frog species link: https://peerj.com/articles/17406 last-modified: 2024-06-07 description: Amphibians are experiencing declines globally, with emerging infectious diseases as one of the main causes. Haematological parameters present a useful method for determining the health status of animals and the effects of particular diseases, but the interpretation of differential cell counts relies on knowing the normal ranges for the species and factors that can affect these counts. However, there is very little data on either normal haematological parameters or guides for blood cell types for free-ranging frog species across the world. This study aims to 1) create a visual guide for three different Australian frog species: Litoria paraewingi, Limnodynastes dumerilii, and Crinia signifera, 2) determine the proportions of erythrocytes to leukocytes and 3) differential leukocytes within blood smears from these three species and 4) assess the association between parasites and differential counts. We collected blood samples from free-ranging frogs and analysed blood smears. We also looked for ectoparasites and tested for the fungal disease chytridiomycosis. Overall, we found that the differentials of erythrocytes to leukocytes were not affected by species, but the proportions of different leukocytes did vary across species. For example, while lymphocytes were the most common type of leukocyte across the three species, eosinophils were relatively common in Limnodynastes dumerilii but rarely present in the other two species. We noted chytridiomycosis infection as well as ectoparasites present in some individuals but found no effect of parasites on blood parameters. Our results add baseline haematological parameters for three Australian frog species and provide an example of how different frog species can vary in their differential blood cell counts. More information is needed on frog haematological data before these parameters can be used to determine the health status of wild or captive frogs. creator: Tara Jadwani-Bungar creator: Nicholas P. Doidge creator: Danielle K. Wallace creator: Laura A. Brannelly uri: https://doi.org/10.7717/peerj.17406 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Jadwani-Bungar et al. title: Comparative study of the gut microbial community structure of Spodoptera frugiperda and Spodoptera literal (Lepidoptera) link: https://peerj.com/articles/17450 last-modified: 2024-06-07 description: BackgroundSpodoptera frugiperda, the fall armyworm is a destructive invasive pest, and S. litura the tobacco cutworm, is a native species closely related to S. frugiperda. The gut microbiota plays a vital role in insect growth, development, metabolism and immune system. Research on the competition between invasive species and closely related native species has focused on differences in the adaptability of insects to the environment. Little is known about gut symbiotic microbe composition and its role in influencing competitive differences between these two insects.MethodsWe used a culture-independent approach targeting the 16S rRNA gene of gut bacteria of 5th instar larvae of S. frugiperda and S. litura. Larvae were reared continuously on maize leaves for five generations. We analyzed the composition, abundance, diversity, and metabolic function of gut microbiomes of S. frugiperda and S. litura larvae.ResultsFirmicutes, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in both species. Enterococcus, ZOR0006, Escherichia, Bacteroides, and Lactobacillus were the genera with the highest abundance in S. frugiperda. Enterococcus, Erysipelatoclostridium, ZOR0006, Enterobacter, and Bacteroides had the highest abundance in S. litura. According to α-diversity analysis, the gut bacterial diversity of S. frugiperda was significantly higher than that of S. litura. KEGG analysis showed 15 significant differences in metabolic pathways between S. frugiperda and S. litura gut bacteria, including transcription, cell growth and death, excretory system and circulatory system pathways.ConclusionIn the same habitat, the larvae of S. frugiperda and S. litura showed significant differences in gut bacterial diversity and community composition. Regarding the composition and function of gut bacteria, the invasive species S. frugiperda may have a competitive advantage over S. litura. This study provides a foundation for developing control strategies for S. frugiperda and S. litura. creator: Yaping Chen creator: Yao Chen creator: Yahong Li creator: Ewei Du creator: Zhongxiang Sun creator: Zhihui Lu creator: Furong Gui uri: https://doi.org/10.7717/peerj.17450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: Agreement and differences between the equations for estimating muscle and bone mass using the anthropometric method in recreational strength trainees link: https://peerj.com/articles/17506 last-modified: 2024-06-07 description: IntroductionThe interest in estimating muscle mass (MM) and bone mass (BM) has grown in the sporting arena, and more specifically in recreational strength trainees, leading to the creation of different strategies to assess them. The aims were: 1) to investigate the agreement between different MM and BM formulas, and the muscle-bone index (MBI), and to establish the differences between them, in a healthy young adult population; and 2) to analyze if there are differences between males and females in the comparison of MM, BM and MBI formulas.MethodsThis study followed a descriptive cross-sectional design. A total of 130 adult active recreational strength trainees were evaluated according to the procedures described by the International Society for the Advancement in Kinanthropometry (ISAK). Estimations were made in kilograms of MM and BM by following the equations by different authors.ResultsThe results showed significant differences between the values obtained by all the MM and BM formulas in the general sample (p < 0.001), and by the majority of formulas for male and female samples. In the general sample, Lin’s coefficient indicated a strong agreement between Kerr, Lee, and Poortmans’ MM estimation equations (concordance correlation coefficient (CCC) = 0.96–0.97). However, when stratifying by sex, this agreement persisted only in males (CCC = 0.90–0.94), in contrast with a lack of agreement observed in females (CCC < 0.90). Discrepancies in bone mass agreement were noted both in the general sample (CCC < 0.15) and when stratified by sex (CCC < 0.12).ConclusionsIn general, differences were found between the values reported by the MM and BM formulas in recreational strength trainees, without an agreement between them. Sex was shown to significantly influence the differences found. The practical implications are that when comparing an individual with reference tables, other studies, or if analyzing an individual’s evolution, the same estimation equation should be used, as they are not interchangeable. creator: Nicolás Baglietto creator: Mario Albaladejo-Saura creator: Francisco Esparza-Ros creator: Raquel Vaquero-Cristóbal uri: https://doi.org/10.7717/peerj.17506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Baglietto et al. title: Research advances in predicting the expansion of hypertensive intracerebral hemorrhage based on CT images: an overview link: https://peerj.com/articles/17556 last-modified: 2024-06-07 description: Hematoma expansion (HE) is an important risk factor for death or poor prognosis in patients with hypertensive intracerebral hemorrhage (HICH). Accurately predicting the risk of HE in patients with HICH is of great clinical significance for timely intervention and improving patient prognosis. Many imaging signs reported in literatures showed the important clinical value for predicting HE. In recent years, the development of radiomics and artificial intelligence has provided new methods for HE prediction with high accuracy. Therefore, this article reviews the latest research progress in CT imaging, radiomics, and artificial intelligence of HE, in order to help identify high-risk patients for HE in clinical practice. creator: Min Ai creator: Hanghang Zhang creator: Junbang Feng creator: Hongying Chen creator: Di Liu creator: Chang Li creator: Fei Yu creator: Chuanming Li uri: https://doi.org/10.7717/peerj.17556 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Ai et al. title: The antimicrobial activity of tea tree oil (Melaleuca alternifolia) and its metal nanoparticles in oral bacteria link: https://peerj.com/articles/17241 last-modified: 2024-06-06 description: Tea tree (Melaleuca alternifolia) oil (TTO) is an antimicrobial agent, and hence, its use in fabricating nanoparticles (NP) may be useful in providing more efficacious antimicrobial agents. The current research aimed to test the antimicrobial efficacy of TTO and its TTO-Metal-NPs against oral microbes: Porphyromonas gingivalis, Enterococcus faecalis, and Streptococcus mutans. The antimicrobial activity of TTO and zinc (Zn) and iron (Fe) nanoparticles (NPs) and the combined effects of antimicrobial agents were investigated using agar well diffusion assays. Fourier-transform infrared spectroscopy (FT-IR) was used to identify the phyto-constituents of TTO. Field emission scanning electron microscopy (FE-SEM), dynamic light scatter (DLS), and zeta potential were utilized to analyze the biogenic nanoparticles’ morphology, size, and potential. The antimicrobial mode of action was determined by assessing the morphological changes under scanning electron microscopy (SEM). The TTO extracts converted Zn and Fe ions to NPs, having an average size of 97.50 (ZnNPs) and 102.4 nm (FeNPs). All tested agents had significant antibacterial efficacy against the tested oral microbes. However, the TTO extract was more efficacious than the NPs. Combination treatment of TTO with antibiotics resulted in partial additive effects against P. gingivalis and partial antagonistic effects against E. faecalis, S. mutans, and common mouthwashes (Oral B and chlorhexidine). TTO and NP-treated bacteria underwent morphological changes on treatment. M. alternifolia phytochemicals could be useful for further research and development of antimicrobial NPs. The current study highlights the variance in activity observed for different types of bacteria and antagonistic effects seen with common mouthwashes, which represent a threat to therapeutic efficacy and heighten the risk of clinical microbial resistance. creator: Afrah E. Mohammed creator: Reham M. Aldahasi creator: Ishrat Rahman creator: Ashwag Shami creator: Modhi Alotaibi creator: Munerah S. BinShabaib creator: Shatha S. ALHarthi creator: Kawther Aabed uri: https://doi.org/10.7717/peerj.17241 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mohammed et al. title: Lumbar extension peak-torque, muscle endurance and motor imagery in junior-elite basketballers with and without a history of low back pain: a pilot study link: https://peerj.com/articles/17508 last-modified: 2024-06-06 description: ObjectivesLow back pain (LBP) is common in elite athletes. Several peripheral and central factors have been identified to be altered in non-athletic LBP populations, however whether these alterations also exist in elite athletes with LBP is unknown. The aim of this study was to determine whether elite basketballers with a history of persistent LBP perform worse than those without LBP at a lumbar muscle endurance task, a lumbar extension peak-torque task, and a lumbar motor imagery task.MethodAn observational pilot study. Twenty junior elite-level male basketballers with (n = 11) and without (n = 9) a history of persistent LBP were recruited. Athletes completed a lumbar extensor muscle endurance (Biering-Sorensen) task, two lumbar extensor peak-torque (modified Biering-Sorensen) tasks and two motor imagery (left/right lumbar and hand judgement) tasks across two sessions (48 hours apart). Performance in these tasks were compared between the groups with and without a history of LBP.ResultsYoung athletes with a history of LBP had reduced lumbar extensor muscle endurance (p < 0.001), reduced lumbar extension peak-torque (p < 0.001), and were less accurate at the left/right lumbar judgement task (p = 0.02) but no less accurate at a left/right hand judgement task (p = 0.59), than athletes without a history of LBP. Response times for both left/right judgement tasks did not differ between groups (lumbar p = 0.24; hand p = 0.58).ConclusionsJunior elite male basketballers with a history of LBP demonstrate reduced lumbar extensor muscle endurance and lumbar extension peak-torque and are less accurate at a left/right lumbar rotation judgement task, than those without LBP. creator: Tim Glazebrook creator: Jennifer Cooke creator: Gordon Waddington creator: Sarah B. Wallwork uri: https://doi.org/10.7717/peerj.17508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Glazebrook et al. title: Movement patterns of two reintegrated African elephant (Loxodonta africana) herds: transitioning from captivity to free-living link: https://peerj.com/articles/17535 last-modified: 2024-06-06 description: With the escalating challenges in captive elephant management, the study of elephant reintegration emerges as a pivotal area of research, primarily addressing the enhancement of animal welfare. The term ‘reintegration’ refers to the process of rehabilitating captive elephants to a natural system, allowing them to roam freely without intensive human intervention. There is a relative paucity of research addressing the behavioural adaptations post-reintegration, despite reintegration of over 20 elephants across various fenced reserves in South Africa. Our study centres on two distinct herds of reintegrated African elephants, monitoring their movement patterns in two South African reserves over a 57-month period post-release. The primary goal of the study was to establish whether the flexibility and adaptability of movement behaviour of reintegrated elephants can be considered as one of the indicators of determining the success of such an operation. The second aim of our study was to investigate if the reintegrated elephants demonstrated an adaptability to their environment through their hourly, daily, and seasonal ranging patterns after a period of free roaming that exceeded 4 years. Our findings indicated that reintegrated elephants, much like their wild counterparts (movement based on literature), displayed notable seasonal and diurnal variations in key movement parameters, such as utilisation distribution areas and reserve utilization. These patterns changed over time, reflecting an adaptive shift in movement patterns after several years of free roaming. Notably, the trajectory of changes in movement parameters varied between herds, indicating unique adaptation responses, likely resulting from differences in the reintegration process (familiarity of reserve, season of release, presence of wild elephants). Although our study is constrained by the limited number of reintegrated herds available for analysis, it underscores the potential of captive elephants to successfully adapt to a free-living environment, emphasising the promising implications of reintegration initiatives. creator: Tenisha Roos creator: Andrew Purdon creator: Victoria Boult creator: Audrey Delsink creator: Brett Mitchell creator: Petrus Johannes Kilian uri: https://doi.org/10.7717/peerj.17535 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Roos et al. title: Electrocortical theta activity may reflect sensory prediction errors during adaptation to a gradual gait perturbation link: https://peerj.com/articles/17451 last-modified: 2024-06-05 description: Locomotor adaptation to abrupt and gradual perturbations are likely driven by fundamentally different neural processes. The aim of this study was to quantify brain dynamics associated with gait adaptation to a gradually introduced gait perturbation, which typically results in smaller behavioral errors relative to an abrupt perturbation. Loss of balance during standing and walking elicits transient increases in midfrontal theta oscillations that have been shown to scale with perturbation intensity. We hypothesized there would be no significant change in anterior cingulate theta power (4–7 Hz) with respect to pre-adaptation when a gait perturbation is introduced gradually because the gradual perturbation acceleration and stepping kinematic errors are small relative to an abrupt perturbation. Using mobile electroencephalography (EEG), we measured gait-related spectral changes near the anterior cingulate, posterior cingulate, sensorimotor, and posterior parietal cortices as young, neurotypical adults (n = 30) adapted their gait to an incremental split-belt treadmill perturbation. Most cortical clusters we examined (>70%) did not exhibit changes in electrocortical activity between 2–50 Hz. However, we did observe gait-related theta synchronization near the left anterior cingulate cortex during strides with the largest errors, as measured by step length asymmetry. These results suggest gradual adaptation with small gait asymmetry and perturbation magnitude may not require significant cortical resources beyond normal treadmill walking. Nevertheless, the anterior cingulate may remain actively engaged in error monitoring, transmitting sensory prediction error information via theta oscillations. creator: Noelle A. Jacobsen creator: Daniel Perry Ferris uri: https://doi.org/10.7717/peerj.17451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Jacobsen et al. title: Fast grassland recovery from viable propagules after reintroducing traditional mowing management on a steep slope link: https://peerj.com/articles/17487 last-modified: 2024-06-05 description: Semi-natural grasslands on steep slopes often show high plant species diversity. These grasslands were traditionally maintained through mowing and/or grazing. The traditional management practices help to maintain species diversity, whereas land abandonment reduces diversity by increasing competition from dominant species and reducing seedling recruitment. The reintroduction of management can reverse species diversity declines, but suitable grassland restoration programs are scarce in Japan. To study the effect of short-term abandonment on seedling ecology, we monitored the vegetation of a Susogari grassland that had been abandoned for 3 years; the grassland occupies a steep slope (ca. 50°) on a hillside above paddy fields, and was traditionally mown. We monitored the vegetation before abandonment, in the 3rd year of abandonment, and in the 1st and 2nd years after restoration of mowing management. Emergence and survival of seedlings was monitored for 18 months after reintroduction of management. We monitored 1,183 seedlings of grassland species and non-target annuals in ten 1-m2 plots. After mowing was reintroduced, most grassland species reappeared or increased in the first and second years. Few seedlings of perennial plants and no seedlings of annuals flowered. An exotic species, Solidago altissima, had a lower survival rate (10%) than grassland species (>30%), and all but two grassland species survived over the 18-month period. Although vegetation composition was not fully recovered, our findings suggest that a steep slope acts as a strong filter that inhibits the establishment of non-target species while enhancing persistence of target grassland species. creator: Susumu Yamada creator: Wakana Yoshida creator: Minori Iida creator: Yoshiko Kitagawa creator: Jonathan Mitchley uri: https://doi.org/10.7717/peerj.17487 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Yamada et al. title: Predictive value of plasma ephrinB2 levels for amputation risk following endovascular revascularization in peripheral artery disease link: https://peerj.com/articles/17531 last-modified: 2024-06-05 description: BackgroundThe aim of this study is to investigate the expression levels of ephrinB2 in patients with lower extremity peripheral arterial disease (PAD) and explore its association with the severity of the disease and the risk of amputation after endovascular revascularization.MethodsDuring the period from March 2021 to March 2023, this study collected blood samples and clinical data from 133 patients diagnosed with lower extremity PAD and 51 healthy volunteer donors. The severity of lower extremity PAD patients was classified using the Rutherford categories. The expression of ephrin-B2 in plasma samples was detected using the Western Blotting.ResultsCompared to the control group, the levels of serum ephrinB2 in patients were significantly elevated (p < 0.001). Moreover, the plasma EphrinB2 levels were positively correlated with white blood cell counts (r = 0.204, p = 0.018), neutrophil counts (r = 0.174, p = 0.045), and neutrophil-to-lymphocyte ratio (NLR) (r = 0.223, p = 0.009). Furthermore, the AUCs of plasma ephrinB2 level, NLR, and their combination as predictors for amputation events within 30 months after lower extremity PAD endovascular revascularization were 0.659, 0.730 and 0.811. In the high-ephrinB2 group, the incidence of amputation events within 30 months after endovascular revascularization was higher.ConclusionsPlasma EphrinB2 levels may be linked to lower extremity PAD development, inflammation, and postoperative amputation. Combining EphrinB2 and NLR can improve amputation prediction accuracy after endovascular revascularization in lower extremity PAD patients. creator: Pengcheng Guo creator: Lei Chen creator: Dafeng Yang creator: Lei Zhang creator: Chang Shu creator: Huande Li creator: Jieting Zhu creator: Jienan Zhou creator: Xin Li uri: https://doi.org/10.7717/peerj.17531 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guo et al. title: Land cover and space use influence coyote carnivory: evidence from stable-isotope analysis link: https://peerj.com/articles/17457 last-modified: 2024-06-04 description: For many species, the relationship between space use and diet composition is complex, with individuals adopting varying space use strategies such as territoriality to facilitate resource acquisition. Coyotes (Canis latrans) exhibit two disparate types of space use; defending mutually exclusive territories (residents) or moving nomadically across landscapes (transients). Resident coyotes have increased access to familiar food resources, thus improved foraging opportunities to compensate for the energetic costs of defending territories. Conversely, transients do not defend territories and are able to redirect energetic costs of territorial defense towards extensive movements in search of mates and breeding opportunities. These differences in space use attributed to different behavioral strategies likely influence foraging and ultimately diet composition, but these relationships have not been well studied. We investigated diet composition of resident and transient coyotes in the southeastern United States by pairing individual space use patterns with analysis of stable carbon (δ13C) and nitrogen (δ15N) isotope values to assess diet. During 2016–2017, we monitored 41 coyotes (26 residents, 15 transients) with GPS radio-collars along the Savannah River area in the southeastern United States. We observed a canopy effect on δ13C values and little anthropogenic food in coyote diets, suggesting 13C enrichment is likely more influenced by reduced canopy cover than consumption of human foods. We also observed other land cover effects, such as agricultural cover and road density, on δ15N values as well as reduced space used by coyotes, suggesting that cover types and localized, resident-like space use can influence the degree of carnivory in coyotes. Finally, diets and niche space did not differ between resident and transient coyotes despite differences observed in the proportional contribution of potential food sources to their diets. Although our stable isotope mixing models detected differences between the diets of resident and transient coyotes, both relied mostly on mammalian prey (52.8%, SD = 15.9 for residents, 42.0%, SD = 15.6 for transients). Resident coyotes consumed more game birds (21.3%, SD = 11.6 vs 13.7%, SD = 8.8) and less fruit (10.5%, SD = 6.9 vs 21.3%, SD = 10.7) and insects (7.2%, SD = 4.7 vs 14.3%, SD = 8.5) than did transients. Our findings indicate that coyote populations fall on a feeding continuum of omnivory to carnivory in which variability in feeding strategies is influenced by land cover characteristics and space use behaviors. creator: Sarah C. Webster creator: Joseph W. Hinton creator: Michael J. Chamberlain creator: Jazmin J. Murphy creator: James C. Beasley uri: https://doi.org/10.7717/peerj.17457 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Webster et al. title: Mitigating NaCl stress in Vigna radiata L. cultivars using Bacillus pseudomycoides link: https://peerj.com/articles/17465 last-modified: 2024-06-04 description: Salt stress is one of the significant abiotic stress factors that exert harmful effects on plant growth and yield. In this study, five cultivars of mung bean (Vigna radiata L.) were treated with different concentrations of NaCl and also inoculated with a salt-tolerant bacterial strain to assess their growth and yield. The bacterial strain was isolated from the saline soil of Sahiwal District, Punjab, Pakistan and identified as Bacillus pseudomycoides. Plant growth was monitored at 15-days interval and finally harvested after 120 days at seed set. Both sodium and potassium uptake in above and below-ground parts were assessed using a flame photometer. Fresh and dry mass, number of pods, seeds per plant, weight of seeds per plant and weight of 100 seeds reduced significantly as the concentration of NaCl increased from 3 to 15 dSm−1. There was a significant reduction in the growth and yield of plants exposed to NaCl stress without bacterial inoculum compared to the plants with bacterial inoculum. The latter plants showed a significant increase in the studied parameters. It was found that the cultivar Inqelab mung showed the least reduction in growth and yield traits among the studied cultivars, while Ramzan mung showed the maximum reduction. Among all the cultivars, maximum Na+ uptake occurred in roots, while the least uptake was observed in seeds. The study concludes that NaCl stress significantly reduces the growth and yield of mung bean cultivars, but Bacillus pseudomycoides inoculum alleviates salt stress. These findings will be helpful to cultivate the selected cultivars in soils with varying concentrations of NaCl. creator: Bushra Bilal creator: Zafar Siddiq creator: Tehreema Iftikhar creator: Muhammad Umar Hayyat uri: https://doi.org/10.7717/peerj.17465 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bilal et al. title: Identification of proteins related to SIS3 by iTRAQ and PRM-based comparative proteomic analysis in cisplatin-induced acute kidney injury link: https://peerj.com/articles/17485 last-modified: 2024-06-04 description: BackgroundCisplatin is a commonly used nephrotoxic drug and can cause acute kidney injury (AKI). In the present study, isobaric tags for relative and absolute quantification (iTRAQ) and parallel reaction monitoring (PRM)-based comparative proteomics were used to analyze differentially expressed proteins (DEPs) to determine the key molecular mechanism in mice with cisplatin-induced AKI in the presence or absence of SIS3, a specific p-smad3 inhibitor, intervention.MethodsThe cisplatin-induced AKI mouse model was established and treated with SIS3. We used iTRAQ to search for DEPs, PRM to verify key DEPs and combined Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for bioinformatics analysis. We then assessed lipid deposition, malondialdehyde (MDA) and reactive oxygen species (ROS) and detected the expression of SREBF1, SCD1, CPT1A, PPARα and NDRG1 in vitro.ResultsProteomic analysis showed that the identified DEPs were mainly enriched in energy metabolism pathways, especially in lipid metabolism. When SIS3 was applied to inhibit the phosphorylation of Smad3, the expression of NDRG1 and fatty acid oxidation key proteins CPT1A and PPARα increased, the expression of lipid synthesis related proteins SREBF1 and SCD1 decreased and the production of lipid droplets, MDA and ROS decreased.ConclusionSIS3 alleviates oxidative stress, reduces lipid accumulation and promotes fatty acid oxidation through NDRG1 in cisplatin-induced AKI. Our study provides a new candidate protein for elucidating the molecular mechanisms of fatty acid metabolism disorders in cisplatin-induced acute kidney injury. creator: Jiayan Huang creator: Jian Ye creator: Yi Gao creator: Yu Wang creator: Qing Zhao creator: Tanqi Lou creator: Weiyan Lai uri: https://doi.org/10.7717/peerj.17485 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Huang et al. title: Role of the transient receptor potential melastatin 4 in inhibition effect of arsenic trioxide on the tumor biological features of colorectal cancer cell link: https://peerj.com/articles/17559 last-modified: 2024-06-04 description: BackgroundTo investigate the effects of arsenic trioxide (ATO) on human colorectal cancer cells (HCT116) growth and the role of transient receptor potential melastatin 4 (TRPM4) channel in this process.MethodsThe viability of HCT116 cells was assessed using the CCK-8 assay. Western blot analysis was employed to examine the protein expression of TRPM4. The apoptosis of HCT116 cells was determined using TUNEL and Flow cytometry. Cell migration was assessed through the cell scratch recovery assay and Transwell cell migration assay. Additionally, Transwell cell invasion assay was performed to determine the invasion ability of HCT116 cells.ResultsATO suppressed the viability of HCT116 cells in a dose-dependent manner, accompanied by a decline in cell migration and invasion, and an increase in apoptosis. 9-phenanthroline (9-Ph), a specific inhibitor of TRPM4, abrogated the ATO-induced upregulation of TRPM4 expression. Additionally, blocking TRPM4 reversed the effects of ATO on HCT116 cells proliferation, including restoration of cell viability, migration and invasion, as well as the inhibition of apoptosis.ConclusionATO inhibits CRC cell growth by inducing TRPM4 expression, our findings indicate that ATO is a promising therapeutic strategy and TRPM4 may be a novel target for the treatment of CRC. creator: Zhan Gao creator: Jing Lv creator: Ting-Ting Tong creator: Kai Zhang creator: Yu-Xuan Han creator: Yu Zhao creator: Mei-Mei Shen creator: Yang Liu creator: Tao Ban creator: Yu Sun uri: https://doi.org/10.7717/peerj.17559 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Gao et al. title: The role of attention bias malleability in experiencing pain and associated disability link: https://peerj.com/articles/17430 last-modified: 2024-06-03 description: BackgroundAttentional processing of pain has been theorized to play a key role in the severity of pain and associated disability. In particular attentional bias towards pain information, resulting in poor pain outcomes, has been extensively researched. Recently, the idea was put forward that attention bias malleability (AM), i.e., the readiness to acquire an attentional bias irrespective of its direction, may be key in predicting poor pain outcomes. We tested this hypothesis in two studies.MethodsIn Study 1, 55 healthy participants completed an AM paradigm, followed by an experimental heat pain paradigm probing pain experience and pain-related task interference. In Study 2, 71 people with chronic pain completed an AM paradigm and questionnaires probing pain experience and associated disability.ResultsIn Study 1, including healthy participants, no relationship was found between AM indices and experimental pain outcomes. In Study 2, including chronic pain patients, results indicated that higher levels of overall AM were related to higher levels of pain experience and disability.ConclusionThis study partially supports the hypotheses that the degree to which individuals can adapt their attentional preference in line with changing environmental conditions is associated with poor pain outcomes. However, future research is needed to clarify inconsistent findings between healthy volunteers and chronic pain patients as well as to determine the causal status of AM in poor pain outcomes. creator: Justine L. Mac Goris creator: Jemma Todd creator: Patrick J.F. Clarke creator: Alicia M. Hughes creator: Claus Vögele creator: Dimitri M.L. Van Ryckeghem uri: https://doi.org/10.7717/peerj.17430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Mac Goris et al. title: Peripheral blood immune cell parameters in patients with high-grade squamous intraepithelial lesion (HSIL) and cervical cancer and their clinical value: a retrospective study link: https://peerj.com/articles/17499 last-modified: 2024-06-03 description: ObjectiveThe objective of this study was to delineate the profile of peripheral blood lymphocytic indices in patients afflicted with high-grade squamous intraepithelial lesions (HSIL) and cervical neoplasms, and to elucidate the correlation of these hematologic markers with the clinicopathological spectra in individuals diagnosed with cervical carcinoma.MethodsWe adopted a retrospective case-control modality for this investigation. An aggregate of 39 HSIL patients and 42 cervical carcinoma patients, who were treated in our facility from July 2020 to September 2023, were meticulously selected. Each case of cervical malignancy was confirmed through rigorous histopathological scrutiny. Concomitantly, 31 healthy female individuals, who underwent prophylactic health evaluations during the corresponding timeframe, were enlisted as the baseline control group. We systematically gathered and analyzed clinical demographics, as well as the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR), from peripheral blood samples. Pearson’s correlation coefficient was deployed to dissect the interrelation between peripheral NLR and PLR concentrations and the clinicopathological features in the cervical cancer group.ResultsInter-group comparative analysis unveiled statistically substantial variances in the PLR and NLR values among the tripartite clusters (F = 36.941, 14.998, P < 0.001, respectively). Although discrepancy in NLR (P = 0.061) and PLR (P = 0.759) measures between the groups of cervical carcinoma and HSIL was not statistically appreciable, these indices were markedly elevated in the cervical carcinoma faction as juxtaposed with the normative control group (t = 5.094, 5.927; P < 0.001 for both parameters). A discernible gradation in peripheral blood PLR and NLR concentrations was noted when stratified by clinical stage and the profundity of myometrial invasion in cervical cancer subjects (P < 0.001). The correlation matrix demonstrated a positive liaison between peripheral blood PLR and the clinical gradation, as well as the invasiveness of the neoplastic cells into the muscularis propria (P < 0.05); a similar trend was observed with the NLR values (P < 0.05).ConclusionAugmented NLR and PLR levels in peripheral blood specimens are indicative of HSIL and cervical malignancy. These hematological parameters exhibit a pronounced interconnection with clinical staging and muscular wall penetration depth, serving as potential discriminative biomarkers for the diagnosis and prognosis of cervical cancer. creator: Ling Wang creator: Yuyan Dong uri: https://doi.org/10.7717/peerj.17499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang and Dong title: Effect of oral tryptamines on the gut microbiome of rats—a preliminary study link: https://peerj.com/articles/17517 last-modified: 2024-06-03 description: BackgroundPsilocybin and related tryptamines have come into the spotlight in recent years as potential therapeutics for depression. Research on the mechanisms of these effects has historically focused on the direct effects of these drugs on neural processes. However, in addition to such neural effects, alterations in peripheral physiology may also contribute to their therapeutic effects. In particular, substantial support exists for a gut microbiome-mediated pathway for the antidepressant efficacy of other drug classes, but no prior studies have determined the effects of tryptamines on microbiota.MethodsTo address this gap, in this preliminary study, male Long Evans rats were treated with varying dosages of oral psilocybin (0.2 or 2 mg/kg), norbaeocystin (0.25 or 2.52 mg/kg), or vehicle and their fecal samples were collected 1 week and 3 weeks after exposure for microbiome analysis using integrated 16S ribosomal DNA sequencing to determine gut microbiome composition.ResultsWe found that although treatment with neither psilocybin nor norbaeocystin significantly affected overall microbiome diversity, it did cause significant dose- and time-dependent changes in bacterial abundance at the phylum level, including increases in Verrucomicrobia and Actinobacteria, and decreases in Proteobacteria.Conclusion and ImplicationsThese preliminary findings support the idea that psilocybin and other tryptamines may act on the gut microbiome in a dose- and time-dependent manner, potentially identifying a novel peripheral mechanism for their antidepressant activity. The results from this preliminary study also suggest that norbaeocystin may warrant further investigation as a potential antidepressant, given the similarity of its effects to psilocybin. creator: Mengyang Xu creator: Andor J. Kiss creator: J. Andrew Jones creator: Matthew S. McMurray creator: Haifei Shi uri: https://doi.org/10.7717/peerj.17517 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Xu et al. title: Characteristics and evolution of hemagglutinin and neuraminidase genes of Influenza A(H3N2) viruses in Thailand during 2015 to 2018 link: https://peerj.com/articles/17523 last-modified: 2024-06-03 description: BackgroundInfluenza A(H3N2) virus evolves continuously. Its hemagglutinin (HA) and neuraminidase (NA) genes have high genetic variation due to the antigenic drift. This study aimed to investigate the characteristics and evolution of HA and NA genes of the influenza A(H3N2) virus in Thailand.MethodsInfluenza A positive respiratory samples from 2015 to 2018 were subtyped by multiplex real-time RT-PCR. Full-length HA and NA genes from the positive samples of influenza A(H3N2) were amplified and sequenced. Phylogenetic analysis with the maximum likelihood method was used to investigate the evolution of the virus compared with the WHO-recommended influenza vaccine strain. Homology modeling and N-glycosylation site prediction were also performed.ResultsOut of 443 samples, 147 (33.18%) were A(H1N1)pdm09 and 296 (66.82%) were A(H3N2). The A(H3N2) viruses circulating in 2015 were clade 3C.2a whereas sub-clade 3C.2a1 and 3C.2a2 dominated in 2016–2017 and 2018, respectively. Amino acid substitutions were found in all antigenic sites A, B, C, D, and E of HA but the majority of the substitutions were located at antigenic sites A and B. The S245N and N329S substitutions in the NA gene affect the N-glycosylation. None of the mutations associated with resistance to NA inhibitors were observed. Mean evolutionary rates of the HA and NA genes were 3.47 × 10−3 and 2.98 × 10−3 substitutions per site per year.ConclusionThe influenza A(H3N2) virus is very genetically diverse and is always evolving to evade host defenses. The HA and NA gene features including the evolutionary rate of the influenza A(H3N2) viruses that were circulating in Thailand between 2015 and 2018 are described. This information is useful for monitoring the genetic characteristics and evolution in HA and NA genes of influenza A(H3N2) virus in Thailand which is crucial for predicting the influenza vaccine strains resulting in high vaccine effectiveness. creator: Sasiprapa Anoma creator: Parvapan Bhattarakosol creator: Ekasit Kowitdamrong uri: https://doi.org/10.7717/peerj.17523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Anoma et al.