title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2023-01 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Iron (oxyhydr)oxides are responsible for the stabilization of Cu and Zn in AMD after treatment with limestone link: https://peerj.com/articles/14663 last-modified: 2023-01-30 description: The formation and transformation of secondary iron (oxyhydr)oxides and their role in the stabilization of copper (Cu) and zinc (Zn) in acid mine drainage (AMD) after limestone treatment are worth studying to better understand the impacts of limestone AMD treatment. In this study, the wastewater from a copper mine ditch was sampled. Two different doses of limestone (S: 5.33 g L−1 and SS: 8.00 g L−1) were applied to adjust the pH range of the sampled AMD. The concentrations of Fe, Cu and Zn in the supernatant and the levels of iron (oxyhydr)oxides and heavy metals in AMD sediments were dynamically monitored for 300 days to analyze the transformation of the secondary iron mineral phase and the role iron (oxyhydr)oxides play in the removal and stabilization of Cu and Zn. The results showed that the pH rose rapidly to 6.82, decreased to 5.82 on the 150th day, and finally decreased to approximately 4.63 by the 300th day, when the dosage of limestone (S) was 5.33 g L−1. Goethite was the main form of iron oxides in the sediments. As the incubation time increased, so did the content of crystalline Fe (oxyhydr)oxides. In addition, the Cu and Zn content in the fraction of crystalline Fe (oxyhydr)oxides increased as the corresponding iron (oxyhydr)oxide increased. When the high dosage of limestone (8.00 g L−1 or SS) was applied, the pH remained at approximately at 7.46 during the whole period and goethite and lepidocrocite were present in the sediment. Amorphous/ poorly crystalline Fe-oxyhydroxide was the main product after SS limestone dosage, indicating that the risk of Cu and Zn reactivation in the sediment was higher with a higher limestone treatment dosage. creator: Yuan Ding creator: Yan Long creator: Weiya Wang creator: Zhe Wei creator: Shuo Cai uri: https://doi.org/10.7717/peerj.14663 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ding et al. title: Modeling knot features using branch scars from Mongolian oak (Quercus mongolica) link: https://peerj.com/articles/14755 last-modified: 2023-01-31 description: Wood quality is an important indicator for modern sawmills. Internal wood characteristics can be derived from their correlations with external appearances. In this study, we developed linear regression models to predict knot size from surface features of Mongolian oak (Quercus mongolica) using data collected from 53 trees. For this, manual measurements and X-ray computed tomography scanning technology was respectively used to obtain internal and external features of 1,297 knots. Our results showed that Mongolian oak knots were generally concentrated in the middle part of oak stems, with fewer knots observed at the top and base. The parameters of knot and scar showed significant correlations (P < 0.01), where length and diameter of the corresponding external scar increase with increasing the length and diameter of a knot. The corresponding external scar can be used as an effective indicator to predict the internal value of oak logs. The accuracy of our constructed model is more than 95% when assessed against independent test samples. These models thus can be applied to improve the practical production of oak timber and reduce commercial loss caused by knots. These additional data can improve the estimation of the influence of knots on wood quality and provide a theoretical foundation for investigating the characteristics of hardwood knots. creator: Xiu-jun Lu creator: Lei Wang creator: Hui-lin Gao creator: Hao Zhan creator: Xiao-lin Zhang uri: https://doi.org/10.7717/peerj.14755 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lu et al. title: The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research link: https://peerj.com/articles/14758 last-modified: 2023-01-31 description: BackgroundContinuous cultivation of ginseng crops in fixed plots can lead to disease outbreaks, yield losses and replanting failures. Fallow periods can help restore soil health and increase the sustainability of agricultural systems; however, taking land out of production for extended periods is often not feasible. Short-term fallow periods could restore soil health, but few studies have examined the effects of short-term fallow treatment on the health of soil in ginseng fields.MethodsIn this preliminary study, we used metagenomic analysis to assess changes in the abundance of major ginseng pathogens and soil health overall following a short-term fallow period in a region in the Changbai Mountains. A sample from a forest plot (Hx0ks), was compared to a sample from a field where ginseng was previously cultivated and then had been left fallow for two years (Hx2), and a sample from a field that had been fallow for two years and was subsequently replanted with ginseng (Clsd).ResultsSoil that was fallow for two years, and then replanted with ginseng, showed reduced nutrient content and lower diversity of soil bacterial and fungal communities than soil that remained fallow. Candidatus Solibacter (5%) and Rhizomicrobium (3%) were the most abudant bacterial genera in Hx2. Rhizomicrobium (4%) and Gemmatimonas (3%) were the most abundant bacterial genera in Clsd. Mortierella (22%) and Peziza (12%) dominated the fungal community in Hx2. Lecanicillium (38%) and Mortierella (13%) dominated the fungal community in Clsd. Fallow periods also increased the functional diversity of soil as predicted by PICRUSt and decreased the relative abundance of the pathogenic fungi.ConclusionsPreliminary findings were consistent with the hypothesis that fallow management in ginseng cultivation can improve soil microbial community structure and function and reduces the number of plant pathogens; however, testing this hypothesis will require replicated plots. creator: Yuqing Li creator: Feyisike Gbolayori Jones creator: Bing Zhang creator: Juntao Cui creator: Wei Zhang uri: https://doi.org/10.7717/peerj.14758 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Effects of lower and upper body fatigue in striking response time of amateur karate athletes link: https://peerj.com/articles/14764 last-modified: 2023-01-31 description: In combat sports, strikes or counter-strikes response time (RT) can be related to performance and sporting success. Moreover, training sessions are usually highly fatiguing, which is expected to impair basic skills, such as RT. Thus, this study aimed to investigate the effect of fatigue on punch and kick RTs of karate practitioners. Twelve individuals of both sexes from different levels (three yellow belts, three red belts, two orange belts, two green belts, one brown belt, and one black belt) were selected. Participants were aged 22 ± 3 years old, with a stature of 169.1 ± 6.5 cm, and a body mass of 65.5 ± 10 kg. Six visits were held with each participant. On the first 2 days, the RT of punches and kicks was measured by a validated smartphone app (TReaction). For the subsequent visits, a randomized incremental test for the upper or lower body was adopted as motor fatigue protocol, immediately followed by punches and kicks RT tests, also in random order. For induction of lower and upper body-specific muscle fatigue, the ITStriker app was used, which operates by emitting sound signals transmitted by a smartphone. One-way repeated measures ANOVA was performed, and significance was set at p ≤ 0.05. Regarding the mean punches RT, significant effects between situations for the upper (F(2,22) = 11.5; ω2 = 0.23; p < 0.001) and lower body (F(2,22) = 14.2; ω2 = 0.18; p < 0.001) fatigue protocols were found. The negative effect of the lower body fatigue protocol in punches RT was evident regardless of the order of the tests (punch RT first: Δ = 10.5%; t = 4.4; p < 0.001; d = 1.0; kick RT first: Δ = 11.4%; t = 4.8; p < 0.001; d = 1.1). Regarding mean kicks RT, significant effects were found between situations for the lower (F(2,22) = 16.6; ω2 = 0.27; p < 0.001) but not for the upper (F(2,22) = 2.3; ω2 = 0.02; p = 0.12) body fatigue protocols. Kick RTs were negatively affected by the lower body fatigue protocol regardless of the RT order applied (punch RT first: Δ = 7.5%; t = 3.0; p = 0.01; d = 0.8; kick RT first: Δ = 14.3%; t = 5.7; p < 0.001; d = 1.5). Upper body fatigue does not impair punch or kick RTs. Thus, it is concluded that the specificity of fatigue protocols and striking order should be considered while performing RT demanding techniques in karate practice. Specifically, lower body motor fatigue may impair both kicks and punches RT, which highlights the role of lower limbs in punches performance. Otherwise, upper body motor fatigue seems to induce impairments that are limited to the specific motor actions of this body segment. creator: Júlio Cesar Carvalho Rodrigues creator: Eduardo Macedo Penna creator: Hugo Enrico Souza Machado creator: Jader Sant’Ana creator: Fernando Diefenthaeler creator: Victor S. Coswig uri: https://doi.org/10.7717/peerj.14764 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rodrigues et al. title: Simultaneous functioning of different light-harvesting complexes—a strategy of adaptation of purple bacterium Rhodopseudomonas palustris to low illumination conditions link: https://peerj.com/articles/14769 last-modified: 2023-01-31 description: Novel peripheral light-harvesting (LH) complex designated as LL LH2 was isolated along with LH4 complex from Rhodopseudomonas palustris cells grown under low light intensity (LL). FPLC-MS/MS allowed to reveal PucABd and PucBabc apoproteins in LL LH2 complex, which is different from previously described LH4 complex containing PucABd, PucABa and PucBb. The main carotenoids in LL LH2 complex were rhodopin and 3,4-didehydrorhodopin. Three-dimensional modeling demonstrated which amino acid residues of all the β-subunits could interact with carotenoids (Car) and bacteriochlorophyll a (BChl a). Analysis of amino acid sequences of α-subunits of both LL complexes showed presence of different C-terminal motifs, IESSVNVG in αa subunit and IESSIKAV in αd subunit, in the same positions of C-termini, which could reflect different retention force of LL LH2 and LH4 on hydroxyl apatite, facilitating successful isolation of these complexes. Differences of these LL complexes in protein and carotenoid composition, in efficiency of energy transfer from Car to BChl a, which is two times lower in LL LH2 than in LH4, allow to assign it to a novel type of light-harvesting complex in Rhodopseudomonas palustris. creator: Olga Petrovna Serdyuk creator: Azat Vadimovich Abdullatypov creator: Lidiya Dmitrievna Smolygina creator: Aleksandr Aleksandrovich Ashikhmin creator: Maxim Alexandrovich Bolshakov uri: https://doi.org/10.7717/peerj.14769 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Serdyuk et al. title: Adjuvant Pam3CSk4 does not improve the immunization against Cryptococcus gattii infection in C57BL/6 mice link: https://peerj.com/articles/14778 last-modified: 2023-01-31 description: BackgroundCryptococcosis is a relevant invasive fungal infection that affects immunocompromised and immunocompetent individuals when caused by Cryptococcus gattii. Host innate and adaptive immune responses can be subverted by C. gattii, that blocks the differentiation of T helper (Th) 1 and Th17 cells, which are involved in the protection against cryptococcosis. Moreover, the macrophage polarization is modulated by C. gattii infection that requires a balance in the macrophage subsets to control the C. gattii infection. Toll-like receptor (TLR) 2 agonists are important immunomodulators favoring a pro-inflammatory response with potential fungicidal activity, and TLR2 agonists have been used as adjuvants in vaccines against infections caused by bacteria or viruses. Therefore, this work aimed to evaluate the immunomodulatory effect of the tripalmitoyl lipopeptide S-glycerol cysteine (Pam3CSK4 or P3C4), a TLR2 agonist, as an adjuvant in the vaccination against C. gattii infection.Methods and ResultsC57BL/6 mice were immunized with 2 × 107 inactivated yeasts of C. gattii via intranasal route on day 1, 14 and 28 (Immunized group). Immunization was associated with 1µg or 10µg of adjuvant P3C4 (Immunized+P3C4-1µg or Immunized+P3C4-10 µg), followed by C. gattii infection on day 42 after the immunization protocol. Immunized+P3C4-1 µg group had reduced levels of IgG1, IgG2a and IgA and no significant difference in the IgG and IgM anti-GXM antibody titer was detected, compared to the Immunized group. High levels of IL-17 and IL-1β in lung tissue of mice from the Immunized+P3C4-1µg group did not promote a predominance of Th17 cells, in contrast, the frequency of TLR2+ cells was increased in immunized mice that received 1 µg of P3C4. The reduction in the relative expression of T-bet and high levels of Foxp3 detected in the lungs of the Immunized+P3C4-1µg group suggest a prevalence of regulatory T cells in the tissue, which did not contribute to the control of C. gattii infection. The immunization protocol associated with 10 µg of adjuvant P3C4 induced high levels of IL-17 in the lung tissue, whereas the levels of pro-inflammatory cytokines were downregulated. To evaluate the effect of adjuvant P3C4 in the control of C. gattii infection, quantification of the fungal burden in the lungs was performed by the CFU assay, and the groups with adjuvant P3C4 showed a pulmonary C. gattii burden that was not significantly altered when compared with the immunized group. The mice that received 1 µg of adjuvant P3C4 had a lower percentage of inflammatory infiltrate in the lungs.ConclusionThe immunomodulatory effect of P3C4, associated with the immunization protocol, plays an imbalance between pro- and anti-inflammatory response in the lungs that did not favor a protection against C. gattii infection, which is related to the immune response characterized by a suppressive/regulatory profile in the pulmonary microenvironment after C. gattii infection. creator: Gabriela Yamazaki de Campos creator: Patrícia Kellen Martins Oliveira-Brito creator: Júlia Garcia Guimarães creator: Letícia Serafim da Costa creator: Javier Emílio Lazo Chica creator: Thiago Aparecido da Silva uri: https://doi.org/10.7717/peerj.14778 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 de Campos et al. title: Bidirectional effect of vitamin D on brown adipogenesis of C3H10T1/2 fibroblast-like cells link: https://peerj.com/articles/14785 last-modified: 2023-01-31 description: BackgroundBrown adipose tissue (BAT) dissipates caloric energy as heat and plays a role in glucose and lipid metabolism. Therefore, augmentation and activation of BAT are the focus of new treatment strategies against obesity, a primary risk factor of metabolic syndrome. The vitamin D system plays a crucial role in mineral homeostasis, bone metabolism, and cell proliferation and differentiation. In this study, we investigated the effects of vitamin D3 [1,25(OH)2D3] on brown adipocyte differentiation.MethodsThe mouse fibroblast-like cell line C3H10T1/2 was differentiated into brown adipocytes in the presence of 1,25(OH)2D3. The effect of 1,25(OH)2D3 on brown adipocyte differentiation was assessed by measuring lipid accumulation, the expression of related genes, and cytotoxicity. The viability of C3H10T1/2 cells was measured using the Cell Counting Kit-8 assay. Gene expression was investigated using quantitative reverse transcription-polymerase chain reaction. Protein expression was estimated using western blotting.Results1,25(OH)2D3 inhibited adipocyte differentiation and exerted a cytotoxic effect at 1 nM. However, in the physiological concentration range (50–250 pM), 1,25(OH)2D3 promoted uncoupling protein 1 (UCP1) expression in C3H10T1/2 cells. This effect was not observed when 1,25(OH)2D3 was added 48 h after the initiation of differentiation, suggesting that the vitamin D system acts in the early phase of the differentiation program. We showed that 1,25(OH)2D3 increased the expression of two key regulators of brown adipogenesis, PR domain containing 16 (Prdm16) and peroxisome proliferator-activated receptor γ coactivator-1α (Pgc1α). Furthermore, 1,25(OH)2D3 increased Ucp1 expression in 3T3-L1 beige adipogenesis in a dose-dependent manner.ConclusionThese data indicate the potential of vitamin D and its analogs as therapeutics for the treatment of obesity and related metabolic diseases. creator: Takako Mukai creator: Tatsuya Kusudo uri: https://doi.org/10.7717/peerj.14785 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mukai and Kusudo title: Hereditary etiology of non-syndromic sensorineural hearing loss in the Republic of North Ossetia–Alania link: https://peerj.com/articles/14514 last-modified: 2023-01-30 description: More than 50% of congenital hearing loss is hereditary, in which the majority form is non-syndromic. In this study we estimate the most prevalent pathogenic genetic changes in an Ossetian cohort of patients. This is useful for local public health officials to promote genetic counseling of affected families with regard to high allele frequencies of prevalent pathogenic variants and assortative mating in the community of people with hearing loss. In this study, genetic heterogeneity of hereditary non-syndromic sensorineural hearing loss (NSNHL) in a cohort of 109 patients and an assessment of the frequency of two GJB2 gene pathogenic variants in a cohort of 349 healthy individuals from the populations of the Republic of North Ossetia–Alania (RNO–Alania) were assessed. The molecular genetic cause of NSNHL in the GJB2 gene in RNO–Alania was confirmed in ~30% of the cases, including ~27% in Ossetians. In Russian patients, the most frequent variant is GJB2:c.35delG (~83%). The GJB2:c.358_360delGAG variant was found to be the most frequent among Ossetians (~54%). Two genetic variants in GJB2, c.35delG and c.358_360delGAG, accounted for 91% of GJB2 pathogenic alleles in the Ossetian patients. A search for large genome rearrangements revealed etiological cause in two Ossetian patients, a deletion at the POU3F4 gene locus associated with X-linked hearing loss (type DFNX2). In another Ossetian patient, a biallelic pathogenic variant in the MYO15A gene caused hearing loss type DFNB3 was identified, and in one Russian family a heterozygous MYH14 gene variant associated with dominant NSNHL was found. Thus, the informative value of the diagnosis was ~37% among all patients with NSNHL from RNO–Alania and ~32% among the Ossetians. These estimates correspond to the literature data on the fraction of recessive genetic forms of hearing loss within the affected population. The importance of this study consists not only in the estimation of the most prevalent pathogenic genetic changes in the Ossetian cohort of patients which could be useful for the public health but also in the genetic counselling of the affected families with regard to the high allele frequencies of revealed pathogenic variants as well as to the assortative mating in community of people with hearing loss. creator: Nika Petrova creator: Inna Tebieva creator: Vitaly Kadyshev creator: Zalina Getoeva creator: Natalia Balinova creator: Andrey Marakhonov creator: Tatyana Vasilyeva creator: Evgeny Ginter creator: Sergey Kutsev creator: Rena Zinchenko uri: https://doi.org/10.7717/peerj.14514 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Petrova et al. title: Alien species revises systematic status: integrative species delimitation of two similar taxa of Symbrenthia Hübner, [1819] (Lepidoptera, Nymphalidae) link: https://peerj.com/articles/14644 last-modified: 2023-01-30 description: Introduction of organisms to new range may impose detrimental effects on local organisms, especially when closely related species are involved. Species delimitation employing an integrative taxonomy approach may provide a quick assessment for the species status between taxa of interest, and to infer ecological competition and/or introgression that may be associated with the introduction. A nymphalid butterfly, Symbrenthia lilaea lunica, was recently introduced to Taiwan, where a closely related local taxon, S. l. formosanus, can be found. We employed multiple species delimitation methods to study the species status between the two taxa, and the results revealed that they can be recognized as two distinct species, revised to S. l. lilaea (syn. nov.) and S. formosanus (stat. rev.) respectively. We further performed a niche modeling approach to investigate the ecological interaction between the two species. The taxonomic status of the two taxa, now elevated to species, has been revised and conservation facing rapid expansion of the introduced species discussed. creator: Yu-Feng Hsu creator: Zong-Yu Shen creator: Hang-Chi Huang creator: Chih-Wei Huang creator: Chen-Chih Lu uri: https://doi.org/10.7717/peerj.14644 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hsu et al. title: Feeding habits of four-finger threadfin fish, Eleutheronema tetradactylum, and its diet interaction with co-existing fish species in the coastal waters of Thailand link: https://peerj.com/articles/14688 last-modified: 2023-01-30 description: This study assessed the feeding habits of four-finger threadfin fish, Eleutheronema tetradactylum, and its diet relationship with other fish species in the tropics. Fish samples were collected from four locations along the coastal regions of Thailand. A whole year field sampling event was conducted to investigate the diet relationship of threadfin fish with other ten co-existing fish species in Pattani Bay during January 2021 and January 2022. E. tetradactylum was an active and specific predator with significant diet shift during ontogeny. Specifically, the juvenile fish fed largely on zooplankton especially Acetes/shrimp postlarvae, and small sized-fish fed on penaeid shrimps, while medium and large-sized fish shifted their diets to a combination of penaeid shrimp, fish and squid. Size and sex of fish as well as site of collection significantly affected gut fullness index and average number of food type (p < 0.05). Transitional sex fish predated almost entirely on other fishes (87.2%), whereas male and female fish fed mainly on penaeid shrimp (66.5%) and other fish (51.3%), respectively. Fish size and mouth opening controlled the size of prey, with the larger fish with larger mouth-opening fed primarily on the larger size of prey. Moreover, E. tetradactylum shared its diets inclusively with Epinephelus coioides, Johnius belangerii, Scomberomorus commerson, Scomberoides lysan, Otolithes ruber and Lutjanus russelli. Penaeid shrimp and teleost fish were the main food types shared by these fishes. This study provided important information on the feeding habits of E. tetradactylum and its diet relationship with other co-existing fish species living in the same habitat of a tropical coastal region. creator: Teuku Haris Iqbal creator: Sukree Hajisamae creator: Apiradee Lim creator: Sitthisak Jantarat creator: Wen-Xiong Wang creator: Karl W.K. Tsim uri: https://doi.org/10.7717/peerj.14688 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Iqbal et al. title: Genetic variants of IFIH1 and DHX58 affect the chronicity of hepatitis C in the Chinese Han population link: https://peerj.com/articles/14740 last-modified: 2023-01-30 description: Hepatitis C remains a major public health problem in the world. The host immune system plays a key role in viral clearance. This study aimed to investigate the connection between retinoic acid-inducible gene I-like (RIG-I-like) receptor gene polymorphism and hepatitis C chronicity in the Chinese Han population. The current study genotyped three SNPs (IFIH1 rs10930046 and DHX58 rs2074158, rs2074160) to assess their association with the chronicity of hepatitis C virus (HCV) infection among 1,590 participants (590 spontaneous HCV clearance cases and 1,000 persistent infection patients). Our research shows that DHX58 rs2074158-G allele (dominant model: adjusted OR = 1.53, 95% CI [1.20–1.95], P = 0.001; additive model: adjusted OR = 1.50, 95% CI [1.27–1.78], P < 0.001) and IFIH1 rs10930046-C allele (additive model: adjusted OR = 1.26, 95% CI [1.07–1.49], P = 0.005) were associated with chronic hepatitis C (CHC). And the risk of CHC increased in people carrying more unfavorable genotypes (rs2074158-AG/GG or rs10930046-CC), with the chronic rates for genotypes number from zero to two in 60.69%, 57.33%, and 85.93%, respectively (adjusted OR = 3.64, 95% CI [2.18–6.08]; P < 0.001). Genetic polymorphism of IFIH1 and DHX58 may be related to CHC in the Chinese Han population. Furthermore, the risk of CHC increases as the number of unfavorable genotypes carried by the HCV-infected person increases. IFIH1 rs10930046, DHX58 rs2074158, age, ALT, and AST levels were all independent predictors of CHC. creator: Peng Huang creator: Jing-Jing Wu creator: Jin-Wei Zhang creator: Yu-Qing Hou creator: Ping Zhu creator: Rong Yin creator: Rong-Bin Yu creator: Yun Zhang creator: Ming Yue creator: Wei Hou uri: https://doi.org/10.7717/peerj.14740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Effects of summer savory (Satureja hortensis L.) and sweet corn (Zea mays L. saccharata) intercropping on crop production and essential oil profiles of summer savory link: https://peerj.com/articles/14753 last-modified: 2023-01-30 description: A 2-year field experiment evaluated the effects of sweet corn-summer savory intercropping on crop productivity and essential oil (EO) composition of summer savory. Five cropping patterns of Corn 100%:Savory 0%, C75:S25, C50:S50, C25:S75, and C0:S100 were tested. The highest corn yield (2,440 kg ha−1) was obtained in a corn monoculture, but was not significantly different from C75:S25 or C50:S50. However, in both years the highest savory yield was obtained in S100 (793.3 g m−2 and 816.6 g m−2, respectively). Savory yields decreased as the proportion of corn increased. The land equivalent ratios in C25:S75, C50:S50, and C75:S25 were 1.54 ± 0.07, 1.56 ± 0.03, and 1.35 ± 0.1, respectively. Monocropped savory had the highest EO value followed by C25:S75 and C50:C50. However, no significant differences were found among these three treatments. Gas chromatography-mass spectrometry (GC–MS) analysis showed that the major components were carvacrol (35.88%–42.96%), γ-terpinene (18.45%–20.03%), ρ-cymene (11.77%–12.24%), and α-terpinene (2.75%–3.96%). The highest amount of carvacrol was recorded in C25:S75 (42.96%). This study suggests that intercropping of corn and savory represents an effective sustainable strategy, especially for smallholders, as a way to increase their overall land productivity and to improve the quality of savory’s EO. creator: Ruhollah Naderi creator: Farzad Bijani creator: Akbar Karami creator: Bhagirath S. Chauhan creator: Todd P. Egan uri: https://doi.org/10.7717/peerj.14753 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Naderi et al. title: Prediction model for missed abortion of patients treated with IVF-ET based on XGBoost: a retrospective study link: https://peerj.com/articles/14762 last-modified: 2023-01-30 description: AimIn this study, we established a model based on XGBoost to predict the risk of missed abortion in patients treated with in vitro fertilization-embryo transfer (IVF-ET), evaluated its prediction ability, and compared the model with the traditional logical regression model.MethodsWe retrospectively collected the clinical data of 1,017 infertile women treated with IVF-ET. The independent risk factors were screened by performing a univariate analysis and binary logistic regression analysis, and then, all cases were randomly divided into the training set and the test set in a 7:3 ratio for constructing and validating the model. We then constructed the prediction models by the traditional logical regression method and the XGBoost method and tested the prediction performance of the two models by resampling.ResultsThe results of the binary logistic regression analysis showed that several factors, including the age of men and women, abnormal ovarian structure, prolactin (PRL), anti-Müllerian hormone (AMH), activated partial thromboplastin time (APTT), anticardiolipin antibody (ACA), and thyroid peroxidase antibody (TPO-Ab), independently influenced missed abortion significantly (P < 0.05). The area under the receiver operating characteristic curve (AUC) score and the F1 score with the training set of the XGBoost model (0.877 ± 0.014 and 0.730 ± 0.019, respectively) were significantly higher than those of the logistic model (0.713 ± 0.013 and 0.568 ± 0.026, respectively). In the test set, the AUC and F1 scores of the XGBoost model (0.759 ± 0.023 and 0.566 ± 0.042, respectively) were also higher than those of the logistic model (0.695 ± 0.030 and 0.550 ± 049, respectively).ConclusionsWe established a prediction model based on the XGBoost algorithm, which can accurately predict the risk of missed abortion in patients with IVF-ET. This model performed better than the traditional logical regression model. creator: Guanghui Yuan creator: Bohan Lv creator: Xin Du creator: Huimin Zhang creator: Mingzi Zhao creator: Yingxue Liu creator: Cuifang Hao uri: https://doi.org/10.7717/peerj.14762 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yuan et al. title: Association of job stress, FK506 binding protein 51 (FKBP5) gene polymorphisms and their interaction with sleep disturbance link: https://peerj.com/articles/14794 last-modified: 2023-01-30 description: BackgroundSleep disturbance is an outcome of multiple factors including environmental and genetic influences. Job stress, a complex environmental factor, likely affects sleep quality, significantly reducing the quality of life of workers. Additionally, FK506 binding protein 51 (FKBP5) may be a pathogenic factor for sleep disturbance as it regulates hypothalamic–pituitary–adrenal (HPA) axis activity, where HPA axis has been found to be involved in the regulation mechanism of sleep and stress response.ObjectivesThe main aim of this study was to investigate the association between job stress and FKBP5 gene polymorphism as well as their interaction with sleep disturbance in Chinese workers; to date, these relationships have not been explored.MethodsThis is a cross-sectional study. A total of 675 railway workers (53.8% male) completed a short Effort-Reward Imbalance questionnaire and the Pittsburgh Sleep Quality Index. The SNaPshot single nucleotide polymorphism (SNP) assay was carried out by screening for FKBP5 SNPs in every participant. Generalized multifactor dimensionality reduction (GMDR) was used to identify the strongest G×E interaction combination.ResultsThe findings showed that job stress was significantly associated with sleep disturbance; specifically, scores on the PSQI subscales (sleep disturbance, sleep medication, and daytime dysfunction) exhibited significant differences between the two job stress groups (X2 = 18.10, p = 0.01). Additionally, the FKBP5 SNP rs1360780-TT (adjusted odds ratio [AOR] = 4.98, 95% confidence interval [CI] = 2.80–8.84) and rs3800373-CC genotype (AOR = 2.06, CI = 1.10–3.86) were associated with an increased risk of sleep disturbance. Job stress and rs1360780 and rs3800373 variants showed a high-dimensional interaction with sleep disturbance as determined by the GMDR model.ConclusionThe FKBP5 gene may increase susceptibility to job stress and result in sleep disturbance, especially in the presence of negative work-related events. These findings contribute to the field of sleep disturbance prevention and treatment. creator: Peixin Li creator: Yuxi Wang creator: Baoying Liu creator: Chuancheng Wu creator: Chenzhou He creator: Xuejie Lv creator: Yu Jiang uri: https://doi.org/10.7717/peerj.14794 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Discrimination of foreign bodies in quinoa (Chenopodium quinoa Willd.) grains using convolutional neural networks with a transfer learning approach link: https://peerj.com/articles/14808 last-modified: 2023-01-30 description: The rising interest in quinoa (Chenopodium quinoa Willd.) is due to its high protein content and gluten-free condition; nonetheless, the presence of foreign bodies in quinoa processing facilities is an issue that must be addressed. As a result, convolutional neural networks have been adopted, mostly because of their data extraction capabilities, which had not been utilized before for this purpose. Consequently, the main objective of this work is to evaluate convolutional neural networks with a learning transfer for foreign bodies identification in quinoa samples. For experimentation, quinoa samples were collected and manually split into 17 classes: quinoa grains and 16 foreign bodies. Then, one thousand images were obtained from each class in RGB space and transformed into four different color spaces (L*a*b*, HSV, YCbCr, and Gray). Three convolutional neural networks (AlexNet, MobileNetv2, and DenseNet-201) were trained using the five color spaces, and the evaluation results were expressed in terms of accuracy and F-score. All the CNN approaches compared showed an F-score ranging from 98% to 99%; both color space and CNN structure were found to have significant effects on the F-score. Also, DenseNet-201 was the most robust architecture and, at the same time, the most time-consuming. These results evidence the capacity of CNN architectures to be used for the discrimination of foreign bodies in quinoa processing facilities. creator: Himer Avila-George creator: Miguel De-la-Torre creator: Jorge Sánchez-Garcés creator: Joel Jerson Coaquira Quispe creator: Jose Manuel Prieto creator: Wilson Castro uri: https://doi.org/10.7717/peerj.14808 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Avila-George et al. title: Exploring the mechanisms by which camel lactoferrin can kill Salmonella enterica serovar typhimurium and Shigella sonnei link: https://peerj.com/articles/14809 last-modified: 2023-01-30 description: There is a continuously increasing pressure associated with the appearance of Salmonella enterica Serovar typhimurium (S. typhimurium) and Shigella sonnei (S. sonnei) that have developed pathogenic multiple antibiotic resistance and the cost of cure and control of these enterobacteriaceae infections increases annually. The current report for first time demonstrated the distinguished antimicrobial action of camel lactoferrin (cLf) obtained from the milk of different clans of camel in Saudi Arabia against S. typhimurium and S. sonnei. These cLf subtypes showed comparable antimicrobial potential when tested against the two bacterial strains but were superior to either bovine (bLf) or human lactoferrin (hLf). The synergism between lactoferrins and antibiotics concerning their antibacterial efficacies against the two bacterial strains was evident. Exploring mechanisms by which camel lactoferrin can kill S. typhimurium and S. sonnei revealed that cLf affects bacterial protein profile. Besides, it interacts with bacterial lipopolysaccharides (LPS) and numerous membrane proteins of S. typhimurium and S. sonnei, with each bacterial strain possessing distinctive binding membrane proteins for lactoferrin. Furthermore, as evidenced by electron microscopy analysis, cLf induces extracellular and intracellular morphological changes in the test bacterial strains when used alone or in combination treatment with antibiotics. Lactoferrin and antibiotics combination strongly disrupts the integrity of the bacterial cells and their membranes. Therefore, cLf can kill S. typhimurium and S. sonnei by four different mechanisms, such as iron chelation, affecting some bacterial proteins, binding to bacterial LPS and membrane proteins, and impairing the integrity of the bacterial cells and their membranes. creator: Hussein A. Almehdar creator: Nawal Abd El-Baky creator: Ehab H. Mattar creator: Raed Albiheyri creator: Atif Bamagoos creator: Abdullah Aljaddawi creator: Vladimir N. Uversky creator: Elrashdy M. Redwan uri: https://doi.org/10.7717/peerj.14809 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Almehdar et al. title: A quantitative approach on environment-food nexus: integrated modeling and indices for cumulative impact assessment of farm management practices link: https://peerj.com/articles/14816 last-modified: 2023-01-30 description: BackgroundBest management practices (BMPs) are promising solutions that can partially control pollution discharged from farmlands. These strategies, like fertilizer reduction and using filter strips, mainly control nutrient (N and P) pollution loads in basins. However, they have secondary impacts on nutrition production and ecosystem. This study develops a method to evaluate the cumulative environmental impacts of BMPs. It also introduces and calculates food’s environmental footprint (FEF) for accounting the total environmental damages per nutrition production.MethodsThis study combines the soil and water assessment tool (SWAT) for basin simulation with the indices of ReCiPe, a life cycle impact assessment (LCIA) method. By these means, the effectiveness of BMPs on pollution loads, production yields, and water footprints (WFs) are evaluated and converted as equivalent environmental damages. This method was verified in Zrebar Lake, western Iran. Here, water consumption, as WFs, and eutrophication are the main indices that are converted into equivalent health and ecological impairments. Two methods, entropy and environmental performance index (EPI), are used for weighting normalized endpoints in last step.ResultsResults showed that using 25–50% less fertilizer and water for irrigation combined with vegetated filter strips reduce N and P pollution about 34–60% and 8–21%, respectively. These can decrease ecosystem damages by 5–9% and health risks by 7–14%. Here, freshwater eutrophication is a more critical damage in ecosystem. However, using less fertilizer adversely reduces total nutrition production by 1.7–3.7%. It means that BMPs can decline total ecological damages and health risks, which threatens nutrition production. FEF presents a tool to solve this dilemma about the sustainability of BMPs. In the study area, a 4–9% decrease in FEF means that BMPs are more environmental friendly than nutrition menacing. Finally, this study concludes that SWAT-ReCiPe with FEF provides a quantitative framework for environment-food nexus assessment. However, due to the uncertainties, this method is recommended as a tool for comparing management strategies instead of reporting certain values. creator: Shervin Jamshidi creator: Anahita Naderi uri: https://doi.org/10.7717/peerj.14816 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jamshidi and Naderi title: Microscopic polyangiitis plasma-derived exosomal miR-1287-5p induces endothelial inflammatory injury and neutrophil adhesion by targeting CBL link: https://peerj.com/articles/14579 last-modified: 2023-01-27 description: BackgroundAn inflammatory environment around the vessel wall caused by leukocyte infiltration is one of the characteristic histopathological features of microscopic polyangiitis (MPA); however, the pathogenic mechanisms are not fully understood. Studies have found that circulating microRNA (miRNA) can be used as potential biomarkers for the diagnosis and classification of anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitides (AAV), and the E3 ubiquitin ligase casitas B-lineage lymphoma (CBL) seems to be associated with inflammation. In addition, evidence indicates that miRNA can be tracked into exosomes and transferred into recipient cells to mediate the process of vascular endothelial injury. Herein, we aimed to identify the profiles of exosomal miRNA, and determine the effect of exosomal miR-1287-5p and its target gene CBL on vascular endothelial cells in MPA.MethodWe isolated plasma exosomes from patients with MPA (MPA-exo) and healthy controls (HC-exo) by ultracentrifugation and conducted exosome small-RNA sequencing to screen differential miRNA expression in MPA-exo (n = 3) compared to HC-exo (n = 3). We measured the expression levels of miR-1303, miR-1287-5p, and miR-129-1-3p using quantitative reverse transcription-polymerase chain reaction (qRT-PCR, n = 6) and performed dual luciferase reporter gene assays to confirm the downstream target gene of miR-1287-5p. In addition, we treated human umbilical vein endothelial cell (HUVEC) with MPA-exo, or transfected them with miR-1287-5p mimic/inhibitor or with CBL-siRNA/CBL-siRNA+ miR-1287-5p inhibitor. After cell culture, we evaluated the effects on vascular endothelial cells by examining the mRNA levels of IL-6, IL-8, MCP-1, ICAM-1 and E-selectin using qRT-PCR and performed neutrophil adhesion assay with haematoxylin staining.ResultTransmission electron microscopy, Western blot and nanoparticle tracking analysis showed that we successfully purified exosomes and MPA-exo could be absorbed into HUVEC. We screened a total of 1,077 miRNA by sequencing and observed a high abundance of miR-1287-5p in the exosomes obtained from MPA plasma. The dual luciferase reporter assay identified CBL as a downstream target gene of miR-1287-5p, and the results revealed that MPA-exo decreased CBL protein expression in HUVEC. In addition, treatment with MPA-exo, up-regulating miR-1287-5p or silencing of CBL in HUVEC significantly increased the mRNA expression of inflammatory factors (including IL-6, IL-8, and MCP-1) and adhesion molecules (including ICAM-1 and E-selection) and promoted the adhesion of neutrophils to HUVEC. However, down-regulating miR-1287-5p had the opposite effect.ConclusionOur study revealed that MPA-exo was involved in the intercellular transfer of miR-1287-5p and subsequently promote the development of acute endothelial injury in MPA. MiR-1287-5p and CBL agonists may be promising therapeutic approach for MPA-induced vascular inflammatory injury. creator: Yan Zhu creator: Liu Liu creator: Liepeng Chu creator: Jingjing Lan creator: Jingsi Wei creator: Wei Li creator: Chao Xue uri: https://doi.org/10.7717/peerj.14579 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhu et al. title: Plain set and stirred yogurt with different additives: implementation of food safety system as quality checkpoints link: https://peerj.com/articles/14648 last-modified: 2023-01-27 description: Hazard Analysis Critical Control Point (HACCP) is a risk management protocol developed to ensure food safety through a precautionary approach that is believed to offer assurances in producing safe food for customers. Yogurt is made in a number of phases, commencing with the collection of raw milk and ending with consumer consumption. While this is happening, major economic and health issues might arise from exposing the manufacturing line to biological, chemical, and/or physical contaminations. As a result, the decision tree approach was used to determine the CCPs during the production of yogurt. Additionally, biological dangers are incorporated as a by-product of the system’s implementation performance. In particular, the plain set and nut puree-honey-fortified stirred yogurt manufacturing techniques are highlighted for the first time in this study. The potential manufacturing risks are described for the first time, together with information on how HACCP plans may guard against major risks that could result in the production of yogurt that is not in compliance with established standards. creator: Aya Allam creator: Noha Shafik creator: Ahmed Zayed creator: Ibrahim Khalifa creator: Ibrahim A. Bakry creator: Mohamed A. Farag uri: https://doi.org/10.7717/peerj.14648 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Allam et al. title: Novel genetic variants in long non-coding RNA MEG3 are associated with the risk of asthma link: https://peerj.com/articles/14760 last-modified: 2023-01-27 description: BackgroundAsthma is the most common chronic inflammatory airway disease worldwide. Asthma is a complex disease whose exact etiologic mechanisms remain elusive; however, it is increasingly evident that genetic factors play essential roles in the development of asthma. The purpose of this study is to identify novel genetic susceptibility loci for asthma in Taiwanese. We selected a well-studied long non-coding RNA (lncRNA), MEG3, which is involved in multiple cellular functions and whose expression has been associated with asthma. We hypothesize that genetic variants in MEG3 may influence the risk of asthma.MethodsWe genotyped four single nucleotide polymorphisms (SNPs) in MEG3, rs7158663, rs3087918, rs11160608, and rs4081134, in 198 patients with asthma and 453 healthy controls and measured serum MEG3 expression level in a subset of controls.ResultsThe variant AG and AA genotypes of MEG3rs7158663 were significantly over-represented in the patients compared to the controls (P = 0.0024). In logistic regression analyses, compared with the wild-type GG genotype, the heterozygous variant genotype (AG) was associated with a 1.62-fold [95% confidence interval (CI) [1.18–2.32], P = 0.0093] increased risk and the homozygous variant genotype (AA) conferred a 2.68-fold (95% CI [1.52–4.83], P = 0.003) increased risk of asthma. The allelic test showed the A allele was associated with a 1.63-fold increased risk of asthma (95% CI [1.25–2.07], P = 0.0004). The AG plus AA genotypes were also associated with severe symptoms (P = 0.0148). Furthermore, the AG and AA genotype carriers had lower serum MEG3 expression level than the GG genotype carriers, consistent with the reported downregulation of MEG3 in asthma patients.ConclusionMEG3 SNP rs7158663 is a genetic susceptibility locus for asthma in Taiwanese. Individuals carrying the variant genotypes have lower serum MEG3 level and are at increased risks of asthma and severe symptoms. creator: Kuo-Liang Chiu creator: Wen-Shin Chang creator: Chia-Wen Tsai creator: Mei-Chin Mong creator: Te-Chun Hsia creator: Da-Tian Bau uri: https://doi.org/10.7717/peerj.14760 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chiu et al. title: Targeting super enhancers for liver disease: a review link: https://peerj.com/articles/14780 last-modified: 2023-01-27 description: BackgroundSuper enhancers (SEs) refer to the ultralong regions of a gene accompanied by multiple transcription factors and cofactors and strongly drive the expression of cell-type-related genes. Recent studies have demonstrated that SEs play crucial roles in regulating gene expression related to cell cycle progression and transcription. Aberrant activation of SEs is closely related to the occurrence and development of liver disease. Liver disease, especially liver failure and hepatocellular carcinoma (HCC), constitutes a major class of diseases that seriously endanger human health. Currently, therapeutic strategies targeting SEs can dramatically prevent disease progression and improve the prognosis of animal models. The associated new approaches to the treatment of related liver disease are relatively new and need systematic elaboration.ObjectivesIn this review, we elaborate on the features of SEs and discuss their function in liver disease. Additionally, we review their application prospects in clinical practice in the future. The article would be of interest to hepatologists, molecular biologists, clinicians, and all those concerned with targeted therapy and prognosis of liver disease.MethodologyWe searched three bibliographic databases (Web of Science Core Collection, Embase, PubMed) from 01/1981 to 06/2022 for peer-reviewed scientific publications focused on (1) gene treatment of liver disease; (2) current status of SE research; and (3) targeting SEs for liver disease. We included English language original studies only.ResultsThe number of published studies considering the role of enhancers in liver disease is considerable. Since SEs were just defined in 2013, the corresponding data on SEs are scarce: approximately 50 papers found in bibliographic databases on the correlation between enhancers (or SEs) and liver disease. Remarkably, half of these papers were published in the past three years, indicating the growing interest of the scientific community in this issue. Studies have shown that treatments targeting components of SEs can improve outcomes in liver disease in animal and clinical trials.ConclusionsThe treatment of liver disease is facing a bottleneck, and new treatments are needed. Therapeutic regimens targeting SEs have an important role in the treatment of liver disease. However, given the off-target effect of gene therapy and the lack of clinical trials, the available experimental data are still fragmented and controversial. creator: Zhongyuan Yang creator: Yunhui Liu creator: Qiuyu Cheng creator: Tao Chen uri: https://doi.org/10.7717/peerj.14780 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Alterations of ecosystem nitrogen status following agricultural land abandonment in the Karst Critical Zone Observatory (KCZO), Southwest China link: https://peerj.com/articles/14790 last-modified: 2023-01-27 description: BackgroundSecondary succession after agricultural land abandonment generally affects nitrogen (N) cycle processes and ecosystem N status. However, changes in soil N availability and NO3– loss potential following secondary succession are not well understood in karst ecosystems.MethodsIn the Karst Critical Zone Observatory (KCZO) of Southwest China, croplands, shrub-grass lands, and secondary forest lands were selected to represent the three stages of secondary succession after agricultural land abandonment by using a space-for-time substitution approach. The contents and 15N natural abundance (δ15N) of leaves, soils, and different-sized aggregates at the three stages of secondary succession were analyzed. The δ15N compositions of soil organic nitrogen (SON) in aggregates and soil to plant 15N enrichment factor (EF = δ15Nleaf −δ15Nsoil), combined with soil inorganic N contents and δ15N compositions were used to indicate the alterations of soil N availability and NO3–loss potential following secondary succession.ResultsLeaf N content and SON content significantly increased following secondary succession, indicating N accumulation in the soil and plant. The δ15N values of SON also significantly decreased, mainly affected by plant δ15N composition and N mineralization. SON content in macro-aggregates and soil NH4+ content significantly increased while δ15N values of NH4+ decreased, implying increases in SON stabilization and improved soil N availability following secondary succession. Leaf δ15N values, the EF values, and the (NO3–-N)/(NH4+-N) ratio gradually decreased, indicating reduced NO3– loss following secondary succession.ConclusionsSoil N availability improves and NO3– leaching loss reduces following secondary succession after agricultural land abandonment in the KCZO. creator: Man Liu creator: Guilin Han uri: https://doi.org/10.7717/peerj.14790 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu and Han title: Relationship between the roots of Hippophae rhamnoides at different stump heights and the root microenvironment in feldspathic sandstone areas link: https://peerj.com/articles/14819 last-modified: 2023-01-27 description: BackgroundTo solve the withering of Hippophae rhamnoides plantation in the feldspathic sandstone areas of Inner Mongolia and to promote the regeneration, rejuvenation, and sustainability of H. rhamnoides forests.MethodsWe stumped aging H. rhamnoides trees at the ground heights of 0, 10, 15, and 20 cm (S1, S2, S3, and S4, respectively) and utilized unstumped trees as the control (CK). We then analyzed the effects of the different stump heights on the roots and the root microenvironment of H. rhamnoides and the relationship between the roots and the root microenvironment in the stumped H. rhamnoides.ResultsThe root fractal features, root branching rate, root length, root soluble proteins, soil moisture content, and soil nutrients among the different treatments were ranked as S3>S2>S1>S4>CK (P < 0.05). The root topological index, root proline, and malondialdehyde among the different treatments were ranked as S320 m depth and coincide with the deepest bathymetric distribution of scattered colonies of Pocillopora. Because DO concentrations in coral reefs of Gorgona Island were comparably low to other coral reefs in the Eastern Tropical Pacific, and the hypoxic threshold of P. capitata was close to the minimum DO record on reefs, hypoxic events could represent a threat if conditions that promote eutrophication (and consequently hypoxia) increase. creator: Ana Lucia Castrillón-Cifuentes creator: Fernando A. Zapata creator: Alan Giraldo creator: Christian Wild uri: https://doi.org/10.7717/peerj.14586 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Castrillon-Cifuentes et al. title: Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples link: https://peerj.com/articles/14596 last-modified: 2023-01-26 description: BackgroundThe accurate identification of SARS-CoV-2 (SC2) variants and estimation of their abundance in mixed population samples (e.g., air or wastewater) is imperative for successful surveillance of community level trends. Assessing the performance of SC2 variant composition estimators (VCEs) should improve our confidence in public health decision making. Here, we introduce a linear regression based VCE and compare its performance to four other VCEs: two re-purposed DNA sequence read classifiers (Kallisto and Kraken2), a maximum-likelihood based method (Lineage deComposition for Sars-Cov-2 pooled samples (LCS)), and a regression based method (Freyja).MethodsWe simulated DNA sequence datasets of known variant composition from both Illumina and Oxford Nanopore Technologies (ONT) platforms and assessed the performance of each VCE. We also evaluated VCEs performance using publicly available empirical wastewater samples collected for SC2 surveillance efforts. Bioinformatic analyses were performed with a custom NextFlow workflow (C-WAP, CFSAN Wastewater Analysis Pipeline). Relative root mean squared error (RRMSE) was used as a measure of performance with respect to the known abundance and concordance correlation coefficient (CCC) was used to measure agreement between pairs of estimators.ResultsBased on our results from simulated data, Kallisto was the most accurate estimator as it had the lowest RRMSE, followed by Freyja. Kallisto and Freyja had the most similar predictions, reflected by the highest CCC metrics. We also found that accuracy was platform and amplicon panel dependent. For example, the accuracy of Freyja was significantly higher with Illumina data compared to ONT data; performance of Kallisto was best with ARTICv4. However, when analyzing empirical data there was poor agreement among methods and variations in the number of variants detected (e.g., Freyja ARTICv4 had a mean of 2.2 variants while Kallisto ARTICv4 had a mean of 10.1 variants).ConclusionThis work provides an understanding of the differences in performance of a number of VCEs and how accurate they are in capturing the relative abundance of SC2 variants within a mixed sample (e.g., wastewater). Such information should help officials gauge the confidence they can have in such data for informing public health decisions. creator: Tunc Kayikcioglu creator: Jasmine Amirzadegan creator: Hugh Rand creator: Bereket Tesfaldet creator: Ruth E. Timme creator: James B. Pettengill uri: https://doi.org/10.7717/peerj.14596 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Emotional Appetite Questionnaire: psychometric properties in Brazilian adult samples before and after the COVID-19 pandemic onset link: https://peerj.com/articles/14597 last-modified: 2023-01-26 description: BackgroundAppetite represents a desire of a person to eat specific food in order to reach satisfaction and pleasure states. This desire may be associated with the experience of negative or positive emotions (emotional appetite). Emotional appetite can influence eating behavior, and its investigation is relevant to avoid possible damage to health resulting from a disordered eating.ObjectivesTo adapt the Emotional Appetite Questionnaire (EMAQ) to the Portuguese language; to assess the validity and reliability of the data; and to assess emotional appetite in three samples of adults collected before and after the outbreak of the COVID-19 pandemic.MethodsThis is a cross-sectional study with non-probabilistic convenience sampling. The Portuguese version of the EMAQ was presented after translation, back-translation, and content analysis. Two studies were conducted, the first before and the second after the pandemic onset. Three samples were formed (2019: Sample 1 (age = 19.7 ± 1.5 years) n = 323; 2020: Sample 2 (age = 21.3 ± 1.8 years) n = 1,011; and Sample 3 (age = 28.9 ± 3.1 years) n = 909). An exploratory strategy with parallel analysis was performed. The analyses were conducted in FACTOR and R (lavaan and semTools packages) software. After determining the best-fit model for the data, emotional appetite was examined considering decrease, non-alteration, and increase in appetite in the face of positive and negative emotions/situations. The profile of emotional appetite was determined using a circumplex model.ResultsThe two-factor model described by the valence of emotions/situations fitted the samples (Comparative Fit Indexminimum-maximum = 0.95–0.98; Tucker-Lewis Index = 0.94–0.98; Root Mean Square Error of Approximation = 0.03–0.08; αord = 0.78–0.88). Increases in appetite were more frequent for positive emotions/situations (52.0–57.5%), and both decreases (35.4–44.5%) and increases (50.0–56.2%) in appetite were observed for negative emotions/situations. Emotions with negative valence and activation were more relevant to appetite reduction, while a significant increase in appetite was observed with anxiety (negative valence and positive activation).ConclusionDifferent emotions and situations may influence appetite in people, and such an investigation may be useful in preparing eating protocols. creator: Bianca G. Martins creator: Nadine V. Vanini creator: Lucas A. Campos creator: Juliana ADB Campos uri: https://doi.org/10.7717/peerj.14597 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Martins et al. title: Next-generation sequencing shows the genomic features of ovarian clear cell cancer and compares the genetic architectures of high-grade serous ovarian cancer and clear cell carcinoma in ovarian and endometrial tissues link: https://peerj.com/articles/14653 last-modified: 2023-01-26 description: Ovarian clear cell carcinoma (OCCC) is a special histological type of epithelial ovarian cancer (EOC) that is not derived from epithelial cells of the ovarian or fallopian tube as the most common type of ovarian cancer, high-grade serous ovarian carcinoma (HGSOC), but is closely related to endometriosis and similar to endometrial clear cell carcinoma (ECCC) at morphologic and phenotypic features. However, limited data was shown in OCCC genomic features and compared with that in OCCC, HGSOC and ECCC. Herein, we utilized next-generation sequencing analysis of a panel of 1,021 genes to profile the mutational alterations in 34 OCCC and compared them to those from HGSOC (402 cases) and ECCC (30 cases). In result, the ARID1A and PIK3CA are high-frequency mutations of OCCC. Clonal architectures showed that all the mutations of genes occur in the later stage in the OCCC progress, whereas KRAS mutation is the earlier event compared with mutation of ARID1A or PIK3CA, which usually occurs in a group of ARID1A or PIK3CA mutations. The mutation frequency of main driver genes is similar between OCCC and ECCC, while TP53 is the main mutation in HGSOC and ECCC. Shared mutational signatures between OCCC and ECCC tissues with commonly observed a C>T change indicated a common carcinogens-exposed between these two carcinomas, but HGSOC and ECCC have common and distinct mutational signatures across cohorts respectively. In addition, we identified some novel CNV gains in NF1, ASXL1, TCF7L2, CREBBP and LRP1B and loss in ATM, FANCM, RB1 and FLT in OCCC. Our study offered a new perspective for OCCC tumorigenesis from two organs, the ovary and uterus, at genomic architectures and revealed novel CNV events for helping to provide theoretical support for OCCC treatment. creator: Meifu Gan creator: Zaixian Tai creator: Yijian Yu creator: Chao Zhang creator: Juan Xu uri: https://doi.org/10.7717/peerj.14653 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gan et al. title: Applicability of VGGish embedding in bee colony monitoring: comparison with MFCC in colony sound classification link: https://peerj.com/articles/14696 last-modified: 2023-01-26 description: BackgroundBee colony sound is a continuous, low-frequency buzzing sound that varies with the environment or the colony’s behavior and is considered meaningful. Bees use sounds to communicate within the hive, and bee colony sounds investigation can reveal helpful information about the circumstances in the colony. Therefore, one crucial step in analyzing bee colony sounds is to extract appropriate acoustic feature.MethodsThis article uses VGGish (a visual geometry group—like audio classification model) embedding and Mel-frequency Cepstral Coefficient (MFCC) generated from three bee colony sound datasets, to train four machine learning algorithms to determine which acoustic feature performs better in bee colony sound recognition.ResultsThe results showed that VGGish embedding performs better than or on par with MFCC in all three datasets. creator: Nayan Di creator: Muhammad Zahid Sharif creator: Zongwen Hu creator: Renjie Xue creator: Baizhong Yu uri: https://doi.org/10.7717/peerj.14696 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Di et al. title: Detection of fungicide resistance to fludioxonil and tebuconazole in Fusarium pseudograminearum, the causal agent of Fusarium crown rot in wheat link: https://peerj.com/articles/14705 last-modified: 2023-01-26 description: Fusarium crown rot (FCR) on wheat is a soil-borne disease that affects the yield and quality of the produce. In 2020, 297 Fusarium pseudograminearum isolates were isolated from diseased FCR wheat samples from eight regional areas across Hebei Province in China. Baseline sensitivity of F. pseudograminearum to fludioxonil (0.0613 ± 0.0347 μg/mL) and tebuconazole (0.2328 ± 0.0840 μg/mL) were constructed based on the in vitro tests of 71 and 83 isolates, respectively. The resistance index analysis showed no resistance isolate to fludioxonil but two low-resistance isolates to tebuconazole in 2020. There was an increased frequency of resistant isolates from 2021 to 2022 based on the baseline sensitivity for tebuconazole. There was no cross-resistance between fludioxonil and tebuconazole. This study provides a significant theoretical and practical basis for monitoring the resistance of F. pseudograminearum to fungicides, especially the control of FCR. creator: Na Zhang creator: Yiying Xu creator: Qi Zhang creator: Le Zhao creator: Yanan Zhu creator: Yanhui Wu creator: Zhen Li creator: Wenxiang Yang uri: https://doi.org/10.7717/peerj.14705 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: Comprehensive profile and contrastive analysis of circular RNA expression in cervical squamous carcinoma and adenocarcinoma link: https://peerj.com/articles/14759 last-modified: 2023-01-26 description: BackgroundNumerous studies have shown circular RNA (circRNA) dysregulation is associated with the pathogenesis of cervical cancer,particularly in individual carcinoma variants. The aim of this study is to investigate and contrastively analyze the expression pattern of circRNAs in cervical squamous carcinoma and adenocarcinoma mediated by human papillomavirus type 16 (HPV-16).MethodsThe expression of circRNAs in cervical squamous carcinoma (SCC), adenocarcinoma (ADC) and adenosquamous carcinoma (ASC) tissues, together with the adjacent normal tissues (ANT), was profiled by high-throughput RNA sequencing (RNA-seq). Bioinformatics analysis and quantitative real time polymerase chain reaction (qRT-PCR) validation of the sequencing data were performed. A network of circRNA-miRNA (microRNA)-mRNA was then constructed according to predicted targets and function of candidate circRNAs.ResultsA total of 11,685 annotated circRNAs were identified in six cervical samples. There were 42 up-regulated and 98 down-regulated circRNAs. 215 circRNAs were up-regulated in SCC but down-regulated circRNAs in ADC, while 50 circRNAs displayed the opposite trend. Function enrichment analysis based on different expressions of circRNAs found that the most enriched pathway in all the three pathologic variants of cervical cancer was the “ubiquitin mediated proteolysis” pathway. Eight key candidate circRNAs derived from this pathway were further validated, and we noticed that several target miRNAs of candidate circRNAs could target the source genes. Based on this we constructed a related competing endogenous RNA (ceRNA) network.ConclusionThrough a comprehensive interpretation of differentially expressed circRNAs in different pathologic variants of cervical cancer, this study provides new insights into the process of tumor differentiation mediated by HPV. Our results may help to complement the molecular typing and stem cell theory of cervical cancer. creator: Hongxue Luo creator: Yi Zhu creator: Jiaqi Wang creator: Yue Wang creator: Lihui Wei uri: https://doi.org/10.7717/peerj.14759 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Luo et al. title: Effects of six weeks of sub-plateau cold environment training on physical functioning and athletic ability in elite parallel giant slalom snowboard athletes link: https://peerj.com/articles/14770 last-modified: 2023-01-26 description: BackgroundHypoxic and cold environments have been shown to improve the function and performance of athletes. However, it is unclear whether the combination of subalpine conditions and cold temperatures may have a greater effect. The present study aims to investigate the effects of 6 weeks of training in a sub-plateau cold environment on the physical function and athletic ability of elite parallel giant slalom snowboard athletes.MethodsNine elite athletes (four males and five females) participated in the study. The athletes underwent 6 weeks of high intensity ski-specific technical training (150 min/session, six times/week) and medium-intensity physical training (120 min/session, six times/week) prior to the Beijing 2021 Winter Olympic Games test competition. The physiological and biochemical parameters were collected from elbow venous blood samples after each 2-week session to assess the athletes’ physical functional status. The athletes’ athletic ability was evaluated by measuring their maximal oxygen uptake, Wingate 30 s anaerobic capacity, 30 m sprint run, and race performance. Measurements were taken before and after participating in the training program for six weeks. The repeated measure ANOVA was used to test the overall differences of blood physiological and biochemical indicators. For indicators with significant time main effects, post-hoc tests were conducted using the least significant difference (LSD) method. The paired-samples t-test was used to analyze changes in athletic ability indicators before and after training.Results(1) There was a significant overall time effect for red blood cells (RBC) and white blood cells (WBC) in males; there was also a significant effect on the percentage of lymphocytes (LY%), serum testosterone (T), and testosterone to cortisol ratio (T/C) in females (p < 0.001 − 0.015, ${\eta }_{p}^{2}=0.81-0.99$ηp2=0.81−0.99). In addition, a significant time effect was also found for blood urea(BU), serum creatine kinase (CK), and serum cortisol levels in both male and female athletes (p = 0.001 − 0.029, ${\eta }_{p}^{2}=0.52-0.95$ηp2=0.52−0.95). (2) BU and CK levels in males and LY% in females were all significantly higher at week 6 (p = 0.001 − 0.038), while WBC in males was significantly lower (p = 0.030). T and T/C were significantly lower in females at week 2 compared to pre-training (p = 0.007, 0.008, respectively), while cortisol (C) was significantly higher in males and females at weeks 2 and 4 (p(male) = 0.015, 0.004, respectively; p(female) = 0.024, 0.030, respectively). (3) There was a noticeable increase in relative maximal oxygen uptake, Wingate 30 s relative average anaerobic power, 30 m sprint run performance, and race performance in comparison to the pre-training measurements (p < 0.001 − 0.027).ConclusionsSix weeks of sub-plateau cold environment training may improve physical functioning and promote aerobic and anaerobic capacity for parallel giant slalom snowboard athletes. Furthermore, male athletes had a greater improvement of physical functioning and athletic ability when trained in sub-plateau cold environments. creator: Tao Ma creator: Jingwang Tan creator: Ran Li creator: Jiatao Li creator: Binghong Gao uri: https://doi.org/10.7717/peerj.14770 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ma et al. title: Energy conservation prospects in water intensive Paddy-Wheat cropping system for groundwater pumping in the semi-arid region of Haryana link: https://peerj.com/articles/14815 last-modified: 2023-01-26 description: The study was aimed at identifying the potential energy saving for groundwater pumping through enhanced efficiency of the pump sets. A total of 65 electrically powered tube wells were selected in the Sonipat district of the north Indian State of Haryana to study the energy use efficiency for groundwater pumping. The existing efficiency as well as the minimum expected overall efficiency of the tubewells were determined based on field survey, measurements, and applicable standard code of the Bureau of India Standards. The overall efficiencies of selected tube wells, computed based on actual measured power consumption, varied from 10.1% to 56.6% in the Sonipat block and 15.3% to 52.8% in the Rai block. The average energy requirement, for the selected tube wells, at the current efficiency level was 4,364.0 and 13,100.4 kWh for wheat and paddy crops, respectively, in the Sonipat block, while it was 3,424.8 and 10,280.9 kWh for wheat and paddy crops, respectively, in the Rai block. Analysis revealed that improving overall efficiency from the current level to the minimum expected level can lead to energy savings of 48.3% and 35.9% for tube wells in the Sonipat and Rai block, respectively. In the Rai block, where the groundwater level has declined significantly, the replacement of inefficient pumps should be done in tandem with crop diversification, improving water application efficiency and groundwater status by employing improved irrigation management practices and adopting groundwater recharge techniques. creator: Kuldeep Singh creator: Raj Kumar Jhorar creator: Manohar Sahai Sidhpuria creator: Mukesh Kumar creator: Mukesh Kumar Mehla uri: https://doi.org/10.7717/peerj.14815 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Singh et al. title: Change in eating habits during the Spanish COVID-19 pandemic lockdown: evidence for a sample of university community link: https://peerj.com/articles/14244 last-modified: 2023-01-25 description: BackgroundThe stress and anxiety caused by COVID-19 lockdown may have changed the eating habits of the population. Our aim is to assess the eating changes that have taken place due to the pandemic.MethodsData were collected through an electronic survey created by the Health Economics Research Group of the University of Cantabria and IDIVAL and conducted between 14/01/2021 and 19/02/2021. A total of 1,417 responses were recorded, but only 507 complete observations were considered. We carried out a cross-sectional analysis through ordered probit regressions.ResultsThe improvement in post-confinement eating habits is associated with higher income level, better self-assessed health status and more physical activity. The worsening of eating habits is associated with having a certain level of nomophobia or the fear of contagion.ConclusionsOur analysis can be used for designing and implementing new strategies to overcome the negative spill overs of the COVID-19 pandemic and improve the dietary patterns. creator: David Cantarero Prieto creator: Paloma Lanza-León creator: Patricia Moreno creator: Carla Blázquez-Fernández creator: Javier Lera creator: Francisco-Jose Gonzalez-Diego creator: Irene González Rodríguez uri: https://doi.org/10.7717/peerj.14244 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cantarero Prieto et al. title: Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, ʻōpeʻapeʻa, across the Hawaiian Islands link: https://peerj.com/articles/14365 last-modified: 2023-01-25 description: Island bat species are disproportionately at risk of extinction, and Hawaiʻi’s only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as ʻōpeʻapeʻa, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988–2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawaiʻi, Maui, Oʻahu, and Kauaʻi. Genetic differentiation occurred between Hawaiʻi and Maui, both of which were differentiated from Oʻahu and Kauaʻi. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawaiʻi and Kauaʻi. Contemporary genetic effective population sizes were smaller on Oʻahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawaiʻi. Our study provides population-level estimates for the genetic diversity and geographic structure of ‘ōpeʻapeʻa, that could be used by agencies tasked with wildlife conservation in Hawaiʻi. creator: Corinna A. Pinzari creator: M. Renee Bellinger creator: Donald Price creator: Frank J. Bonaccorso uri: https://doi.org/10.7717/peerj.14365 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development link: https://peerj.com/articles/14406 last-modified: 2023-01-25 description: Glutathione S-transferase (GSTs), a large and diverse group of multi-functional enzymes (EC 2.5.1.18), are associated with cellular detoxification, various biotic and abiotic stress responses, as well as secondary metabolites transportation. Here, 53 members of the FcGST gene family were screened from the genome database of fig (Ficus carica), which were further classified into five subfamilies, and the tau and phi were the major subfamilies. These genes were unevenly distributed over all the 13 chromosomes, and 12 tandem and one segmental duplication may contribute to this family expansion. Syntenic analysis revealed that FcGST shared closer genetic evolutionary origin relationship with species from the Ficus genus of the Moraceae family, such as F. microcarpa and F. hispida. The FcGST members of the same subfamily shared similar gene structure and motif distribution. The α helices were the chief structure element in predicted secondary and tertiary structure of FcGSTs proteins. GO and KEGG indicated that FcGSTs play multiple roles in glutathione metabolism and stress reactions as well as flavonoid metabolism. Predictive promoter analysis indicated that FcGSTs gene may be responsive to light, hormone, stress stimulation, development signaling, and regulated by MYB or WRKY. RNA-seq analysis showed that several FcGSTs that mainly expressed in the female flower tissue and peel during ‘Purple-Peel’ fig fruit development. Compared with ‘Green Peel’, FcGSTF1, and FcGSTU5/6/7 exhibited high expression abundance in the mature fruit purple peel. Additionally, results of phylogenetic sequences analysis, multiple sequences alignment, and anthocyanin content together showed that the expression changes of FcGSTF1, and FcGSTU5/6/7 may play crucial roles in fruit peel color alteration during fruit ripening. Our study provides a comprehensive overview of the GST gene family in fig, thus facilitating the further clarification of the molecular function and breeding utilization. creator: Longbo Liu creator: Shuxuan Zheng creator: Dekun Yang creator: Jie Zheng uri: https://doi.org/10.7717/peerj.14406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Evidence of validity and reliability of Jumpo 2 and MyJump 2 for estimating vertical jump variables link: https://peerj.com/articles/14558 last-modified: 2023-01-25 description: BackgroundWe investigated the concurrent validity and test-retest reliability of the Jumpo 2 and MyJump 2 apps for estimating jump height, and the mean values of force, velocity, and power produced during countermovement (CMJ) and squat jumps (SJ).MethodsPhysically active university aged men (n = 10, 20 ± 3 years, 176 ± 6 cm, 68 ± 9 kg) jumped on a force plate (i.e., criterion) while being recorded by a smartphone slow-motion camera. The videos were analyzed using Jumpo 2 and MyJump 2 using a Samsung Galaxy S7 powered by the Android system. Validity and reliability were determined by regression analysis, typical error of estimates and measurements, and intraclass correlation coefficients.ResultsBoth apps provided a reliable estimate of jump height and the mean values of force, velocity, and power. Furthermore, estimates of jump height for CMJ and SJ and the mean force of the CMJ were valid. However, the apps presented impractical or poor validity correlations for velocity and power. Compared with criterion, the apps underestimated the velocity of the CMJ.ConclusionsTherefore, Jumpo 2 and MyJump 2 both provide a valid measure of jump height, but the remaining variables provided by these apps must be viewed with caution since the validity of force depends on jump type, while velocity (and as consequence power) could not be well estimated from the apps. creator: Amilton Vieira creator: Gabriela L. Ribeiro creator: Victor Macedo creator: Valdinar de Araújo Rocha Junior creator: Roberto de Souza Baptista creator: Carlos Gonçalves creator: Rafael Cunha creator: James Tufano uri: https://doi.org/10.7717/peerj.14558 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Vieira et al. title: Facilitation of a free-roaming apex predator in working lands: evaluating factors that influence leopard spatial dynamics and prey availability in a South African biodiversity hotspot link: https://peerj.com/articles/14575 last-modified: 2023-01-25 description: Apex predators ideally require vast intact spaces that support sufficient prey abundances to sustain them. In a developing world, however, it is becoming extremely difficult to maintain large enough areas to facilitate apex predators outside of protected regions. Free-roaming leopards (Panthera pardus) are the last remaining apex predator in the Greater Cape Floristic Region, South Africa, and face a multitude of threats attributable to competition for space and resources with humans. Using camera-trap data, we investigated the influence of anthropogenic land modification on leopards and the availability of their natural prey species in two contrasting communities—primarily protected (Cederberg) and agriculturally transformed (Piketberg). Potential prey species composition and diversity were determined, to indicate prey availability in each region. Factors influencing spatial utilisation by leopards and their main prey species were also assessed. Estimated potential prey species richness (Cederberg = 27, Piketberg = 26) and diversity indices (Cederberg—H′ = 2.64, Ds = 0.90; Piketberg—H′ = 2.46, Ds = 0.89), supported by both the Jaccard’s Index (J = 0.73) and Sørensen’s Coefficient (CC = 0.85), suggested high levels of similarity across the two regions. Main leopard prey species were present in both regions, but their relative abundances differed. Grey rhebok, klipspringer, and rock hyrax were more abundant in the Cederberg, while Cape grysbok, Cape porcupine, chacma baboon, and common duiker were more abundant in Piketberg. Leopards persisted across the agriculturally transformed landscape despite these differences. Occupancy modelling revealed that the spatial dynamics of leopards differed between the two regions, except for both populations preferring areas further away from human habitation. Overall, anthropogenic factors played a greater role in affecting spatial utilisation by leopards and their main prey species in the transformed region, whereas environmental factors had a stronger influence in the protected region. We argue that greater utilisation of alternative main prey species to those preferred in the protected region, including livestock, likely facilitates the persistence of leopards in the transformed region, and believe that this has further implications for human-wildlife conflict. Our study provides a baseline understanding of the potential direct and indirect impacts of agricultural landscape transformation on the behaviour of leopards and shows that heavily modified lands have the potential to facilitate mammalian diversity, including apex predators. We iterate that conservation measures for apex predators should be prioritised where they are present on working lands, and encourage the collaborative development of customised, cost-effective, multi-species conflict management approaches that facilitate coexistence. creator: Eugene Greyling creator: Jessica Comley creator: Michael I. Cherry creator: Alison J. Leslie creator: Lana Müller uri: https://doi.org/10.7717/peerj.14575 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Greyling et al. title: Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study link: https://peerj.com/articles/14595 last-modified: 2023-01-25 description: Background and ObjectiveEpidemiological studies report associations between coronavirus disease 2019 (COVID-19) and periodontitis; however, causality has not been proven. The aim of this study is to assess the associations between COVID-19 susceptibility and periodontitis with two-sample Mendelian randomization (MR) analyses.MethodsA two-sample summary MR analysis was performed using data for outcome and exposure from the OpenGWAS database on people of European descent. Periodontal complex traits (PCTs) were chosen as a proxy for the periodontitis phenotype. The causal association between PCT3 (Aggregatibacter actinomycetemcomitans), PCT5 (Porphyromonas gingivalis), and gingival crevicular fluid (GCF) interleukin-1β (IL-1β) and COVID-19 were considered. Genome-wide association study (GWAS) data with the two largest sample sizes were selected as COVID-19 outcomes (datasets ebi-a-GCST010776 and ebi-a-GCST010777). Single-nucleotide polymorphisms (SNPs) associated with PCT3, PCT5, and GCF IL-1β at statistical significance at genome-wide level (P < 5 × 10−8) were identified as genetic instruments. We used two-sample summary MR methods and tested the existence of a pleiotropic effect with MR-Egger.ResultsInverse-variance weighted (IVW) estimates showed that there was a positive association between COVID-19 risk and periodontitis (ebi-a-GCST010776: odds ratio [OR] = 1.02 (95% confidence interval (CI), 1.00–1.05), P = 0.0171; ebi-a-GCST010777: OR = 1.03 (95% CI, 1.00–1.05), P = 0.0397). The weighted median also showed directionally similar estimates. Exploration of the causal associations between other PCTs and COVID-19 identified a slight effect of local inflammatory response (GCF IL-1β) on COVID-19 risk across the two datasets (ebi-a-GCST010776: IVW OR = 1.02 (95% CI, [1.01–1.03]), P < 0.001; ebi-a-GCST010777: IVW OR = 1.03 (95% CI, [1.02–1.04]), P < 0.001). The intercepts of MR-Egger yielded no proof for significant directional pleiotropy for either dataset (ebi-a-GCST010776: P = 0.7660; ebi-a-GCST010777: P = 0.6017).ConclusionsThe findings suggests that periodontitis and the higher GCF IL-1β levels is causally related to increase susceptibility of COVID-19. However, given the limitations of our study, the well-designed randomized controlled trials are needed to confirm its findings, which may represent a new non-pharmaceutical intervention for preventing COVID-19. creator: Zhaoqiang Meng creator: Yujia Ma creator: Wenjing Li creator: Xuliang Deng uri: https://doi.org/10.7717/peerj.14595 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Meng et al. title: Combination of Vitamin C and Lenvatinib potentiates antitumor effects in hepatocellular carcinoma cells in vitro link: https://peerj.com/articles/14610 last-modified: 2023-01-25 description: Lenvatinib has become a first-line drug in the treatment of advanced hepatocellular carcinoma (HCC). Investigating its use in combination with other agents is of great significance to improve the sensitivity and durable response of Lenvatinib in advanced HCC patients. Vitamin C (L-ascorbic acid, ascorbate, VC) is an important natural antioxidant, which has been reported to show suppressive effects in cancer treatment. Here, we investigated the effect of the combination of VC and Lenvatinib in HCC cells in vitro. We found that treatment of VC alone significantly inhibited the proliferation, migration and invasion in HCC cells. Additionally, VC was strongly synergistic with Lenvatinib in inhibition of the proliferative, migratory and invasive capacities of HCC cells in vitro. In conclusion, our results demonstrate that the combination of VC and Lenvatinib has synergistic antitumor activities against HCC cells, providing a promising therapeutic strategy to improve the prognosis of HCC patients. creator: Xinyue Wang creator: Songyi Qian creator: Siyi Wang creator: Sheng Jia creator: Nishang Zheng creator: Qing Yao creator: Jian Gao uri: https://doi.org/10.7717/peerj.14610 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2023 Wang et al. title: Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep link: https://peerj.com/articles/14689 last-modified: 2023-01-25 description: BackgroundStevia straw is a byproduct of sugar crop stevia. It is a good feed material because of richness in nutrients and active substances (steviosides and flavonoids). However, due to improper utilization such as piling, burning and so on, it became a large amount of wasted straw resources and lead to environmental pollution.MethodsWe added 0%, 0.2%, 0.4%, 0.6%, 0.8%, 1.0% and 1.5% of stevia stalk to study the effects of different stevia stalk concentrations on nutrient utilization and rumen fermentation in sheep (based on sheep diet). In vitro fermentation method was used, with 17 repetitions for each treatment. All fermentation substrate based on sheep diet with different stevia stalk concentrations were fermented for 2 h, 6 h, 12 h, 24 h and 48 h, then the gas production, dry matter degradability (DMD), crude protein degradability (CPD), neutral detergent fiber degradability (NDFD), acid detergent fiber degradability (ADFD), pH, ammonia nitrogen (NH3-N) and volatile fatty acids (VFAs) were determined.ResultsThe results showed that at different fermentation time, the change trend of gas production in each teatment was basically same, but the maximum occurred in 1.0% treatment at 48 h. The DMD, CPD, NDFD and ADFD of sheep diets increased with fermentation time increasing, especially the CPD48h, NDFD48h and ADFD48h of diets in 0.8%, 1.0% and 1.5% treatments were significantly higher than those in control (P < 0.05). The pH of fermentation substrate in each treatment remained within the normal range of 6.21∼7.25. NH3-N24h–48hin 0.8%, 1.0% and 1.5% treatments were higher than that in control. At 6 h–12 h, the total acid content of 0.8% and 1.0% treatments were significantly higher than those of other treatments (P < 0.05), it reached the highest in 1.0% treatment. According to overall evaluation, effect ranking of stevia stalk on sheep nutrient utilization was as follows: 1.0% >0.8% >1.5% >0.4% >0.6% >0.2%. Overall, 1.0% stevia stalk could promote nutrient degradation and sheep rumen fermentation. creator: Xia Zhang creator: Ting Jiao creator: Shumin Ma creator: Xin Chen creator: Zhengwen Wang creator: Shengguo Zhao creator: Yue Ren uri: https://doi.org/10.7717/peerj.14689 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance link: https://peerj.com/articles/14709 last-modified: 2023-01-25 description: Acinetobacter baumannii is one of the most successful pathogens that can cause difficult-to-treat nosocomial infections. Outbreaks and infections caused by multi-drug resistant A. baumannii are prevalent worldwide, with only a few antibiotics are currently available for treatments. Plasmids represent an ideal vehicle for acquiring and transferring resistance genes in A. baumannii. Five extensively drug-resistant A. baumannii clinical isolates from three major Jordanian hospitals were fully sequenced. Whole-Genome Sequences (WGS) were used to study the antimicrobial resistance and virulence genes, sequence types, and phylogenetic relationship of the isolates. Plasmids were characterized In-silico, followed by conjugation, and plasmid curing experiments. Eight plasmids were recovered; resistance plasmids carrying either aminoglycosides or sulfonamide genes were detected. Chromosomal resistance genes included blaOXA-66, blaOXA-91, and blaOXA-23,and the detected virulence factors were involved in biofilm formation, adhesion, and many other mechanisms. Conjugation and plasmid curing experiments resulted in the transfer or loss of several resistance phenotypes. Plasmid profiling along with phylogenetic analyses revealed high similarities between two A. baumannii isolates recovered from two different intensive care units (ICU). The high similarities between the isolates of the study, especially the two ICU isolates, suggest that there is a common A. baumannii strain prevailing in different ICU wards in Jordanian hospitals. Three resistance genes were plasmid-borne, and the transfer of the resistance phenotype emphasizes the role and importance of conjugative plasmids in spreading resistance among A. baumannii clinical strains. creator: Qutaiba Ababneh creator: Sara Al Sbei creator: Ziad Jaradat creator: Sebawe Syaj creator: Neda’a Aldaken creator: Hamza Ababneh creator: Zeina Inaya uri: https://doi.org/10.7717/peerj.14709 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ababneh et al. title: Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells link: https://peerj.com/articles/14722 last-modified: 2023-01-25 description: BackgroundS100 calcium-binding protein A9 (S100A9) is a commonly known pro-inflammatory factor involved in various inflammatory responses. Clostridium perfringens (C. perfringens ) type C is known to cause diarrhea in piglets. However, the role of S100A9 in C. perfringens type C-induced infectious diarrhea is unclear.MethodsHere, the S100A9 gene was overexpressed and knocked down in the IPEC-J2 cells, which were treated with C. perfringens beta2 (CPB2) toxin. The role of S100A9 in CPB2 toxin-induced injury in IPEC-J2 cells was assessed by measuring the levels of inflammatory cytokines, reactive oxygen species (ROS), lactate dehydrogenase (LDH), cell proliferation, and tight junction-related proteins.ResultsThe results showed elevated expression of S100A9 in diarrhea-affected piglet tissues, and the elevation of S100A9 expression after CPB2 toxin treatment of IPEC-J2 was time-dependent. In CPB2 toxin-induced IPEC-J2 cells, overexpression of S100A9 had the following effects: the relative expression of inflammatory factors IL-6, IL8, TNF-α, and IL-1β was increased; the ROS levels and LDH viability were significantly increased; cell viability and proliferation were inhibited; the G0/G1 phase cell ratio was significantly increased. Furthermore, overexpression of S100A9 reduced the expression of tight junction proteins in CPB2-induced IPEC-J2 cells. The knockdown of S100A9 had an inverse effect. In conclusion, our results confirmed that S100A9 exacerbated inflammatory injury in CPB2 toxin-induced IPEC-J2 cells, inhibited cell viability and cell proliferation, and disrupted the tight junctions between cells. Thus, decreased S100A9 expression alleviates CPB2 toxin-induced inflammatory injury in IPEC-J2 cells. creator: Jie Li creator: Xiaoyu Huang creator: Kaihui Xie creator: Juanli Zhang creator: Jiaojiao Yang creator: Zunqiang Yan creator: Shuangbao Gun uri: https://doi.org/10.7717/peerj.14722 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing link: https://peerj.com/articles/14733 last-modified: 2023-01-25 description: BackgroundThe Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated.MethodsIn this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function.ResultsAfter filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan. creator: Shifang Wu creator: Xiaoli Yang creator: Haina Gao creator: Chengrui Shi creator: Longlin Wang creator: Deyuan Lu creator: Yiheng Li creator: Jinliang Zhang creator: Weibing Zhang creator: Pengcheng Wen uri: https://doi.org/10.7717/peerj.14733 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wu et al. title: Comparison of urine proteomes from tumor-bearing mice with those from tumor-resected mice link: https://peerj.com/articles/14737 last-modified: 2023-01-25 description: ObjectiveThis study aimed to address on the most important concern of surgeons—whether to completely resect tumor. Urine can indicate early changes associated with physiological or pathophysiological processes. Based on these ideas, we conducted experiments to explore changes in the urine proteome between tumor-bearing mice and tumor-resected mice.MethodThe tumor-bearing mouse model was established with MC38 mouse colon cancer cells, and the mice were divided into the control group, tumor-resected group, and tumor-bearing group. Urine was collected 7 and 30 days after tumor resection. Liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) was used to identify the urine proteome, which was analyzed for differentially expressed proteins and functional annotation.Results(1) Seven days after tumor resection, 20 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included circadian rhythm, Notch signaling pathway, leukocyte cell–cell adhesion, and heterophilic cell–cell adhesion via plasma membrane cell adhesion molecules. (2) Thirty days after tumor resection, 33 differentially expressed proteins distinguished the tumor-resected group and the tumor-bearing group. The identified biological processes included cell adhesion; complement activation, the alternative pathway; the immune system process; and angiogenesis. (3) The difference in the urine proteome between the tumor-resected group and the healthy control group was smaller 30 days after tumor resection.ConclusionChanges in the urinary proteome can reflect the complete resection of MC38 tumors. creator: Ziqi Heng creator: Chenyang Zhao creator: Youhe Gao uri: https://doi.org/10.7717/peerj.14737 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Heng et al. title: Inferring fish behaviour at the trawl mouth from escape location link: https://peerj.com/articles/14746 last-modified: 2023-01-25 description: In this study, we used escape location underneath the trawl to understand groundfish herding behaviour at the trawl mouth. Three collecting bags (port, center, starboard) were mounted under the trawl and behind the footgear to collect escapees. The escape-at-length of species that escaped into the center bag were compared to the two wing bags to infer fish response behaviour, herding behaviour, and swimming capacity at the trawl mouth. For roundfish, smaller-sized individuals escaped more in the center for both Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus), <20 and 11 cm, respectively, indicating that larger-sized fish were to a greater extent seeking to escape under the trawl at the wings, vs small fish being herded to the center and likely overrun due to reduced swimming capacity. For flatfish and monkfish (Lophius piscatorius), results varied. European plaice (Pleuronectes platessa), American plaice (Hippoglossoides platessoides), and monkfish were caught most often in the wings, though not significantly for American plaice. Catches of dab (Limanda limanda) between 18 and 27 cm were significantly higher in the center, with no difference for smaller and larger individuals. The differences between fish escape location likely result from a combination of varying herding behaviour, size, and swimming capacity. Here, we were able to show how these size-dependent behaviours relate to fish response behaviour, escape behaviour, size, and likely swimming capacity. creator: Vang Y. Nguyen creator: Shannon M. Bayse creator: Haraldur Arnar Einarsson creator: Ólafur Arnar Ingólfsson uri: https://doi.org/10.7717/peerj.14746 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Nguyen et al. title: Response of photosynthesis, the xanthophyll cycle, and wax in Japanese yew (Taxus cuspidata L.) seedlings and saplings under high light conditions link: https://peerj.com/articles/14757 last-modified: 2023-01-25 description: In order to understand the adaptative changes of the Japanese yew (Taxus cuspidate L.) to high light conditions, this study investigated gas-exchange, chlorophyll fluorescence, chlorophyll, and the impact of epicuticular wax on the gas-exchange and photoinhibition of Japanese yew seedlings and saplings. The chlorophyll content per unit area and photosynthetic rate in seedling leaves were significantly lower than in sapling leaves. When leaves from seedlings and saplings were exposed to 1,200 μmol·m−2·s−1 photon flux density (PFD) for 2 h, seedling leaves exhibited a greater down-regulation of maximum quantum yield (Fv/Fm) and actual photosystem II efficiency ($\Phi$ΦPSII). Non-photochemical quenching (NPQ) and high energy quenching (qE) in sapling leaves were much higher than in seedling leaves when both were exposed to 1,200 μmol·m−2·s−1 PFD for 2 h. At a low level of O2, the photorespiration rate (Pr) and the ratio of photorespiration/gross photosynthetic rate (Pr/Pg) in seedling leaves were lower than in sapling leaves when both were exposed to 1,200 μmol·m−2·s−1 PFD, but this difference did not reach statistical significance (P < 0.05). Compared with sapling leaves, seedling leaves exhibited lower levels of xanthophyll pool. Epicuticular wax content on seedling leaves was significantly lower than on sapling leaves. The results of this study showed that wax coverage on the leaf surface decreased the photosynthetic rate in sapling leaves as a consequence of decreased stomatal conductance. Epicuticular wax is related to tree age and photoinhibition prevention in the Japanese yew. It is possible that lower photosynthetic rate, lower NPQ depending on the xanthophyll cycle, and lower deposition of epicuticular wax results in seedling plants that are not adapted to high light conditions. creator: Wei Li creator: Jiacheng Li creator: Jia Wei creator: Chunda Niu creator: Deguang Yang creator: Baiwen Jiang uri: https://doi.org/10.7717/peerj.14757 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Construction of a ceRNA network of regulated ferroptosis in doxorubicin-induced myocardial injury link: https://peerj.com/articles/14767 last-modified: 2023-01-25 description: BackgroundFerroptosis and long-noncoding RNAs (lncRNAs) play crucial roles in doxorubicin (DOX)-induced myocardial injury (DIMI). Nevertheless, there is no research to construct competing endogenous RNAs (ceRNAs) network between lncRNAs and ferroptosis-related key gene. So our research was designed to screen ferroptosis-related genes from differentially expressed mRNAs in DIMI and construct lncRNAs regulated ferroptosis-related key gene ceRNAs network.MethodsThe male mice were injected with DOX intraperitoneally to induce myocardial injury, myocardial injury was evaluated by hematoxylin and eosin (HE) staining, and ferroptosis-related protein-glutathione peroxidase 4 (GPx4) protein expression was detected. The differentially expressed lncRNAs and mRNAs were detected by microarray, and the ferroptosis-related genes were screened to construct a protein-protein associations (PPA) network, the highest maximal clique centrality (MCC) score gene were identified by Cytoscape software, miRNAs bound to key genes and lncRNAs bound to miRNAs were predicted; then, the obtained lncRNAs were intersected with differentially expressed lncRNAs detected by microarray. Finally, the lncRNA/miRNA/mRNA ceRNA network of the highest MCC score gene regulating ferroptosis in DIMI was constructed. The expressions of the key components in ceRNA network were detected by qRT-PCR.ResultsCompared with the control group, in the DOX group, myocardial enzymes and HE staining showed that myocardium structure was changed, and GPx4 protein expression was decreased. The differentially expressed 10,265 lncRNAs and 6,610 mRNAs in the DOX group were detected via microarray. Among them, 114 ferroptosis-related genes were obtained to construct PPA networks, and Becn1 was identified as the key gene. Finally, the ceRNA network including Becn1, three miRNAs and four lncRNAs was constructed by predicting data of the Starbase database. The relative expressions of these components in ceRNA net were up-regulated and consistent with microarray results.ConclusionsBased on the microarray detection results and bioinformatics analysis, we screened ferroptosis-related gene Becn1 and constructed the lncRNA/miRNA/mRNA ceRNA network of regulated ferroptosis in DIMI. creator: Hongwei Ye creator: Yuping Li creator: Lu Li creator: Yuhui Huang creator: Jiahui Wang creator: Qin Gao uri: https://doi.org/10.7717/peerj.14767 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ye et al. title: Scaling patterns of body plans differ among squirrel ecotypes link: https://peerj.com/articles/14800 last-modified: 2023-01-25 description: Body size is often hypothesized to facilitate or constrain morphological diversity in the cranial, appendicular, and axial skeletons. However, how overall body shape scales with body size (i.e., body shape allometry) and whether these scaling patterns differ between ecological groups remains poorly investigated. Here, we test whether and how the relationships between body shape, body size, and limb lengths differ among species with different locomotor specializations, and describe the underlying morphological components that contribute to body shape evolution among squirrel (Sciuridae) ecotypes. We quantified the body size and shape of 87 squirrel species from osteological specimens held at museum collections. Using phylogenetic comparative methods, we first found that body shape and its underlying morphological components scale allometrically with body size, but these allometric patterns differ among squirrel ecotypes: chipmunks and gliding squirrels exhibited more elongate bodies with increasing body sizes whereas ground squirrels exhibited more robust bodies with increasing body size. Second, we found that only ground squirrels exhibit a relationship between forelimb length and body shape, where more elongate species exhibit relatively shorter forelimbs. Third, we found that the relative length of the ribs and elongation or shortening of the thoracic region contributes the most to body shape evolution across squirrels. Overall, our work contributes to the growing understanding of mammalian body shape evolution and how it is influenced by body size and locomotor ecology, in this case from robust subterranean to gracile gliding squirrels. creator: Tate J. Linden creator: Abigail E. Burtner creator: Johannah Rickman creator: Annika McFeely creator: Sharlene E. Santana creator: Chris J. Law uri: https://doi.org/10.7717/peerj.14800 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Linden et al. title: Face matching and metacognition: investigating individual differences and a training intervention link: https://peerj.com/articles/14821 last-modified: 2023-01-25 description: BackgroundAlthough researchers have begun to consider metacognitive insight during face matching, little is known about the underlying mechanism. Here, I investigated whether objective ability, as well as self-assessed ability, were able to predict metacognitive performance, that is, the ability to differentiate correct and incorrect responses in terms of confidence. In addition, I considered whether a training intervention resulted in improvements to both face matching performance and metacognitive insight.MethodsIn this experiment (N = 220), participants completed a face matching task, with either a diagnostic feature training course or a control course presented at the halfway point. In addition, a second face matching task, as well as a self-report questionnaire regarding ability, were completed to provide measures of objective and self-assessed ability respectively.ResultsHigher self-assessed ability with faces, as well as higher objective ability with face matching, predicted better metacognitive performance, i.e., greater confidence in correct, in comparison with incorrect, responses. This pattern of results was evident both when objective ability was measured through performance on the same task used to measure metacognitive insight and when a different task was used. Finally, the training intervention failed to produce improvements in face matching performance and showed no evidence of altering metacognitive ability.DiscussionThe current work begins to address the mechanism underlying individual differences in metacognitive insight during face matching. Although support was provided for a competence-based account, where better face matchers showed greater performance on the task and were more successful in monitoring their performance, further work might focus on decoupling task performance and competence in order to more conclusively explain why some people are more insightful than others. creator: Robin S. S. Kramer uri: https://doi.org/10.7717/peerj.14821 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kramer title: Pepper growth promotion and biocontrol against Xanthomonas euvesicatoria by Bacillus cereus and Bacillus thuringiensis formulations link: https://peerj.com/articles/14633 last-modified: 2023-01-24 description: BackgroundBacillus genus has been used in horticultural crops as a biocontrol agent against insect pests, microbial phytopathogens, and plant growth-promoting bacteria (PGPB), representing an alternative to agrochemicals. In particular, B. cereus (Bc) and B. thuringiensis (Bt) have been studied for their fungicidal and insecticidal activities. However, their use as biofertilizer formulations and biocontrol agents against phytopathogenic bacteria is limited.ObjectiveTo evaluate Bc and Bt formulations as PGPB and biocontrol agents against the bacterial spot agent Xanthomonas euvesicatoria (Xe) in greenhouse-grown chili peppers.MethodsBc and Bt isolates obtained from soil samples were identified and characterized using conventional biochemical and multiplex PCR identification methods. Bioassays to determine Bc and Bt isolates potential as PGPB were evaluated on chili pepper seedlings in seedbeds. In addition, formulations based on Bc (F-BC26 and F-BC08) and Bt (F-BT24) strains were assessed as biofertilizers on pepper, under controlled conditions. Furthermore, in vitro antagonism assays were performed by confronting Bc and Bt isolate formulations against Xe isolates in direct (foliage) and indirect (resistance induction) phytopathogen biocontrol assays on pepper plants, which were grown under controlled conditions for 15 d after formulations treatment.ResultsIsolates were identified as Bc and Bt. Formulations significantly improved pepper growth in seedbeds and pots, whereas in vitro bioassays demonstrated the bactericidal effect of Bc and Bt strains against Xe isolates. Furthermore, assays showed significant plant protection by F-BC26, F-BC08, and F-BT24 formulated strains against Xe.ConclusionResults indicated that F-BT24 and F-BC26 isolates formulations promoted pepper growth and protected it against Xanthomonas euvesicatoria. creator: Jared Hernández-Huerta creator: Patricia Tamez-Guerra creator: Ricardo Gomez-Flores creator: Ma. Carmen E. Delgado-Gardea creator: Loreto Robles-Hernández creator: Ana Cecilia Gonzalez-Franco creator: Rocio Infante-Ramirez uri: https://doi.org/10.7717/peerj.14633 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hernández-Huerta et al. title: Mesenchymal stem cell-derived extracellular vesicles, osteoimmunology and orthopedic diseases link: https://peerj.com/articles/14677 last-modified: 2023-01-24 description: Mesenchymal stem cells (MSCs) play an important role in tissue healing and regenerative medicine due to their self-renewal and multi-directional differentiation properties. MSCs exert their therapeutic effects mainly via the paracrine pathway, which involves the secretion of extracellular vesicles (EVs). EVs have a high drug loading capacity and can transport various molecules, such as proteins, nucleic acids, and lipids, that can modify the course of diverse diseases. Due to their ability to maintain the therapeutic effects of their parent cells, MSC-derived EVs have emerged as a promising, safe cell-free treatment approach for tissue regeneration. With advances in inflammation research and emergence of the field of osteoimmunology, evidence has accumulated pointing to the role of inflammatory and osteoimmunological processes in the occurrence and progression of orthopedic diseases. Several studies have shown that MSC-derived EVs participate in bone regeneration and the pathophysiology of orthopedic diseases by regulating the inflammatory environment, enhancing angiogenesis, and promoting the differentiation and proliferation of osteoblasts and osteoclasts. In this review, we summarize recent advances in the application and functions of MSC-derived EVs as potential therapies against orthopedic diseases, including osteoarthritis, intervertebral disc degeneration, osteoporosis and osteonecrosis. creator: Maoxiao Ma creator: Guofeng Cui creator: Youwen Liu creator: Yanfeng Tang creator: Xiaoshuai Lu creator: Chen Yue creator: Xue Zhang uri: https://doi.org/10.7717/peerj.14677 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ma et al. title: RNAi-based knockdown of candidate gut receptor genes altered the susceptibility of Spodoptera frugiperda and S. litura larvae to a chimeric toxin Cry1AcF link: https://peerj.com/articles/14716 last-modified: 2023-01-24 description: BackgroundA multitude of Cry toxins (secreted by Bacillus thuringiensis or Bt) has been deployed globally either via transgenic mean or bio-pesticidal formulations in order to manage insect pests. However, Bt resistance development in insects is emerging as a major concern. To avoid this problem, multiple gene pyramiding or protein-engineered chimeric toxin-based strategy has been analyzed.MethodsIn the present study, one such chimeric toxin Cry1AcF (contain the swapped domains of Cry1Ac and Cry1F) was used to investigate its in vivo pathogenesis process in lepidopteran pests Spodoptera frugiperda and S. litura. A number of biochemical and molecular analysis were performed.ResultsOral ingestion of Cry1AcF caused greater toxicity in S. frugiperda than S. litura with larvae displaying increased hemolymph melanization. Histopathology of the midgut transverse sections exhibited Cry1AcF-induced extensive gut damage in both the test insects followed by cytotoxicity in terms of reduced hemocyte numbers and viability. Elevated hemolymph phenoloxidase activity indicated the immune-stimulatory nature of Cry1AcF. In order to analyze the role of gut receptor proteins in Cry1AcF intoxication in test insects, we performed RNAi-mediated silencing using bacterially-expressed dsRNAs of individual receptor-encoding genes including CAD, ABCC2, ALP1 and APN. Target-specific induced downregulation of receptor mRNAs differentially altered the insect susceptibility to Cry1AcF toxin in our study. The susceptibility of ALP1 and APN dsRNA pre-treated S. frugiperda was considerably decreased when treated with Cry1AcF in LD50 and LD90 doses, whereas susceptibility of CAD and ABCC2 dsRNA pre-treated S. litura was significantly reduced when ingested with Cry1AcF in different doses. CAD/ABCC2-silenced S. frugiperda and ALP1/APN-silenced S. litura were vulnerable to Cry1AcF alike of control larvae. In conclusion, our results indicate ALP1/APN and CAD/ABCC2 as the functional receptor for Cry1AcF toxicity in S. frugiperda and S. litura, respectively. creator: Tushar K. Dutta creator: Kodhandaraman Santhoshkumar creator: Arudhimath Veeresh creator: Chandramani Waghmare creator: Chetna Mathur creator: Rohini Sreevathsa uri: https://doi.org/10.7717/peerj.14716 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Dutta et al. title: Effects of the environmental conditions and seasonality on a population survey of the Andean condor Vultur gryphus in the tropical Andes link: https://peerj.com/articles/14763 last-modified: 2023-01-24 description: BackgroundAmong the New World vultures, the Andean condor is considered one of the most culturally and ecologically important species. However, their populations are declining over their entire distributional range. In response, conservation strategies have been implemented in many countries to reverse the increasing extinction risk of this species. The initiatives rely on extensive population surveys to gather basic information necessary to implement policies and to intervene efficiently. Still, there is a need to standardize the surveys based on seasonality and suitable environmental conditions throughout the species distribution. Here, we provide the first assessment of how daily temperature, rainfall, and seasonality influence surveys of Andean condors on a communal roost in the central Peruvian Andes.MethodsUsing an autoregressive generalized linear model, we associated environmental variables with visual surveys of adult and young condors at three different times of the day and three times a week between June 2014 and March 2015.ResultsWe found that both adults and young Andean condors showed a threefold reduction in the use of the communal roost after the beginning of the rainy season. Colder and drier days (dry season) are preferable for surveying, as we expect the total number of condors using communal roosts to reduce under rainy (rainfall = −0.53 ± 0.16) and warmer days (temperature = −0.04 ± 0.02) days. Therefore, the significant variation in the use of roosts across seasons and hours should be carefully accounted for in national surveys, at the risk of undermining the full potential of the communal roost surveys. Moreover, we also found a strong bias towards immatures (about 76%) in the adult:immature ratio and a remarkable absence of Andean condors during the wet season. These results suggest that the species might be using other unknown communal roosts hierarchically. Such results provide key information for selecting priority areas for conservation and selecting the best time to survey this species in the tropical Andes. Finally, it may open a fruitful avenue for further research on the protection of the Andean condor. creator: Sandra Márquez-Alvis creator: Luis Martin Vallejos creator: Santiago Paredes-Guerrero creator: Luis Pollack-Velasquez creator: Gabriel Silva Santos uri: https://doi.org/10.7717/peerj.14763 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Márquez-Alvis et al. title: Verification of the detachment–transport coupling relationship of rill erosion using colluvium material in steep nonerodible slopes link: https://peerj.com/articles/14766 last-modified: 2023-01-24 description: The detachment–transport coupling equation by Foster and Meyer is a classical equation that describes the relationship between detachment and transport. The equation quantifies the relationship between sediment loads and soil detachment rates, deepens the understanding of soil erosion and provides a reliable basis for the establishment of an erosion model. However, the applicability of this equation to slopes with gradients greater than 47% is limited. In this work, the detachment–transport coupling relationship is investigated using the colluvium material of Benggang. A nonerodible rill flume 4 m long and 0.12 m wide was adopted. The slope gradient ranged from 27% to 70%, the unit flow discharge ranged from 0.56 × 10−3 to 3.33 × 10−3 m2 s−1, and the sediment transport capacity (Tc) was measured under each slope and discharge combination. The sediment was inputted into the flume according to the predetermined sediment addition rate (from 0% to 100% of Tc), and the detachment rate (Dr) under each combination of the slope and discharge was measured. Dr linearly decreased with increasing sediment loads, which is consistent with the detachment–transport coupling equation by Foster and Meyer. The linear equations can predict the detachment capacity (Dc) and Tc well (Nash–Sutcliffe efficiency coefficient (NSE) = 0.98 for Dc, and NSE = 0.99 for Tc). The detachment–transport coupling equation can adequately predict the Dr (NSE = 0.89). However, its applicability to slopes of <47% (NSE: 0.92–0.96) was greater than that to slopes of ≥47% (NSE: 0.81–0.89), and the predicted Dr under Tc levels of 20% and 40% were higher than the measured values, while the predicted value under a Tc level of 80% was lower than the measured value. In summary, the detachment–transport coupling equation by Foster and Meyer can accurately reflect the negative feedback relationship between detachments and transports along steep-slope fixed beds and is suitable for colluvial deposit research. The results provide a basis for the construction of steep-slope colluvial deposit erosion models. In the future, the study of the hydrodynamic characteristics of sediment transport processes should be strengthened to clarify the detachment–transport effect of flows through hydrodynamics. creator: Libo Chen creator: Pengyu Gao creator: Xiaolin Li creator: Qin Zhu creator: Zumei Wang creator: Fang Shuai creator: Yue Zhang creator: Jinshi Lin creator: Yanhe Huang creator: Fangshi Jiang uri: https://doi.org/10.7717/peerj.14766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chen et al. title: Body mass index and the risk of basal cell carcinoma: evidence from Mendelian randomization analysis link: https://peerj.com/articles/14781 last-modified: 2023-01-24 description: ObjectiveWe aim to test whether body mass index (BMI) is causally associated with the risk of basal cell carcinoma (BCC) using Mendelian randomization (MR) analysis.MethodsSingle-nucleotide polymorphisms (SNPs) associated with four BMI-related traits were screened via a genome-wide association study (GWAS) with 681,275, 336,107, 454,884, and 461,460 European-descent individuals, respectively. Summary-level data for BCC (17,416 cases and 375,455 controls) were extracted from UK Biobank. An inverse variance weighted (IVW) method was employed as the primary MR analysis. Sensitivity analyses were conducted via MR-Egger regression, heterogeneity test, pleiotropy test, and leave-one-out sensitivity test. The assumption that exposure causes outcome was verified using the MR Steiger test. Meta-analysis was also used to estimate the average genetically predicted effect of BMI on BCC.ResultsTwo-sample MR analysis showed inverse associations between genetically predicted BMI and BCC risk. Moreover, when exposure and outcome were switched to see if reverse causation was possible, there was no evidence of a cause-and-effect relationship from BCC to BMI. Finally, the meta-analysis also showed a strong negative causal relationship between BMI and BCC.ConclusionGenetical predicted higher BMI were associated with lower BCC risk. Further research is required to comprehend the mechanisms underlying this putative causative association. creator: Likui Lu creator: Bangbei Wan creator: Hongtao Zeng creator: Jun Guo creator: Min Li creator: Miao Sun uri: https://doi.org/10.7717/peerj.14781 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lu et al. title: Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time link: https://peerj.com/articles/14598 last-modified: 2023-01-23 description: Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial. creator: Raphael Eisenhofer creator: Kylie L. Brice creator: Michaela DJ Blyton creator: Scott E. Bevins creator: Kellie Leigh creator: Brajesh K. Singh creator: Kristofer M. Helgen creator: Ian Hough creator: Christopher B. Daniels creator: Natasha Speight creator: Ben D. Moore uri: https://doi.org/10.7717/peerj.14598 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Eisenhofer et al. title: Relationship between fruit phenotypes and domestication in hexaploid populations of biribá (Annona mucosa) in Brazilian Amazonia link: https://peerj.com/articles/14659 last-modified: 2023-01-23 description: BackgroundBiribá (Annona mucosa Jacq.) is a fruit tree domesticated in Amazonia and has polyploid populations. The species presents ample phenotypic variation in fruit characteristics, including weight (100–4,000 g) and differences in carpel protrusions. Two cytotypes are recorded in the literature (2n = 28, 42) and genome size records are divergent (2C = 4.77, 5.42 and 6.00 pg). To decipher the role of polyploidy in the domestication of A. mucosa, we examined the relationships among phenotypic variation, chromosome number and genome size, and which came first, polyploidization or domestication.MethodologyWe performed chromosome counts of A. mucosa from central and western Brazilian Amazonia, and estimated genome size by flow cytometry. We performed phylogenetic reconstruction with publicly available data using a Bayesian framework, time divergence analysis and reconstructed the ancestral chromosome number for the genus Annona and for A. mucosa.ResultsWe observed that variation in fruit phenotypes is not associated with variation in chromosome number and genome size. The most recent common ancestor of A. mucosa is inferred to be polyploid and diverged before domestication.ConclusionsWe conclude that, when domesticated, A. mucosa was already polyploid and we suggest that human selection is the main evolutionary force behind fruit size and fruit morphological variation in Annona mucosa. creator: Giulia Melilli Serbin creator: Diego Sotero de Barros Pinangé creator: Raquel Moura Machado creator: Santelmo Vasconcelos creator: Bruno Sampaio Amorim creator: Charles Roland Clement uri: https://doi.org/10.7717/peerj.14659 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Serbin et al. title: Monitoring algorithm of hospitalized patients in a medical center with SARS-CoV-2 (Omicron variant) infection: clinical epidemiological surveillance and immunological assessment link: https://peerj.com/articles/14666 last-modified: 2023-01-23 description: PurposeCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major healthcare threat worldwide. Since it was first identified in November 2021, the Omicron (B.1.1.529) variant of SARS-CoV-2 has evolved into several lineages, including BA.1, BA.2–BA.4, and BA.5. SARS-CoV-2 variants might increase transmissibility, pathogenicity, and resistance to vaccine-induced immunity. Thus, the epidemiological surveillance of circulating lineages using variant phenotyping is essential. The aim of the current study was to characterize the clinical outcome of Omicron BA.2 infections among hospitalized COVID-19 patients and to perform an immunological assessment of such cases against SARS-CoV-2.Patients and MethodsWe evaluated the analytical and clinical performance of the BioIC SARS-CoV-2 immunoglobulin (Ig)M/IgG detection kit, which was used for detecting antibodies against SARS-CoV-2 in 257 patients infected with the Omicron variant.ResultsPoor prognosis was noted in 38 patients, including eight deaths in patients characterized by comorbidities predisposing them to severe COVID-19. The variant-of-concern (VOC) typing and serological analysis identified time-dependent epidemic trends of BA.2 variants emerging in the outbreak of the fourth wave in Taiwan. Of the 257 specimens analyzed, 108 (42%) and 24 (9.3%) were positive for anti-N IgM and IgG respectively.ConclusionThe VOC typing of these samples allowed for the identification of epidemic trends by time intervals, including the B.1.1.529 variant replacing the B.1.617.2 variant. Moreover, antibody testing might serve as a complementary method for COVID-19 diagnosis. The combination of serological testing results with the reverse transcription-polymerase chain reaction cycle threshold value has potential value in disease prognosis, thereby aiding in epidemic investigations conducted by clinicians or the healthcare department. creator: Chi-Sheng Chen creator: Ming-Jr Jian creator: Chih-Kai Chang creator: Hsing-Yi Chung creator: Shih-Yi Li creator: Jung-Chung Lin creator: Kuo-Ming Yeh creator: Ya-Sung Yang creator: Chien-Wen Chen creator: Shan-Shan Hsieh creator: Sheng-Hui Tang creator: Cherng-Lih Perng creator: Feng-Yee Chang creator: Hung-Sheng Shang uri: https://doi.org/10.7717/peerj.14666 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Effects of prohexadione calcium spraying during the booting stage on panicle traits, yield, and related physiological characteristics of rice under salt stress link: https://peerj.com/articles/14673 last-modified: 2023-01-23 description: Prohexadione calcium (Pro-Ca), as a growth retardant, can effectively alleviate the damage of salt stress to plants. In order to explore the effects of NaCl stress on the physiological characteristics and panicle traits of rice plants as well as the alleviating effect of Pro-Ca at the booting stage, we performed pot experiments on two rice cultivars: conventional rice ‘Huanghuazhan’ and hybrid rice ‘Xiangliangyou900’. Rice plants were treated with 0.3% NaCl 48 hours after Pro-Ca (100 mg L−1) treatment to study the effects of Pro-Ca on the physiological characteristics of the leaves and panicles, as well as the panicle and yield traits of rice under salt stress. Our analysis indicated that NaCl treatment inhibited the morphological growth parameters and photosynthetic efficiency, destroyed the antioxidant defense systems of leaves and panicles, increased soluble protein and proline in both rice cultivars. Foliar application of Pro-Ca significantly increased the leaf area, uppermost internode length, panicle length, panicle weight, number of primary branches, number of grains per panicle, seed setting rate and yield under salt stress. Pro-Ca application significantly affected chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and apparent mesophyll conductance (AMC) in NaCl-treated rice cultivars compared with NaCl treatment alone. Moreover, Pro-Ca also increased ascorbic acid (AsA) content, enhanced superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) activity, and further increased the accumulation of soluble protein and proline in leaves and panicles. These results illustrated that foliar application of Pro-Ca at the booting stage could alleviate the damage caused by NaCl stress by regulating the physiological and metabolic processes of rice plants, thereby enhancing the stress resistance of the plants, increasing total rice yield in salt stress conditions. creator: XiXin Huang creator: Dianfeng Zheng creator: Naijie Feng creator: Anqi Huang creator: Rongjun Zhang creator: Fengyan Meng creator: Yin Jie creator: Baomin Mu creator: Dewei Mu creator: Hang Zhou uri: https://doi.org/10.7717/peerj.14673 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Assessing the breeding phenology of a threatened frog species using eDNA and automatic acoustic monitoring link: https://peerj.com/articles/14679 last-modified: 2023-01-23 description: BackgroundClimate change has driven shifts in breeding phenology of many amphibians, causing phenological mismatches (e.g., predator-prey interactions), and potentially population declines. Collecting data with high spatiotemporal sensitivity on hibernation emergence and breeding times can inform conservation best practices. However, monitoring the phenology of amphibians can be challenging because of their cryptic nature over much of their life cycle. Moreover, most salamanders and caecilians do not produce conspicuous breeding calls like frogs and toads do, presenting additional monitoring challenges.MethodsIn this study, we designed and evaluated the performance of an environmental DNA (eDNA) droplet digital PCR (ddPCR) assay as a non-invasive tool to assess the breeding phenology of a Western Chorus Frog population (Pseudacris maculata mitotype) in Eastern Ontario and compared eDNA detection patterns to hourly automatic acoustic monitoring. For two eDNA samples with strong PCR inhibition, we tested three methods to diminish the effect of inhibitors: diluting eDNA samples, adding bovine serum albumin to PCR reactions, and purifying eDNA using a commercial clean-up kit.ResultsWe recorded the first male calling when the focal marsh was still largely frozen. Chorus frog eDNA was detected on April 6th, 6 days after acoustic monitoring revealed this first calling male, but only 2 days after males attained higher chorus activity. eDNA signals were detected at more sampling locales within the marsh and eDNA concentrations increased as more males participated in the chorus, suggesting that eDNA may be a reasonable proxy for calling assemblage size. Internal positive control revealed strong inhibition in some samples, limiting detection probability and quantification accuracy in ddPCR. We found diluting samples was the most effective in reducing inhibition and improving eDNA quantification.ConclusionsAltogether, our results showed that eDNA ddPCR signals lagged behind male chorusing by a few days; thus, acoustic monitoring is preferable if the desire is to document the onset of male chorusing. However, eDNA may be an effective, non-invasive monitoring tool for amphibians that do not call and may provide a useful complement to automated acoustic recording. We found inhibition patterns were heterogeneous across time and space and we demonstrate that an internal positive control should always be included to assess inhibition for eDNA ddPCR signal interpretations. creator: Ying Chen creator: Orianne Tournayre creator: Haolun Tian creator: Stephen C. Lougheed uri: https://doi.org/10.7717/peerj.14679 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2023 Chen et al. title: Hydrometeorological characterization and estimation of landfill leachate generation in the Eastern Amazon/Brazil link: https://peerj.com/articles/14686 last-modified: 2023-01-23 description: The complex physical-chemical and microbiological composition of leachate in sanitary landfills sets the adequate treatment for different waste types. However, before the final disposal of wastes in receptor waterbodies, it is essential to use specific methods to quantitatively prevent internal flows to find proper treatments. The aim of the present research is to use hydrological models to estimate monthly leachate flow generation in Macapá’s Municipal Sanitary Landfill (ASMM), Amapá State, Brazil. Disregarding the temporal trend bias, the average (0.45 m3s−1), minimum (0.07 m3s−1) and maximum (0.72 m3s−1) flows were estimated based on hydrological models in the literature (Rmax = 99%, p < 0.05). The results estimated from different hydrological gauges pointed towards significant spatial variations in final discharge. Thus, estimated flows worked as reference to calculate the loads of coproducts and nutrients concerning different operational stages in ASMM. Therefore, rain intensity estimates have pointed out precipitation variability, and it has significantly affected leachate flow. In conclusion, there would be a proportional increase in leachate flow during extreme maximum precipitation events; overflow would be the effect of such flows and it would assumingly have impact on its surrounding areas. It is also possible estimating some degree of rainfall impact over ASMM’s infrastructure in the long term (>10 years), since it could influence its lifespan. creator: Carlos Armando Reyes Flores creator: Helenilza Ferreira Albuquerque Cunha creator: Alan Cavalcanti da Cunha uri: https://doi.org/10.7717/peerj.14686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Reyes Flores et al. title: Musculoskeletal simulations to examine the effects of accentuated eccentric loading (AEL) on jump height link: https://peerj.com/articles/14687 last-modified: 2023-01-23 description: BackgroundDuring counter movement jumps, adding weight in the eccentric phase and then suddenly releasing this weight during the concentric phase, known as accentuated eccentric loading (AEL), has been suggested to immediately improve jumping performance. The level of evidence for the positive effects of AEL remains weak, with conflicting evidence over the effectiveness in enhancing performance. Therefore, we proposed to theoretically explore the influence of implementing AEL during constrained vertical jumping using computer modelling and simulation and examined whether the proposed mechanism of enhanced power, increased elastic energy storage and return, could enhance work and power.MethodsWe used a simplified model, consisting of a ball-shaped body (head, arm, and trunk), two lower limb segments (thigh and shank), and four muscles, to simulate the mechanisms of AEL. We adjusted the key activation parameters of the muscles to influence the performance outcome of the model. Numerical optimization was applied to search the optimal solution for the model. We implemented AEL and non-AEL conditions in the model to compare the simulated data between conditions.ResultsOur model predicted that the optimal jumping performance was achieved when the model utilized the whole joint range. However, there was no difference in jumping performance in AEL and non-AEL conditions because the model began its push-off at the similar state (posture, fiber length, fiber velocity, fiber force, tendon length, and the same activation level). Therefore, the optimal solution predicted by the model was primarily driven by intrinsic muscle dynamics (force-length-velocity relationship), and this coupled with the similar model state at the start of the push-off, resulting in similar push-off performance across all conditions. There was also no evidence of additional tendon-loading effect in AEL conditions compared to non-AEL condition.DiscussionOur simplified simulations did not show improved jump performance with AEL, contrasting with experimental studies. The reduced model demonstrates that increased energy storage from the additional mass alone is not sufficient to induce increased performance and that other factors like differences in activation strategies or movement paths are more likely to contribute to enhanced performance. creator: Eric Yung-Sheng Su creator: Timothy J. Carroll creator: Dominic J. Farris creator: Glen A. Lichtwark uri: https://doi.org/10.7717/peerj.14687 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Su et al. title: Genome-wide identification and expression reveal the involvement of the FCS-like zinc finger (FLZ) gene family in Gossypium hirsutum at low temperature link: https://peerj.com/articles/14690 last-modified: 2023-01-23 description: FCS-like zinc finger (FLZ) is a plant-specific gene family that plays an important regulatory role in plant growth and development and its response to stress. However, studies on the characteristics and functions of cotton FLZ family genes are still lacking. This study systematically identified members of the cotton FLZ gene family based on cotton genome data. The cotton FLZ family genes were systematically analyzed by bioinformatics, and their expression patterns in different tissues and under low-temperature stress were analyzed by transcriptome and qRT–PCR. The G. hirsutum genome contains 56 FLZ genes distributed on 20 chromosomes, and most of them are located in the nucleus. According to the number and evolution analysis of FLZ family genes, FLZ family genes can be divided into five subgroups in cotton. The G. hirsutum FLZ gene has a wide range of tissue expression types, among which the expression is generally higher in roots, stems, leaves, receptacles and calyx. Through promoter analysis, it was found that it contained the most cis-acting elements related to methyl jasmonate (MeJA) and abscisic acid (ABA). Combined with the promoter and qRT–PCR results, it was speculated that GhFLZ11, GhFLZ25, GhFLZ44 and GhFLZ55 were involved in the response of cotton to low-temperature stress. Taken together, our findings suggest an important role for the FLZ gene family in the cotton response to cold stress. This study provides an important theoretical basis for further research on the function of the FLZ gene family and the molecular mechanism of the cotton response to low temperature. creator: JunDuo Wang creator: Zhiqiang Li creator: Yajun Liang creator: Juyun Zheng creator: Zhaolong Gong creator: Guohui Zhou creator: Yuhui Xu creator: Xueyuan Li uri: https://doi.org/10.7717/peerj.14690 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: A clustering method for small scRNA-seq data based on subspace and weighted distance link: https://peerj.com/articles/14706 last-modified: 2023-01-23 description: BackgroundIdentifying the cell types using unsupervised methods is essential for scRNA-seq research. However, conventional similarity measures introduce challenges to single-cell data clustering because of the high dimensional, high noise, and high dropout.MethodsWe proposed a clustering method for small ScRNA-seq data based on Subspace and Weighted Distance (SSWD), which follows the assumption that the sets of gene subspace composed of similar density-distributing genes can better distinguish cell groups. To accurately capture the intrinsic relationship among cells or genes, a new distance metric that combines Euclidean and Pearson distance through a weighting strategy was proposed. The relative Calinski-Harabasz (CH) index was used to estimate the cluster numbers instead of the CH index because it is comparable across degrees of freedom.ResultsWe compared SSWD with seven prevailing methods on eight publicly scRNA-seq datasets. The experimental results show that the SSWD has better clustering accuracy and the partitioning ability of cell groups. SSWD can be downloaded at https://github.com/ningzilan/SSWD. creator: Zilan Ning creator: Zhijun Dai creator: Hongyan Zhang creator: Yuan Chen creator: Zheming Yuan uri: https://doi.org/10.7717/peerj.14706 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ning et al. title: Dauer fate in a Caenorhabditis elegans Boolean network model link: https://peerj.com/articles/14713 last-modified: 2023-01-23 description: Cellular fates are determined by genes interacting across large, complex biological networks. A critical question is how to identify causal relationships spanning distinct signaling pathways and underlying organismal phenotypes. Here, we address this question by constructing a Boolean model of a well-studied developmental network and analyzing information flows through the system. Depending on environmental signals Caenorhabditis elegans develop normally to sexual maturity or enter a reproductively delayed, developmentally quiescent ‘dauer’ state, progressing to maturity when the environment changes. The developmental network that starts with environmental signal and ends in the dauer/no dauer fate involves genes across 4 signaling pathways including cyclic GMP, Insulin/IGF-1, TGF-β and steroid hormone synthesis. We identified three stable motifs leading to normal development, each composed of genes interacting across the Insulin/IGF-1, TGF-β and steroid hormone synthesis pathways. Three genes known to influence dauer fate, daf-2, daf-7 and hsf-1, acted as driver nodes in the system. Using causal logic analysis, we identified a five gene cyclic subgraph integrating the information flow from environmental signal to dauer fate. Perturbation analysis showed that a multifactorial insulin profile determined the stable motifs the system entered and interacted with daf-12 as the switchpoint driving the dauer/no dauer fate. Our results show that complex organismal systems can be distilled into abstract representations that permit full characterization of the causal relationships driving developmental fates. Analyzing organismal systems from this perspective of logic and function has important implications for studies examining the evolution and conservation of signaling pathways. creator: Alekhya Kandoor creator: Janna Fierst uri: https://doi.org/10.7717/peerj.14713 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kandoor et al. title: Magnetic fields generated by submarine power cables have a negligible effect on the swimming behavior of Atlantic lumpfish (Cyclopterus lumpus) juveniles link: https://peerj.com/articles/14745 last-modified: 2023-01-23 description: Submarine power cables carry electricity over long distances. Their geographic distribution, number, and areal coverage are increasing rapidly with the development of, for example, offshore wind facilities. The flow of current passing through these cables creates a magnetic field (MF) that can potentially affect marine organisms, particularly those that are magnetosensitive. The lumpfish (Cyclopterus lumpus) is a migratory species that is widely distributed in the North Atlantic Ocean and Barents Sea. It migrates between coastal spawning grounds and pelagic offshore feeding areas. We tested whether lumpfish respond to MFs of the same intensity as those emitted by high voltage direct current (HVDC) submarine power cables. Laboratory experiments were conducted by placing juvenile lumpfish in an artificial MF gradient generated by a Helmholtz coil system. The intensity of the artificial MF used (230 µT) corresponded to the field at 1 m from a high-power submarine cable. The fish were filmed for 30 min with the coil either on or off. Swimming speeds, and presence in the different parts of a raceway, were extracted from the videos and analyzed. Juvenile lumpfish activity, defined as the time that the fish spent swimming relative to stationary pauses (attached to the substrate), and the distance travelled, were unaffected by exposure to the artificial MF. The swimming speed of juvenile lumpfish was reduced (by 16%) when the coil was on indicating that the fish could either sense the MF or the induced electric field created by the movement of the fish through the magnetic field. However, it seems unlikely that a 16% decrease in swimming speed occurring within 1 m of HVDC cables would significantly affect Atlantic lumpfish migration or homing. creator: Caroline M. F. Durif creator: Daniel Nyqvist creator: Bastien Taormina creator: Steven D. Shema creator: Anne Berit Skiftesvik creator: Florian Freytet creator: Howard I. Browman uri: https://doi.org/10.7717/peerj.14745 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Durif et al. title: Potential use of essential oils from Origanum vulgare and Syzygium aromaticum to control Tetranychus urticae Koch (Acari: Tetranychidae) on two host plant species link: https://peerj.com/articles/14475 last-modified: 2023-01-20 description: Plant extracts and essential oils are considered alternatives to synthetic chemicals with toxic effects on insects and mites. Acaricidal, repellent, and oviposition effects of commercially available essential oils of Origanum vulgare L. (Lamiaceae) and Syzygium aromaticum (L.) (Myrtaceae) were investigated in this study on Tetranychus urticae Koch (Acari: Tetranychidae), one of the main pests in agriculture, on two host plant species using leaf disc bioassays. O. vulgare essential oil showed higher toxicity to T. urticae protonymphs and adult females inhabiting both bean and tomato leaves than S. aromaticum essential oil. The LC50 values of O. vulgare essential oil were found to be 1.67 and 2.05 µl L−1 air for the bean populations in protonymphs and adult females and 1.87 and 3.07 µl L−1 air for the tomato populations, respectively. Five percent concentration of S. aromaticum essential oil had the highest repellent effect on the bean population of T. urticae after 1, 24, and 48 h, resulting in 61.22%, 40.81%, and 18% repellence, respectively. Although O. vulgare showed higher toxic effects, S. aromaticum was a better repellent against the bean population of T. urticae. The mortality rates of adult females of T. urticae treated with either O. vulgare or S. aromaticum essential oil increased with the increasing concentration and time on both host plants. Both essential oils caused a decrease in egg number and larvae hatching in both bean and tomato populations of T. urticae. In the light of the results obtained, O. vulgare and S. aromatium essential oils have the potential to be used in the control programs against T. urticae in both host plants. creator: Hilal Susurluk uri: https://doi.org/10.7717/peerj.14475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Susurluk title: No changes in the abundance of selected fecal bacteria during increased carbohydrates consumption period associated with the racing season in amateur road cyclists link: https://peerj.com/articles/14594 last-modified: 2023-01-20 description: BackgroundCyclists often use high-carbohydrate, low-fiber diets to optimize the glycogen stores and to avoid the gastrointestinal distress during both, the trainings and the competitions. The impact of such dietary changes on gut microbiota is not fully known.MethodsWe assessed the abundances of Faecalibacterium prausnitzii, Akkermansia muciniphila, Bifidobacterium spp., and Bacteroides spp. and the fecal pH in 14 amateur cyclists during the racing season. Eleven healthy men formed the control group.ResultsDespite significant differences in the diet composition and physical endurance levels of amateur cyclists before the competition season (1st term) and control group (carbohydrates: 52.2% ± 4.9% vs 41.9% ± 6.6%; VO2max: 56.1 ± 6.0 vs 39.7 ± 7.7; p < 0.01; respectively), we did not observe any significant differences in studied gut bacteria abundances or fecal pH between the groups. Although the cyclists’ carbohydrates consumption (2nd term) have increased throughout the season (4.48 g/kg b.w. ± 1.56 vs 5.18 g/kg b.w. ± 1.99; p < 0.05), the studied gut bacteria counts and fecal pH remained unchanged. It seems that the amateur cyclists’ diet with increased carbohydrates intake does not alter the gut microbiota, but further research is needed to assess the potential impact of even higher carbohydrates consumption (over 6 g/kg b.w.). creator: Jakub Wiącek creator: Joanna Szurkowska creator: Jakub Kryściak creator: Miroslawa Galecka creator: Joanna Karolkiewicz uri: https://doi.org/10.7717/peerj.14594 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wiącek et al. title: Cyclic fatigue resistance of EdgeTaper Platinum, Protaper Gold, and TruNatomy Prime rotary files before and after autoclave sterilization link: https://peerj.com/articles/14656 last-modified: 2023-01-20 description: BackgroundThis in vitro investigation aimed to determine the influence of multiple autoclave cycles on the cyclic fatigue resistance of three heat-treated nickel-titanium (NiTi) files: EdgeTaper Platinum (ETP), ProTaper Gold (PTG), and TruNatomy Prime (TN).MaterialsSixty NiTi files, twenty of each NiTi file type: ETP 25/.06, PTG 25/.08, and TN 26/.04 were randomly divided into four equal subgroups (n = 5). The files for the control group were left un-autoclaved. Different autoclave sterilization cycles (one, five, and ten) were used for the other three groups. The files were then placed in a metal canal block and rotated according to the manufacturer’s instructions until fracture. The length of the broken segment and the time taken for fracture were measured. The fractured surfaces were subsequently subjected to SEM imaging. The Kruskal-Wallis test was used to analyze the data, followed by Dunn-Bonferroni pairwise comparisons. Statistical significance was set at p < 0.05.ResultsETP showed significantly greater resistance to cyclic fatigue than TN in all autoclave groups and PTG after five autoclave cycles (p = 0.014). Fatigue resistance was not affected by the number of autoclaving cycles, except for ETP. After the first and tenth autoclaving cycles, they required significantly more rotations to failure than the non-sterilized files (p = 0.039 and p = 0.021, respectively). The fractured segments of the ETP files in these two groups were also longer than those in the control group (p = 0.010).ConclusionThe cyclic fatigue resistance of ETP was greater than that of TN in all tested conditions. Repeated autoclave cycles of sterilization improved the cyclic fatigue resistance of the ETP files only and did not affect the cyclic fatigue resistance of TN and PTG. However, the ETP files separated at a longer distance from the tip with increased autoclaving cycles. creator: Rahaf A. Almohareb creator: Reem M. Barakat creator: Fahda N. Algahtani creator: Manal F. Alkadi uri: https://doi.org/10.7717/peerj.14656 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Almohareb et al. title: Hygiene practices and factors influencing intestinal parasites among food handlers in the province of Belgarn, Saudi Arabia link: https://peerj.com/articles/14700 last-modified: 2023-01-20 description: BackgroundThis study aimed to evaluate the association between socio-demographic status, and hygienic habits among food handlers with intestinal parasitic infections.MethodsIt was a cross-sectional study in which 112 participants were recruited, from Belgarn province of Saudi Arabia. The descriptive analysis was used to evaluate demographic data and categorical variables. The association between sociodemographic characteristics and Relative Risk regression analysis was performed for each investigated factor. p-value of <0.05, was assumed to be statistically significant.ResultsOne hundred and twelve food handlers with a mean age of 33.5 ± 9.2 years were included in this study. The food handlers were from 15 different countries (11 Asians and four Africans). The majority of the food handlers were cooks (87, 77.7%), and waiters and dish washers (24, 21.4%). Among them, 106 (94.6%) used uniforms, and gloves at work. In hand washing practices, 104 (92.9%) wash their hands with soap before handling and preparing food and eight (7.1%) wash without soap, 98 (87.5%) wash with soap before meals and 14 (12.5%) wash without soap, 105 (93.8%) wash with soap after visiting toilets and seven (6.2%) wash without soap. Twenty-five (42.3%) of infected food handlers are not used to trim their fingernails. Intestinal infection was observed in 59 (52.68%) participants with mean age (32.5 ± 8.1 years) for infected participants.ConclusionIn this study, food handlers had a high prevalence of intestinal parasites. Although some of the food handlers had a high level of education, the infection with intestinal parasites was detected. In addition to regular screening for intestinal parasites among food handlers, there is a need for educational programs on proper hygiene habits, modes of transmission and prevention of the infection. creator: Abdulrahman S. Alqarni creator: Majed H. Wakid creator: Hattan S. Gattan uri: https://doi.org/10.7717/peerj.14700 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Alqarni et al. title: Perspectives of the Saudi medical students toward the impact of lockdowns on their physical activity level and lifestyle during the COVID-19 pandemic link: https://peerj.com/articles/14725 last-modified: 2023-01-20 description: BackgroundPhysical activity (PA) level is affected by various factors in university students. Due to the pandemic of COVID-19, the Saudi Ministry of Education announced the closure of schools and universities as a preventive measure. This cross-sectional study aimed to evaluate the impact of the COVID-19 pandemic lockdown on PA levels and other lifestyle aspects among the Saudi medical students and to explore their perspectives toward it.MethodsThree hundred ninety-six medical students have completed the survey, which consisted of three sections: (1) participant’s demographic data; (2) five statements about the PA and the lockdown; and (3) the International PA Questionnaire—Short Form (IPAQ-SF).ResultsAbout 63.9% of the participants were female, and 60.4% were of normal weight. Approximately 80% of participants were classified as inactive. Regarding the perspective of the students, 52.8% reported that they were not exercising regularly in the gym before the lockdown, and 46.9% reported that the lockdown and transition to online learning affected their compliance with exercise. During the lockdown and shift to online learning, the majority of participants experienced decreased PA levels, 42.4% experienced weight gain, and 53.6% reported a negative impact on their psychological status.ConclusionGenerally, the results of this study showed that the COVID-19 had a negative influence on the PA level, as well as other lifestyle aspects (e.g., gaining weight) and psychological status of medical students. This study highlights aspects where universities and institutions delivering medical education can use resources to improve students’ well-being during pandemics. creator: Asma Alrushud creator: Dalyah Alamam creator: Muneera Almurdi creator: Ghaliah A. Dablan creator: Alanoud A. Alghamdi creator: Fatimah K. Almazyad creator: Malak A. Alhamdani creator: Khlood A. Alqarni creator: Hosam Alzahrani uri: https://doi.org/10.7717/peerj.14725 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Alrushud et al. title: Identification of the potential biomarkers associated with circadian rhythms in heart failure link: https://peerj.com/articles/14734 last-modified: 2023-01-20 description: BackgroundHeart failure (HF) is a syndrome with multiple clinical symptoms resulting from damage to the heart’s structure and/or function with various pathogenic factors, which has developed as one of the most severe threats to human health. Approximately 13% of genes and about 8% of proteins contained in the heart are rhythmic, which could lead to HF if disrupted. Herein, we aimed to identify the circadian rhythms-related hub genes as potential biomarkers contributing to the identification and treatment of HF.MethodsExpression data of ischemic and dilated cardiomyopathy samples with or without HF were collected from the GEO database. First, genes with differential expression in HF and healthy samples were identified, named as differentially expressed genes (DEGs), which were then intersected with circadian rhythms-related genes to identify circadian rhythms-related DEGs. A protein-protein interaction (PPI) network was established to screen hub genes. The performance of the hub genes to identify HF among healthy controls was assessed by referring to the receiver operating characteristic (ROC) curve. Additionally, quantitative real-time polymerase chain reaction (RT-PCR) was run to further validate the hub genes depending on clinical human peripheral blood samples.ResultsA total of 10,163 DEGs were determined, composed of 4,615 up-regulated genes and 5,548 down-regulated genes in HF patients in comparison to healthy controls. By overlapping the circadian rhythms-related genes in the Circadian Gene DataBase (CGDB), 723 circadian rhythms-related DEGs were obtained, mainly enriched in regulating lipid metabolic process, circadian rhythm and AMPK signaling pathway. Eight hub genes were screened out through the PPI network. The ROC curve indicated the high accuracy of five hub genes with AUC > 0.7, which also showed high accuracy validated by the external validation dataset. Furthermore, according to the results of quantitative RT-PCR, the HF group showed significantly increased relative mRNA expression of CRY2 and BHLHE41 while the decreased ARNTL and NPAS2 in comparison to controls, indicating the four hub genes as potential biomarkers of HF.ConclusionOur study validated that ARNTL, CRY2, BHLHE41 and NPAS2 could serve as potential biomarkers of circadian rhythm in HF. These results may provide a reference for employing novel markers or targets for the diagnosis and treatment of HF. creator: Qiang Sun creator: Jun Zhao creator: Li Liu creator: Xiaoliang Wang creator: Xinshun Gu uri: https://doi.org/10.7717/peerj.14734 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sun et al. title: Mendelian randomization investigation identified the causal relationship between body fat indexes and the risk of bladder cancer link: https://peerj.com/articles/14739 last-modified: 2023-01-20 description: BackgroundObservational studies have suggested that obesity is associated with the risk of bladder cancer (BCa). However, their causal relationship remains unclear. This study aimed to prove the causal relationship between obesity and the risk of BCa by using Mendelian randomization.MethodsSingle-nucleotide polymorphisms (SNPs) correlated with body fat indexes were screened from several genome-wide association studies (GWAS) with more than 300,000 individuals. Summary-level genetic data of BCa-related GWAS were obtained from a European cohort with a sample size of 218,792. An inverse-variance-weighted (IVW) method was used as the major MR analysis. The MR-Egger regression, IVW regression, leave-one-out test, and MR-Pleiotropy Residual Sum and Outlier methods were used to test the reliability and stability of MR results.ResultsGenetically predicted per 1-SD increase in body fat indexes (whole body fat mass, and the right leg, left leg, right arm, left arm, and trunk fat mass) were associated with increased BCa risk with values of 51.8%, 77.9%, 75.1%, 67.2%, 59.7%, and 36.6%, respectively. Sensitivity analyses suggested that the genetically determined risk effect of obesity on BCa was stable and reliable.ConclusionsOur study provided powerful evidence to support the causal hypothesis that the genetically predicted high body fat mass was associated with a risk increase for BCa. The finding is a new idea for drawing up prevention strategies for BCa. creator: Bangbei Wan creator: Ning Ma creator: Weiying Lu uri: https://doi.org/10.7717/peerj.14739 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wan et al. title: Almost nothing is known about the tiger shark in South Atlantic waters link: https://peerj.com/articles/14750 last-modified: 2023-01-20 description: The tiger shark (Galeocerdo cuvier) has been relatively well assessed concerning biology and ecology aspects in both Atlantic and Pacific North America and in Caribbean waters. The amount of data in these regions has led to the species protection under capture quotas and with the creation of sanctuaries. The reality in developing countries, however, is the exact opposite, with scarce information on the species in the southern hemisphere, namely South American and African waters. In these regions, protection measures are insufficient, and studies on tiger shark biology and ecology are scarce, significantly hindering conservation and management efforts. Thus, the aim of this study was to compile scientific literature on the tiger shark in the South Atlantic and discuss the impact of these data (or lack thereof) distributed within a total of ten research categories for guiding management plans. In total, 41 scientific publications on different G. cuvier biology and ecology aspects were obtained. The most studied topics were Feeding Ecology (n = 12), followed by Human Interactions (n = 8), and Movements and Migration (n = 7). Northeastern Brazil (Southwest Atlantic) was the most researched area, probably due to the higher coastal abundance of tiger sharks in this area, alongside a high number of recorded attacks, justifying funding for studies in the region. No studies carried out in other South American or African countries were found. It is important to mention that even though some research topics are relatively well covered, a severe knowledge gap is noted for risk assessments and fisheries management, with a proposition for the implementation of sanctuaries noted. This is, however, particularly worrisome, as the South Atlantic is mostly unexplored in this regard for tiger sharks. It is also important to note how different the attention given to this species is in the North Atlantic when compared to the South region. Lastly, we highlight that the existence of sub-populations, the lack of migratory corridors geographically connecting distinct areas used by the species, and the lack of fisheries statistics on tiger shark landings, all increase the vulnerability of this species in the South Atlantic. creator: Samuel Balanin creator: Rachel Ann Hauser-Davis creator: Eloísa Giareta creator: Patricia Charvet creator: Natascha Wosnick uri: https://doi.org/10.7717/peerj.14750 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Balanin et al. title: A comparative study on third trimester fetal biometric parameters with maternal age link: https://peerj.com/articles/14528 last-modified: 2023-01-19 description: BackgroundAdvanced maternal age is an important parameter associated with increased risk of feto-maternal complications and it is an evolving trend in society for women planning for pregnancy in late ages. However there are no studies done whether advanced maternal age has its effects on expression of growth pattern in the fetus. So this study was done to compare the maternal age with the third trimester fetal biometric parameters.MethodsThis study was done in 100 antenatal women and divided into two groups: Group 1: optimal maternal age group between 21–29 years of age and Group 2: advanced maternal age 30 and above. The pre-pregnant maternal weight, gestational age and third trimester fetal biometrics using ultrasound are noted and compared between the groups.ResultsThe maternal weight gain between the groups was optimal but the third trimester fetal parameters were significantly less in advanced maternal age. The abdominal circumference in optimal age group and head circumference in advanced maternal age group was closer to calculated estimated date of delivery (EDD) and would be specific in calculating the gestational age.ConclusionsThough there is no significant difference in maternal weight gain, there are fetal growth restrictions in advanced maternal age group due to which the third trimester fetal parameters are lesser than the optimal age group. Head circumference would be specific in calculating the estimated date of delivery in advanced maternal age group. creator: Yogitha Poojari creator: Prudhvinath reddy Annapureddy creator: Sharmila Vijayan creator: Vinoth Kumar Kalidoss creator: Yuvaraj Mf creator: Sankaran Pk uri: https://doi.org/10.7717/peerj.14528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Poojari et al. title: N6-methyladenosine (m6A) reader IGF2BP1 facilitates clear-cell renal cell carcinoma aerobic glycolysis link: https://peerj.com/articles/14591 last-modified: 2023-01-18 description: Emerging articles have reported that N6-methyladenosine (m6A) modification is mainly involved in clear-cell renal cell carcinoma (ccRCC) tumorigenesis. However, the regulatory mechanisms of m6A reader IGF2BP1 involved in ccRCC tumor energy metabolism are currently unknown. Results showed that the m6A reader IGF2BP1 exhibited significantly higher expression in ccRCC cells. Functionally, results by gain/loss functional assays indicated that IGF2BP1 promoted the glycolytic characteristics, including glucose uptake, lactate production and extracellular acidification rate (ECAR). Mechanistically, IGF2BP1 recognized the m6A modified sites on LDHA mRNA and enhanced its mRNA stability, thereby accelerating tumor energy metabolism. Thus, our work reveals a novel facet of the m6A that promoted mRNA stability and highlighted the functional importance of IGF2BP1 as m6A readers in post-transcriptional gene regulation. creator: Bao Yuan creator: Jin Zhou uri: https://doi.org/10.7717/peerj.14591 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yuan and Zhou title: Transcriptomic differences between bleached and unbleached hydrozoan Millepora complanata following the 2015-2016 ENSO in the Mexican Caribbean link: https://peerj.com/articles/14626 last-modified: 2023-01-18 description: The 2015-2016 El Niño-southern oscillation or “ENSO” caused many M. complanata colonies that live in the Mexican Caribbean to experience extensive bleaching. The purpose of this work was to analyze the effect of bleaching on the cellular response of M. complanata, employing a transcriptomic approach with RNA-seq. As expected, bleached specimens contained a significantly lower chlorophyll content than unbleached hydrocorals. The presence of algae of the genera Durusdinium and Cladocopium was only found in tissues of unbleached M. complanata, which could be associated to the greater resistance that these colonies exhibited during bleaching. We found that 299 genes were differentially expressed in M. complanata bleached colonies following the 2015-2016 ENSO in the Mexican Caribbean. The differential expression analysis of bleached M. complanata specimens evidenced enriched terms for functional categories, such as ribosome, RNA polymerase and basal transcription factors, chaperone, oxidoreductase, among others. Our results suggest that the heat-shock response mechanisms displayed by M. complanata include: an up-regulation of endogenous antioxidant defenses; a higher expression of heat stress response genes; up-regulation of transcription-related genes, higher expression of genes associated to transport processes, inter alia. This study constitutes the first differential gene expression analysis of the molecular response of a reef-forming hydrozoan during bleaching. creator: Víctor H. Hernández Elizárraga creator: Norma Olguín-López creator: Rosalina Hernández-Matehuala creator: Juan Caballero-Pérez creator: César Ibarra-Alvarado creator: Alejandra Rojas-Molina uri: https://doi.org/10.7717/peerj.14626 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hernández Elizárraga et al. title: Microplastic contamination in canned fish sold in Türkiye link: https://peerj.com/articles/14627 last-modified: 2023-01-18 description: The presence of microplastics (MPs) in processed seafood is a growing concern. In this study, 33 different canned fish brands belonging to seven producers were purchased from the Turkish market and investigated. MPs composition, possible sources, and potential intake were assessed. Light microscopy was used to quantify potential MPs, and micro-Raman microscopy was used to identify the polymer types. The results showed that all the samples had at least one MPs particle, and fragments were the most abundant (57.3%) shape of MPs. Polyolefin (21.88%) was the most common polymer type. The results showed that packaging and the production processes are the main possible sources of MPs. Human intake estimation risk is relatively lower since canned fish consumption is relatively low. The findings suggest that the risk related to MPs in canned fish should be considered one of the components of food safety management systems. creator: Sedat Gündoğdu creator: Ali Riza Köşker uri: https://doi.org/10.7717/peerj.14627 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gundogdu and Kosker title: Potato bacterial wilt in Ethiopia: history, current status, and future perspectives link: https://peerj.com/articles/14661 last-modified: 2023-01-18 description: BackgroundPotato is an essential food staple and a critical tuber crop for rural livelihoods in Ethiopia, where many pathogenic pests are threatening production. Bacterial wilt, also known as brown rot of potato, ranks among the diseases that most affect many potato farmers in Ethiopia and the disease losses dramatically threatening the vibrant potato sector even in the highlands of the country where it has been uncommon so far.MethodologyTo devise a strategy towards boosting potato productivity in Ethiopia where food insecurity is most prevalent, production constraints should be investigated and properly addressed. Hence, we have used existing reviews and reports on the subjects, such as textbooks, and proceeding and conference abstracts in Plant Protection Society of Ethiopia; Web of Science; Google Scholar; Research Gate and CIP’s database to document most relevant information on the occurrence, distribution, and disease management of bacterial wilt in Ethiopia.ResultsProvision of comprehensive information on potato bacterial wilt occurrence, distribution, and management techniques are crucial for potato growers, researchers and stakeholders engaged on potato industry. In this review, we provided insights on the history, status, and future perspectives of potato bacterial wilt in Ethiopia.ConclusionsAwareness of potato bacterial wilt and integrated disease management approaches could bring a fundamental impact to the farming community mostly to smallholder farmers in developing countries. This document compiled such imperative information targeting bacterial wilt management techniques to ensure food security. creator: Gebrehanna Lemma Tessema creator: Hussen Ebrahim Seid uri: https://doi.org/10.7717/peerj.14661 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gebrehanna and Hussen title: The energetic effect of hip flexion and retraction in walking at different speeds: a modeling study link: https://peerj.com/articles/14662 last-modified: 2023-01-18 description: In human walking, power for propulsion is generated primarily via ankle and hip muscles. The addition of a ‘passive’ hip spring to simple bipedal models appears more efficient than using only push-off impulse, at least, when hip spring associated energetic costs are not considered. Hip flexion and retraction torques, however, are not ‘free’, as they are produced by muscles demanding metabolic energy. Studies evaluating the inclusion of hip actuation costs, especially during the swing phase, and the hip actuation’s energetic benefits are few and far between. It is also unknown whether these possible benefits/effects may depend on speed. We simulated a planar flat-feet model walking stably over a range of speeds. We asked whether the addition of independent hip flexion and retraction remains energetically beneficial when considering work-based metabolic cost of transport (MCOT) with different efficiencies of doing positive and negative work. We found asymmetric hip actuation can reduce the estimated MCOT relative to ankle actuation by up to 6%, but only at medium speeds. The corresponding optimal strategy is zero hip flexion and some hip retraction actuation. The reason for this reduced MCOT is that the decrease in collision loss is larger than the associated increase in hip negative work. This leads to a reduction in total positive mechanical work, which results in an overall lower MCOT. Our study shows how ankle actuation, hip flexion, and retraction actuation can be coordinated to reduce MCOT. creator: Jian Jin creator: Dinant Kistemaker creator: Jaap H. van Dieën creator: Andreas Daffertshofer creator: Sjoerd M. Bruijn uri: https://doi.org/10.7717/peerj.14662 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jin et al. title: A geospatial risk analysis graphical user interface for identifying hazardous chemical emission sources link: https://peerj.com/articles/14664 last-modified: 2023-01-18 description: BackgroundPerforming back trajectory and forward trajectory using the Hybrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT) is a reliable approach for assessing particle transport after release among mid-field atmospheric models. HYSPLIT has an externally facing online interface that allows non-expert users to run the model trajectories without requiring extensive training or programming. However, the existing HYSPLIT interface is limited if simulations have a large amount of meteorological data and timesteps that are not coincident. The objective of this study is to design and develop a more robust tool to rapidly evaluate hazard transport conditions and to perform risk analysis, while still maintaining an intuitive and user-friendly interface.MethodsHYSPLIT calculates forward and backward trajectories of particles based on wind speed, wind direction, and the corresponding location, timestamp, and Pasquill stability classes of the regions of the atmosphere in terms of the wind speed, the amount of solar radiation, and the fractional cloud cover. The computed particle transport trajectories, combined with the online Proton Transfer Reaction-Mass Spectrometry (PTR-MS) data (https://figshare.com/articles/dataset/ARL_Data_from_PROS_station_at_Hanford_site/19993964), can be used to identify and quantify the sources and affected area of the hazardous chemicals’ emission using the potential source distribution function (PSDF). PSDF is an improved statistical function based on the well-known potential source contribution function (PSCF) in establishing the air pollutant source and receptor relationship. Performing this analysis requires a range of meteorological and pollutant concentration measurements to be statistically meaningful. The existing HYSPLIT graphical user interface (GUI) does not easily permit computations of trajectories of a dataset of meteorological data in high temporal frequency. To improve the performance of HYSPLIT computations from a large dataset and enhance risk analysis of the accidental release of material at risk, a geospatial risk analysis tool (GRAT-GUI) is created to allow large data sets to be processed instantaneously and to provide ease of visualization.ResultsThe GRAT-GUI is a native desktop-based application and can be run in any Windows 10 system without any internet access requirements, thus providing a secure way to process large meteorological datasets even on a standalone computer. GRAT-GUI has features to import, integrate, and convert meteorological data with various formats for hazardous chemical emission source identification and risk analysis as a self-explanatory user interface. The tool is available at https://figshare.com/articles/software/GRAT/19426742. creator: Hongfei Hou creator: Huiying Ren creator: Patrick Royer creator: Xiao-Ying Yu uri: https://doi.org/10.7717/peerj.14664 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hou et al. title: Patterns and controlling factors of soil carbon sequestration in nitrogen-limited and -rich forests in China—a meta-analysis link: https://peerj.com/articles/14694 last-modified: 2023-01-18 description: Soil organic carbon (SOC) management has the potential to contribute to climate change mitigation by reducing atmospheric carbon dioxide (CO2). Understanding the changes in forest nitrogen (N) deposition rates has important implications for C sequestration. We explored the effects of N enrichment on soil carbon sequestration in nitrogen-limited and nitrogen-rich Chinese forests and their controlling factors. Our findings reveal that N inputs enhanced net soil C sequestration by 5.52–18.46 kg C kg−1 N, with greater impacts in temperate forests (8.37–13.68 kg C kg−1 N), the use of NH4NO3 fertilizer (7.78 kg Ckg−1 N) at low N levels (<30 kg Ckg−1 N; 9.14 kg Ckg−1 N), and in a short period (<3 years; 12.95 kg C kg−1 N). The nitrogen use efficiency (NUE) varied between 0.24 and 13.3 (kg C kg−1 N) depending on the forest type and was significantly controlled by rainfall, fertilizer, and carbon-nitrogen ratio rates. Besides, N enrichment increased SOC concentration by an average of 7% and 2% for tropical and subtropical forests, respectively. Although soil carbon sequestration was higher in the topsoil compared to the subsoil, the relative influence indicated that nitrogen availability strongly impacts the SOC, followed by dissolved organic carbon concentration and mean annual precipitation. This study highlights the critical role of soil NUE processes in promoting soil C accumulation in a forest ecosystem. creator: Mbezele Junior Yannick Ngaba creator: Yves Uwiragiye creator: Jianbin Zhou uri: https://doi.org/10.7717/peerj.14694 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ngaba et al. title: HLA-A*01:01 allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire link: https://peerj.com/articles/14707 last-modified: 2023-01-18 description: In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. However, much less attention was paid to the T-cell response and the presentation of virus peptides by MHC-I molecules. In this study, we compared the features of the HLA-I genotype in symptomatic patients with COVID-19 in the first and third waves of the pandemic. As a result, we could identify the diminishing of carriers of the HLA-A*01:01 allele in the third wave and demonstrate the unique properties of this allele. Thus, HLA-A*01:01-binding immunoprevalent epitopes are mostly derived from ORF1ab. A set of epitopes from ORF1ab was tested, and their high immunogenicity was confirmed. Moreover, analysis of the results of single-cell phenotyping of T-cells in recovered patients showed that the predominant phenotype in HLA-A*01:01 carriers is central memory T-cells. The predominance of T-lymphocytes of this phenotype may contribute to forming long-term T-cell immunity in carriers of this allele. Our results can be the basis for highly effective vaccines based on ORF1ab peptides. creator: Maxim Shkurnikov creator: Stepan Nersisyan creator: Darya Averinskaya creator: Milena Chekova creator: Fedor Polyakov creator: Aleksei Titov creator: Dmitriy Doroshenko creator: Valery Vechorko creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.14707 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Shkurnikov et al. title: Analysing the SPAD dynamics of water-stressed vs. well-watered sesame (Sesamum indicum L.) accessions and establishing their relationship with seed yield link: https://peerj.com/articles/14711 last-modified: 2023-01-18 description: BackgroundThe chlorophyll content is susceptible to deficit moisture stress and may affect the plant yield. Leaf chlorophyll content is directly related to tolerance and higher productivity under deficit moisture stress (WS). The SPAD meter is an excellent tool for rapid analysis of crop chlorophyll content. Therefore, establishing a relationship between leaf chlorophyll content and seed yield is crucial in sesame, particularly under deficit moisture stress.MethodsSeeds of 37 sesame genotypes with checks were used in this study. These genotypes were mostly landraces, adapted to different agro-ecological zones in India. The selected genotypes were evaluated under well water (WW) and deficit moisture stress (WS) conditions. The SPAD readings were recorded ten (10) times each at every seven days intervals from the juvenile/first bud (30–35 days after sowing) to ripening/ physiological maturity (95–100 days after sowing) stage. This study aimed to identify the association between leaf SPAD readings (recorded at 7-days interval) and seed yield of sesame genotypes.ResultsThe analysis of variance revealed the presence of significant variation in SPAD readings due to treatment (WW and WS), genotypes, and their interaction effects. The SPAD readings at all stages were positively correlated with seed yield in both WW and WS. High values of correlation coefficients were observed at 52 (r: 0.672) and 59 (r: 0.655) DAS under WS; whereas at 59 (r: 0.960), 66 (r: 0.972) and 73 (r: 0.974) DAS under WW at one percent significance level (p < 0.01), which coincided with the mid-bloom stage of the sesame crop. The best-fit multiple regression model revealed that the dependence of sesame seed yield is significantly influenced by SPAD reading at 52 DAS under WS and 59 to 73 DAS under WW. Both these models provide a good fit with the chi-squared test, which compares the predicted and observed yield. creator: Lora Anusha Pallavolu creator: Ratnakumar Pasala creator: Ramesh Kulasekaran creator: Brij Bihari Pandey creator: Umamahesh Virupaksham creator: Sandhyarani Perika uri: https://doi.org/10.7717/peerj.14711 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pallavolu et al. title: Prevalence and risk factors of COVID-19-related generalized anxiety disorder among the general public in China: a cross-sectional study link: https://peerj.com/articles/14720 last-modified: 2023-01-18 description: ObjectiveThis study aimed to estimate the prevalence of generalized anxiety disorder in China during the coronavirus disease 2019 (COVID-19) pandemic and identify its associated factors.MethodsA cross-sectional study was conducted among the general population in China from March 16 to April 2, 2020. The participants were recruited using stratified random sampling. Data on demographic characteristics and COVID-19 related factors were obtained using self-administered questionnaires. The anxiety score was measured based on the Chinese version of the Generalized Anxiety Disorder 7-item Scale (GAD-7).ResultsThe study comprised 10,824 participants, of which 37.69% had symptoms of anxiety. The risk factors for anxiety symptoms included poor self-reported health (OR = 1.672, p < 0.001), chronic diseases (OR = 1.389, p < 0.001), and quarantine (OR = 1.365, p < 0.001), while participants’ perceptions that COVID-19 would be controlled was a protective factor (OR = 0.774, p < 0.001). The interactions between quarantine and self-reported health (p < 0.001), as well as between perceptions of COVID-19 and self-reported health (p < 0.001) were found to have a significant effect on GAD-7 scores.ConclusionsSelf-reported health status, chronic diseases, quarantine, and perceptions of COVID-19 were significantly associated with GAD-7 scores, indicating that mental health interventions are urgently needed during pandemics, especially for high-risk groups. creator: Yi Xia creator: Qi Wang creator: Lushaobo Shi creator: Zengping Shi creator: Jinghui Chang creator: Richard Xu creator: Huazhang Miao creator: Dong Wang uri: https://doi.org/10.7717/peerj.14720 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xia et al. title: Biologging as an important tool to uncover behaviors of cryptic species: an analysis of giant armadillos (Priodontes maximus) link: https://peerj.com/articles/14726 last-modified: 2023-01-18 description: Advances in biologging have increased the understanding of how animals interact with their environment, especially for cryptic species. For example, giant armadillos (Priodontes maximus) are the largest extant species of armadillo but are rarely encountered due to their fossorial and nocturnal behavior. Through the analysis of speed, turning angles, and accelerometer activity counts, we estimated behavioral states, characterized activity budgets, and investigated the state-habitat associations exhibited by individuals monitored with GPS telemetry in the Brazilian Pantanal from 2019 to 2020. This methodology is proposed as a useful framework for the identification of priority habitat. Using the non-parametric Bayesian mixture model for movement (M3), we estimated four latent behavioral states that were named ‘vigilance-excavation’, ‘local search’, ‘exploratory’, and ‘transit’. These states appeared to correspond with behavior near burrows or termite mounds, foraging, ranging, and rapid movements, respectively. The first and last hours of activity presented relatively high proportions of the vigilance-excavation state, while most of the activity period was dominated by local search and exploratory states. The vigilance-excavation state occurred more frequently in regions between forest and closed savannas, whereas local search was more likely in high proportions of closed savanna. Exploratory behavior probability increased in areas with high proportions of both forest and closed savanna. Our results establish a baseline for behavioral complexity, activity budgets, and habitat associations in a relatively pristine environment that can be used for future work to investigate anthropogenic impacts on giant armadillo behavior and fitness. The integration of accelerometer and GPS-derived movement data through our mixture model has the potential to become a powerful methodological approach for the conservation of other cryptic species. creator: Joshua A. Cullen creator: Nina Attias creator: Arnaud L.J. Desbiez creator: Denis Valle uri: https://doi.org/10.7717/peerj.14726 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cullen et al. title: Acteoside alleviates UUO-induced inflammation and fibrosis by regulating the HMGN1/TLR4/TREM1 signaling pathway link: https://peerj.com/articles/14765 last-modified: 2023-01-18 description: PurposeActeoside (Act), a phenylethanoid compound that was first isolated from mullein, has been widely used for the investigation of anti-inflammatory and anti-fibrotic effect. However, the mechanism of Act against unilateral ureteral obstruction (UUO)-mediated renal injury is largely unknown. Therefore, this study aimed to explore the effects of Act on UUO rats and possible mechanisms.MethodsA total of 20 Sprague-Dawley (SD) rats were divided randomly into three groups (n ≥ 6): (i) sham-operated group (Sham); (ii) UUO group (UUO+Saline); and (iii) UUO + Act 40 mg/kg/day, (UUO+Act); Continuous gavage administration for 2 weeks postoperatively, while the rats in Sham and UUO+saline groups were given equal amounts of saline. All rats were sacrificed after 14 days, the urine and blood samples were collected for biochemical analysis, the renal tissues were collected for pathological staining and immunohistochemistry. Correlations between individual proteins were analyzed by Pearson correlation analysis.ResultsThe results of renal function indexes and histopathological staining showed that Act could improve renal function by reducing serum creatinine, blood urea nitrogen and urine protein at the same time, Act could alleviate renal inflammation and fibrosis. In addition, the results of immunohistochemistry showed that Act could reduce the expression of inflammation and kidney injury-related proteins F4/80, Mcp-1, KIM-1 proteins, as well as the expression of fibrosis-related protein α-SMA and β-catenin. More importantly, Act can also reduce the expression of HMGN1, TLR4 and TREM-1 proteins.ConclusionThese data demonstrate that Act can ameliorate UUO-induced renal inflammation and fibrosis in rats probably through triggering HMGN1/TLR4/TREM-1 pathway. creator: Yan Mao creator: Jiali Yu creator: Jingjing Da creator: Fuxun Yu creator: Yan Zha uri: https://doi.org/10.7717/peerj.14765 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mao et al. title: Differential expression of lysine acetylation proteins in gastric cancer treated with a new antitumor agent bioactive peptide chelate selenium link: https://peerj.com/articles/14384 last-modified: 2023-01-17 description: The method of anticancer bioactive peptide (ACBP) functionalized selenium particle (Se), which has enhanced anticancer activity, inhibited the growth of gastric cancer (GC) cells, and increased the ability of apoptosis in vitro, has been reported in previous studies. We used tandem mass spectrometry (TMT) labeling to construct a complete atlas of the acetylation-modified proteome in GC MKN-45 cells treated with ACBP-Se. The proteomics data database was searched and analyzed by bioinformatics: Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), functional enrichment, and protein-protein interaction network. Finally, we conducted a quantitative PRM analysis of the selected target-modified peptides. We identified 4,958 acetylation sites from 1,926 proteins in this research. Among these, 4,467 acetylation sites corresponding to 1,777 proteins were quantified. Based on the above data and standards, we found that in the ACBP-Se group vs. the control group, 297 sites were upregulated, and 665 sites were downregulated. We systematically assessed the proteins containing quantitative information sites, including protein annotation, functional classification, and functional enrichment, cluster analysis supported by functional enrichment, domain structures, and protein interaction networks. Finally, we evaluated differentially expressed lysine acetylation sites. We revealed that SHMT2 K200 and PGK1 K97 were the most critical acetylated non-histone proteins, which may have an essential role in ACBP-Se treatment. Here, we identified and quantified the lysine acetylation proteins in GC cells treated with ACBP-Se. The characterization of acetylation indicates that acetylated proteins might be pivotal in the biological process, molecular binding, and metabolic pathways of ACBP-Se treatment progress. Our findings provide a broad understanding of acetylation ACBP-Se treatment of GC, suggesting a potential application for molecular targeted therapy. creator: Yanan Xu creator: Jianxun Wen creator: Wenyan Han creator: Jin Yan creator: Wei Jia creator: Xiulan Su uri: https://doi.org/10.7717/peerj.14384 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Bacterial incidence and drug resistance from pathogens recovered from blood, cerebrospinal and pleural fluids in 2019–2020. Results of the Invifar network link: https://peerj.com/articles/14411 last-modified: 2023-01-17 description: BackgroundAntimicrobial resistance is a global concern. Analysis of sterile fluids is essential because microorganisms are defined as significant in most cases. Blood, cerebrospinal, and pleural fluids are frequently received in the microbiology lab because they are associated with considerable rates of morbi-mortality. Knowledge of epidemiology in these samples is needed to choose proper empirical treatments due to the importance of reducing selection pressure.MethodsWe used retrospective laboratory data of blood, CSF, and pleural fluid collected from patients in Mexico between 2019 and 2020. Each laboratory identified the strains and tested susceptibility using its routine methods. For Streptococcus pneumoniae, a comparative analysis was performed with data from the broth microdilution method.ResultsForty-five centers participated in the study, with 30,746 clinical isolates from blood, 2,429 from pleural fluid, and 2,275 from CSF. For blood and CSF, Staphylococcus epidermidis was the most frequent. For blood, among gram negatives, the most frequent was Escherichia coli. Among Enterobacterales, 9.8% of K. pneumoniae were carbapenem-resistant. For S. pneumoniae, similar resistance percentages were observed for levofloxacin, cefotaxime, and vancomycin. For CSF, the most frequent gram-negative was E. coli. In Acinetobacter baumannii, carbapenem resistance was 71.4%. The most frequent species detected for pleural fluid was E. coli; in A. baumannii, carbapenem resistance was 96.3%.ConclusionGram-negative bacteria, with E. coli most prevalent, are frequently recovered from CSF, blood, and pleural fluid. In S. pneumoniae, the routine, conventional methods showed good agreement in detecting resistance percentages for erythromycin, levofloxacin, and vancomycin. creator: Elvira Garza-González creator: Adrian Camacho-Ortiz creator: Alfredo Ponce-de-Leon creator: Edgar Ortiz-Brizuela creator: Luis Esaú López-Jácome creator: Claudia Colin creator: Fabian Rojas-Larios creator: Oscar A. Newton-Sánchez creator: Gabriela Echaniz-Aviles creator: Maria Noemi Carnalla-Barajas creator: Araceli Soto creator: Paola Bocanegra-Ibarias creator: Ana María del Rocío Hernández-Dueñas creator: María del Consuelo Velázquez-Acosta creator: Laura Karina Avilés-Benítez creator: Juan Pablo Mena-Ramirez creator: Daniel Romero creator: Isela Mora-Jiménez creator: Margarita Alcaraz-Espejel creator: José Manuel Feliciano-Guzmán creator: Maribel López-García creator: Patricia Rodriguez-Zulueta creator: María Angelina Quevedo-Ramos creator: Cecilia Padilla-Ibarra creator: Carlos Antonio Couoh-May creator: Maria Carolina Rivera-Ferreira creator: Cecilia Teresita Morales-de-la-Peña creator: Hector Zubiate creator: Raúl Peralta-Catalán creator: Carlos Miguel Cetina-Umaña creator: Joaquin Rincón-Zuno creator: Maria Lucia Perez-Ricardez creator: Iris Yazmin Hernández-Cordova creator: Eduardo López-Gutiérrez creator: Mariana Gil creator: Efren Aguirre-Burciaga creator: Guadalupe Soledad Huirache-Villalobos creator: Scarlett Munoz creator: Nicolás Rogelio Eric Barlandas-Rendón creator: Enrique Bolado-Martinez creator: Luis Javier Quintanilla-Cazares creator: Abraham C. Gómez-Choel creator: Laura Lopez creator: Juan Carlos Tinoco creator: Rosa Areli Martínez-Gamboa creator: Alejandro Molina creator: Samuel Pavel Escalante-Armenta creator: Lizbeth Duarte creator: Luis Alberto Ruiz-Gamboa creator: Dulce Isabel Cobos-Canul creator: Dulce López creator: Irma Elena Barroso-Herrera-y-Cairo creator: Eduardo Rodriguez-Noriega creator: Rayo Morfin-Otero uri: https://doi.org/10.7717/peerj.14411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Garza-González et al. title: Upper Norian conodonts from the Baoshan block, western Yunnan, southwestern China, and implications for conodont turnover link: https://peerj.com/articles/14517 last-modified: 2023-01-17 description: The Sevatian of the late Norian is one of the key intervals in biotic turnover and in changes of paleoclimate and paleoenvironments. Conodont faunas recovered from two sections of upper Norian strata of the Dashuitang and Nanshuba formations near Baoshan City in western Yunnan province provide new insights into the diversity and biostratigraphy of the Sevatian conodonts within China as well as globally. A lower Mockina (M.) bidentata Zone and an upper Parvigondolella (P.) andrusovi Zone are identified in this area according to the first occurrences of M. bidentata and of P. andrusovi. Rich conodont fauna of M. zapfei is detailed and presents various intraspecific forms. A total of 19 forms of P1 elements are presented, which, when combined with the reported conodonts in the M. bidentata Zone, suggest that there was a peak in conodont diversity within the M. bidentata Zone. A biotic crisis in the uppermost M. bidentata Zone is recognized from the contrast between the diverse conodont fauna in the M. bidentata Zone and the rare conodonts in the P. andrusovi Zone. The conodont turnover during the middle Sevatian highlights the fact that the prolonged phases of the end-Triassic mass extinction probably began in the transition interval from M. bidentata Zone to P. andrusovi Zone. creator: Weiping Zeng creator: Haishui Jiang creator: Yan Chen creator: James Ogg creator: Muhui Zhang creator: Hanxinshuo Dong uri: https://doi.org/10.7717/peerj.14517 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zeng et al. title: Low temperature upregulating HSP70 expression to mitigate the paclitaxel-induced damages in NHEK cell link: https://peerj.com/articles/14630 last-modified: 2023-01-17 description: Scalp cooling is the most approved treatment for preventing chemotherapy-induced alopecia (CIA). However, the protective mechanism of scalp cooling has rarely been reported. The goal of the present study was to study the relationship between paclitaxel concentration and temperature and the inhibitory effect of low temperature on paclitaxel-induced alopecia. The results showed that the dose of paclitaxel should not exceed 60–70 mg/mL during scalp cooling treatment, and the optimal cooling temperature under different paclitaxel concentrations was determined. Normal human epidermal keratinocytes (NHEK) cells were analyzed by global transcriptome analysis, functional annotation and pathway analysis of differentially expressed genes (DEGs) and ELISA kit to analyze the mechanism of low temperature therapy. The expression of HSPA8, HSPA1A and HSPA1B, which belongs to HSP70, was up-regulated by low temperature. These genes are important target genes of low temperature treatment, which were confirmed by ELISA. The up-regulation of PLK2 and the down-regulation of TXNIP expression are the upstream of mitochondrial dysfunction and ROS, inhibiting the accumulation of ROS and up-regulating the mitochondrial membrane potential. Our research partially elucidates the therapeutic mechanism of scalp cooling, which provides a new idea on the drug research and development in CIA. creator: Liang Chen creator: Yi Xu uri: https://doi.org/10.7717/peerj.14630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen and Xu title: Detect feature edges for diagnosis of bacterial vaginosis link: https://peerj.com/articles/14667 last-modified: 2023-01-17 description: One of the most common diseases among women of reproductive age is bacterial vaginosis (BV). However, the etiology of BV remains unknown. In this study, we modeled the temporal sample of the vaginal microbiome as a network and investigated the relationship between the network edges and BV. Furthermore, we used feature selection algorithms including decision tree (DT) and ReliefF (RF) to select the network feature edges associated with BV and subsequently validated these feature edges through logistic regression (LR) and support vector machine (SVM). The results show that: machine learning can distinguish vaginal community states (BV, ABV, SBV, and HEA) based on a few feature edges; selecting the top five feature edges of importance can achieve the best accuracy for the feature selection and classification model; the feature edges selected by DT outperform those selected by RF in terms of classification algorithm LR and SVM, and LR with DT feature edges is more suitable for diagnosing BV; two feature selection algorithms exhibit differences in the importance of ranking of edges; the feature edges selected by DT and RF cannot construct sub-network associated with BV. In short, the feature edges selected by our method can serve as indicators for personalized diagnosis of BV and aid in the clarification of a more mechanistic interpretation of its etiology. creator: Jie Li creator: Yaotang Li uri: https://doi.org/10.7717/peerj.14667 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li and Li title: Prenatal diagnosis of fetuses conceived by assisted reproductive technology by karyotyping and chromosomal microarray analysis link: https://peerj.com/articles/14678 last-modified: 2023-01-17 description: BackgroundInvasive prenatal evaluation by chromosomal microarray analysis (CMA) and karyotyping might represent an important option in pregnant women, but limited reports have applied CMA and karyotyping of fetuses conceived by assisted reproductive technology (ART). This study aimed to examine the value of CMA and karyotyping in prenatal diagnosis after ART.MethodsThis retrospective study included all singleton fetuses conceived by ART from January 2015 to December 2021. Anomalies prenatally diagnosed based on karyotyping and CMA were analyzed. Prevalence rates for various CMA and karyotyping results were stratified based on specific testing indications including isolated—and non-isolated ART groups. The rates of CMA findings with clinical significance (pathogenic/likely pathogenic) and karyotype anomalies were assessed and compared to those of local control individuals with naturally conceived pregnancies and without medical indications.ResultsIn total, 224 subjects were assessed by karyotyping and CMA. In the examined patients, chromosomal and karyotype abnormality rates were 3.57% (8/224) and 8.93% (20/224), respectively. This finding indicated a 5.35% (12/224)-incremental rate of abnormal CMA was obtained over karyotype analysis (p = 0.019). The risk of CMA with pathogenic findings for all pregnancies conceived by ART (5.80%, 13/224) was markedly elevated in comparison with the background value obtained in control individuals (1.47%, 9/612; p = 0.001). In addition, risk of CMA with clinically pathogenic results in isolated ART groups was significant higher compared to the background risk reported in the control cohort (p = 0.037).ConclusionsPrenatal diagnosis including karyotyping and CMA is recommended for fetuses conceived by ART, with or without ultrasound findings. creator: Huan Guo creator: Rui Sheng creator: Xiu Zhang creator: Xuemei Jin creator: Wenjing Gu creator: Ting Liu creator: Haixin Dong creator: Ran Jia uri: https://doi.org/10.7717/peerj.14678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: Hard-bottom habitats support commercially important fish species: a systematic review for the North Atlantic Ocean and Baltic Sea link: https://peerj.com/articles/14681 last-modified: 2023-01-17 description: Hard-bottom habitats span a range of natural substrates (e.g., boulders, cobble) and artificial habitats (e.g., the base of wind turbines, oil platforms). These hard-bottom habitats can provide a variety of ecosystem services, ranging from the enhancement of fish biomass and production to providing erosion control. Management decisions regarding the construction or fate of hard-bottom habitats require information on the ecological functions of these habitats, particularly for species targeted in ecosystem-based fisheries management. This study provides a systematic review of the relationships of various hard-bottom habitats to individual commercially harvested species that are managed jointly across the Atlantic by the International Council for the Exploration of the Sea (ICES). We systemically reviewed peer-reviewed publications on hard-bottom habitats including both natural and artificial reefs, after applying various exclusion criteria. Most studies were conducted on near-shore hard-bottom habitats, and habitat importance varied according to fish species and region. We quantified the frequency with which studies demonstrate that natural and artificial hard-bottom habitats function as spawning grounds, settlement and nursery areas, and foraging grounds, as well as provide stepping-stones during migration, or new home ranges. Hard-bottom habitats generally support higher fish densities than surrounding habitat types, although not all fish species benefit from hard-bottom habitats. Of the commercially important species, cod (Gadus morhua) was the most frequently studied species, with enhanced biomass, density, feeding, and spawning on hard-bottom habitats compared to unstructured habitats. Moreover, hard-bottom habitats appear to be of particular importance for spawning of herring (Clupea harengus). Collectively, data indicate that loss of hard-bottom habitats may translate into less-favourable conditions for spawning and biomass of diverse commercial species, including cod and herring. creator: Hugo Flávio creator: Rochelle Seitz creator: David Eggleston creator: Jon C. Svendsen creator: Josianne Støttrup uri: https://doi.org/10.7717/peerj.14681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Flávio et al. title: The root enrichment of bacteria is consistent across different stress-resistant plant species link: https://peerj.com/articles/14683 last-modified: 2023-01-17 description: Bacteria, inhabiting around and in plant roots, confer many beneficial traits to promote plant growth and health. The secretion of root exudates modulates the nutritional state of the rhizosphere and root area, further selecting specific bacteria taxa and shaping the bacteria communities. Many studies of the rhizosphere effects have demonstrated that selection by the plant rhizosphere consistently enriches a set of bacteria taxa, and this is conserved across different plant species. Root selection effects are considered to be stronger than the rhizosphere selection effects, yet studies are limited. Here, we focus on the root selection effects across a group of 11 stress-resistant plant species. We found that the root selection consistently reduced the alpha diversity (represented by total number of observed species, Shannon’s diversity, and phylogenetic diversity) and altered the structure and composition of bacteria communities. Furthermore, root selection tended to enrich for clusters of bacteria genera including Pantoea, Akkermansia, Blautia, Acinetobacter, Burkholderia-Paraburkholderia, Novosphingobium, Massilia, Pseudomonas, Chryseobacterium, and Stenotrophomonas. Our study offers some basic knowledge for understanding the microbial ecology of the plant root, and suggests that several bacteria genera are of interest for future studies. creator: Feng Huang creator: Congyi Zhu creator: Minli Huang creator: Xiaobing Song creator: Aitian Peng uri: https://doi.org/10.7717/peerj.14683 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Solithromycin inhibits IL-13-induced goblet cell hyperplasia and MUC5AC, CLCA1, and ANO1 in human bronchial epithelial cells link: https://peerj.com/articles/14695 last-modified: 2023-01-17 description: Solithromycin is a novel fluoroketolide antibiotic belonging to the class of macrolide antibiotics. Activation of the interleukin (IL)-13 receptor leads to STAT6 activation and subsequent induction of SAM pointed domain containing ETS transcription factor (SPDEF), chloride channel accessory 1 (CLCA1), and anoctamin-1 (ANO1), all of which are associated with the induction of MUC5AC. We examined the effects of solithromycin on mucin production led by IL-13 signaling. Normal human bronchial epithelial cells were grown at the air-liquid interface with IL-13 with/without solithromycin for 14 days. Histochemical analysis was performed using hematoxylin and eosin staining and MUC5AC immunostaining. MUC5AC, SPDEF, CLCA1, and ANO1 mRNA expressions were examined using real-time polymerase chain reaction. Western blot analysis was performed to assess CLCA1 and ANO1 proteins, and phosphorylation of STAT6 and ERK. Solithromycin attenuated IL-13 induction of goblet cell hyperplasia and MUC5AC, CLCA1 and ANO1 mRNA and protein expression induced by IL-13, but had no effect on the phosphorylation of STAT6 and ERK. Our results indicate that solithromycin could attenuate goblet cell hyperplasia and MUC5AC induced by IL-13 through inhibition of CLCA1 and ANO1 mRNA and protein expression. However, much more information is required to clarify the molecular mechanisms underlying the inhibition of CLCA1 and ANO1 by solithromycin. creator: Yasuhiro Kimura creator: Masahiro Shinoda creator: Masaharu Shinkai creator: Takeshi Kaneko uri: https://doi.org/10.7717/peerj.14695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kimura et al. title: Genome-wide identification and expression profile analysis of SWEET genes in Chinese jujube link: https://peerj.com/articles/14704 last-modified: 2023-01-17 description: The novel sugar transporter known as SWEET (sugars will eventually be exported transporter) is involved in the transport and distribution of photosynthesis products in plants. The SWEET protein is also involved in pollen development, nectar secretion, stress responses, and other important physiological processes. Although SWEET genes have been characterized and identified in model plants, such as Arabidopsis and rice, little is known about them in jujube. In this study, the molecular characteristics of the SWEET gene family in the Chinese jujube (Ziziphus jujuba Mill.) and their expression patterns in different organs, at different fruit developmental stages, and under abiotic stress were analyzed. A total of 19 ZjSWEET genes were identified in jujube through a genome-wide study; these were classified into four sub-groups based on their phylogenic relationships. The gene structure analysis of ZjSWEET genes showed that all the members had introns. The expression patterns of different ZjSWEET genes varied significantly in different organs (root, shoot, leave, flower, fruit), which indicated that ZjSWEETs play different roles in multiple organs. According to the expression profiles by quantitative real-time PCR analysis during fruit development, the expression levels of the two genes (ZjSWEET11, ZjSWEET18) gradually increased with the development of the fruit and reached a high level at the full-red fruit stage. A prediction of the cis-acting regulatory elements indicated that the promoter sequences of ZjSWEETs contained nine types of phytohormone-responsive cis-regulatory elements and six environmental factors. In addition, the expression profiles by quantitative real-time PCR analysis showed that some of the ZjSWEETs responded to environmental changes; ZjSWEET2 was highly induced in response to cold stress, and ZjSWEET8 was significantly up-regulated in response to alkali and salt stresses. This study showed that the functions of the ZjSWEET family members of jujube are different, and some may play an important role in sugar accumulation and abiotic stress in jujube. creator: Chong Yang creator: Xuan Zhao creator: Zhi Luo creator: Lihu Wang creator: Mengjun Liu uri: https://doi.org/10.7717/peerj.14704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Nitrogen and potassium interactions optimized asynchronous spikelet filling and increased grain yield of japonica rice link: https://peerj.com/articles/14710 last-modified: 2023-01-17 description: Poor grain filling severely reduces rice yield. Fertilizers play a vital role in regulating grain filling, especially nitrogen (N) and potassium (K). In this field study we aimed to investigate the interactive effects of N and K on the asynchronous filling properties of superior and inferior spikelets of japonica rice. We looked at grain filling under three N rates (0, 90, and 180 kg N ha−1) and three K rates (0, 60, and 120 kg K2O ha−1) during 2020 and 2021. Across two years, the results showed that the combined use of N and K on superior and inferior spikelets significantly increased their weight by 1.29 mg and 2.31 mg, their maximum grain filling rate by 0.24 mg d−1 and 0.07 mg d−1, and their average grain filling rate by 0.21 mg d−1 and 0.06 mg d−1, respectively, in comparison with the control (N0K0) treatment. Likewise, K supply increased the average contribution rate of superior and inferior spikelets to yield by 9.1% and 10.0%, respectively. Correlation analysis showed that the grain filling rate of superior and inferior spikelets was an important factor in determining the spikelet weight, whereas the grain filling time was not. We also found that the 1,000-grain weight mainly increased after increasing the spikelets’ maximum grain filling rate and average grain filling rate. Collectively, these results illustrate that the combined use of N and K can optimize the asynchronous filling of superior and inferior spikelets and, in particular, enhance inferior spikelet weight with higher rice yield. creator: Weitao Xu creator: Jianming Li creator: Jiancheng Feng creator: Zhenzhu Shao creator: Yidan Huang creator: Wenfeng Hou creator: Qiang Gao uri: https://doi.org/10.7717/peerj.14710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Comparative transcriptome analysis of Armillaria gallica 012m in response to ethephon treatment link: https://peerj.com/articles/14714 last-modified: 2023-01-17 description: Background Gastrodia elata, known as a rootless, leafless, achlorophyllous and fully mycoheterotrophic orchid, needs to establish symbionts with particular Armillaria species to acquire nutrition and energy. Previous research findings had approved that ethylene (ET) played an important role in plant-fungi interaction and some receptors of ET had been discovered in microorganisms. However, the molecular mechanisms underlying the role of ET in the interaction between G. elata and Armillaria species remain unknown.MethodsExiguous ethephon (ETH) was added to agar and liquid media to observe the morphological features of mycelium and count the biomass respectively. Mycelium cultured in liquid media with exiguous ETH (0.1 ppm, 2.0 ppm, 5.0 ppm) were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing). The DEGs of growth-related genes and candidate ET receptor domains were predicted on SMART.ResultsETH-0.1 ppm and ETH-2 ppm could significantly improve the mycelium growth of A. gallica 012m, while ETH-5 ppm inhibited the mycelium growth in both solid and liquid media. The number of up-regulated or down-regulated genes increased along with the concentrations of ETH. The growth of mycelia might benefit from the up-regulated expression of Pyr_redox (Pyridine nucleotide-disulphide oxidoreductase), GAL4 (C6 zinc finger) and HMG (High Mobility Group) genes in the ETH-0.1 ppm and ETH-2 ppm. Therefore, the growth of mycelia might be impaired by the down-regulated expression of ZnF_C2H2 and ribosomal protein S4 proteins in the ETH-5 ppm. Seven ET receptor domains were predicted in A. gallica 012m. Based on cluster analysis and comparative studies of proteins, the putative ETH receptor domains of A. gallica 012m have a higher homologous correlation with fungi.ConclusionsThe responses of A. gallica 012m to ETH had a concentration effect similar to the plants’ responses to ET. Therefore, the number of up-regulated or down-regulated genes are increased along with the concentrations of ETH. Seven ET receptor protein domains were predicted in the genome and transcriptome of A. gallica 012m. We speculate that ETH receptors exist in A. gallica 012m and ethylene might play an important role in the plant-fungi interaction. creator: Haiying Yang creator: Kaixiang He creator: Yapu Cao creator: Zhihao Li creator: Qiaolin Ji creator: Jingxian Sun creator: Ganpeng Li creator: Xin Chen creator: Haiying Mo creator: Gang Du creator: Qingqing Li uri: https://doi.org/10.7717/peerj.14714 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: A cross-sectional survey of avian influenza knowledge among poultry farmworkers in Indonesia link: https://peerj.com/articles/14600 last-modified: 2023-01-16 description: BackgroundAvian influenza (AI) poses a serious threat to global public health, especially the highly pathogenic form. Awareness and protective behavior among the public, particularly the high-risk populations, are essential for prevention and control. This study aimed to ascertain the level of AI knowledge among Indonesia’s poultry farmworkers.MethodsThis was a cross-sectional study conducted online. A predesigned standardized questionnaire, containing six demographic questions and 14 questions on AI knowledge, was used. The questionnaire was distributed via WhatsApp and email platforms. Volunteers (respondents) included 119 men and 81 women, aged 18–50 years, who work on poultry farms in Indonesia. Data were analyzed using the chi-squared and Fisher exact tests.ResultsThe study’s findings revealed that more than two-thirds (67.0%) of the respondents had heard about AI. Their primary sources of information were health workers (36.0%) and media, especially television (34.0%). The majority of the participants (91.3%) had good knowledge about AI as a contagious infection, transmissible from birds to other birds, animals, or humans. A total of 76.8% of the respondents believed that poultry workers and veterinarians were at high risk of contracting AI infection.ConclusionsThe study concluded that poultry workers had good knowledge about AI infection, transmission, and risk variables. Health workers and television were the main sources of information on AI. The level of AI knowledge was high among the respondents. creator: Saifur Rehman creator: Aamir Shehzad creator: Lisa Dyah Andriyani creator: Mustofa Helmi Effendi creator: Zain Ul Abadeen creator: Muhammad Ilyas Khan creator: Muhammad Bilal uri: https://doi.org/10.7717/peerj.14600 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rehman et al. title: Transcription analyses of differentially expressed mRNAs, lncRNAs, circRNAs, and miRNAs in the growth plate of rats with glucocorticoid-induced growth retardation link: https://peerj.com/articles/14603 last-modified: 2023-01-16 description: BackgroundGlucocorticoids (GCs) are commonly used to treat autoimmune diseases and malignancies in children and adolescents. Growth retardation is a common adverse effect of GC treatment in pediatric patients. Accumulating evidence indicates that non-coding RNAs (ncRNAs) are involved in the pathogenesis of glucocorticoid-induced growth retardation (GIGR), but the roles of specific ncRNAs in growth remain largely unknown.MethodsIn this study, 2-week-old male Sprague-Dawley rats had been treated with 2 mg/kg/d of dexamethasone for 7 or 14 days, after which the growth plate tissues were collected for high-throughput RNA sequencing to identify differentially expressed mRNAs, lncRNAs, circRNAs, and miRNAs in GIGR rats.ResultsTranscriptomic analysis identified 1,718 mRNAs, 896 lncRNAs, 60 circRNAs, and 72 miRNAs with different expression levels in the 7d group. In the 14d group, 1,515 mRNAs, 880 lncRNAs, 46 circRNAs, and 55 miRNAs with differential expression were identified. Four mRNAs and four miRNAs that may be closely associated with the development of GIGR were further validated by real-time quantitative fluorescence PCR. Function enrichment analysis indicated that the PI3K-Akt signaling pathway, NF-kappa B signaling pathway, and TGF-β signaling pathway participated in the development of the GIGR. Moreover, the constructed ceRNA networks suggested that several miRNAs (including miR-140-3p and miR-127-3p) might play an important role in the pathogenesis of GIGR.ConclusionsThese results provide new insights and important clues for exploring the molecular mechanisms underlying GIGR. creator: Mingyue Yin creator: Junqi Wang creator: Juanjuan Zhang creator: Wei Wang creator: Wenli Lu creator: Fei Xu creator: Xiaoyu Ma creator: Sheng Lyu creator: Lifen Chen creator: Lidan Zhang creator: Zhiya Dong creator: Yuan Xiao uri: https://doi.org/10.7717/peerj.14603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yin et al. title: High and low dose of luzindole or 4-phenyl-2-propionamidotetralin (4-P-PDOT) reverse bovine granulosa cell response to melatonin link: https://peerj.com/articles/14612 last-modified: 2023-01-16 description: BackgroundCommunication between oocytes and granulosa cells ultimately dictate follicle development or atresia. Melatonin is also involved in follicle development. This study aimed to investigate the effects of melatonin and its receptor antagonists on hormone secretion, as well as gene expression related to hormone synthesis, TGF-β superfamily, and follicle development in bovine granulosa cells, and assess the effects of melatonin in the presence of 4-P-PDOT and luzindole.MethodsBovine ovaries were collected from a local abattoir and follicular fluid (follicle diameter 5–8 mm) was collected for granulosa cell isolation and culture. Granulosa cells and culture medium were collected 48 h after treatment with melatonin at high dose concentrations (10−5 M) and low dose concentrations (10−9 M) in the absence/presence of 4-P-PDOT and luzindole (10−5 M or 10−9 M). Furthermore, the expression level of genes related to hormonal synthesis (CYP11A1, CYP19A1, StAR, and RUNX2), TGF-β superfamily (BMP6, INHA, INHBA, INHBB, and TGFBR3), and development (EGFR, DNMT1A, and FSHR) were detected in each experimental group by real-time quantitative PCR. In addition, the level of hormones in culture medium were detected using ELISA.ResultsBoth 10−5 M and 10−9 M melatonin doses promoted the secretion of inhibin A and progesterone without affecting the production of inhibin B and estradiol. In addition, both promoted the gene expression of INHA, StAR, RUNX2, TGFBR3, EGFR, and DNMT1A, and inhibited the expression of BMP6, INHBB, CYP11A1, CYP19A1, and FSHR. When combined with different doses of 4-P-PDOT and luzindole, they exhibited different effects on the secretion of inhibin B, estradiol, inhibin A, and progesterone, and the expression of CYP19A1, RUNX2, BMP6, INHBB, EGFR, and DNMT1A induced by melatonin.ConclusionHigh and low dose melatonin receptor antagonists exhibited different effects in regulating hormone secretion and the expression of various genes in response to melatonin. Therefore, concentration effects must be considered when using luzindole or 4-P-PDOT. creator: Wenju Liu creator: Zhihao Chen creator: Rui Li creator: Menghao Zheng creator: Xunsheng Pang creator: Aiyou Wen creator: Bing Yang creator: Shujuan Wang uri: https://doi.org/10.7717/peerj.14612 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Comparative studies of two AA10 family lytic polysaccharide monooxygenases from Bacillus thuringiensis link: https://peerj.com/articles/14670 last-modified: 2023-01-16 description: Bacillus thuringiensis, known to be one of the most important biocontrol microorganisms, contains three AA10 family lytic polysaccharide monooxygenases (LPMOs) in its genome. In previous reports, two of them, BtLPMO10A and BtLPMO10B, have been preliminarily characterized. However, some important biochemical features and substrate preference, as well as their potential applications in chitin degradation, still deserve further investigation. Results from present study showed that both BtLPMO10A and BtLPMO10B exhibit similar catalytic domains as well as highly conserved substrate-binding planes. However, unlike BtLPMO10A, which has comparable binding ability to both crystalline and amorphous form of chitins, BtLPMO10B exhibited much stronger binding ability to colloidal chitin, which mainly attribute to its carbohydrate-binding module-5 (CBM5). Interestingly, the relative high binding ability of BtLPMO10B to colloidal chitin does not lead to high catalytic activity of the enzyme. In contrast, the enzyme exhibited higher activity on β-chitin. Further experiments showed that the binding of BtLPMO10B to colloidal chitin was mainly non-productive, indicating a complicated role for CBM5 in LPMO activity. Furthermore, synergistic experiments demonstrated that both LPMOs boosted the activity of the chitinase, and the higher efficiency of BtLPMO10A can be overridden by BtLPMO10B. creator: Huiyan Zhang creator: Haichuan Zhou creator: Yong Zhao creator: Tang Li creator: Heng Yin uri: https://doi.org/10.7717/peerj.14670 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Inter-rater and intra-rater reliability of isotonic exercise monitoring device for measuring active knee extension link: https://peerj.com/articles/14672 last-modified: 2023-01-16 description: BackgroundThe goal of this study was to assess the reliability of electromyography and range of motion measurements obtained using a knee exercise monitoring system. This device was developed to collect data on knee exercise activities.MethodsTwenty healthy individuals performed isotonic quadriceps exercises in this study. The vastus medialis surface electromyography (sEMG) and range of motion (ROM) of the knee were recorded during the exercise using the isotonic knee exercise monitoring device, the Mobi6-6b, and a video camera system. Each subject underwent a second measuring session at least 24 h after the first session. To determine reliability, the intraclass correlation coefficients (ICCs) and standard error of measurement (SEM) at the 95% confidence interval were calculated, and a Bland–Altman analysis was performed.ResultsFor inter-rater reliability, the ICCs of the mean absolute value (MAV) and root mean square (RMS) of sEMG were 0.73 (0.49, 0.86) and 0.79 (0.61, 0.89), respectively. ROM had an ICC of 0.93 (0.02, 0.98). The intra-rater reliability of the MAV of the sEMG was 0.89 (0.71, 0.96) and the intra-rater reliability of RMS of the sEMG was 0.88 (0.70, 0.95). The ROM between days had an intra-rater reliability of 0.82 (0.54, 0.93). The Bland–Altman analysis demonstrated no systematic bias in the MAV and RMS of sEMG, but revealed a small, systematic bias in ROM (−0.8311 degrees).ConclusionFor sEMG and range of motion measures, the isotonic knee exercise monitoring equipment revealed moderate to excellent inter- and intra-rater agreement. However, the confidence interval of ROM inter-rater reliability was quite large, indicating a small agreement bias; hence, the isotonic knee exercise monitor may not be suitable for measuring ROM. This isotonic knee exercise monitor could detect and collect information on a patient’s exercise activity for the benefit of healthcare providers. creator: Chonnanid Limsakul creator: Kiattisak Sengchuai creator: Rakkrit Duangsoithong creator: Nattha Jindapetch creator: Jermphiphut Jaruenpunyasak uri: https://doi.org/10.7717/peerj.14672 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Limsakul et al. title: Stories told by corals, algae, and sea-urchins in a Mesoamerican coral reef: degradation trumps succession link: https://peerj.com/articles/14680 last-modified: 2023-01-16 description: Understanding the mechanisms that allow the permanence of coral reefs and the constancy of their characteristics is necessary to alleviate the effects of chronic environmental changes. After a disturbance, healthy coral reefs display trajectories that allow regaining coral cover and the establishment of framework building corals. Through a comparative approach, in a patch reef partially affected by a ship grounding, we analyzed the successional trajectories in affected and unaffected sectors. Fleshy algae (which do not promote the recruitment of corals) dominated the reef surface irrespective of the impact of the ship grounding incident. Acropora species had near-zero contributions to community structure, whereas non-framework building corals like Porites sp. had a slightly higher recruitment. Cover of coral and calcareous crustose algae decreased over time, and neither the latter nor adult coral colonies had any effect on the occurrence probabilities of small corals. Sea urchin (Diadema antillarum) densities were generally low, and thus unlikely to contribute to reverting algal dominance. The successional trajectories of the community in the impacted and non-impacted sectors of the coral patch reef agree with the inhibition successional model, leading to the development of a degraded state dominated by fleshy algae. It is probable that the stability and resilience of this degraded state are high due to the ability of fleshy algae to monopolize space, along with low coral recovery potential. creator: Isael Victoria-Salazar creator: Edgar J. González creator: Jorge A. Meave creator: Miguel-Ángel Ruiz-Zárate creator: Héctor A. Hernández-Arana uri: https://doi.org/10.7717/peerj.14680 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Victoria-Salazar et al. title: Molecular marker development and genetic diversity exploration in Medicago polymorpha link: https://peerj.com/articles/14698 last-modified: 2023-01-16 description: Medicago polymorpha L. (bur clover), an invasive plant species of the genus Medicago, has been traditionally used in China as an edible vegetable crop because of its high nutritive value. However, few molecular markers for M. polymorpha have been identified. Using the recently published high-quality reference genome of M. polymorpha, we performed a specific-locus amplified fragment sequencing (SLAF-seq) analysis of 10 M. polymorpha accessions to identify molecular markers and explore genetic diversity. A total of 52,237 high-quality single nucleotide polymorphisms (SNPs) were developed. These SNPs were mostly distributed on pseudochromosome 3, least distributed on pseudochromosome 7, and relatively evenly distributed on five other pseudochromosomes of M. polymorpha. Phenotypic analysis showed that there was a great difference in phenotypic traits among different M. polymorpha accessions. Moreover, clustering all M. polymorpha accessions based on their phenotypic traits revealed three groups. Both phylogenetic analysis and principal component analysis (PCA) of all M. polymorpha accessions based on SNP markers consistently indicated that all M. polymorpha accessions could be divided into three distinct groups (I, II, and III). Subsequent genetic diversity analysis for the 10 M. polymorpha accessions validated the effectiveness of the M. polymorpha germplasm molecular markers in China. Additionally, SSR mining analysis was also performed to identify polymorphic SSR motifs, which could provide valuable candidate markers for the further breeding of M. polymorpha. Since M. polymorpha genetics have not been actively studied, the molecular markers generated from our research will be useful for further research on M. polymorpha resource utilization and marker-assisted breeding. creator: Hailong Ren creator: Zhenwu Wei creator: Bo Zhou creator: Xiang Chen creator: Qiang Gao creator: Zhibin Zhang uri: https://doi.org/10.7717/peerj.14698 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ren et al. title: Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs link: https://peerj.com/articles/14288 last-modified: 2023-01-13 description: Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S rRNA ahead of a large-scale port deepening event. For the first time, this study established baseline bacterial community characterizations and their patterns of diversity prior to and after a maintenance dredging event. PEI samples were collected for two consecutive years 2020 (Phase I, before maintenance dredging) and 2021 (Phase II, after maintenance dredging) from PEI sediments and adjacent coral reef sediments. In spite of their proximity and tidal connections through the PEI, reef and PEI sediment microbial communities were distinct. Changes in microbial diversity within the intracoastal waterway (ICW), a route for community exchange or transfers, were the greatest after maintenance dredging occurred. Microbial diversity in reef sediments also changed after dredging, indicating potential influence from resuspended sediments due to an associated increase in trace metals and decrease in cyanobacterial diversity. Sediments were identified as a possible source of human and coral pathogens, although dredging did not affect the relative abundances of these indicator microorganisms. This study highlighted the utility and relative ease of applying current molecular ecology methods to address macroscale questions with environmental management ramifications. creator: Lauren E. Krausfeldt creator: Jose Victor Lopez creator: Catherine Margaret Bilodeau creator: Hyo Won Lee creator: Shelby L. Casali uri: https://doi.org/10.7717/peerj.14288 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Krausfeldt et al. title: Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches link: https://peerj.com/articles/14319 last-modified: 2023-01-13 description: Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene. creator: Jorge Salazar-Bravo creator: Nicolás Tinoco creator: Horacio Zeballos creator: Jorge Brito creator: Daniela Arenas-Viveros creator: David Marín-C creator: José Daniel Ramírez-Fernández creator: Alexandre R. Percequillo creator: Thomas E. Lee, Jr. creator: Sergio Solari creator: Javier Colmenares-Pinzon creator: Carlos Nivelo creator: Bernal Rodríguez Herrera creator: William Merino creator: Cesar E. Medina creator: Oscar Murillo-García creator: Ulyses F.J. Pardiñas uri: https://doi.org/10.7717/peerj.14319 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Salazar-Bravo et al. title: Immunoexpression of stem cell markers SOX-2, NANOG AND OCT4 in ameloblastoma link: https://peerj.com/articles/14349 last-modified: 2023-01-13 description: BackgroundAmeloblastoma (AME) is characterized by a locally invasive growth pattern. In an attempt to justify the aggressiveness of neoplasms, the investigation of the role of stem cells has gained prominence. The SOX-2, NANOG and OCT4 proteins are important stem cell biomarkers.MethodologyTo verify the expression of these proteins in tissue samples of AME, dentigerous cyst (DC) and dental follicle (DF), immunohistochemistry was performed and indirect immunofluorescence were performed on the human AME (AME-hTERT) cell line.ResultsRevealed expression of SOX-2, NANOG and OCT4 in the tissue samples and AME-hTERT lineage. Greater immunostaining of the studied proteins was observed in AME compared to DC and DF (p < 0.001).ConclusionsThe presence of biomarkers indicates a probable role of stem cells in the genesis and progression of AME. creator: Karolyny Martins Balbinot creator: Felippe José Almeida Loureiro creator: Giordanna Pereira Chemelo creator: Ricardo Alves Mesquita creator: Aline Maria Pereira Cruz Ramos creator: Rommel Thiago Jucá Ramos creator: Artur Luiz da Costa da Silva creator: Sílvio Augusto Fernandes de Menezes creator: Maria Sueli da Silva Kataoka creator: Sergio de Melo Alves Junior creator: João de Jesus Viana Pinheiro uri: https://doi.org/10.7717/peerj.14349 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Martins Balbinot et al. title: Variations induced by the use of unstable surface do not facilitate motor adaptation to a throwing skill link: https://peerj.com/articles/14434 last-modified: 2023-01-13 description: Induced variability by the use of unstable surfaces has been proposed to enhance proprioceptive control to deal with perturbations in the support base better. However, there is a lack of evidence about its benefits facilitating motor adaptions in upper body skills. In this experiment, practice on an unstable surface was applied to analyze the adaptations in an upper limb precision throwing skill. After a pretest, twenty-one participants were randomly allocated into two groups: one group practiced the throwing task on a stable surface and the other group practiced the same task on an unstable support base. Differences in throwing performance between pre- and post-practice were analyzed in accuracy, hand movement kinematics and variability of the throw in both surface conditions. Fuzzy entropy of the horizontal force was calculated to assess the complexity dynamics of postural sway. Participants improved their performance on the stable and the unstable surface. Induced variability using an unstable surface reduced participants’ variability and the complexity of postural sway, but it did not facilitate a superior adaptation of the throwing task. The results suggest that the variations induced by unstable surfaces would fall far from the family of specific motor solutions and would not facilitate additional motor performance of the throwing task. creator: Francisco J. Moreno creator: David Barbado creator: Carla Caballero creator: Tomás Urbán creator: Rafael Sabido uri: https://doi.org/10.7717/peerj.14434 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Moreno et al. title: Genetic characterization of hepatitis B virus genotypes among patients with chronic infection in Sulaimaniyah city, Iraq link: https://peerj.com/articles/14454 last-modified: 2023-01-13 description: BackgroundHepatitis B virus (HBV) genotypes are distributed unevenly throughout the world’s regions. The researchers’ goal in this study was to find out which HBV genotypes are now prevalent in the blood of chronic HBV patients in Iraq’s Kurdistan Region’s Sulaimaniyah governorate.MethodsGenotyping was carried out utilizing Polymerase Chain Reaction (PCR) type-specified primers. Thirty-three chronic HBV patients were included in the HBV genotyping assay. Phylogenic trees of Pre-S1/Pre S2/S genes’ nucleotide sequences were constructed using 36 HBV isolates.ResultsAll the patients had HBV genotype D. Additionally, two samples were further analyzed by sequencing and deposited in GenBank as HBV/Sul-1/2021 accession numbers MZ077051 and HBV/Sul-2/2021 accession numbers MZ077052. Phylogenic analysis indicated that the HBV isolates belong to sub-genotype D1/serotype ayw2. The HBV/Sul-2/2021 had two sequence deletion mutations from G61del-T87del, which accounted for 27 amino acid deletions, and ten other mutations were identified in the carboxylic terminus of the pre-S1 from Q104del-R113del. Accordingly, 37 amino acids were deleted in the S promoter region. Several other substitution mutations were recorded in both HBV isolates.ConclusionPatients with chronic HBV were found to have the HBV sub-genotype D1/subtype ayw2 with no mixed genotypes. HBV/Sul-1/2022, a new strain with a 37-amino acid mutation, was found to be distinct from any previously known HBV isolates. creator: Mardin Othman Abdulqadir creator: Peshnyar Muhammad Atta Rashid creator: Ali Hattem Hussain creator: Heshu Sulaiman Rahman creator: Shahow Abdulrehman Ezzaddin uri: https://doi.org/10.7717/peerj.14454 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Abdulqadir et al. title: Surviving on the edge: present and future effects of climate warming on the common frog (Rana temporaria) population in the Montseny massif (NE Iberia) link: https://peerj.com/articles/14527 last-modified: 2023-01-13 description: The Montseny massif shelters the southernmost western populations of common frogs (Rana temporaria) that live in a Mediterranean climate, one which poses a challenge for the species’ persistence in a scenario of rising temperatures. We evaluated the effect of climate change at three levels. First, we analysed if there has been an advancement in the onset of spawning period due to the increase in temperatures. Second, we analysed the impact of climatic variables on the onset of the spawning period and, third, how the distribution of this species could vary according to the predictions with regard to rising temperatures for the end of this century. From 2009 to 2021, we found there had been an increase in temperatures of 0.439 °C/decade, more than the 0.1 °C indicated by estimates for the second half of the previous century. We found an advancement in the onset of the reproduction process of 26 days/decade for the period 2009–2022, a change that has been even more marked during the last eight years, when data were annually recorded. Minimum temperatures and the absence of frost days in the week prior to the onset of the spawning period determine the start of reproduction. Predictions on habitat availability for spawning provided by climatic niche analysis for the period 2021–2100 show a potential contraction of the species range in the Montseny and, remarkably, much isolation from the neighbouring populations. creator: Albert Montori creator: Fèlix Amat uri: https://doi.org/10.7717/peerj.14527 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Montori and Amat title: Diagnostic biomarker panels of osteoarthritis: UPLC-QToF/MS-based serum metabolic profiling link: https://peerj.com/articles/14563 last-modified: 2023-01-13 description: Osteoarthritis (OA) is the most common joint disease in the world, characterized by pain and loss of joint function, which has led to a serious reduction in the quality of patients’ lives. In this work, ultrahigh performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-QToF/MS) in conjunction with multivariate pattern recognition methods and an univariate statistical analysis scheme were applied to explore the serum metabolic signatures within OA group (n = 31), HC (healthy controls) group (n = 57) and non-OA group (n = 19) for early diagnosis and differential diagnosis of OA. Based on logistic regression analysis and receiver operating characteristic (ROC) curve analysis, seven metabolites, including phosphatidylcholine (18:0/22:6), p-cresol sulfate and so on, were identified as critical metabolites for the diagnosis of OA and HC and yielded an area under the curve (AUC) of 0.978. The other panel of unknown m/z 239.091, phosphatidylcholine (18:0/18:0) and phenylalanine were found to distinguish OA from non-OA and achieved an AUC of 0.888. These potential biomarkers are mainly involved in lipid metabolism, glucose metabolism and amino acid metabolism. It is expected to reveal new insight into OA pathogenesis from changed metabolic pathways. creator: Xinxin Lin creator: Shiqi He creator: Suyu Wu creator: Tianwen Zhang creator: Sisi Gong creator: Tang Minjie creator: Yao Gao uri: https://doi.org/10.7717/peerj.14563 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lin et al. title: Occurrence of two myxosporean parasites in the gall bladder of white seabream Diplodus sargus (L.) (Teleostei, Sparidae), with the morphological and molecular description of Ceratomyxa sargus n. sp. link: https://peerj.com/articles/14599 last-modified: 2023-01-13 description: Myxosporeans are widespread cnidarian parasites that usually parasitize fish as part of their complex life cycle, thus constituting a potential threat for the aquaculture industry. White seabream Diplodus sargus (L.) is a commercially valuable sparid fish reared in Southern European aquacultures. Nonetheless, knowledge on myxosporean infections potentially harming the sustainable production of this fish is extremely limited. In this study, a myxosporean survey was conducted on D. sargus specimens reared in two Southern Portuguese fish farms. Two coelozoic myxosporeans were detected infecting the gall bladder, and are herein reported based on microscopic and molecular procedures: Ceratomyxa sargus n. sp. and Zschokkella auratis Rocha et al., 2013, previously described from reared stocks of gilthead seabream Sparus aurata in the same geographic locality. Ceratomyxa sargus n. sp. is the 12th species of the genus to be reported from Southern European sparids, reinforcing a substantial radiation of Ceratomyxa within this fish family and geographic region. SSU rRNA-based Bayesian inference and maximum likelihood analyses revealed C. sargus n. sp. positioned separately from other sparid-infecting Ceratomyxa spp. reported from Southern European countries, demonstrating that this species does not share a more immediate common ancestor with its closest relatives based on host affinity and geography. The recognition of a novel sparid-infecting lineage within the Ceratomyxa clade strengthens the contention that this genus entered sparid fish multiple times, namely in the Southern European region. The identification of Zschokkella auratis infections in D. sargus demonstrates that host shift has occurred among sparids reared in the Southern Portuguese coast. This agrees with the broad host specificity that is usually attributed to this genus, and that may be suggested to be the outcome of the capacity of the Zschokkella morphotype to undergo host shift/switch based on our findings and the limited molecular data available for this genus. Thus, a better understanding of Zschokkella host-associated diversification and dispersal mechanisms requires the increasing availability of molecular data from infections of the same species occurring in multiple hosts and geographical locations. creator: Sónia Rocha creator: Luís Filipe Rangel creator: Graça Casal creator: Ricardo Severino creator: Florbela Soares creator: Pedro Rodrigues creator: Maria João Santos uri: https://doi.org/10.7717/peerj.14599 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rocha et al. title: Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East link: https://peerj.com/articles/14623 last-modified: 2023-01-13 description: The taxonomic concept of the genus Stenocaris Sars, 1909 is uncertain because none of the synapomorphies for the species of Stenocaris are defined. Detailed comparison of previous records of Stenocaris minor (T. Scott, 1892) from different localities reveals that this species represents a species complex composed of two species, S. minor s. str. and S. minor sensu Cottarelli & Venanzetti, 1989. Because the latter species has fundamental differences in the nature of the fifth leg in females and the sexual dimorphism of the second leg in males, we propose a new species for S. minor sensu Cottarelli & Venanzetti, 1989, S. figaroloensis sp. nov. We also suggest that S. minor sensu Apostolov, 1971, S. minor sensu Marinov, 1971, and S. minor sensu Apostolov & Marinov, 1988 from the Black Sea and S. minor sensu Wilson, 1932 from North America should be relegated to species inquirenda in the genus. Taxonomic review of the morphology of all Stenocaris species indicated that the generic concept must be restricted to accommodate S. minor s. str., S. gracilis Sars, 1909, S. intermedia Itô, 1972, S. figaroloensis sp. nov., and the South Korean new species, S. marcida sp. nov., based on the synapomorphic condition of the confluent fifth leg in males. As a result of our analysis, two Stenocaris species, S. baltica Arlt, 1983 and S. pygmaea Noodt, 1955, are transferred to the genus Vermicaris Kornev & Chertoprud, 2008 as V. baltica (Arlt, 1983) comb. nov. and V. pygmaea (Noodt, 1955) comb. nov. based on the synapomorphic characters of a reduced condition of the second and fifth legs. Additionally, S. arenicola Wilson, 1932 and S. kliei (Kunz, 1938) are allocated to a new genus, Huysicaris gen. nov., mainly characterized by obvious caudal rami with a recurved dorsal spinous process and convex inner margins, as H. arenicola (Wilson, 1932) comb. nov. and H. kliei (Kunz, 1938) comb. nov. A marine interstitial harpacticoid collected from the subtidal substrate off Dok-do Island in the East Sea of South Korea is proposed as S. marcida sp. nov. and the distribution of S. intermedia, originally known from its type locality in Japanese waters only, is extended to the East Sea of Korea and Russia. We provide their detailed descriptions and illustrations and discuss the morphological characters supporting their identities. creator: Jong Guk Kim creator: Kyuhee Cho creator: Seong Myeong Yoon creator: Jimin Lee uri: https://doi.org/10.7717/peerj.14623 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kim et al. title: Chinese striped-neck turtles vocalize underwater and show differences in peak frequency among different age and sex groups link: https://peerj.com/articles/14628 last-modified: 2023-01-13 description: BackgroundTurtle vocalizations play an important role throughout their lives by expressing individual information (position, emotion, or physiological status), reflecting mating preferences, and synchronizing incubation. The Chinese striped-neck turtle (Mauremys sinensis) is one of the most widely distributed freshwater turtles in China, whose wild population is critically endangered. However, its vocalization has not been studied, which can be the basis for behavioral and ecological studies.MethodsFive different sex–age groups of turtles were recorded underwater in a soundproof room. Cluster analysis and principal component analysis for classification of Chinese striped-neck turtle calls were unreasonable. The turtle calls were manually sought using visual and aural inspection of the recordings in Raven Pro 1.5 software and classified according to differences perceived through auditory inspection and the morphological characteristics of the spectrograms. The results of similarity analysis verified the reliability of manual classification. We compared the peak frequency of the calls among different age and sex groups.ResultsWe identified ten M. sinensis call types, displayed their spectra and waveforms, and described their auditory characteristics. Most calls produced by the turtles were low-frequency. Some high-frequency call types, that are common in other turtle species were also produced. Similar to other turtles, the Chinese striped-neck turtle generates harmonic vocalizations. Courtship behaviors were observed when one of the call types occurred in the mixed-sex group. Adult females produced more high-frequency call types, and subadult males had higher vocalizations than other groups. These results provide a basis for future research on the function of vocalizations, field monitoring, and conservation of this species. creator: Lu Zhou creator: Jinhong Lei creator: Xiaofei Zhai creator: Haitao Shi creator: Jichao Wang uri: https://doi.org/10.7717/peerj.14628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhou et al. title: Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber link: https://peerj.com/articles/14637 last-modified: 2023-01-13 description: BackgroundThe calmodulin-like (CML) protein is a crucial Ca2+-binding protein that can sense and conduct the Ca2+ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable.MethodsIn this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR).ResultsForty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development-related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs. creator: Yunfen Liu creator: Feilong Yin creator: Lingyan Liao creator: Liang Shuai uri: https://doi.org/10.7717/peerj.14637 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies link: https://peerj.com/articles/14642 last-modified: 2023-01-13 description: The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms’ shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC. creator: Joyce Dutra creator: Rosimeire Gomes creator: Glen Jasper Yupanqui García creator: Danitza Xiomara Romero-Cale creator: Mariana Santos Cardoso creator: Vinicius Waldow creator: Claudia Groposo creator: Rubens N. Akamine creator: Maira Sousa creator: Henrique Figueiredo creator: Vasco Azevedo creator: Aristóteles Góes-Neto uri: https://doi.org/10.7717/peerj.14642 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Dutra et al. title: Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil link: https://peerj.com/articles/14657 last-modified: 2023-01-13 description: The construction of high-speed roads has resulted in large amounts of steep and exposed cut slopes, posing more potential hazards in areas with mountains and hills. Vegetation restoration is an effective and environmentally-friendly way to restore exposed slopes using outside soil spray seeding, though it is difficult to establish a vegetation cover. Spraying artificial soil on high and steep slopes is a challenging task as it is difficult to keep the fluid mixture on sloped surfaces. Because of these challenges, this study applied different combinations of cement and soil aggregates in artificial soil, measuring final soil properties after one growing season. Experimental results showed that there were substantial differences in all basic soil parameters and in the soil quality index after different treatments. In particular, adding 5–10% cement content could improve the adhesion of artificial soil without remarkably reducing soil quality; adding 0.09% of soil aggregate was also beneficial to soil nutrient availability. These findings indicate that the combination of cement and soil aggregates could be applied in artificial soils for the ecological restoration of steep slope vegetation. Adding cement to the soil increased the alkaline levels of the soil, so it is important to reduce artificial soil pH in the future. The application of a cement and soil aggregate should be considered in the field for the ecological restoration of slope vegetation, and the impact of this addition on slope stability and vegetation growth should be explored with further research. creator: Zhuxin Mao creator: Qian Li creator: Yuchao Wang uri: https://doi.org/10.7717/peerj.14657 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mao et al. title: Systematic identification of smORFs in domestic silkworm (Bombyx mori) link: https://peerj.com/articles/14682 last-modified: 2023-01-13 description: The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species. creator: Linrong Wan creator: Wenfu Xiao creator: Ziyan Huang creator: Anlian Zhou creator: Yaming Jiang creator: Bangxing Zou creator: Binbin Liu creator: Cao Deng creator: Youhong Zhang uri: https://doi.org/10.7717/peerj.14682 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wan et al. title: A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain) link: https://peerj.com/articles/14692 last-modified: 2023-01-13 description: Hybotidae fly species, also known as dance flies, in Cretaceous ambers have been described from Lebanon, France, Myanmar, Russia, and Canada. Here we describe Grimaldipeza coelicagen. et sp. n., and recognize another two un-named species, in Spanish amber from the middle Albian El Soplao and lower Cenomanian La Hoya outcrops. The fore tibial gland is present in the new genus, which is characteristic of the family Hybotidae. We compare Grimaldipeza coelicagen. et sp. n. with the holotypes of Trichinites cretaceusHennig, 1970 and Ecommocydromia difficilisSchlüter, 1978, and clarify some morphological details present in the latter two species. Further taxonomic placement beyond family of the here described new genus was not possible and remains incertae sedis within Hybotidae until extant subfamilies are better defined. We provide new paleoecological data of the hybotids, together with paleogeographical and life paleoenvironmental notes. A table with the known Cretaceous Hybotidae is provided. Furthermore, the La Hoya amber-bearing outcrop is described in detail, filling the information gap for this deposit. creator: Mónica M. Solórzano-Kraemer creator: Bradley J. Sinclair creator: Antonio Arillo creator: Sergio Álvarez-Parra uri: https://doi.org/10.7717/peerj.14692 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Solórzano-Kraemer et al. title: A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology link: https://peerj.com/articles/14717 last-modified: 2023-01-13 description: After its original description, the Middle Miocene gekkotan Palaeogekko risgoviensis remained an enigma for palaeontologists due to a rather poor knowledge of its osteology and relationships. Coming from a single locality in southern Germany, this gecko lived in central Europe during a period when a single gekkotan lineage (i.e., euleptine sphaerodactylids) is confidently reported to have inhabited the continent. However, it is unclear whether P. risgoviensis may represent a member of this same lineage or a second clade of Gekkota. In order to shed light on this issue, the type material of P. risgoviensis is here redescribed, refigured and extensively compared with extinct and extant geckos from Europe. A phylogenetic analysis is also conducted in order to investigate its relationships. The new observations confirm the validity of the German species as a distinct taxon, and exclude the previously-suggested chimeric status of the type material of this gecko (with the exception of a single dentary included in the type series, which clearly belong to a different lizard). Phylogenetic relationships of Palaeogekko are still unclear, though, with different positions within the gekkotan tree recovered for the taxon. Nevertheless, it is confidently supported as a non-eublepharid gekkonoid, in agreement with hypothesys presented by other scholars. creator: Andrea Villa uri: https://doi.org/10.7717/peerj.14717 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Villa title: Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study link: https://peerj.com/articles/14732 last-modified: 2023-01-13 description: BackgroundTensiomyography (TMG) is a non-invasive instrument for measuring mechanical muscle contraction characteristics and measuring the maximum displacement of the muscle belly in the radial direction with respect to the muscle and the time needed to achieve this from electrical stimulation. There have been only been a reports of TMG in healthy adults. A systematic review of TMG reported a low proportion of female participants, with a small sample size. Therefore, it is unclear whether there is a difference in TMG parameters according to sex and between dominant and non-dominant feet. Furthermore, the relationship between TMG parameters and evaluations commonly used in clinical practice has not been clarified. This study aimed to clarify the characteristics of muscle contraction of the rectus femoris using TMG according to sex among healthy college students and its relationship with muscle function evaluation, such as lower limb muscle mass and muscle strength.MethodsThis cross-sectional study included 91 healthy university students (18–24 years). Five tools were used: TMG, lower-limb muscle mass, rectus femoris thickness, isometric knee joint extension torque, and thigh circumference. Each parameter was compared by the generalized linear mixed model (GLMM) and Bonferroni’s multiple comparison test, with sex as the without-subject factor and dominant/non-dominant foot as the within-subject factor. The correlation between the TMG parameters and other parameters was examined using Pearson’s correlation coefficient for both males and females.ResultsThe results of the GLMM, in terms of the TMG parameters, an interaction was observed for maximum displacement (Dm); in the results of the multiple comparison test, Dm for the non-dominant leg was significantly lower in females than in males. A main effect and interaction were not observed for delay time (Td) and contraction time (Tc) by sex, dominant foot, or non-dominant foot. There was a main effect of sex on muscle function evaluation parameters (ρ ≤ 0.05). The correlation between TMG parameters for males and females and lower limb muscle mass, muscle thickness, joint torque, and thigh circumference were significantly correlated with some TMG parameters, lower limb muscle mass and muscle thickness (ρ ≤ 0.05). The absolute value of the correlation coefficient was low overall (0.20–0.38).ConclusionIn healthy college students, TMG parameters for the rectus femoris showed sex differences in Dm, and there was a weak correlation between TMG parameters and lower limb muscle mass. TMG parameter evaluation may indicate a different function compared to the traditional muscle function assessment used in clinical practice. When using the Dm of the TMG as an evaluation battery for the rectus femoris muscle, it is important to consider sex-related differences. creator: Yasuaki Kusumoto creator: Hayato Goto creator: Kohei Chiba creator: Sakiko Oonishi creator: Junko Tsuchiya uri: https://doi.org/10.7717/peerj.14732 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kusumoto et al. title: Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems link: https://peerj.com/articles/14445 last-modified: 2023-01-12 description: The Costa Rican Paramo is a unique ecosystem with high levels of endemism that is geographically isolated from the Andean Paramos. Paramo ecosystems occur above Montane Forests, below the permanent snow level, and their vegetation differs notably from that of adjacent Montane Forests. We compared the composition and beta diversity of blooming plant species using phenological data from functional plant groups (i.e., insect-visited, bird-visited and insect + bird-visited plants) between a Paramo and a Montane Forest site in Costa Rica and analyzed seasonal changes in blooming plant diversity between the rainy and dry seasons. Species richness was higher in the Montane Forest for all plant categories, except for insect-visited plants, which was higher in the Paramo. Beta diversity and blooming plant composition differed between both ecosystems and seasons. Differences in species richness and beta diversity between Paramo and the adjacent Montane Forest are likely the result of dispersal events that occurred during the last glacial period and subsequent isolation, as climate turned to tropical conditions after the Pleistocene, and to stressful abiotic conditions in the Paramo ecosystem that limit species establishment. Differences in blooming plant composition between both ecosystems and seasons are likely attributed to differential effects of climatic cues triggering the flowering events in each ecosystem, but phylogenetic conservatism cannot be discarded. Analyses of species composition and richness based on flowering phenology data are useful to evaluate potential floral resources for floral visitors (insects and birds) and how these resources change spatially and temporarily in endangered ecosystems such as the Paramo. creator: E. Jacob Cristóbal-Pérez creator: Gilbert Barrantes creator: Alfredo Cascante-Marín creator: Ruth Madrigal-Brenes creator: Paul Hanson creator: Eric J. Fuchs uri: https://doi.org/10.7717/peerj.14445 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cristóbal-Pérez et al. title: Primate tooth crown nomenclature revisited link: https://peerj.com/articles/14523 last-modified: 2023-01-12 description: Cusp patterning on living and extinct primate molar teeth plays a crucial role in species diagnoses, phylogenetic inference, and the reconstruction of the evolutionary history of the primate clade. These studies rely on a system of nomenclature that can accurately identify and distinguish between the various structures of the crown surface. However, studies at the enamel-dentine junction (EDJ) of some primate taxa have demonstrated a greater degree of cusp variation and expression at the crown surface than current systems of nomenclature allow. In this study, we review the current nomenclature and its applicability across all the major primate clades based on investigations of mandibular crown morphology at the enamel-dentine junction revealed through microtomography. From these observations, we reveal numerous new patterns of lower molar accessory cusp expression in primates. We highlight numerous discrepancies between the expected patterns of variation inferred from the current academic literature, and the new patterns of expected variation seen in this study. Based on the current issues associated with the crown nomenclature, and an incomplete understanding of the precise developmental processes associated with each individual crown feature, we introduce these structures within a conservative, non-homologous naming scheme that focuses on simple location-based categorisations. Until there is a better insight into the developmental and phylogenetic origin of these crown features, these categorisations are the most practical way of addressing these structures. Until then, we also suggest the cautious use of accessory cusps for studies of taxonomy and phylogeny. creator: Simon A. Chapple creator: Matthew M. Skinner uri: https://doi.org/10.7717/peerj.14523 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chapple and Skinner title: Models of ultrasonic radiomics and clinical characters for lymph node metastasis assessment in thyroid cancer: a retrospective study link: https://peerj.com/articles/14546 last-modified: 2023-01-12 description: BackgroundPreoperative prediction of cervical lymph node metastasis in papillary thyroid carcinoma provided a basis for tumor staging and treatment decision. This study aimed to investigate the utility of machine learning and develop different models to preoperatively predict cervical lymph node metastasis based on ultrasonic radiomic features and clinical characteristics in papillary thyroid carcinoma nodules.MethodsData from 400 papillary thyroid carcinoma nodules were included and divided into training and validation group. With the help of machine learning, clinical characteristics and ultrasonic radiomic features were extracted and selected using randomforest and least absolute shrinkage and selection operator regression before classified by five classifiers. Finally, 10 models were built and their area under the receiver operating characteristic curve, accuracy, sensitivity, specificity, positive predictive value and negative predictive value were measured.ResultsAmong the 10 models, RF-RF model revealed the highest area under curve (0.812) and accuracy (0.7542) in validation group. The top 10 variables of it included age, seven textural features, one shape feature and one first-order feature, in which eight were high-dimensional features.ConclusionsRF-RF model showed the best predictive performance for cervical lymph node metastasis. And the importance features selected by it highlighted the unique role of higher-dimensional statistical methods for radiomics analysis. creator: Hui Zhu creator: Bing Yu creator: Yanyan Li creator: Yuhua Zhang creator: Juebin Jin creator: Yao Ai creator: Xiance Jin creator: Yan Yang uri: https://doi.org/10.7717/peerj.14546 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhu et al. title: The impact of hypertension on the prognosis of patients with hypertrophic cardiomyopathy: a single-center retrospective study link: https://peerj.com/articles/14614 last-modified: 2023-01-12 description: BackgroundHypertrophic cardiomyopathy (HCM) and hypertension coexist fairly frequently in clinical practice. However, the evidence about the impact of hypertension on the prognosis of HCM is limited. The present study aims to investigate the impact of hypertension on the prognosis of HCM patients.MethodsA total of 468 HCM patients were enrolled, and patients were divided into hypertension group (31.8%) and non-hypertension group (68.2%). The primary study endpoint was HCM-related death, consisting of heart failure (HF)-related death, stroke-related death and sudden cardiac death (SCD). Associations between hypertension and HCM-related death were analyzed by Cox regression models with the use of propensity score matching (PSM) as primary analysis.ResultsThere were 55 HCM-related death during a median follow-up time of 4.6 years, and the mortality rate was 2.53 per 100 person years. Kaplan-Meier analysis based on the crude cohort or PSM cohort revealed no significant difference regarding the HCM-related death between the two groups. In the crude cohort, both univariable and multivariable Cox regression analysis indicated that hypertension was not significantly associated with HCM-related death with hazard ratios (HR) at 0.74 (95% CI [0.40–1.36], p value: 0.329) and 0.77 (95% CI [0.35–1.71], p value: 0.521), respectively. Similarly, no strong evidence for an association was observed between hypertension and HCM-related death in the PSM cohort with unadjusted HR at 0.90 (95% CI [0.34–2.41]; p value: 0.838) and adjusted HR at 0.77 (95% CI [0.35–1.71]; p value: 0.521), respectively. Other propensity score methods, including overlap weighting and inverse probability treatment weighting demonstrated similar results. Sensitivity analysis also indicated that the concomitant hypertension did not significantly increase the risk of HF-related death, stroke-related death or SCD in HCM patients.ConclusionHCM-related death did not significantly differ between hypertension and non-hypertension groups, suggesting a negative impact of hypertension on the clinical prognosis of HCM patients. creator: Ziqiong Wang creator: Yi Zheng creator: Haiyan Ruan creator: Liying Li creator: Muxin Zhang creator: Linjia Duan creator: Sen He uri: https://doi.org/10.7717/peerj.14614 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Development and validation of a novel risk model in newly diagnosed de novo bone metastatic prostate cancer (M1b): a retrospective study link: https://peerj.com/articles/14615 last-modified: 2023-01-12 description: BackgroundPrevious studies suggested that bone metastasis has a significant effect on the time of progression to metastatic castration-resistant prostate cancer (CRPC) for newly diagnosed de novo bone metastatic hormone-sensitive prostate cancer (mHSPC). Nevertheless, the effect of different bone metastasis sites was not fully evaluated. This study aimed to develop and validate a novel bone metastatic risk model.MethodsWe enrolled 122 patients who were newly diagnosed with de novo bone metastatic prostate cancer following primary androgen deprivation based therapy at our institution from January 2008 to June 2021. The metastatic bone sites were classified into six sites: skull; cervical, thoracic, and lumbar vertebrae; chest (ribs and sternum); pelvis; upper limbs; and lower limbs. We calculated the bone metastatic score (BMS) for each site: 0 points were assigned for non-metastasis and 1 point was assigned for metastasis. The X-tile was adopted to acquire optimal cutoff points of BMS. We defined high-risk group (HRG) as BMS ≥ 3 and low-risk group (LRG) as BMS < 3. The new bone risk stratification was validated by calculating the area under the receiver operating characteristic curve (AUC). Subsequently, the relevant clinical prognostic variables were added to construct a predictive nomogram for predicting CRPC.ResultsThe median patient age was 73 years. Most patients had Gleason score ≤8 (93 cases, 76.2%). The median follow-up duration was 11.5 months (range: 2–92 months). Eighty-six patients progressed to CRPC during the follow-up. The most common bone metastatic site was the pelvis (90.2%). The median BMS was 4. Seventy-six patients had HRG, while forty-six had LRG. The 1-, 2-, and 3-year AUCs for H/LRG were 0.620, 0.754, and 0.793, respectively. The HRG was associated with earlier time to CRPC. A nomogram based on four parameters (Gleason score, H/LRG, prostate-specific antigen [PSA] nadir, and time to PSA nadir) was developed to predict CRPC. Internal validation using bootstrapping demonstrated good accuracy for predicting the CRPC (C-index: 0.727). The calibration analysis demonstrated that the model performed well.ConclusionWe established a novel H/LRG risk model for newly diagnosed de novo bone metastatic prostate cancer, which provided evidence to support clinical decision-making. creator: Yang Zhang creator: Junqi Wang creator: Li Ding creator: Yuxin Zheng creator: Chuang Wu creator: Kun Wang creator: Wentao Xia creator: Peng Ge uri: https://doi.org/10.7717/peerj.14615 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Modulation of lower limb muscles and trajectory correction in the bipedal stance during visual perturbation link: https://peerj.com/articles/14631 last-modified: 2023-01-12 description: The ability to actively track posture using visual targets as indicators is important for improving impairments in whole-body coordination, and accurate visual feedback on tasks is considered effective in promoting sensory-motor integration and behavioral success. In the present study, we examined inter- and intramuscular modulation between the two lower limbs in response to visual perturbation. Sixteen healthy young subjects (age: 21.3 ± 0.7 years) were asked to move their weight back and forth while tracking a visual target displayed on a monitor in front of them for 30 s. Three types of target movements were examined: a sinusoidal wave (i.e., a predictable pattern), more complex patterns (random), and no movement (stationary). Electromyography (EMG) was used to assess intra- and intermuscular coherence modulation of the plantar flexor muscles (right and left soleus and right and left medial gastrocnemius). The ability to adjust posture to follow the target signal was assessed using a stabilometer. Inter- and intramuscular coherence increased during the visual perturbation task compared to the stationary task. In addition, left-right differences in lower limb modulation were observed during the visual perturbation task. Furthermore, interlimb coherence was related to the motor accuracy of tracking. The muscles of both lower limbs cooperated in response to visual perturbation, suggesting that these muscles control visually induced anteroposterior postural sway. Since such visual perturbations promote coordination between both lower extremities, this relationship may indicate the potential for rehabilitation training to help individuals acquire and improve the motor functions necessary to efficiently and stably perform activities of daily living. creator: Tadayoshi Minamisawa creator: Noboru Chiba creator: Eizaburo Suzuki uri: https://doi.org/10.7717/peerj.14631 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Minamisawa et al. title: Heat treatment-induced autophagy promotes breast cancer cell invasion and metastasis via TGF-β2-mediated epithelial-mesenchymal transitions link: https://peerj.com/articles/14640 last-modified: 2023-01-12 description: BackgroundInsufficient thermal ablation can accelerate malignant behaviors and metastases in some solid tumors, and epithelial-mesenchymal transition (EMT) and autophagy are involved in tumor metastasis. It has been found that TGF-β2 which belongs to the family of transforming growth factors often associated with cancer cell invasiveness and EMT. However, whether the interactions between autophagy and TGF-β2 induce EMT in breast cancer (BC) cells following insufficient microwave ablation (MWA) remains unclear.MethodsBC cells were treated with sublethal heat treatment to simulate insufficient MWA, and the effects of heat treatment on the BC cell phenotypes were explored. CCK-8, colony formation, flow cytometry, Transwell, and wound healing assays were performed to evaluate the influence of sublethal heat treatment on the proliferation, apoptosis, invasion, and migration of BC cells. Western blotting, real-time quantitative PCR, immunofluorescence, and transmission electron microscopy were carried out to determine the changes in markers associated with autophagy and EMT following sublethal heat treatment.ResultsResults showed that heat treatment promoted the proliferation of surviving BC cells, which was accompanied by autophagy induction. Heat treatment-induced autophagy up-regulated TGF-β2/Smad2 signaling and promoted EMT phenotype, thereby enhancing BC cells’ migration and invasion abilities. An increase or decrease of TGF-β2 expression resulted in the potentiation and suppression of autophagy, as well as the enhancement and abatement of EMT. Autophagy inhibitors facilitated apoptosis and repressed proliferation of BC cells in vitro, and thwarted BC cell tumor growth and pulmonary metastasis in vivo.ConclusionHeat treatment-induced autophagy promoted invasion and metastasis via TGF-β2/Smad2-mediated EMTs. Suppressing autophagy may be a suitable strategy for overcoming the progression and metastasis of residual BC cells following insufficient MWA. creator: Zhennan Li creator: Cheng Lu creator: Fengliang Wang creator: Haowei Guo creator: Zhipeng Wang creator: Hong Yin creator: Jian Li uri: https://doi.org/10.7717/peerj.14640 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: The circadian calling activity of a lebinthine cricket with high-frequency calls is unaffected by cicada choruses in the day link: https://peerj.com/articles/14641 last-modified: 2023-01-12 description: BackgroundMany factors can influence circadian rhythms in animals. For acoustically communicating species, both abiotic cues (such as light and temperature) and biotic cues (such as the activity of other animals), can influence the timing of signalling activity. Here we compare the 24-h singing activity of the cricket Lebinthus luae in the laboratory and field to assess whether the presence of other singing insects influences circadian rhythm.MethodsAcoustic monitors were placed in four localities in Singapore and the number of L. luae calls were counted for 10 min of each hour. Individuals from the same localities were captured and recorded in the laboratory in silence but with similar abiotic conditions (temperature and light cycle) as they experience in the field, and the number of calls over 24 h was quantified.ResultsThe 24-h pattern of L. luae singing was not significantly different between laboratory and field recordings. Singing activity peaked in the morning, with a secondary peak in the afternoon and a smaller peak at night. In the field, L. luae sang in the same locations and at the same time as diurnally singing cicadas, suggesting that the sympatric cicada chorus did not affect the circadian rhythm of communication in this species. Acoustic niche partitioning could potentially explain the ability of this cricket to call alongside cicadas: L. luae sings at higher frequencies than sympatric cicadas, unlike nocturnally singing cricket species that overlap with cicadas in frequency. creator: Ming Kai Tan creator: Tony Robillard creator: Hannah ter Hofstede uri: https://doi.org/10.7717/peerj.14641 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tan et al. title: Modeling geographic distribution of arbuscular mycorrhizal fungi from molecular evidence in soils of Argentinean Puna using a maximum entropy approach link: https://peerj.com/articles/14651 last-modified: 2023-01-12 description: The biogeographic region of Argentinean Puna mainly extends at elevations higher than 3,000 m within the Andean Plateau and hosts diverse ecological communities highly adapted to extreme aridity and low temperatures. Soils of Puna are typically poorly evolved and geomorphology is shaped by drainage networks, resulting in highly vegetated endorheic basins and hypersaline basins known as salar or salt flats. Local communities rely on soil fertility for agricultural practices and on pastures for livestock rearing. From this perspective, investigating the scarcely explored microbiological diversity of these soils as indicators of ecosystems functioning might help to predict the fragility of these harsh environments. In this study we collected soil samples from 28 points, following a nested design within three different macro-habitats, i.e., Puna grassland, hypersaline salar and family-run crop fields. Total fungi and arbuscular mycorrhizal fungi (AMF) occurrence were analyzed using eDNA sequencing. In addition, the significance of soil salinity and organic matter content as significant predictors of AMF occurrence, was assessed through Generalized Linear Mixed Modeling. We also investigated whether intensive grazing by cattle and lama in Puna grasslands may reduce the presence of AMF in these highly disturbed soils, driving or not major ecological changes, but no consistent results were found, suggesting that more specific experiments and further investigations may address the question more specifically. Finally, to predict the suitability for AMF in the different macro-habitats, Species Distribution Modeling (SDM) was performed within an environmental coherent area comprising both the phytogeographic regions of Puna and Altoandino. We modeled AMF distribution with a maximum entropy approach, including bioclimatic and edaphic predictors and obtaining maps of environmental suitability for AMF within the predicted areas. To assess the impact of farming on AMF occurrence, we set a new series of models excluding the cultivated Chaupi Rodeo samples. Overall, SDM predicted a lower suitability for AMF in hypersaline salar areas, while grassland habitats and a wider temperature seasonality range appear to be factors significantly related to AMF enrichment, suggesting a main role of seasonal dynamics in shaping AMF communities. The highest abundance of AMF was observed in Vicia faba crop fields, while potato fields yielded a very low AMF occurrence. The models excluding the cultivated Chaupi Rodeo samples highlighted that if these cultivated areas had theoretically remained unmanaged habitats of Puna and Altoandino, then large-scale soil features and local bioclimatic constraints would likely support a lower suitability for AMF. Using SDM we evidenced the influence of bioclimatic, edaphic and anthropic predictors in shaping AMF occurrence and highlighted the relevance of considering human activities to accurately predict AMF distribution. creator: Davide Nepote Valentin creator: Samuele Voyron creator: Florencia Soteras creator: Hebe Jorgelina Iriarte creator: Andrea Giovannini creator: Erica Lumini creator: Mónica A. Lugo uri: https://doi.org/10.7717/peerj.14651 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Nepote Valentin et al. title: Genome-wide identification of MAXs genes for strigolactones synthesis/signaling in solanaceous plants and analysis of their potential functions in tobacco link: https://peerj.com/articles/14669 last-modified: 2023-01-12 description: The more axillary growth (MAX) gene family is a group of key genes involved in the synthesis and signal transduction of strigolactones (SLs) in plants. Although MAX genes play vital roles in plant growth and development, characterization of the MAX gene family has been limited in solanaceous crops, especially in tobacco. In this study, 74 members of the MAX family were identified in representative Solanaceae crops and classified into four groups. The physicochemical properties, gene structure, conserved protein structural domains, cis-acting elements, and expression patterns could be clearly distinguished between the biosynthetic and signal transduction subfamilies; furthermore, MAX genes in tobacco were found to be actively involved in the regulation of meristem development by responding to hormones. MAX genes involved in SL biosynthesis were more responsive to abiotic stresses than genes involved in SL signaling. Tobacco MAX genes may play an active role in stress resistance. The results of this study provide a basis for future in-depth analysis of the molecular mechanisms of MAX genes in tobacco meristem development and stress resistance. creator: Lixianqiu Wang creator: Bingjie Li creator: Changbo Dai creator: Anming Ding creator: Weifeng Wang creator: Haoqi Shi creator: Mengmeng Cui creator: Yuhe Sun creator: Jing Lv uri: https://doi.org/10.7717/peerj.14669 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe link: https://peerj.com/articles/14684 last-modified: 2023-01-12 description: When the wastewater volume exceeds the sewer pipe capacity during extreme rainfall events, untreated sewage discharges directly into rivers as combined sewer overflow (CSO). To compare the impacts of CSOs and stormwater on urban waterways, we assessed physicochemical water quality, the 16S rRNA gene-based bacterial community structure, and EcoPlate-based microbial functions during rainfall periods in an urban waterway before and after a stormwater storage pipe was commissioned. A temporal variation analysis showed that CSOs have significant impacts on microbial function and bacterial community structure, while their contributions to physicochemical parameters, bacterial abundance, and chlorophyll a were not confirmed. Heat map analysis showed that the impact of CSO on the waterway bacterial community structure was temporal and the bacterial community composition in CSO is distinct from that in sewers. Hierarchical clustering analysis revealed that the waterway physicochemical water qualities, bacterial community composition, and microbial community function were distinguishable from the upper reach of the river, rather than between CSO and stormwater. Changes in the relative abundance of tetracycline resistance (tet) genes—especially tet(M)—were observed after CSOs but did not coincide with changes in the microbial community composition, suggesting that the parameters affecting the microbial community composition and relative abundance of tet genes differ. After pipe implementation, however, stormwater did not contribute to the abundance of tet genes in the waterway. These results indicate that CSO-induced acute microbial disturbances in the urban waterway were alleviated by the implementation of a stormwater storage pipe and will support the efficiency of storage pipe operation for waterway management in urban areas. creator: Kazuaki Matsui creator: Takeshi Miki uri: https://doi.org/10.7717/peerj.14684 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Matsui and Miki title: Comprehensive genomic signature of pyroptosis-related genes and relevant characterization in hepatocellular carcinoma link: https://peerj.com/articles/14691 last-modified: 2023-01-12 description: BackgroundCurrently, the most predominant type of liver cancer is hepatocellular carcinoma (HCC), which is also the fourth leading cause of cancer-related death in the global population. Pyroptosis is an emerging form of cell death that affects the prognosis of cancer patients by modulating tumor cell migration, proliferation and invasion. However, the evaluation of pyroptosis in the prognosis of HCC is still insufficient.MethodsA total of 365 HCC patients from the TCGA-LIHC cohort were classified into two distinct subtypes using consensus clustering of pyroptosis-related genes (PRGs). Following univariate Cox analysis of differentially expressed genes between subtypes, we established a prognostic model (PRGs-score, PRGS) by LASSO Cox analysis. We further tested the predictive power of the prognostic model in the ICGC (LIRI-JP) and GEO (GSE14520) cohorts. The tumor microenvironment (TME) was studied using the CIBERSORT. The enrichment scores for immune cells and immune functions in low- and high-PRGS groups were assessed using ssGSEA. The IMvigor210 cohort was used to investigate the immunotherapy efficacy. Furthermore, we validated the expression of prognostic genes in PRGS by RT-qPCR in vitro.ResultsThe subtyping of HCC based on PRGs exhibited distinct clinical characteristics. We developed a prognostic model PRGS by differentially expressed genes between different subtypes. The results showed that PRGS could well forecast the survival of HCC patients in different cohorts and was associated with the immune microenvironment. Moreover, PRGS was considered to be an independent prognostic risk factor and superior to other pyroptosis-related signatures. Low-PRGS implied greater immune cell infiltration and better overall survival with immunotherapy. The results of RT-qPCR also showed that prognostic genes were significantly dysregulated in HCC.ConclusionsPRGS has promising application in forecasting the prognosis of HCC patients, and its relationship with the immune microenvironment provides a basis for the subsequent treatment and research of HCC. creator: Sheng Wang creator: Songsen Gao creator: Liang Shan creator: Xueyi Qian creator: Jiajie Luan creator: Xiongwen Lv uri: https://doi.org/10.7717/peerj.14691 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Arsenic and mercury tolerant rhizobacteria that can improve phytoremediation of heavy metal contaminated soils link: https://peerj.com/articles/14697 last-modified: 2023-01-12 description: BackgroundMining deposits often contain high levels of toxic elements such as mercury (Hg) and arsenic (As) representing strong environmental hazards. The purpose of this study was the isolation for plant growth promoting bacteria (PGPBs) that can improve phytoremediation of such mine waste deposits.MethodsWe isolated native soil bacteria from the rhizosphere of plants of mine waste deposits and agricultural land that was previously mine tailings from Tlalpujahua Michoacán, Mexico, and were identified by their fatty acid profile according to the MIDI Sherlock system. Plant growth promoting traits of all bacterial isolates were examined including production of 3-indoleacetic acid (IAA), siderophores, biofilm formation, and phosphate solubilization. Finally, the response of selected bacteria to mercury and arsenic was examined an in-vitro assay.ResultsA total 99 bacterial strains were isolated and 48 identified, representing 34 species belonging to 23 genera. Sixty six percent of the isolates produced IAA of which Pseudomonas fluorescens TL97 produced the most. Herbaspirillum huttiense TL36 performed best in terms of phosphate solubilization and production of siderophores. In terms of biofilm formation, Bacillus atrophaeus TL76 was the best.DiscussionMost of the bacteria isolates showed high level of tolerance to the arsenic (as HAsNa2O4 and AsNaO2), whereas most isolates were susceptible to HgCl2. Three of the selected bacteria with PGP traits Herbispirillum huttiense TL36, Klebsiella oxytoca TL49 and Rhizobium radiobacter TL52 were also tolerant to high concentrations of mercury chloride, this might could be used for restoring or phytoremediating the adverse environmental conditions present in mine waste deposits. creator: Daniel Rojas-Solis creator: John Larsen creator: Roberto Lindig-Cisneros uri: https://doi.org/10.7717/peerj.14697 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Rojas-Solis et al. title: Effects of high-intensity interval exercise on cardiac troponin elevation when comparing with moderate-intensity continuous exercise: a systematic review and meta-analysis link: https://peerj.com/articles/14508 last-modified: 2023-01-11 description: BackgroundThis systematic review and meta-analysis aimed to compare the effects of high-intensity interval exercise (HIIE) with different recovery modes versus moderate-intensity continuous exercise (MICE) on cardiac troponin (cTn) elevation.MethodologyA literature search was conducted in four databases: Scopus, PubMed, EBSCO and Web of Science from January 2010 to June 2022. The articles were screened, evaluated for quality before data were extracted. The review protocol was registered at PROSPERO (CRD42021245649). Standardized mean differences (SMD) of peak cTn were analyzed with a 95% confidence interval (95% CI) using Revman 5.4 software.ResultsSix studies satisfied the inclusion criteria with a total of 92 and 79 participants for HIIE and MICE, respectively. Overall, there was no significant difference between HIIE and MICE in the elevation of cardiac troponin T (SMD: 0.41 [95% CI [−0.21, 1.03]], p = 0.20, I2 = 77%, p for heterogeneity <0.01). In subgroup analysis, HIIE with passive recovery elicits greater release of cardiac troponin T than MICE (SMD: 0.85 [95% CI [0.44, 1.27]], p < 0.01, I2 = 32%, p for heterogeneity = 0.22). Changes of cardiac troponin T (SMD: 0.41 [95% CI [−0.21, 1.03]], p = 0.20, I2 = 77%, p for heterogeneity < 0.01) after HIIE with active recovery were not significantly different from those of MICE.ConclusionsThere was no significant difference between HIIE and MICE in the elevation of cardiac troponin T. However, HIIE with passive recovery elicited more cardiac troponin T elevation than MICE, which should be considered when developing exercise programs. creator: Shuoqi Li creator: Shazlin Shaharudin creator: Rafel Cirer-Sastre creator: Feifei Li creator: Faizal Abdul Manaf creator: Mohd Faiz Mohd Shukri uri: https://doi.org/10.7717/peerj.14508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species link: https://peerj.com/articles/14526 last-modified: 2023-01-11 description: Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in this group is S. mystax, and its phenotypic diversity has been recognized as three subspecies—S. mystax mystax, S. mystax pileatus and S. mystax pluto—with non-overlapping geographic distributions. In this sense, we carried out an extensive field survey in their distribution areas and used a framework of taxonomic hypothesis testing of genomic data combined with an integrative taxonomic decision-making framework to carry out a taxonomic revision of S. mystax. Our tests supported the existence of three lineages/species. The first species corresponds to Saguinus mystax mystax from the left bank of the Juruá River, which was raised to the species level, and we also discovered and described animals from the Juruá–Tefé interfluve previously attributed to S. mystax mystax as a new species. The subspecies S. m. pileatus and S. m. pluto are recognized as a single species, under a new nomenclatural combination. However, given their phenotypic distinction and allopatric distribution, they potentially are a manifestation of an early stage of speciation, and therefore we maintain their subspecific designations. creator: Gerson Paulino Lopes creator: Fábio Rohe creator: Fabrício Bertuol creator: Erico Polo creator: Ivan Junqueira Lima creator: João Valsecchi creator: Tamily Carvalho Melo Santos creator: Stephen D. Nash creator: Maria Nazareth Ferreira da Silva creator: Jean P. Boubli creator: Izeni Pires Farias creator: Tomas Hrbek uri: https://doi.org/10.7717/peerj.14526 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lopes et al. title: Senile dementia and psychiatric stigma among community health service providers and relatives of diagnosed and suspected dementia patients: a cross-sectional study link: https://peerj.com/articles/14613 last-modified: 2023-01-11 description: BackgroundThe number of people suffering from dementia is increasing rapidly in China. Early identification, referral, and intervention for dementia patients within communities are important to public health. However, these measures could be impacted by misconceptions about dementia and associated psychiatric stigma from community health professionals and relatives of dementia patients.MethodsA cross-sectional survey was conducted on 249 participants, which included community doctors, community nurses, and relatives of diagnosed and suspected dementia patients in Guiyang, China. Participants were recruited through convenient sampling. The Chinese version of Dementia Knowledge Assessment Scale (DKAS) and the Perceived Psychiatric Stigma Scale (PPSS) were used to evaluate the participants’ knowledge of dementia and dementia-related psychiatric stigma.ResultsA total of 249 participants completed the questionnaire. The participants had moderate overall knowledge of dementia and the associated psychiatric stigma. Participants who were ≥45 years old, had a low level of education, had a low monthly income, or gained knowledge of dementia through non-media channels had lower awareness of dementia and stronger psychiatric stigma. In the “Communication & behavior” subscale of DKAS, all participants had a low level of awareness. Relatives of diagnosed and suspected dementia patients had higher total PPSS and “Marital preclusion” subscale scores than community doctors and nurses but lower psychiatric stigma based on the PPSS “Self-deprecation” subscale score.ConclusionsDespite their profession, community doctors and nurses did not show an absolute advantage over relatives of diagnosed and suspected dementia patients in the dementia knowledge, and they even showed higher psychiatric stigma in some subscales. The self-deprecation subscale is related to the identification with negative labels such as “people with a mental illness are the weak”. This study shows that reducing stigma on the “Self-deprecation” subscale should be a core component of training and educational programs targeted at improving dementia knowledge among community health service providers. creator: Qiwen Zhang creator: Jing Deng creator: Huanyue Luo creator: Li Wang uri: https://doi.org/10.7717/peerj.14613 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Anatomical and physiological responses of Aechmea blanchetiana (Bromeliaceae) induced by silicon and sodium chloride stress during in vitro culture link: https://peerj.com/articles/14624 last-modified: 2023-01-11 description: Salt stress is one of the most severe abiotic stresses affecting plant growth and development. The application of silicon (Si) is an alternative that can increase the tolerance of plants to various types of biotic and abiotic stresses. The objective was to evaluate salt stress’s effect in vitro and Si’s mitigation potential on Aechmea blanchetiana plants. For this purpose, plants already established in vitro were transferred to a culture medium with 0 or 14 µM of Si (CaSiO3). After growth for 30 days, a stationary liquid medium containing different concentrations of NaCl (0, 100, 200, or 300 µM) was added to the flasks. Anatomical and physiological analyses were performed after growth for 45 days. The plants cultivated with excess NaCl presented reduced root diameter and effective photochemical quantum yield of photosystem II (PSII) (ΦPSII) and increased non-photochemical dissipation of fluorescence (qN). Plants that grew with the presence of Si also had greater content of photosynthetic pigments and activity of the enzymes of the antioxidant system, as well as higher values of maximum quantum yield of PSII (FV/FM), photochemical dissipation coefficient of fluorescence (qP) and fresh weight bioaccumulation of roots and shoots. The anatomical, physiological and biochemical responses, and growth induced by Si mitigated the effect of salt stress on the A. blanchetiana plants cultivated in vitro, which can be partly explained by the tolerance of this species to grow in sandbank (Restinga) areas. creator: Rosiane Cipriano creator: João Paulo Rodrigues Martins creator: Lorenzo Toscano Conde creator: Mariela Mattos da Silva creator: Diolina Moura Silva creator: Andreia Barcelos Passos Lima Gontijo creator: Antelmo Ralph Falqueto uri: https://doi.org/10.7717/peerj.14624 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cipriano et al. title: Mass media pressure on physical build, psychological well-being and physical-healthy profile. An explanatory model in adulthood link: https://peerj.com/articles/14652 last-modified: 2023-01-11 description: BackgroundThe pressure exerted by the media on mental image, psychological well-being and the physical-dietary sphere is of vital interest in understanding human behavioral patterns at different stages of development. The present research reflects the objectives of developing an explanatory model of the associations between media pressure and physical build on psychological well-being, physical activity and the Mediterranean diet and testing the structural model using a multi-group model according to participants’ stage of adulthood development.MethodsA descriptive, non-experimental, cross-sectional study was carried out on a sample of 634 participants aged between 18 and 65 years (35.18 ± 9.68). An ad hoc socio-demographic questionnaire, Sociocultural Attitudes Towards Appearance Questtionnaire-4, Psychological Well-Being Scale, Predimed questtionnaire and International Physical Activity Questionnaire-Short Form were used for data collection.ResultsParticipants in early adulthood show higher scores for media pressure and for pressure on physical build. It is also observed that participants in middle adulthood show higher scores for psychological well-being and physical activity levels.ConclusionsIn conclusion, it can be seen that there are a large number of physical, physical-health and psychological differences in each of the phases of adulthood. creator: Eduardo Melguizo-Ibáñez creator: Gabriel González-Valero creator: Georgian Badicu creator: Wilhelm Robert Grosz creator: Marius Bazgan creator: Pilar Puertas Molero uri: https://doi.org/10.7717/peerj.14652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Melguizo-Ibáñez et al. title: Transcriptome and metabolome response of eggplant against Ralstonia solanacearum infection link: https://peerj.com/articles/14658 last-modified: 2023-01-11 description: Bacterial wilt is a soil-borne disease that represents ubiquitous threat to Solanaceae crops. The whole-root transcriptomes and metabolomes of bacterial wilt-resistant eggplant were studied to understand the response of eggplant to bacterial wilt. A total of 2,896 differentially expressed genes and 63 differences in metabolites were identified after inoculation with Ralstonia solanacearum. Further analysis showed that the biosynthesis pathways for phytohormones, phenylpropanoids, and flavonoids were altered in eggplant after inoculation with R. solanacearum. The results of metabolomes also showed that phytohormones played a key role in eggplant response to bacterial wilt. Integrated analyses of the transcriptomic and metabolic datasets indicated that jasmonic acid (JA) content and gene involved in the JA signaling pathway increased in response to bacterial wilt. These findings remarkably improve our understanding of the mechanisms of induced defense response in eggplant and will provide insights intothe development of disease-resistant varieties of eggplant. creator: Xi Ou Xiao creator: Wenqiu Lin creator: Enyou Feng creator: Xiongchang Ou uri: https://doi.org/10.7717/peerj.14658 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xiao et al. title: Distribution, conservation status and proposed measures for preservation of Radiodiscus microgastropods in Chile link: https://peerj.com/articles/14027 last-modified: 2023-01-10 description: The genus Radiodiscus includes minute terrestrial snails occurring throughout the American continent. We assessed the conservation status of eight poorly known Chilean Radiodiscus species using the International Union for Conservation of Nature (IUCN) and NatureServe categories and criteria. Under the IUCN guidelines the species were assessed using the Criterion B of geographic range, which considers the extent of occurrence (EOO) and area of occupancy (AOO) as subcriteria. For NatureServe we used these two parameters plus the number of occurrences, ecological viability, and threats. Considering species rarity and possible sampling bias, we also used ecological niche modeling to determine climate and environmental tolerances and predict potential species distributions analyzing bioclimatic and geographical layers. Radiodiscus australis, R. coarctatus and R. quillajicola were listed as Critically Endangered by IUCN and NatureServe standards; R. coppingeri, R. flammulatus, R. magellanicus and R. villarricensis as Endangered by both methods; while R. riochicoensis as Endangered by IUCN standards and Vulnerable by NatureServe standards. Niche modeling results indicated that Radiodiscus species respond to different environmental conditions and that the predicted distribution areas contain suitable habitats beyond the current ranges, which may be helpful for future management plans. Nature-based sport tourism, forestry activities, urbanization, roads, pollution, mining, forest fires, livestock, volcanism, tsunamis, soil erosion and introduced species are among the major threats affecting these snails. Based on the low number of occurrences and the threats identified, the most at-risk species are R. coarctatus and R. quillajicola (one record), R. australis (two records) and R. villarricensis (three records); the latter two lacking occurrences within protected areas. Compiling our findings, we propose a list of actions to preserve Chilean Radiodiscus species. creator: Gonzalo A. Collado creator: Rodrigo B. Salvador creator: Marcela Vidal creator: Fernanda Parra Aravena creator: Vannia Delgado creator: Cristian Torres-Díaz uri: https://doi.org/10.7717/peerj.14027 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Collado et al. title: RNA-Seq and genetic diversity analysis of faba bean (Vicia faba L.) varieties in China link: https://peerj.com/articles/14259 last-modified: 2023-01-10 description: BackgroundFaba bean (Vicia faba L) is one of the most important legumes in the world. However, there is relatively little genomic information available for this species owing to its large genome. The lack of data impedes the discovery of molecular markers and subsequent genetic research in faba bean. The objective of this study was to analyze the faba bean transcriptome, and to develop simple sequence repeat (SSR) markers to determine the genetic diversity of 226 faba bean varieties derived from different regions in China.MethodsFaba bean varieties with different phenotype were used in transcriptome analysis. The functions of the unigenes were analyzed using various database. SSR markers were developed and the polymorphic markers were selected to conduct genetic diversity analysis.ResultsA total of 92.43 Gb of sequencing data was obtained in this study, and 133,487 unigene sequences with a total length of 178,152,541 bp were assembled. A total of 5,200 SSR markers were developed on the basis of RNA-Seq analysis. Then, 200 SSR markers were used to evaluate polymorphisms. In total, 103 (51.5%) SSR markers showed significant and repeatable bands between different faba bean varieties. Clustering analysis revealed that 226 faba bean materials were divided into five groups. Genetic diversity analysis revealed that the relationship between different faba beans in China was related, especially in the same region. These results provided a valuable data resource for annotating genes to different categories and developing SSR markers. creator: Wanwei Hou creator: Xiaojuan Zhang creator: Yuling Liu creator: Yujiao Liu creator: Bai li Feng uri: https://doi.org/10.7717/peerj.14259 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hou et al. title: Flexor hallucis brevis motor unit behavior in response to moderate increases in rate of force development link: https://peerj.com/articles/14341 last-modified: 2023-01-10 description: BackgroundStudies on motor unit behaviour with varying rates of force development have focussed predominantly on comparisons between slow and ballistic (i.e., very fast) contractions. It remains unclear how motor units respond to less extreme changes in rates of force development. Here, we studied a small intrinsic foot muscle, flexor hallucis brevis (FHB) where the aim was to compare motor unit discharge rates and recruitment thresholds at two rates of force development. We specifically chose to investigate relatively slow to moderate rates of force development, not ballistic, as the chosen rates are more akin to those that presumably occur during daily activity.MethodsWe decomposed electromyographic signals to identify motor unit action potentials obtained from indwelling fine-wire electrodes in FHB, from ten male participants. Participants performed isometric ramp-and-hold contractions from relaxed to 50% of a maximal voluntary contraction. This was done for two rates of force development; one with the ramp performed over 5 s (slow condition) and one over 2.5 s (fast condition). Recruitment thresholds and discharge rates were calculated over the ascending limb of the ramp and compared between the two ramp conditions for matched motor units. A repeated measures nested linear mixed model was used to compare these parameters statistically. A linear repeated measures correlation was used to assess any relationship between changes in recruitment threshold and mean discharge rate between the two conditions.ResultsA significant increase in the initial discharge rate (i.e., at recruitment) in the fast (mean: 8.6 ±  2.4 Hz) compared to the slow (mean: 7.8 ± 2.3 Hz) condition (P = 0.027), with no changes in recruitment threshold (P = 0.588), mean discharge rate (P = 0.549) or final discharge rate (P = 0.763) was observed. However, we found substantial variability in motor unit responses within and between conditions. A small but significant negative correlation (R2 = 0.33, P = 0.003) was found between the difference in recruitment threshold and the difference in mean discharge rate between the two conditions.ConclusionThese findings suggest that as force increases for contractions with slower force development, increasing the initial discharge rate of recruited motor units produces the increase in rate of force development, without a change in their recruitment thresholds, mean or final discharge rate. However, an important finding was that for only moderate changes in rate of force development, as studied here, not all units respond similarly. This is different from what has been described in the literature for ballistic contractions in other muscle groups, where all motor units respond similarly to the increase in neural drive. Changing the discharge behaviour of a small group of motor units may be sufficient in developing force at the required rate rather than having the discharge behaviour of the entire motor unit pool change equally. creator: Jeroen Aeles creator: Luke A. Kelly creator: Andrew G. Cresswell uri: https://doi.org/10.7717/peerj.14341 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Aeles et al. title: The bony cap and its distinction from the distal phalanx in humans, cats, and horses link: https://peerj.com/articles/14352 last-modified: 2023-01-10 description: It has been recognized as early as the Victorian era that the apex of the distal phalanx has a distinct embryological development from the main shaft of the distal phalanx. Recent studies in regenerative medicine have placed an emphasis on the role of the apex of the distal phalanx in bone regrowth. Despite knowledge about the unique aspects of the distal phalanx, all phalanges are often treated as equivalent. Our morphological study reiterates and highlights the special anatomical and embryological properties of the apex of the distal phalanx, and names the apex “the bony cap” to distinguish it. We posit that the distal phalanx shaft is endochondral, while the bony cap is intramembranous and derived from the ectodermal wall. During development, the bony cap may be a separate structure that will fuse to the endochondral distal phalanx in the adult, as it ossifies well before the distal phalanges across taxa. Our study describes and revives the identity of the bony cap, and we identify it in three mammalian species: humans, cats, and horses (Homo sapiens, Felis catus domestica, and Equus caballus). During the embryonic period, we show the bony cap has a thimble-like shape that surrounds the proximal endochondral distal phalanx. The bony cap may thus play an inductive role in the differentiation of the corresponding nail, claw, or hoof (keratin structures) of the digit. When it is not present or develops erroneously, the corresponding keratin structures are affected, and regeneration is inhibited. By terming the bony cap, we hope to inspire more attention to its distinct identity and role in regeneration. creator: Shannon Smith creator: Laurel R. Yohe creator: Nikos Solounias uri: https://doi.org/10.7717/peerj.14352 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Smith et al. title: Yield-based drought tolerance index evaluates the drought tolerance of cotton germplasm lines in the interaction of genotype-by-environment link: https://peerj.com/articles/14367 last-modified: 2023-01-10 description: BackgroundCotton is an economically important crop in China, and drought has seriously affected cotton production. Understanding genetic variation, genotype ×environment interactions, and the associations between these traits is critical for developing improved cotton varieties with high drought tolerance.MethodsTo screen ideal drought-resistant cotton germplasm lines and excellent genotypes, the yield traits of 103 cotton germplasm lines were analyzed. Cotton resource material was planted under normal watering and water deficit conditions for three consecutive years. The yield traits under normal irrigation and water stress conditions were measured, and then five screening indicators were calculated based on the cotton yield per plant under the two water treatments to determine the ideal genotype and most accurate identification indicators.ResultsThe results of correlation analysis and principal component analysis showed that the geometric mean productivity (GMP), mean productivity (MP), and stress tolerance index (STI) were significantly positively correlated with yield under water stress and could be used to distinguish genotypes with high drought tolerance. Among the experimental germplasm lines, some had higher STI and GMP values, indicating their higher drought tolerance. This result indicates that best linear unbiased prediction (BLUP) analysis of the STI and GMP under drought stress can effectively improve screening for drought tolerance in cotton germplasm lines. The results from the screening index, three-dimensional map, and genotype ×environment (GGE) biplots were consistent with the above results. We determined that CQJ-5, Xin lu zao 45, Bellsno, Zhong R 2016 and ND 359-5 are drought-tolerant genotypes that can be used to breed drought-tolerant germplasm lines that produce high and stable yields. creator: Fenglei Sun creator: Quanjia Chen creator: Qin Chen creator: Menghui Jiang creator: Yanying Qu uri: https://doi.org/10.7717/peerj.14367 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sun et al. title: Diagnostic value and mechanism of plasma S100A1 protein in acute ischemic stroke: a prospective and observational study link: https://peerj.com/articles/14440 last-modified: 2023-01-10 description: BackgroundPlasma S100A1 protein is a novel inflammatory biomarker associated with acute myocardial infarction and neurodegenerative disease’s pathophysiological mechanisms. This study aimed to determine the levels of this protein in patients with acute ischemic stroke early in the disease progression and to investigate its role in the pathogenesis of acute ischemic stroke.MethodsA total of 192 participants from hospital stroke centers were collected for the study. Clinically pertinent data were recorded. The volume of the cerebral infarction was calculated according to the Pullicino formula. Multivariate logistic regression analysis was used to select independent influences. ROC curve was used to analyze the diagnostic value of AIS and TIA. The correlation between S100A1, NF-κB p65, and IL-6 levels and cerebral infarction volume was detected by Pearson correlation analysis.ResultsThere were statistically significant differences in S100A1, NF-κB p65, and IL-6 among the AIS,TIA, and PE groups (S100A1, [230.96 ± 39.37] vs [185.85 ± 43.24] vs [181.47 ± 27.39], P < 0.001; NF-κB p65, [3.99 ± 0.65] vs [3.58 ± 0.74] vs [3.51 ± 0.99], P = 0.001; IL-6, [13.32 ± 1.57] vs [11.61 ± 1.67] vs [11.42 ± 2.34], P < 0.001). Multivariate logistic regression analysis showed that S100A1 might be an independent predictive factor for the diagnosis of disease (P < 0.001). The AUC of S100A1 for diagnosis of AIS was 0.818 (P < 0.001, 95% CI [0.749–0.887], cut off 181.03, Jmax 0.578, Se 95.0%, Sp 62.7%). The AUC of S100A1 for diagnosis of TIA was 0.720 (P = 0.001, 95% CI [0.592–0.848], cut off 150.14, Jmax 0.442, Se 50.0%, Sp 94.2%). There were statistically significant differences in S100A1, NF-κB p65, and IL-6 among the SCI,MCI, and LCI groups (S100A1, [223.98 ± 40.21] vs [225.42 ± 30.92] vs [254.25 ± 37.07], P = 0.001; NF-κB p65, [3.88 ± 0.66] vs [3.85 ± 0.64] vs [4.41 ± 0.45], P < 0.001; IL-6, [13.27 ± 1.65] vs [12.77 ± 1.31] vs [14.00 ± 1.40], P = 0.007). Plasma S100A1, NF-κB p65, and IL-6 were significantly different from cerebral infarction volume (S100A1, r = 0.259, P = 0.002; NF-κB p65, r = 0.316, P < 0.001; IL-6, r = 0.177, P = 0.036). There was a positive correlation between plasma S100A1 and IL-6 with statistical significance (R = 0.353, P < 0.001). There was no significant positive correlation between plasma S100A1 and NF-κB p65 (R < 0.3), but there was statistical significance (R = 0.290, P < 0.001). There was a positive correlation between IL-6 and NF-κB p65 with statistical significance (R = 0.313, P < 0.001).ConclusionS100A1 might have a better diagnostic efficacy for AIS and TIA. S100A1 was associated with infarct volume in AIS, and its level reflected the severity of acute cerebral infarction to a certain extent. There was a correlation between S100A1 and IL-6 and NF-κB p65, and it was reasonable to speculate that this protein might mediate the inflammatory response through the NF-κB pathway during the pathophysiology of AIS. creator: Guo Hong creator: Tingting Li creator: Haina Zhao creator: Zhaohao Zeng creator: Jinglei Zhai creator: Xiaobo Li creator: Xiaoguang Luo uri: https://doi.org/10.7717/peerj.14440 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: UHPLC-ESI-QE-Orbitrap-MS based metabolomics reveals the antioxidant mechanism of icaritin on mice with cerebral ischemic reperfusion link: https://peerj.com/articles/14483 last-modified: 2023-01-10 description: BackgroundIcaritin (ICT) has been previously demonstrated to display protective effects against cerebral ischemic reperfusion (I/R) by inhibiting oxidative stress, but the mechanism remains unclear. This study aimed to explore the mechanism from the perspective of metabolomics.MethodsA mice cerebral artery occlusion/reperfusion (MCAO/R) model was explored to mimic cerebral ischemic reperfusion and protective effect of ICT was assessed by neurologic deficit scoring, infarct volume and brain water content. Ultra-high-performance liquid chromatography electrospray ionization orbitrap tandem mass spectrometry (UHPLC-ESI-QE-Orbitrap-MS) based metabolomic was performed to explore potential biomarkers. Brain tissue metabolic profiles were analyzed and metabolic biomarkers were identified through multivariate data analysis. The protein levels of Nrf2, HO-1 and HQO1 were assayed by western blot. The release of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT) were detected using corresponding assay kits.ResultsThe results showed that after ICT treatment, the neurological deficit, cerebral infarction area, brain edema and the level of MDA in brain tissue of MCAO/R mice were significantly reduced. Meanwhile, ICT enhanced the activity of SOD, CAT and GSH-Px. Western blot results confirmed that ICT up-regulated the protein levels of antioxidant-related protein including Nrf2, HO-1 and NQO1. According to the metabolomic profiling of brain tissues, clear separations were observed among the Sham, Model and ICT groups. A total of 44 biomarkers were identified, and the identified biomarkers were mainly related to linoleic acid metabolism, arachidonic acid metabolism, alanine, aspartate and glutamate metabolism, arginine biosynthesis, arginine and proline metabolism, D-glutamine and D-glutamate metabolism, taurine and hypotaurine metabolism and purine metabolism, respectively. At the same time, the inhibitory effect of ICT on arachidonic acid and linoleic acid in brain tissue, as well as the promoting effect on taurine, GABA, NAAG, may be the key factors for the anti-neurooxidative function of mice after MCAO/R injury.ConclusionOur results demonstrate that ICT has benefits for MCAO/R injury, which are partially related to the suppression of oxidative stress via stimulating the Nrf2 signaling and regulating the production of arachidonic acid, linoleic acid, taurine, GABA, NAAG in brain tissue. creator: Yunfeng Tang creator: Lixin Sun creator: Yun Zhao creator: Jingchun Yao creator: Zhong Feng creator: Zhong Liu creator: Guimin Zhang creator: Chenghong Sun uri: https://doi.org/10.7717/peerj.14483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Tang et al. title: A data integration framework for spatial interpolation of temperature observations using climate model data link: https://peerj.com/articles/14519 last-modified: 2023-01-10 description: Meteorological station measurements are an important source of information for understanding the weather and its association with risk, and are vital in quantifying climate change. However, such data tend to lack spatial coverage and are often plagued with flaws such as erroneous outliers and missing values. Alternative meteorological data exist in the form of climate model output that have better spatial coverage, at the expense of bias. We propose a probabilistic framework to integrate temperature measurements with climate model (reanalysis) data, in a way that allows for biases and erroneous outliers, while enabling prediction at any spatial resolution. The approach is Bayesian which facilitates uncertainty quantification and simulation based inference, as illustrated by application to two countries from the Middle East and North Africa region, an important climate change hotspot. We demonstrate the use of the model in: identifying outliers, imputing missing values, non-linear bias correction, downscaling and aggregation to any given spatial configuration. creator: Theo Economou creator: Georgia Lazoglou creator: Anna Tzyrkalli creator: Katiana Constantinidou creator: Jos Lelieveld uri: https://doi.org/10.7717/peerj.14519 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Economou et al. title: Computed tomography-based radiomics machine learning models for prediction of histological invasiveness with sub-centimeter subsolid pulmonary nodules: a retrospective study link: https://peerj.com/articles/14559 last-modified: 2023-01-10 description: To improve the accuracy of preoperative diagnoses and avoid over- or undertreatment, we aimed to develop and compare computed tomography-based radiomics machine learning models for the prediction of histological invasiveness using sub-centimeter subsolid pulmonary nodules. Three predictive models based on radiomics were built using three machine learning classifiers to discriminate the invasiveness of the sub-centimeter subsolid pulmonary nodules. A total of 203 sub-centimeter nodules from 177 patients were collected and assigned randomly to the training set (n = 143) or test set (n = 60). The areas under the curve of the predictive models were 0.743 (95% confidence interval CI [0.661–0.824]) for the logistic regression, 0.828 (95% CI [0.76–0.896]) for the support vector machine, and 0.917 (95% CI [0.869–0.965]) for the XGBoost classifier models in the training set, and 0.803 (95% CI [0.694–0.913]), 0.726 (95% CI [0.598–0.854]), and 0.874 (95% CI [0.776–0.972]) in the test set, respectively. In addition, the decision curve showed that the XGBoost model added more net benefit within the range of 0.06 to 0.93. creator: Haochuan Zhang creator: Shixiong Wang creator: Zhenkai Deng creator: Yangli Li creator: Yingying Yang creator: He Huang uri: https://doi.org/10.7717/peerj.14559 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Isopsoralen suppresses receptor activator of nuclear factor kappa-β ligand-induced osteoclastogenesis by inhibiting the NF-κB signaling link: https://peerj.com/articles/14560 last-modified: 2023-01-10 description: Osteoporosis is a serious systemic metabolic bone system disease.This study aimed to identify the target genes of isopsoralen and the signaling pathways involved in the differential expression of the genes involved in osteoclast differentiation. We hypothesized that isopsoralen may inhibit osteoclast differentiation by blocking the nuclear factor kappa-B (NF-κB) signaling pathway and verified our hypothesis through basic experiments. The 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay was used to detect the effect of isopsoralen on the proliferation and viability of primary mouse bone marrow monocytes (BMMCs). The effect of isopsoralen on receptor activator of nuclear factor kappa-B ligand (RANKL)-induced osteoclast differentiation was determined by using tartrate-resistant acid phosphatase (TRAP) staining. Quantitative real-time PCR (qRT-PCR) and Western blot were used to detect the expression of the related genes and proteins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of isopsoralen target genes were obtained through comprehensive analysis using the STITCH database, Cytoscape 3.8.2, and R-Studio software. Differentially expressed genes (DEGs) were found in osteoclasts induced by RANKL before and after 3 days using R-Studio, following which KEGG analysis was performed. Next, enrichment analysis was performed on the KEGG pathway shared by the target genes of isopsoralen and the differentially expressed genes during osteoclast differentiation to predict the signaling pathway underlying the inhibition of osteoclast differentiation by isopsoralen. Finally, Western blot was used to detect the effect of isopsoralen on the activation of signaling pathways to verify the results of our bioinformatics analysis. Based on the enrichment analysis of isopsoralen target genes and differentially expressed genes during osteoclastogenesis, we believe that isopsoralen can inhibit RANKL-induced osteoclastogenesis by inhibiting the NF-κB signaling pathway. creator: Wanda Zhan creator: Binjia Ruan creator: Hui Dong creator: Chaoyong Wang creator: Shuangshi Wu creator: Hang Yu creator: Xiaohang Xu creator: Hao Sun creator: Jun Cai uri: https://doi.org/10.7717/peerj.14560 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhan et al. title: No detectable changes in reproductive behaviour of Caenorhabditis elegans males after 97 generations under obligatory outcrossing link: https://peerj.com/articles/14572 last-modified: 2023-01-10 description: In Caenorhabditis elegans, a species reproducing mostly via self-fertilization, numerous signatures of selfing syndrome are observed, including differences in reproductive behaviour compared to related obligatory outcrossing species. In this study we investigated the effect of nearly 100 generations of obligatory outcrossing on several characteristics of male reproductive behaviour. A genetically uniform ancestral population carrying a mutation changing the reproductive system to obligatory outcrossing was split into four independent populations. We predicted that the transition from the natural reproductive system, where males were extremely rare, to obligatory outcrossing, where males comprise 50% of the population and are necessary for reproduction, will increase the selection pressure on higher effectiveness of mating behaviour. Several characteristics of male mating behaviour during a 15 min interaction as well as copulation success were compared between the ancestral and evolved populations. No significant differences in male mating behaviour or fertilization success were detected between generations 1 and 97 of obligatory outcrossing populations. We found, however, that longer contact with females increased chances of successful copulation, although this effect did not differ between populations. We conclude that either selection acting on male mating behaviour has not been strong enough, or mutational input of new adaptive variants has not been sufficient to cause noticeable behavioural differences after 97 generations of evolution starting from genetically uniform population. creator: Weronika Antoł creator: Jagoda Byszko creator: Alicja Dyba creator: Joanna Palka creator: Wiesław Babik creator: Zofia Prokop uri: https://doi.org/10.7717/peerj.14572 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Antoł et al. title: Pemafibrate prevents choroidal neovascularization in a mouse model of neovascular age-related macular degeneration link: https://peerj.com/articles/14611 last-modified: 2023-01-10 description: BackgroundPathological choroidal neovascularization (CNV) is one of the major causes of visual impairment in neovascular age-related macular degeneration (AMD). CNV has been suppressed by using anti-vascular endothelial growth factor (VEGF) antibodies. However, some clinical cases have demonstrated the failure of anti-VEGF therapies. Furthermore, anti-VEGF agents might induce the development of ocular atrophy. Recently, peroxisome proliferator-activated receptor alpha (PPARα) activation using pemafibrate treatment was suggested as one of the promising therapeutic targets in the prevention of ocular ischemia. However, the preventive role of pemafibrate remains unclear in CNV. We aimed to examine the preventive role of pemafibrate on laser-induced pathological CNV.MethodsAdult male C57BL/6 mice were orally supplied pemafibrate (0.5 mg/kg) for four days, followed by laser irradiation. Then, pemafibrate was consecutively given to mice with the same condition. CNV was visualized with isolectin-IB4. The eye (retina and/or retinal pigment epithelium [RPE]-choroid), liver, and serum were used for biomolecular analyses.ResultsWe found that pemafibrate administration suppressed CNV volumes. Pemafibrate administration activated PPARα downstream genes in the liver and eye (especially, RPE-choroid). Furthermore, pemafibrate administration elevated serum fibroblast growth factor 21 levels and reduced serum levels of triglycerides.ConclusionsOur data suggest a promising pemafibrate therapy for suppressing CNV in AMD. creator: Deokho Lee creator: Ayaka Nakai creator: Yukihiro Miwa creator: Kazuno Negishi creator: Yohei Tomita creator: Toshihide Kurihara uri: https://doi.org/10.7717/peerj.14611 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lee et al. title: Comprehensive analysis of fatty acid metabolism-related gene signatures for predicting prognosis in patients with prostate cancer link: https://peerj.com/articles/14646 last-modified: 2023-01-10 description: Fatty acid metabolism (FAM) is an important factor in tumorigenesis and development. However, whether fatty acid metabolism (FAM)-related genes are associated with prostate cancer (PCa) prognosis is not known. Therefore, we established a novel prognostic model based on FAM-related genes to predict biochemical recurrence in PCa patients. First, PCa sequencing data were acquired from TCGA as the training cohort and GSE21032 as the validation cohort. Second, a prostate cancer prognostic model containing 10 FAM-related genes was constructed using univariate Cox and LASSO. Principal component analysis and t-distributed stochastic neighbour embedding analysis showed that the model was highly effective. Third, PCa patients were divided into high- and low-risk groups according to the model risk score. Survival analysis, ROC curve analysis, and independent prognostic analysis showed that the high-risk group had short recurrence-free survival (RFS), and the risk score was an independent diagnostic factor with diagnostic value in PCa patients. External validation using GSE21032 also showed that the prognostic model had high reliability. A nomogram based on a prognostic model was constructed for clinical use. Fourth, tumor immune correlation analyses, such as the ESTIMATE, CIBERSORT algorithm, and ssGSEA, showed that the high-risk group had higher immune cell infiltration, lower tumour purity, and worse RFS. Various immune checkpoints were expressed at higher levels in high-risk patients. In summary, this prognostic model is a promising prognostic biomarker for PCa that should improve the prognosis of PCa patients. These data provide new ideas for antitumour immunotherapy and have good potential value for the development of targeted drugs. creator: Hongbo Wang creator: Zhendong Liu creator: Yubo Wang creator: Dali Han creator: Yuelin Du creator: Bin Zhang creator: Yang He creator: Junyao Liu creator: Wei Xiong creator: Xingxing Zhang creator: Yanzheng Gao creator: Panfeng Shang uri: https://doi.org/10.7717/peerj.14646 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: CMTM6 is highly expressed in lung adenocarcinoma and can be used as a biomarker of a poor diagnosis link: https://peerj.com/articles/14668 last-modified: 2023-01-10 description: BackgroundCMTM6 which is chemokine-like factor (CKLF)-like Marvel transmembrane domain containing family member 6 is involved in the occurrence and progression of various tumors. However, the role of CMTM6 is still unclear in lung adenocarcinoma (LUAD).MethodsImmunohistochemical, Western blotting and RT‒PCR methods were used to detect the expression of CMTM6 in LUAD. Cox regression and the Kaplan‒Meier method were performed to assess overall survival. Immunogenic features were evaluated according to immune cell infiltrations, immune checkpoints. The sensitivity to chemotherapy agents was estimated using the pRRophetic package.ResultsIn LUAD, the expression of CMTM6 was obviously upregulated and was significantly associated with T stage (p = 0.008) and lymph node metastasis (p = 0.018). Multivariate Cox regression analysis demonstrated that CMTM6 was a specialty prognostic risk factor. Based on GSEA enrichment analysis, we found that high expression of CMTM6 is associated with multiple immune signaling pathways. The group with high CMTM6 expression showed a positive association with various types of tumor-infiltrating cells. Moreover, a total of 36 chemotherapeutic drugs were significantly correlated with the expression of CMTM6. Among them, two chemotherapeutic drugs had better therapeutic effects in the high CMTM6 expression group, while 34 chemotherapeutic drugs had therapeutic effects in the low CMTM6 expression group.ConclusionThis study confirmed that CMTM6 is highly expressed in LUAD and is a new independent poor prognostic factor. In addition, the high expression of CMTM6 is closely related to the tumor microenvironment and immunotherapy, providing new ideas for the treatment of posterior LUAD. creator: Daqi Jia creator: Li Xiong creator: Honggang Xue creator: Jidong Li uri: https://doi.org/10.7717/peerj.14668 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jia et al. title: The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses link: https://peerj.com/articles/14063 last-modified: 2023-01-09 description: The GAGA protein (also known as GAF) is a transcription factor encoded by the Trl gene in D. melanogaster. GAGA is involved in the regulation of transcription of many genes at all stages of fly development and life. Recently, we investigated the participation of GAGA in spermatogenesis and discovered that Trl mutants experience massive degradation of germline cells in the testes. Trl underexpression induces autophagic death of spermatocytes, thereby leading to reduced testis size. Here, we aimed to determine the role of the transcription factor GAGA in the regulation of ectopic germline cell death. We investigated how Trl underexpression affects gene expression in the testes. We identified 15,993 genes in three biological replicates of our RNA-seq analysis and compared transcript levels between hypomorphic TrlR85/Trl362 and Oregon testes. A total of 2,437 differentially expressed genes were found, including 1,686 upregulated and 751 downregulated genes. At the transcriptional level, we detected the development of cellular stress in the Trl-mutant testes: downregulation of the genes normally expressed in the testes (indicating slowed or abrogated spermatocyte differentiation) and increased expression of metabolic and proteolysis-related genes, including stress response long noncoding RNAs. Nonetheless, in the Flybase Gene Ontology lists of genes related to cell death, autophagy, or stress, there was no enrichment with GAGA-binding sites. Furthermore, we did not identify any specific GAGA-dependent cell death pathway that could regulate spermatocyte death. Thus, our data suggest that GAGA deficiency in male germline cells leads to an imbalance of metabolic processes, impaired mitochondrial function, and cell death due to cellular stress. creator: Svetlana Fedorova creator: Natalya V. Dorogova creator: Dmitriy A. Karagodin creator: Dmitry Yu Oshchepkov creator: Ilya I. Brusentsov creator: Natalya V. Klimova creator: Elina M. Baricheva uri: https://doi.org/10.7717/peerj.14063 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Fedorova et al. title: Substantial changes in Gaseous pollutants and health effects during COVID-19 in Delhi, India link: https://peerj.com/articles/14489 last-modified: 2023-01-09 description: BackgroundCoronavirus disease has affected the entire population worldwide in terms of physical and environmental consequences. Therefore, the current study demonstrates the changes in the concentration of gaseous pollutants and their health effects during the COVID-19 pandemic in Delhi, the national capital city of India.MethodologyIn the present study, secondary data on gaseous pollutants such as nitrogen dioxide (NO2), carbon monoxide (CO), sulfur dioxide (SO2), ammonia (NH3), and ozone (O3) were collected from the Central Pollution Control Board (CPCB) on a daily basis. Data were collected from January 1, 2020, to September 30, 2020, to determine the relative changes (%) in gaseous pollutants for pre-lockdown, lockdown, and unlockdown stages of COVID-19.ResultsThe current findings for gaseous pollutants reveal that concentration declined in the range of 51%–83% (NO), 40%–69% (NOx), 31%–60% (NO2), and 25%–40% (NH3) during the lockdown compared to pre-lockdown period, respectively. The drastic decrease in gaseous pollutants was observed due to restricted measures during lockdown periods. The level of ozone was observed to be higher during the lockdown periods as compared to the pre-lockdown period. These gaseous pollutants are linked between the health risk assessment and hazard identification for non-carcinogenic. However, in infants (0–1 yr), Health Quotient (HQ) for daily and annual groups was found to be higher than the rest of the exposed group (toddlers, children, and adults) in all the periods.ConclusionThe air quality values for pre-lockdown were calculated to be “poor category to “very poor” category in all zones of Delhi, whereas, during the lockdown period, the air quality levels for all zones were calculated as “satisfactory,” except for Northeast Delhi, which displayed the “moderate” category. The computed HQ for daily chronic exposure for each pollutant across the child and adult groups was more than 1 (HQ > 1), which indicated a high probability to induce adverse health outcomes. creator: Bhupendra Singh creator: Puneeta Pandey creator: Saikh Mohammad Wabaidur creator: Ram Avtar creator: Pramod Kumar creator: Shakilur Rahman uri: https://doi.org/10.7717/peerj.14489 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Singh et al. title: Clasnip: a web-based intraspecies classifier and multi-locus sequence typing for pathogenic microorganisms using fragmented sequences link: https://peerj.com/articles/14490 last-modified: 2023-01-09 description: Bioinformatic approaches for the identification of microorganisms have evolved rapidly, but existing methods are time-consuming, complicated or expensive for massive screening of pathogens and their non-pathogenic relatives. Also, bioinformatic classifiers usually lack automatically generated performance statistics for specific databases. To address this problem, we developed Clasnip (www.clasnip.com), an easy-to-use web-based platform for the classification and similarity evaluation of closely related microorganisms at interspecies and intraspecies levels. Clasnip mainly consists of two modules: database building and sample classification. In database building, labeled nucleotide sequences are mapped to a reference sequence, and then single nucleotide polymorphisms (SNPs) statistics are generated. A probability model of SNPs and classification groups is built using Hidden Markov Models and solved using the maximum likelihood method. Database performance is estimated using three replicates of two-fold cross-validation. Sensitivity (recall), specificity (selectivity), precision, accuracy and other metrics are computed for all samples, training sets, and test sets. In sample classification, Clasnip accepts inputs of genes, short fragments, contigs and even whole genomes. It can report classification probability and a multi-locus sequence typing table for SNPs. The classification performance was tested using short sequences of 16S, 16–23S and 50S rRNA regions for 12 haplotypes of Candidatus Liberibacter solanacearum (CLso), a regulated plant pathogen associated with severe disease in economically important Apiaceous and Solanaceous crops. The program was able to classify CLso samples with even only 1–2 SNPs available, and achieved 97.2%, 98.8% and 100.0% accuracy based on 16S, 16–23S, and 50S rRNA sequences, respectively. In comparison with all existing 12 haplotypes, we proposed that to be classified as a new haplotype, given samples have at least 2 SNPs in the combined region of 16S rRNA (OA2/Lsc2) and 16–23S IGS (Lp Frag 4–1611F/Lp Frag 4–480R) regions, and 2 SNPs in the 50S rplJ/rplL (CL514F/CL514R) regions. Besides, we have included the databases for differentiating Dickeya spp., Pectobacterium spp. and Clavibacter spp. In addition to bacteria, we also tested Clasnip performance on potato virus Y (PVY). 251 PVY genomes were 100% correctly classified into seven groups (PVYC, PVYN, PVYO, PVYNTN, PVYN:O, Poha, and Chile3). In conclusion, Clasnip is a statistically sound and user-friendly bioinformatic application for microorganism classification at the intraspecies level. Clasnip service is freely available at www.clasnip.com. creator: Jiacheng Chuan creator: Huimin Xu creator: Desmond L. Hammill creator: Lawrence Hale creator: Wen Chen creator: Xiang Li uri: https://doi.org/10.7717/peerj.14490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chuan et al. title: How to measure ego-resiliency in the face of various life-changing crises: Measurement invariance, convergent and discriminant validity and reliability of the Polish version of the Revised Ego-Resiliency Scale (ER89-R12) link: https://peerj.com/articles/14499 last-modified: 2023-01-09 description: This study examines the generalizability of the latent structure of the Polish version of the Ego-Resiliency Scale (ER89-R12), a brief self-report scale that measures ego-resiliency. We investigated the measurement invariance, validity, and reliability of ER89-R12 among three groups of individuals who were facing various major, long-term, life-changing crises (N = 512): parents of children with Down’s syndrome, women with breast cancer, and individuals after divorce. The analysis of the measurement invariance confirmed the two-factor structure of the questionnaire and the high reliability of this measure in those studied groups. A multigroup confirmatory factor analysis provided evidence of configural, metric, scalar, and residual invariance across the three groups. Moreover, the correlation patterns were similar across the groups. Ego-resiliency was strongly and consistently positively correlated with mental health: psychological well-being, perceived social support, self-esteem, and post-traumatic growth, and negatively correlated with perceived stress. The presented results indicate the potential usefulness of the ER89-R12 tool in studies on people experiencing various crises in their lives. creator: Anna Kołodziej-Zaleska creator: Michalina Ilska creator: Anna Brandt-Salmeri creator: Anna Jazłowska creator: Hanna Przybyła-Basista uri: https://doi.org/10.7717/peerj.14499 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kołodziej-Zaleska et al. title: Co-circulation of all the four Dengue virus serotypes during 2018–2019: first report from Eastern Uttar Pradesh, India link: https://peerj.com/articles/14504 last-modified: 2023-01-09 description: Dengue fever is an endemic disease in India, transmitted by an infected mosquito bite. In India, the number of concurrent infections and the circulation of multiple dengue virus (DENV) serotypes has increased in recent decades. Molecular surveillance among the DENV serotype is important to keep track of the circulating serotypes, evolutionary changes, and key mutations that can alter the diagnostics. The current study included patients admitted for dengue in the Eastern Uttar Pradesh (E-UP) region during 2018–2019. The genetic characterization of the circulating DENV was accomplished through partial CprM (511 bp) gene amplification via reverse transcriptase polymerase chain reaction and sequencing. Phylogenetic analysis revealed the circulation of all four DENV1-4 serotypes. DENV-2 was the most abundant serotype (44%, 27/61), followed by DENV-3 (32%, 20/61). DENV-1 had a 16% (10/61) predominance, while DENV-4 (6%, 4/61) was found to be the least abundant serotype. DENV-2 genotypes were distributed among lineages I (7.4%), II (85%) and III (7.4%) of genotype IV, DENV-3 to lineage III of genotype III, DENV-1 to genotype III; DENV-2 to lineage B (75%) and C (25%) of genotype I. This primary report on the co-circulation of DENV1-4 serotypes from the E-UP region highlights the requirement of continuous molecular surveillance for monitoring circulating DENV serotypes. creator: Sthita Pragnya Behera creator: Pooja Bhardwaj creator: Hirawati Deval creator: Neha Srivastava creator: Rajeev Singh creator: Brij Ranjan Misra creator: Awdhesh Agrawal creator: Asif Kavathekar creator: Rajni Kant uri: https://doi.org/10.7717/peerj.14504 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Behera et al. title: The impacts of math anxiety, science anxiety, and gender on arts versus sciences choices in Qatari secondary schools link: https://peerj.com/articles/14510 last-modified: 2023-01-09 description: Previous studies showed small-to-moderate associations between students’ performances in math and science and math anxiety and science anxiety, respectively. Accordingly, the high prevalence of these two forms of topic anxiety represent severe obstructions to the worldwide demand calling for improving the quality of math and science achievements and, subsequently, increasing career success in science, technology, engineering, and math (STEM) domains. Therefore, this study examined math anxiety and science anxiety among female and male students who were enrolled in Sciences vs Arts tracks in Grades 11 and 12 in a Middle Eastern Arabic-speaking country (Qatar), and investigated how gender, math anxiety and science anxiety could predict this enrollment. Results showed that students in the Arts track experienced higher levels of math anxiety and science anxiety than those in the Sciences track, regardless of the students’ gender. However, a binary logistic regression analysis showed that science learning anxiety, but not evaluation science anxiety nor math learning or evaluation anxieties, significantly predicts students’ enrollment in Arts and Sciences tracks. Therefore, STEM career success is associated with good knowledge of STEM domains and positive emotions towards math and science. creator: Ahmed M. Megreya creator: Ahmed A. Al-Emadi uri: https://doi.org/10.7717/peerj.14510 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Megreya and Al-Emadi title: Assessing factors influencing students’ perceptions towards animal species conservation link: https://peerj.com/articles/14553 last-modified: 2023-01-09 description: BackgroundThe way humans perceive and interact with non-human animals is particular to each person, from antipathetic interactions evidenced by fear, aversion or repulsion, to empathy evidenced by feelings of affection, enchantment and interest in the animal. In this sense, herein we investigated the perception of university students about species belonging to different classes of wild vertebrates and the influence of social and educational factors on that.MethodsData were obtained through online forms answered by 700 university students from nine Brazilian states, 328 females and 372 males, aged between 18 and 65 years. The form had eight sentences to be answered in relation to 17 species of wild vertebrates. The agreement level for each of these sentences was to be indicated using a five-point Likert scale. The sentences were designed to assess aesthetic, risk, utilitarian, and preservation perceptions attributed to each species by students.ResultsWe found that species perceived as useful by the students are generally also perceived as beautiful and as those that should be preserved. On the other hand, we found similarity between the species perceived as ugly and those that should not be preserved; and between the species perceived as harmful and those considered dangerous. Female and lower-income students more often agree that animals are harmful. We found that perceptions of danger in relation to animals were predominantly associated with younger respondents. However, this did not lead to less support for conservation among these students, as students of all age groups agree that species should be preserved. Our results show that students’ knowledge area was an important predictor associated with empathetic and antipathetic perceptions. Environmental area students showed greater empathy in all analyzed categories (beauty, usefulness, harmlessness, and preservation) than non-environmental areas students. On the other hand, students from the area of the exact sciences showed greater dislike in all analyzed categories than students from other areas. We found a strong relationship between the areas “Environmental” and “Humanities, Languages and Arts” for the attitudinal factors associated with utility and preservation, suggesting a similar empathetic worldview for students in these areas.ConclusionsWe found that the perception directed towards wild vertebrates varies according to the gender, age, income and study area of the students, in addition to the taxon considered. Finally, our results indicate that negative perceptions should be taken into account in environmental education efforts, educational policies and in planning fauna conservation plans which should incorporate the most diverse audiences, and not only encompass charismatic species but extend to animals that arouse great aversion from the part of people. creator: Heliene Mota Pereira creator: Franciany Braga-Pereira creator: Luane Maria Melo Azeredo creator: Luiz Carlos Serramo Lopez creator: Rômulo Romeu Nóbrega Alves uri: https://doi.org/10.7717/peerj.14553 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mota Pereira et al. title: Differences in histomorphology and expression of key lipid regulated genes of four adipose tissues from Tibetan pigs link: https://peerj.com/articles/14556 last-modified: 2023-01-09 description: Tibetan pigs, an indigenous pig breed in China, have high overall fat deposition and flavorful and tasty meat. They are thus good models for studying adipogenesis. Few studies have been conducted focusing on expression of lipid regulated genes in different adipose tissues of Tibetan pigs. Therefore, we compared the difference of histomorphology and expression level of lipid regulated genes through qPCR and western blot in subcutaneous fat, perirenal fat, omental adipose tissue, and inguinal fat of Tibetan pigs. Our results showed that the area of subcutaneous adipocytes in Tibetan pigs was smaller, while the other three adipose tissues (perirenal fat, greater omentum fat, inguinal fat) had cell areas of similar size. The gene expression of FABP4, FASN, FABP3, and ME1 in subcutaneous fat was significantly higher than that in perirenal fat. Furthermore, the protein expression of FABP4 was significantly lower in subcutaneous fat than in perirenal fat (p < 0.05), and the expression of FASN was higher in greater omentum fat than in subcutaneous fat (p = 0.084). The difference in adipocyte cell size and expression of lipid-regulated genes in adipose tissues from the various parts of the pig body is likely due to the different cellular lipid metabolic processes. Specially, FABP4 and FASN may be involved in the regulation of fat deposition in different adipose tissues of Tibetan pigs. creator: Chenghong Lin creator: Zexia Dong creator: Jia Song creator: Sutian Wang creator: Ying Yang creator: Hua Li creator: Zheng Feng creator: Yangli Pei uri: https://doi.org/10.7717/peerj.14556 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lin et al. title: The effects of soil drought stress on growth characteristics, root system, and tissue anatomy of Pinus sylvestris var. mongolica link: https://peerj.com/articles/14578 last-modified: 2023-01-09 description: The main purpose of this study was to study the changes in growth, root system, and tissue anatomical structure of Pinus sylvestris var. mongolica under soil drought conditions. In this study, the growth indexes and photosynthesis of P. sylvestris var. mongolica seedlings under soil drought stress were studied by pot cultivation. Continuous pot water control experiment of the indoor culture of P. sylvestris var. mongolica was carried out, ensuring that the soil water content of each treatment reached 80%, 40%, and 20% of the field moisture capacity as control, moderate drought and severe drought, respectively. The submicroscopic structures of the needles and roots were observed using a scanning electron microscope and a transmission electron microscope. The response of soil roots to drought stress was studied by root scanning. Moderate drought stress increased needle stomatal density, while under severe drought stress, stomatal density decreased. At the same time, the total number of root tips, total root length, root surface area, and root volume of seedlings decreased with the deepening of the drought. Furthermore, moderate drought and severe drought stress significantly reduced the chlorophyll a and chlorophyll b content in P. sylvestris var. mongolica seedlings compared to the control group. The needle cells were deformed and damaged, and chloroplasts and mitochondria were damaged, gradually disintegrated, and the number of osmiophiles increased. There was also an increase in nuclear vacuolation. creator: Fanjun Meng creator: Tianze Zhang creator: Dachuan Yin uri: https://doi.org/10.7717/peerj.14578 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Meng et al. title: Eight single nucleotide polymorphisms and their association with food habit domestication traits and growth traits in largemouth bass fry (Micropterus salmoides) based on PCR-RFLP method link: https://peerj.com/articles/14588 last-modified: 2023-01-09 description: BackgroundThe largemouth bass (Micropterus salmoides), an economically important freshwater fish species widely farmed in China, is traditionally cultured using a diet of forage fish. However, given the global decline in forage fish fisheries and increasing rates of waterbody pollution and disease outbreaks during traditional culturing, there is a growing trend of replacing forage fish with formulated feed in the largemouth bass breeding industry. The specific molecular mechanisms associated with such dietary transition in this fish are, nevertheless, poorly understood.MethodsTo identify single nucleotide polymorphisms (SNPs) related to food habit domestication traits and growth traits in largemouth bass fry, we initially genotyped fry using eight candidate SNPs based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, with genetic parameters being determined using Popgen32 and Cervus 3.0. Subsequently, we assessed the associations between food habit domestication traits of largemouth bass fry and these SNPs using the Chi-square test or Fisher’s exact test. Furthermore, we used a general linear model to assess the relationships between the growth traits of largemouth bass fry and these SNPs. The Pearson correlation coefficient between growth traits and the SNPs was also determined using bivariate correlation analysis in IBM SPSS Statistics 22. Finally, the phenotypic variation explained (PVE) by the SNPs was calculated by regression analysis in Microsoft Excel.ResultsThe genotyping results obtained based on PCR-RFLP analysis were consistent with those of direct sequencing. Five SNPs (SNP01, SNP02, SNP04, SNP05, and SNP06) were found to be significantly correlated with the food habit domestication traits of fry (P < 0.05); SNP01 (P = 0.0011) and SNP04 (P = 0.0055) particularly, had showed highly significant associations. With respect to growth traits, we detected significant correlations with the two SNPs (SNP01 and SNP07) (P < 0.05), with SNP01 being significantly correlated with body length, and height (P < 0.05), and SNP07 being significantly correlated with body height only (P < 0.05).ConclusionsOur findings indicated that the PCR-RFLP can be used as a low-cost genotyping method to identify SNPs related to food habit domestication and growth traits in largemouth bass, and that these trait-related SNPs might provide a molecular basis for the future breeding of new varieties of largemouth bass. creator: Jiao Cui creator: Zhou Jiang creator: Zerui Wang creator: Jiaqi Shao creator: Chuanju Dong creator: Lei Wang creator: Xuejun Li creator: Jinxing Du creator: Shengjie Li creator: Zhigang Qiao creator: Meng Zhang uri: https://doi.org/10.7717/peerj.14588 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cui et al. title: Novel ethyl p-methoxy cinnamate rich Kaempferia galanga (L.) essential oil and its pharmacological applications: special emphasis on anticholinesterase, anti-tyrosinase, α-amylase inhibitory, and genotoxic efficiencies link: https://peerj.com/articles/14606 last-modified: 2023-01-09 description: BackgroundKaempferia galanga (L.) is one of the prospective therapeutic plants with an aromatic rhizome, and belongs to the Zingiberaceae family. This herb is commonly used by local practitioners in traditional Asian medicine.MethodsIn the present investigation, the novel Kaempferia galanga rhizome essential oil rich in ethyl p-methoxy cinnamate (EMCKG) was evaluated using GC/MS for chemical composition analysis. EMCKG was analyzed for its possible antimicrobial, neurodegenerative inhibitory, acetylcholinesterase, anti-inflammatory, and antioxidant activities as well as for the genotoxic effects using the standard methodologies. ANOVA and post hoc was performed to test the statistical significance of the study.ResultsGC/MS analysis identified ethyl p-methoxy cinnamate as the major component of EMCKG essential oil with an area percentage of 66.39%. The EMCKG exhibited moderate (DPPH assay IC50 = 15.64 ± 0.263 µg/mL; ABTS assay IC50 = 16.93 ± 0.228 µg/mL) antioxidant activity than standard ascorbic acid (DPPH assay IC50 = 21.24 ± 0.413 µg/mL; ABTS assay IC50 = 21.156 ± 0.345 µg/mL). Similarly, EMCKG showed comparable activity in albumin denaturation (IC50 = 2.93 ± 0.59 µg/mL) and protease inhibitor assay (IC50 = 17.143 ± 0.506 µg/mL) to that of standard sodium diclofenac (IC50 = 23.87 ± 0.729 µg/mL and IC50 = 19.18 ± 0.271 µg/mL, respectively). The EMCKG exhibited a dose-dependent antimicrobial activity pattern with the highest inhibitory activity at 500 µg/mL against Staphylococcus aureus and considerable anticholinesterase activities (IC50 = 21.94 ± 0.109 µg/mL) compared to the standard galanthamine (IC50 = 27.18 ± 0.511 µg/mL). EMCKG also showed strong anti-diabetic activity (IC50 = 18.503 ± 0.480 µg/mL) and anti-tyrosinase activity (IC50 = 14.756 ± 0.325 µg/mL) as compared to the standards used (acarbose IC50 = 20.39 ± 0.231 µg/mL and kojic acid IC50 = 17.73 ± 0.192 µg/mL) in the study. Genotoxicity analysis of EMCKG revealed that at 1 µg/mL concentration has no toxic effects in mitosis of Allium cepa roots (Mitotic Index MI = 13.56% and chromosomal aberration CA = 07.60%). The ANOVA confirmed that except for the anticholinesterase activity, there is insignificant difference for essential oil and standards used for all the other bioactivities thus confirming their interchangeable applicability.ConclusionsCurrent research provides the basis for the fact that besides being a rich source of ethyl p-methoxycinnamate, EMCKG has the potential for future formulation and development of an inexpensive skin-care agent and for the preparation of anti-diabetic drugs. creator: Twahira Begum creator: Roktim Gogoi creator: Neelav Sarma creator: Sudin Kumar Pandey creator: Mohan Lal uri: https://doi.org/10.7717/peerj.14606 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Begum et al. title: Exosomes derived from M1 macrophages inhibit the proliferation of the A549 and H1299 lung cancer cell lines via the miRNA-let-7b-5p-GNG5 axis link: https://peerj.com/articles/14608 last-modified: 2023-01-09 description: BackgroundAlmost all cells are capable of secreting exosomes (Exos) for intercellular communication and regulation. Therefore, Exos can be used as a natural therapeutic platform to regulate genes or deliver drugs to treat diseases. M1 macrophages inhibit tumor growth by releasing pro-inflammatory factors. This study explored the applicability of M1 macrophage exosomes (M1-Exos) as gene carriers and the effects on GNG5 protein, and further examined whether macrophage repolarization could inhibit tumor activity.MethodsM0 macrophages were polarized toward M1 using vitexin. Exos were obtained from M1 macrophages by ultra-centrifugation. The transwell non-contact co-culture system was used to co-culture M1 macrophages with HLF-α human lung epithelial cells or A549 or H1299 lung cancer cells. MTT, scratch, and transwell assays were used to detect the cell viability, migration, and invasion ability of cells in the four groups. Flow cytometry was used to detect the apoptosis rate of each group, and western blot (WB) analysis was performed to detect the change in the expression of proliferation- and apoptosis-related proteins. We screened the differentially expressed microRNAs using quantitative polymerase chain reaction technology. Luciferase reporter analysis was performed to explore the interaction between miRNA and protein. We used Xenografted A549 tumors in nude mice to study the effect of M1-Exos on tumor cell growth in vivo.ResultsThe results showed that, under the M1 macrophage co-culture system, lung cancer cell viability, invasion, and migration ability decreased, and the number of apoptotic cells increased, will all indicators being statistically significant (P < 0.05). The expression levels of PCNA, KI67, and Bcl-2 decreased significantly, but that of Bax increased (P < 0.05). Exosomes can have the same effect on tumor cells as M1 macrophages. Exosomes can transport miR-let-7b-5p to tumor cells, and miR-let-7b-5p can inhibit tumor cell proliferation and promote tumor cell apoptosis by regulating the GNG5 protein level.ConclusionsM1-Exos inhibit the proliferation, invasion, and metastasis of lung cancer cells through miRNA-let-7b-5p and GNG5 signaling pathways and inhibit the anti-apoptotic ability of lung cancer cells. creator: Jingcui Peng creator: Sa Li creator: Bin Li creator: WenXia Hu creator: Cuimin Ding uri: https://doi.org/10.7717/peerj.14608 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Peng et al. title: The relationship of low-density lipoprotein cholesterol and all-cause or cardiovascular mortality in patients with type 2 diabetes: a retrospective study link: https://peerj.com/articles/14609 last-modified: 2023-01-09 description: BackgroundThe optimal levels of low-density lipoprotein cholesterol (LDL-C) in patients with type 2 diabetes (T2D) are not currently clear. In this study, we determined the relationship between various mean LDL-C and all-cause or cardiovascular mortality risks in patients with T2D, stratifying by albumin level, age, sex, and antilipid medication use. We also evaluated the association of LDL-C standard deviation (LDL-C-SD) and all-cause and cardiovascular mortality by type of antilipid medication use.MethodsA total of 46,675 T2D patients with a prescription for antidiabetic agents >6 months from outpatient visits (2003–2018) were linked to Taiwan’s National Death Registry to identify all-cause and cardiovascular mortality. The Poisson assumption was used to estimate mortality rates, and the Cox proportional hazard regression model was used to assess the relative hazards of respective mortality in relation to mean LDL-C in patient cohorts by albumin level, age, sex, and antilipid use adjusting for medications, comorbidities, and laboratory results. We also determined the overall, and anti-lipid-specific mortality rates and relative hazards of all-cause and cardiovascular mortality associated with LDL-C-SD using the Poisson assumption and Cox proportional hazard regression model, respectively.ResultsAll-cause and cardiovascular mortality rates were the lowest in T2D patients with a mean LDL-C > 90-103.59 mg/dL in the normal albumin group (≥ 3.5 g/dL). Compared to T2D patients with a mean LDL-C > 90–103.59 mg/dL, those with a mean LDL-C ≤ 77 mg/dL had an elevated risk of all-cause mortality in both the normal and lower albumin groups. T2D patients with a mean LDL-C ≤ 90 and > 103.59–119 mg/dL had relatively higher risk of cardiovascular mortality in the normal albumin group, but in the lower albumin group (<3.5 g/dL), any level of mean LDL-C ≤ 119 mg/dL was not significantly associated with cardiovascular mortality. Increased risks of all-cause and cardiovascular mortality were observed in patients with a mean LDL-C ≤ 77 mg/dL in both sexes and in all age groups except in those aged <50 years, a lower mean LDL-C was not associated with cardiovascular mortality. Similarly, patients with an LDL-C-SD <10th and > 90th percentiles were associated with significant risks of all-cause and cardiovascular mortality. In statin users, but not fibrate users, lower and higher levels of mean LDL-C and LDL-C-SD were both associated with elevated risks of all-cause and cardiovascular mortality.ConclusionsThe optimal level of LDL-C was found to be >90–103.59 mg/dL in T2D patients. Lower and higher levels of mean LDL-C and LDL-C-SD were associated with all-cause and cardiovascular mortality, revealing U-shaped associations. Further studies are necessary to validate the relationship between optimal LDL-C levels and all-cause and cardiovascular mortality in patients with diabetes. creator: Chin-Huan Chang creator: Shu-Tin Yeh creator: Seng-Wei Ooi creator: Chung-Yi Li creator: Hua-Fen Chen uri: https://doi.org/10.7717/peerj.14609 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chang et al. title: Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies link: https://peerj.com/articles/14616 last-modified: 2023-01-09 description: BackgroundIn metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.MethodsWe investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.ResultsThe reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6–1% of the Amplicon Sequence Variants (ASVs). creator: Francesco Mugnai creator: Federica Costantini creator: Anne Chenuil creator: Michèle Leduc creator: José Miguel Gutiérrez Ortega creator: Emese Meglécz uri: https://doi.org/10.7717/peerj.14616 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mugnai et al. title: Different types of plantar vibration affect gait characteristics differently while walking on different inclines link: https://peerj.com/articles/14619 last-modified: 2023-01-09 description: BackgroundPlantar vibration has been widely used to strengthen the sensation of the somatosensory system, further enhancing balance during walking on a level surface in patients with stroke. However, previous studies with plantar vibration only involved the level surface, which neglected the importance of inclined/declined walking in daily life. Thus, combining the plantar vibration and inclined/declined walking might answer a critical research question: whether different types of plantar vibration had different effects on gait characteristics during walking on different inclines.MethodsEighteen healthy young adults were recruited. Fifteen walking conditions were assigned randomly to these healthy adults (no, sub-, and supra-threshold plantar vibration × five different inclines: +15%, +8%, 0%, −8%, −15% grade). A motion capture system with eight cameras captured 12 retro-reflective markers and measured the stride time, stride length, step width, and respective variabilities.ResultsA significant interaction between vibration and inclination was observed in the stride time (p < 0.0001) and step width (p = 0.015). Post hoc comparisons found that supra-threshold vibration significantly decreased the stride time (−8%: p < 0.001; −15%: p < 0.001) while the sub-threshold vibration significantly increased the step width (−8%: p = 0.036) in comparison with no plantar vibration.ConclusionsWhen walking downhill, any perceivable (supra-threshold) vibration on the plantar area decreased the stride time. Also, the increase in step width was observed by non-perceivable (sub-threshold) plantar vibration while walking uphill. These observations were crucial as follows: (1) applying sub-threshold plantar vibrations during uphill walking could increase the base of support, and (2) for those who may need challenges in locomotor training, applying supra-threshold vibration during downhill walking could reach this specific training goal. creator: Haoyu Xie creator: Haolan Liang creator: Jung H. Chien uri: https://doi.org/10.7717/peerj.14619 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xie et al. title: Dominance of Bacillus species in the wheat (Triticum aestivum L.) rhizosphere and their plant growth promoting potential under salt stress conditions link: https://peerj.com/articles/14621 last-modified: 2023-01-09 description: Wheat (Triticum aestivum L.) is a major source of calorific intake in its various forms and is considered one of the most important staple foods. Improved wheat productivity can contribute substantially to addressing food security in the coming decades. Soil salinity is the most serious limiting factor in crop production and fertilizer use efficiency. In this study, 11 bacteria were isolated from wheat rhizosphere and examined for salt tolerance ability. WGT1, WGT2, WGT3, WGT6, WGT8, and WGT11 were able to tolerate NaCl salinity up to 4%. Bacterial isolates were characterized in vitro for plant growth-promoting properties including indole-3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, zinc solubilization, biofilm formation, and cellulase-pectinase production. Six isolates, WGT1, WGT3, WGT4, WGT6, WGT8, and WGT9 showed IAA production ability ranging from 0.7–6 µg m/L. WGT8 displayed the highest IAA production. Five isolates, WGT1, WGT2, WGT5, WGT10, and WGT11, demonstrated phosphate solubilization ranging from 1.4–12.3 µg m/L. WGT2 showed the highest phosphate solubilization. Nitrogen fixation was shown by only two isolates, WGT1 and WGT8. Zinc solubilization was shown by WGT1 and WGT11 on minimal media. All isolates showed biofilm formation ability, where WGT4 exhibited maximum potential. Cellulase production ability was noticed in WGT1, WGT2, WGT4, and WGT5, while pectinase production was observed in WGT2 and WGT3. Phylogenetic identification of potential bacteria isolates confirmed their close relationship with various species of the genus Bacillus. WGT1, WGT2, and WGT3 showed the highest similarity with B. cereus, WGT6 with B. tianshenii, WGT8 with B. subtilis, and WGT11 with B. thuringiensis. Biofertilizer characteristics of salt-tolerant potential rhizospheric bacteria were evaluated by inoculating wheat plants under controlled conditions and field experiments. B. cereus WGT1 and B. thuringiensis WGT11 displayed the maximum potential to increase plant growth parameters and enhance grain yield by 37% and 31%, respectively. Potential bacteria of this study can tolerate salt stress, have the ability to produce plant growth promoting substances under salt stress and contribute significantly to enhance wheat grain yield. These bacterial isolates have the potential to be used as biofertilizers for improved wheat production under salinity conditions and contribute to the sustainable agriculture. creator: Syeda Tahseen Zahra creator: Mohsin Tariq creator: Muhammad Abdullah creator: Farrukh Azeem creator: Muhammad Arslan Ashraf uri: https://doi.org/10.7717/peerj.14621 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zahra et al. title: Construction of an anthropometric discriminant model for identification of elite swimmers: an adaptive lasso approach link: https://peerj.com/articles/14635 last-modified: 2023-01-09 description: BackgroundAnthropometric characteristics are important factors that affect swimming performance. The aim of this study is to build a discriminant model using anthropometric factors to identify elite short-to-medium-distance freestyle swimmers through an adaptive Lasso approach.MethodsThe study recruited 254 swimmers (145 males and 109 females) who were divided them into elite (aged 17.9 ± 2.2 years, FINA points 793.8 ± 73.8) and non-elite (aged 17.1 ± 1.3 years, FINA points 560.6 ± 78.7) groups. Data for 73 variables were obtained, including basic information, anthropometric and derivative indicators. After filtering out highly correlated variables, 24 candidate variables were retained to be used in adaptive Lasso to select variables for prediction of elite swimmers. Deviance and area under the curve (AUC) were applied to assess the goodness of fit and prediction accuracy of the model, respectively.ResultsThe adaptive Lasso selected 12 variables using the whole sample, with an AUC being 0.926 (95% CI [0.895–0.956]; P = 2.42 × 10−29). In stratified analysis by gender, nine variables were selected for male swimmers with an AUC of 0.921 (95% CI [0.880–0.963]; P = 8.82 × 10−17), and eight variables were for female swimmers with an AUC of 0.941 (95% CI [0.898–0.984]; P = 7.67 × 10−15).ConclusionThe adaptive Lasso showed satisfactory performance in selecting anthropometric characteristics to identify elite swimmers. Additional studies with longitudinal data or data from other ethnicities are needed to validate our findings. creator: Qile Pan creator: Rongxin Zhu creator: Jun Qiu creator: Guang Cai uri: https://doi.org/10.7717/peerj.14635 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pan et al. title: Integrated omics analysis reveals the immunologic characteristics of cystic Peyer’s patches in the cecum of Bactrian camels link: https://peerj.com/articles/14647 last-modified: 2023-01-09 description: Bactrian camels have specific mucosa-associated lymphoid tissue (MALT) throughout the large intestine, with species-unique cystic Peyer’s patches (PPS) as the main type of tissue. However, detailed information about the molecular characteristics of PPS remains unclear. This study applied a transcriptomic analysis, untargeted metabolomics, and 16S rDNA sequencing to compare the significant differences between PPS and the adjacent normal intestine tissues (NPPS) during the healthy stage of three young Bactrian camels. The results showed that samples from PPS could be easily differentiated from the NPPS samples based on gene expression profile, metabolites, and microbial composition, separately indicated using dimension reduction methods. A total of 7,568 up-regulated and 1,266 down-regulated differentially expressed genes (DEGs) were detected, and an enrichment analysis found 994 DEGs that participated in immune-related functions, and a co-occurance network analysis identified nine hub genes (BTK, P2RX7, Pax5, DSG1, PTPN2, DOCK11, TBX21, IL10, and HLA-DOB) during multiple immunologic processes. Further, PPS and NPPS both had a similar pattern of most compounds among all profiles of metabolites, and only 113 differentially expressed metabolites (DEMs) were identified, with 101 of these being down-regulated. Deoxycholic acid (DCA; VIP = 37.96, log2FC = −2.97, P = 0), cholic acid (CA; VIP = 13.10, log2FC = −2.10, P = 0.01), and lithocholic acid (LCA; VIP = 12.94, log2FC = −1.63, P = 0.01) were the highest contributors to the significant dissimilarities between groups. PPS had significantly lower species richness (Chao1), while Firmicutes (35.92% ± 19.39%), Bacteroidetes (31.73% ± 6.24%), and Proteobacteria (13.96% ± 16.21%) were the main phyla across all samples. The LEfSe analysis showed that Lysinibacillus, Rikenellaceae_RC9_gut_group, Candidatus_Stoquefichus, Mailhella, Alistipes, and Ruminococcaceae_UCG_005 were biomarkers of the NPPS group, while Escherichia_Shigella, Synergistes, Pyramidobacter, Odoribacter, Methanobrevibacter, Cloacibacillus, Fusobacterium, and Parabacteroides were significantly higher in the PPS group. In the Procrustes analysis, the transcriptome changes between groups showed no significant correlations with metabolites or microbial communities, whereas the alteration of metabolites significantly correlated with the alteration of the microbial community. In the co-occurrence network, seven DEMs (M403T65-neg, M329T119-neg, M309T38-neg, M277T42-2-neg, M473T27-neg, M747T38-1-pos, and M482t187-pos) and 14 genera (e.g., Akkermansia, Candidatus-Stoquefichus, Caproiciproducens, and Erysipelatoclostridium) clustered much more tightly, suggesting dense interactions. The results of this study provide new insights into the understanding of the immune microenvironment of the cystic PPS in the cecum of Bactrian camels. creator: Xiao shan Wang creator: Pei xuan Li creator: Bao shan Wang creator: Wang dong Zhang creator: Wen hui Wang uri: https://doi.org/10.7717/peerj.14647 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: A more reliable species richness estimator based on the Gamma–Poisson model link: https://peerj.com/articles/14540 last-modified: 2023-01-06 description: BackgroundAccurately estimating the true richness of a target community is still a statistical challenge, particularly in highly diverse communities. Due to sampling limitations or limited resources, undetected species are present in many surveys and observed richness is an underestimate of true richness. In the literature, methods for estimating the undetected richness of a sample are generally divided into two categories: parametric and nonparametric estimators. Imposing no assumptions on species detection rates, nonparametric methods demonstrate robust statistical performance and are widely used in ecological studies. However, nonparametric estimators may seriously underestimate richness when species composition has a high degree of heterogeneity. Parametric approaches, which reduce the number of parameters by assuming that species-specific detection probabilities follow a given statistical distribution, use traditional statistical inference to calculate species richness estimates. When species detection rates meet the model assumption, the parametric approach could supply a nearly unbiased estimator. However, the infeasibility and inefficiency of solving maximum likelihood functions limit the application of parametric methods in ecological studies when the model assumption is violated, or the collected data is sparse.MethodTo overcome these estimating challenges associated with parametric methods, an estimator employing the moment estimation method instead of the maximum likelihood estimation method is proposed to estimate parameters based on a Gamma-Poisson mixture model. Drawing on the concept of the Good-Turing frequency formula, the proposed estimator only uses the number of singletons, doubletons, and tripletons in a sample for undetected richness estimation.ResultsThe statistical behavior of the new estimator was evaluated by using real and simulated data sets from various species abundance models. Simulation results indicated that the new estimator reduces the bias presented in traditional nonparametric estimators, presents more robust statistical behavior compared to other parametric estimators, and provides confidence intervals with better coverage among the discussed estimators, especially in assemblages with high species composition heterogeneity. creator: Chun-Huo Chiu uri: https://doi.org/10.7717/peerj.14540 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chiu title: The biomarkers discovery of hyperuricemia and gout: proteomics and metabolomics link: https://peerj.com/articles/14554 last-modified: 2023-01-06 description: BackgroundHyperuricemia and gout are a group of disorders of purine metabolism. In recent years, the incidence of hyperuricemia and gout has been increasing, which is a severe threat to people’s health. Several studies on hyperuricemia and gout in proteomics and metabolomics have been conducted recently. Some literature has identified biomarkers that distinguish asymptomatic hyperuricemia from acute gout or remission of gout. We summarize the physiological processes in which these biomarkers may be involved and their role in disease progression.MethodologyWe used professional databases including PubMed, Web of Science to conduct the literature review. This review addresses the current landscape of hyperuricemia and gout biomarkers with a focus on proteomics and metabolomics.ResultsProteomic methods are used to identify differentially expressed proteins to find specific biomarkers. These findings may be suggestive for the diagnosis and treatment of hyperuricemia and gout to explore the disease pathogenesis. The identified biomarkers may be mediators of the link between hyperuricemia, gout and kidney disease, metabolic syndrome, diabetes and hypertriglyceridemia. Metabolomics reveals the main influential pathways through small molecule metabolites, such as amino acid metabolism, lipid metabolism, or other characteristic metabolic pathways. These studies have contributed to the discovery of Chinese medicine. Some traditional Chinese medicine compounds can improve the metabolic disorders of the disease.ConclusionsWe suggest some possible relationships of potential biomarkers with inflammatory episodes, complement activation, and metabolic pathways. These biomarkers are able to distinguish between different stages of disease development. However, there are relatively few proteomic as well as metabolomic studies on hyperuricemia and gout, and some experiments are only primary screening tests, which need further in-depth study. creator: Xinghong Wu creator: Chongge You uri: https://doi.org/10.7717/peerj.14554 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wu and You title: On the origin of mitochondria: a multilayer network approach link: https://peerj.com/articles/14571 last-modified: 2023-01-06 description: BackgoundThe endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method.MethodsWe used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa.ResultsIn our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades.ConclusionBy leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies. creator: Dérick Gabriel F. Borges creator: Daniel S. Carvalho creator: Gilberto C. Bomfim creator: Pablo Ivan P. Ramos creator: Jerzy Brzozowski creator: Aristóteles Góes-Neto creator: Roberto F. S. Andrade creator: Charbel El-Hani uri: https://doi.org/10.7717/peerj.14571 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Borges et al. title: Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit link: https://peerj.com/articles/14581 last-modified: 2023-01-06 description: Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucmá cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Umán cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates. creator: Omar Oltehua-López creator: Mario A. Arteaga-Vázquez creator: Victoria Sosa uri: https://doi.org/10.7717/peerj.14581 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Oltehua-López et al. title: The role of subjective significance, valence and arousal in the explicit processing of emotion-laden words link: https://peerj.com/articles/14583 last-modified: 2023-01-06 description: Emotional categorisation (deciding whether a word is emotional or not) is a task that employs the explicit analysis of the emotional meaning of words. Therefore, it allows for assessing the role of emotional factors, i.e., valence, arousal, and subjective significance, in emotional word processing. The aim of the current experiment was to investigate the role of subjective significance, a reflective form of activation that is similar to arousal (the automatic form), in the processing of emotional meaning. We applied the orthogonal manipulation of three emotional factors. Thus, we were able to precisely differentiate the effects of each factor and search for interactions between them. We expected valence to shape the late positive complex LPC component, while subjective significance and arousal were expected to shape the P300 and N400 components. We observed the effects of subjective significance throughout the whole span of processing, while the arousal effect was present only in the LPC component. We also observed that amplitudes for N400 and LPC discriminated negative from positive valence. The results showed that all factors included in the analysis should be taken into account while explaining the processing of emotion-laden words; especially interesting is the subjective significance, which was shown to shape processing individually, as well as to come into interaction with valence and arousal. creator: Kamil K. Imbir creator: Joanna Duda-Goławska creator: Adrianna Wielgopolan creator: Adam Sobieszek creator: Maciej Pastwa creator: Jaroslaw Zygierewicz uri: https://doi.org/10.7717/peerj.14583 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Imbir et al. title: No effect of attentional modulation by spatial cueing in a masked numerical priming paradigm using continuous flash suppression (CFS) link: https://peerj.com/articles/14607 last-modified: 2023-01-06 description: One notion emerging from studies on unconscious visual processing is that different “blinding techniques” seem to suppress the conscious perception of stimuli at different levels of the neurocognitive architecture. However, even when only the results from a single suppression method are compared, the picture of the scope and limits of unconscious visual processing remains strikingly heterogeneous, as in the case of continuous flash suppression (CFS). To resolve this issue, it has been suggested that high-level semantic processing under CFS is facilitated whenever interocular suppression is attenuated by the removal of visuospatial attention. In this behavioral study, we aimed to further investigate this “CFS-attenuation-by-inattention” hypothesis in a numerical priming study using spatial cueing. Participants performed a number comparison task on a visible target number (“compare number to five”). Prime-target pairs were either congruent (both numbers smaller, or both larger than five) or incongruent. Based on the “CFS-attenuation-by-inattention” hypothesis, we predicted that reaction times (RTs) for congruent prime-target pairs should be faster than for incongruent ones, but only when the prime was presented at the uncued location. In the invisible condition, we observed no priming effects and thus no evidence in support of the “CFS-attenuation-by-inattention” hypothesis. In the visible condition, we found an inverse effect of prime-target congruency. Our results agree with the notion that the representation of CF-suppressed stimuli is fractionated, and limited to their basic, elemental features, thus precluding semantic processing. creator: Juliane Handschack creator: Marcus Rothkirch creator: Philipp Sterzer creator: Guido Hesselmann uri: https://doi.org/10.7717/peerj.14607 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Handschack et al. title: A novel fatty acid metabolism-related gene prognostic signature and candidate drugs for patients with hepatocellular carcinoma link: https://peerj.com/articles/14622 last-modified: 2023-01-06 description: Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Fatty acid metabolism (FAM) is associated with the development and treatment of HCC. This study aimed to build a FAM-related gene model to assess the prognosis of HCC and provide guidance for individual treatment. RNA-sequencing data of patients with HCC from The Cancer Genome Atlas and Gene Expression Omnibus database (GSE14520) were extracted as the training and validation sets, respectively. A FAM-related gene predictive signature was built, and the performance of prognostic model was assessed. The immune infiltration and drug sensitivity were also evaluated. Quantitative real-time polymerase chain reaction and western blot were performed to evaluate the levels of the model genes. A 12-gene FAM-related risk signature was constructed; patients with a higher risk score had poorer prognosis than those with a lower risk score. Risk score was shown as an independent risk factor for overall survival of HCC, and the signature was further confirmed as an effective and accurate model. A nomogram was constructed, and it exhibited the good performance in the prognostic prediction. In addition, the immune cell infiltration and sensitivity to chemotherapy drugs were correlated with different risk levels. Finally, quantitative real-time polymerase chain reaction and western blot proved the changes of above genes. Differential expression of FAM-related genes can be used to predict response to immunotherapy and chemotherapy, and improve the clinical prognosis evaluation of patients with HCC, which provides new clues for further experimental exploration and verification on FAM-related genes in HCC. creator: Jingze Yang creator: Xin Yang creator: Jinlu Guo creator: Shi Liu uri: https://doi.org/10.7717/peerj.14622 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Evaluating the effect of the incidence angle of ALOS-2 PALSAR-2 on detecting aquaculture facilities for sustainable use of coastal space and resources link: https://peerj.com/articles/14649 last-modified: 2023-01-06 description: BackgroundDriven by the growing world population, aquaculture plays a key role in meeting the increasing demand for food. However, aquaculture facilities in Japan are widely installed in coastal waters where natural disasters, such as typhoons and tsunamis, might wash these facilities away, thereby interfering with maritime navigation safety. Therefore, it is imperative to efficiently monitor the state of aquaculture facilities daily, particularly after a disaster in real time. To this end, several new space-borne L-band synthetic aperture radars (SARs) continue to be launched now and in the future, whose utilizations are expected to increase nationally and internationally. An example is the Japan Aerospace Exploration Agency, currently operating a SAR that can be operated day and night, and even under cloudy conditions, called ALOS-2 PALSAR-2.MethodsBased on the above facts, this study evaluated the effect of the incidence angle of ALOS-2 PALSAR-2 HH single-polarization data, using 3 m spatial resolution, on aquaculture raft detection. As the study site, we selected Ago Bay, located on the Pacific coast of Mie Prefecture in central Japan since the Nankai Trough Megathrust Earthquake and tsunamis have been predicted to occur in the future around this area. Then, we analyzed the sigma zero (backscattering coefficient) of aquaculture rafts and their surrounding sea surfaces, including the relationships between satellite orbits and aquaculture raft directions.ResultsInvestigations revealed that the optimum incidence angle for detecting aquaculture rafts in this study was 33.8°–45.1°. Differences in the sigma zero values existed between the ascending and descending orbits. However, the incidence angles differed on the orbits. Then, differences in the median sigma zero values across a range of incidence angles were evaluated under the descending orbit. In addition, when the directions of the aquaculture rafts were closely perpendicular to the satellite orbit, aquaculture rafts tended to show the highest values of sigma zero due to Bragg resonance scattering. Hence, this knowledge may allow for the rapid detection of aquaculture rafts during an emergency without going on-site. creator: Hiroki Murata creator: Toyonobu Fujii creator: Chinatsu Yonezawa uri: https://doi.org/10.7717/peerj.14649 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Murata et al. title: Depletion of PSMD14 suppresses bladder cancer proliferation by regulating GPX4 link: https://peerj.com/articles/14654 last-modified: 2023-01-06 description: ObjectiveThe aim of this study was to investigate the role of deubiquitinase (DUB) 26S proteasome non-ATPase regulatory subunit 14 (PSMD14) in patients with bladder cancer.MethodsFrom 2016 to 2018, 181 patients diagnosed with primary bladder cancer at the Affiliated Hospital of Qingdao University were recruited. The expression of PSMD14 in bladder cancer tissues was tested by immunochemistry. The association between PSMD14 expression and clinical and pathological data and outcomes of bladder cancer patients was determined. Overexpression and knockdown cells were constructed to evaluate the effects of PSMD14 on proliferation of bladder cancer cells.ResultsOur results showed that PSMD14 was significantly overexpressed in bladder cancer tissues compared to adjacent non-tumor tissues (76.24% vs 23.76%, P = 0.02). The expression of PSMD14 was significantly higher in patients with larger tumor diameters (85.14% vs 70.09%, P = 0.019) and patients with a family history of cancer (92.16% vs 70.00%, P = 0.002). Patients with high expression of PSMD14 had poor disease-free survival (DFS) (HR = 2.89, 95% CI [1.247–6.711], P = 0.013). Gain and loss of function experiments demonstrated that PSMD14 deficiency inhibited bladder cancer cell proliferation. Additionally, depletion of PSMD14 suppressed bladder cancer cell growth via down-regulation of GPX4, and the promotion of PSMD14-induced cell growth was observably reversed by the GPX4 inhibitor RSL3.ConclusionWe determined that PSMD14 is highly expressed in bladder cancer tissues, and that PSMD14 expression correlated with poor disease-free survival. Depletion of PSMD14 could inhibit the proliferation of bladder cancer cells through the downregulation of GPX4. Therefore, PSMD14 may be an effective target for the treatment of bladder cancer. creator: Changxin Jia creator: Xin Zhang creator: Tingting Qu creator: Xiuyun Wu creator: Yu Li creator: Yang Zhao creator: Lijiang Sun creator: Qing Wang uri: https://doi.org/10.7717/peerj.14654 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Jia et al. title: Immune fitness and lifestyle habits of Saudi medical students: a cross sectional study link: https://peerj.com/articles/14363 last-modified: 2023-01-05 description: IntroductionImmune function reaches an optimum level in young adults. However, young adults are more likely to adopt potentially harmful habits that may pose a risk to their long-term health and immune fitness, and which eventually may put a substantial burden on the healthcare system. This study aimed to assess the status of medical students’ immune fitness, using the immune status questionnaire (ISQ) and exploring the association with the commonly adopted lifestyle habits hypothesized to have an impact on immune functions.MethodsA descriptive, cross-sectional study was conducted among preclinical students attending the medical school of King Abdulaziz University. An online self-reported questionnaire was used to assess the immune status (ISQ), perceived (momentary) immune fitness, general health, lifestyle habits and students’ perception of these lifestyle-associated impacts on immune fitness. Descriptive, Spearman’s correlation and stepwise linear regression analyses were performed.ResultsIn a pooled sample of 211 participants, the overall ISQ score was 6.00 ± 5.0 with statistically significant abnormally lower scores in females (ISQ 5.00 ± 5.0, p < 0.001). 49.29% of respondents experienced poor immune fitness as measured by the ISQ (<6). The ISQ score was significantly correlated with fast and fatty food consumption (p = 0.003), daytime sleepiness (p = 0.001), and BMI subgroups (p = 0.028) negatively and positively correlated with adherence to a program of exercise (p = 0.005). A total of 41.23% of participants who reported a normal immune health, rated at ≥6 were graded below 6 on the ISQ score. Only 62.6% of students were able to correctly identify the effects of fast and fatty food consumption on immune fitness.ConclusionPoor immune fitness was common among medical students in KAU and associated significantly with their adopted lifestyle habits. Although, other factors can be significant contributors, biased immune health perception and lack of awareness of these lifestyle-associated impacts on immune fitness and general health may hinder the adoption of healthier habits. Immune biomarkers should be implemented in future work. creator: Azzah S. Alharbi uri: https://doi.org/10.7717/peerj.14363 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Alharbi title: Serratia marcescens antibiotic resistance mechanisms of an opportunistic pathogen: a literature review link: https://peerj.com/articles/14399 last-modified: 2023-01-05 description: Serratia marcescens is a ubiquitous bacterium from order Enterobacterales displaying a high genetic plasticity that allows it to adapt and persist in multiple niches including soil, water, plants, and nosocomial environments. Recently, S. marcescens has gained attention as an emerging pathogen worldwide, provoking infections and outbreaks in debilitated individuals, particularly newborns and patients in intensive care units. S. marcescens isolates recovered from clinical settings are frequently described as multidrug resistant. High levels of antibiotic resistance across Serratia species are a consequence of the combined activity of intrinsic, acquired, and adaptive resistance elements. In this review, we will discuss recent advances in the understanding of mechanisms guiding resistance in this opportunistic pathogen. creator: Faviola Tavares-Carreon creator: Karla De Anda-Mora creator: Idalia C. Rojas-Barrera creator: Angel Andrade uri: https://doi.org/10.7717/peerj.14399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tavares-Carreon et al. title: Validation of low-density lipoprotein cholesterol equations in pediatric population link: https://peerj.com/articles/14544 last-modified: 2023-01-05 description: Several studies have shown a high prevalence of dyslipidemia in children. Since childhood lipid concentrations continue into adulthood, recognition of lipid abnormalities in the early period is crucial to prevent the development of future coronary heart disease (CHD). Low density lipoprotein cholesterol (LDL-C) is one of the most used parameters in the initiation and follow-up of treatment in patients with dyslipidemia. It is a well known fact that LDL-C lowering therapy reduces the risk of future CHD. Therefore, accurate determination of the LDL-C levels is so important for the management of lipid abnormalities. This study aimed to validate different LDL-C estimating equations in the Turkish population, composed of children and adolescents. A total of 3,908 children below 18 years old at Sivas Cumhuriyet University Hospital (Sivas, Turkey) were included in this study. LDL-C was directly measured by direct homogeneous assays, i.e., Roche, Beckman, Siemens and estimated by Friedewald’s, Martin/Hopkins’, extended Martin-Hopkins’ and Sampson’s formulas. The concordances between the estimations obtained by the formulas and the direct measurements were evaluated both overall and separately for the LDL-C, triglycerides (TG) and non-high-density lipoprotein cholesterol (non-HDL-C) sublevels. Linear regression analysis was performed and residual error plots were generated between each estimation and direct measurement method. Coefficient of determination (R2) and mean absolute deviations were also evaluated. The overall concordance of Friedewald, Sampson, Martin-Hopkins and the extended Martin-Hopkins formula were 64.6%, 69.9%, 69.4%, and 84.3% for the Roche direct assay, 69.8%, 71.6%, 73.6% and 80.4% for the Siemens direct assay, 66.5%, 68.8%, 68.9% and 82.1% for the Beckman direct assay, respectively. The extended Martin-Hopkins formula had the highest concordance coefficient in both overall and all sublevels of LDL-C, non-HDL-C, and TG. When estimating the LDL-C categories, the highest underestimation degrees were obtained with the Friedewald formula. Our analysis, conducted in a large pediatric population, showed that the extended Martin-Hopkins equation gives more reliable results in estimation of LDL-C compared to other equations. creator: Gözde Ertürk Zararsız creator: Serkan Bolat creator: Ahu Cephe creator: Necla Kochan creator: Serra Ilayda Yerlitaş creator: Halef Okan Doğan creator: Gökmen Zararsız uri: https://doi.org/10.7717/peerj.14544 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ertürk Zararsız et al. title: Comparing diversity patterns and processes of microbial community assembly in water column and sediment in Lake Wuchang, China link: https://peerj.com/articles/14592 last-modified: 2023-01-05 description: The study compare the diversity patterns and processes of microbial community assembly in the water and sediment of Lake Wuchang (China) using high-throughput sequencing of 16S rRNA gene amplicons. A higher microbial α-diversity in the sediment was revealed (P < 0.01), and the most common bacterial phyla in water column were Proteobacteria, Cyanobacteria and Actinobacteria, while Proteobacteria, Acidobacteria, Chloroflexi and Nitrospirae were dominant in sediment. Functions related to phototrophy and nitrogen metabolism primarily occurred in the water column and sediment, respectively. The microbial communities in water column from different seasons were divided into three groups, while no such dispersion in sediment based on PCoA and ANOSIM. According to Pearson correlation analysis, water temperature, dissolved oxygen, water depth, total nitrogen, ammonium, and nitrite were key factors in determining microbial community structure in water column, while TN in sediment, conductivity, and organic matter were key factors in sediment. However, the stochastic processes (|βNTI| < 2) dominated community assembly in both the water column and sediment of Lake Wuchang. These data will provide a foundation for microbial development and utilization in lake water column and sediment under the circumstances of increasing tendency of lake ecological fishery in China. creator: Xuemei Li creator: Zihao Meng creator: Kang Chen creator: Feifei Hu creator: Lu Liu creator: Tingbing Zhu creator: Deguo Yang uri: https://doi.org/10.7717/peerj.14592 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Short-term improvement of heat tolerance in naturally growing Acropora corals in Okinawa link: https://peerj.com/articles/14629 last-modified: 2023-01-05 description: Mass bleaching and subsequent mortality of reef corals by heat stress has increased globally since the late 20th century, due to global warming. Some experimental studies have reported that corals may increase heat tolerance for short periods, but only a few such studies have monitored naturally-growing colonies. Therefore, we monitored the survival, growth, and bleaching status of Acropora corals in fixed plots by distinguishing individual colonies on a heat-sensitive reef flat in Okinawa, Japan. The level of heat stress, assessed by the modified version of degree heating week duration in July and August, when the seawater temperature was the highest, was minimally but significantly higher in 2017 than in 2016; however, the same colonies exhibited less bleaching and mortality in 2017 than in 2016. Another study conducted at the same site showed that the dominant unicellular endosymbiotic algal species did not change before and after the 2016 bleaching, indicating that shifting and switching of the Symbiodiniaceae community did not contribute to improved heat tolerance. Colonies that suffered from partial mortality in 2016 were completely bleached at higher rates in 2017 than those without partial mortality in 2016. The present results suggest that either genetic or epigenetic changes in coral hosts and/or algal symbionts, or the shifting or switching of microbes other than endosymbionts, may have improved coral holobiont heat tolerance. creator: Tanya Singh creator: Kazuhiko Sakai creator: Jun Ishida-Castañeda creator: Akira Iguchi uri: https://doi.org/10.7717/peerj.14629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Singh et al. title: A systematic analysis of anti-diabetic medicinal plants from cells to clinical trials link: https://peerj.com/articles/14639 last-modified: 2023-01-05 description: BackgroundDiabetes is one of the fastest-growing health emergencies of the 21st century, placing a severe economic burden on many countries. Current management approaches have improved diabetic care, but several limitations still exist, such as decreased efficacy, adverse effects, and the high cost of treatment, particularly for developing nations. There is, therefore, a need for more cost-effective therapies for diabetes management. The evidence-based application of phytochemicals from plants in the management of diseases is gaining traction.MethodologyVarious plants and plant parts have been investigated as antidiabetic agents. This review sought to collate and discuss published data on the cellular and molecular effects of medicinal plants and phytochemicals on insulin signaling pathways to better understand the current trend in using plant products in the management of diabetes. Furthermore, we explored available information on medicinal plants that consistently produced hypoglycemic effects from isolated cells to animal studies and clinical trials.ResultsThere is substantial literature describing the effects of a range of plant extracts on insulin action and insulin signaling, revealing a depth in knowledge of molecular detail. Our exploration also reveals effective antidiabetic actions in animal studies, and clear translational potential evidenced by clinical trials.ConclusionWe suggest that this area of research should be further exploited in the search for novel therapeutics for diabetes. creator: Simeon Omale creator: Kennedy I. Amagon creator: Titilayo O. Johnson creator: Shaun Kennedy Bremner creator: Gwyn W. Gould uri: https://doi.org/10.7717/peerj.14639 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Omale et al. title: Retrospective validation of bone risk stratification criteria for men with de novo metastatic hormone-naive prostate cancer in China link: https://peerj.com/articles/14500 last-modified: 2023-01-04 description: BackgroundBone metastasis has been suggested to be a significant impactor on the prognosis of newly diagnosed de novo metastatic hormone-sensitive prostate cancer (mHSPC), and some risk stratification models have been proposed on the basis of this hypothesis. However, the effectiveness of these risk stratification criteria has not been fully evaluated in China. This study aimed to evaluate the effectiveness of the risk stratification models in China.MethodsA total of 140 patients who were newly diagnosed with metastatic prostate cancer followed by primary androgen deprivation-based therapy from January 2008 to June 2021 at our institution were enrolled in this study. The patients were divided into different groups on the basis of high- and low-volume disease (H/LVD) criteria, high-and low-risk disease (H/LRD) criteria, extremity bone metastasis criteria (EBM), and extent of disease (EOD) criteria. The area under the receiver operating characteristic (ROC) curve (AUC) and decision curve analysis (DCA) were used to compare the validity and net benefit of these models. Using the Cox proportional hazards model, we performed univariable and multivariable analyses of the factors influencing overall survival (OS) and the time of progression to metastatic castration-resistant prostate cancer (CRPC).ResultsThe median patient age was 72 years. Most patients had a Gleason score ≥8 (102 cases, 72.9%) and clinical T stage >2 (75 cases, 53.6%). The median follow-up time was 25 months (range, 2–95 months). Ninety-two patients progressed to CRPC and fifty-seven patients died during the follow-up. The AUC of OS and CRPC showed that the EOD model had higher validity than the other risk stratification models. DCA shows that the net benefit of the EOD model on OS was better than that of the other risk stratification models. As for CRPC, the net benefit of the EOD model was second only to that of the H/LRD model when the threshold was <0.5; however, when the threshold was >0.5, the EOD model outperformed the other models. The effectiveness of EOD as an independent prognostic variable was verified through univariable and multivariable analyses.ConclusionThe EOD model yields reasonable risk stratification for use in Chinese mHSPC patients, providing further evidence supporting its role in clinical decision-making. creator: Yang Zhang creator: Li Ding creator: Yuxin Zheng creator: Kun Wang creator: Wentao Xia creator: Junqi Wang creator: Peng Ge uri: https://doi.org/10.7717/peerj.14500 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Novice assessors demonstrate good intra-rater agreement and reliability when determining pressure pain thresholds; a cross-sectional study link: https://peerj.com/articles/14565 last-modified: 2023-01-04 description: BackgroundExperienced assessors show good intra-rater reproducibility (within-session and between-session agreement and reliability) when using an algometer to determine pressure pain thresholds (PPT). However, it is unknown whether novice assessors perform equally well. This study aimed to determine within and between-session agreement and reliability of PPT measurements performed by novice assessors and explored whether these parameters differed per assessor and algometer type.MethodsTen novice assessors measured PPTs over four test locations (tibialis anterior muscle, rectus femoris muscle, extensor carpi radialis brevis muscle and paraspinal muscles C5-C6) in 178 healthy participants, using either a Somedic Type II digital algometer (10 raters; 88 participants) or a Wagner Force Ten FDX 25 digital algometer (nine raters; 90 participants). Prior to the experiment, the novice assessors practiced PPTs for 3 h per algometer. Each assessor measured a different subsample of ~9 participants. For both the individual assessor and for all assessors combined (i.e., the group representing novice assessors), the standard error of measurement (SEM) and coefficient of variation (CV) were calculated to reflect within and between-session agreement. Reliability was assessed using intraclass correlation coefficients (ICC1,1).ResultsWithin-session agreement expressed as SEM ranged from 42 to 74 kPa, depending on the test location and device. Between-session agreement, expressed as SEM, ranged from 36 to 76 kPa and the CV ranged from 9–16% per body location. Individual assessors differed from the mean group results, ranging from −55 to +32 kPa or from −9.5 to +6.6 percentage points. Reliability was good to excellent (ICC1,1: 0.87 to 0.95). Results were similar for both types of algometers.ConclusionsFollowing 3 h of algometer practice, there were slight differences between assessors, but reproducibility in determining PPTs was overall good. creator: Roland R. Reezigt creator: Geranda E. C. Slager creator: Michel W. Coppieters creator: Gwendolyne G. M. Scholten-Peeters uri: https://doi.org/10.7717/peerj.14565 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Reezigt et al. title: Effect of oval foramen restriction and premature contraction of the arterial catheter on right heart function of fetuses and infants link: https://peerj.com/articles/14702 last-modified: 2023-01-04 description: ObjectiveThe effect of fetal oval foramen restriction and premature contraction of the arterial catheter for the right heart function of fetuses and infants was studied by evaluating the right and left ventricular (RV/LV) ratios, the tricuspid annular plane systolic excursion (TAPSE) value, and the Tei index of right heart function parameters.MethodsThis study was approved by the Ethics Committee of First Affiliated Hospital of Hebei North University (K20190116). We collected 257 fetuses between March 2020 and December 2021. Among these, 98 fetuses that did not have any heart abnormalities were assigned to group A, 91 fetuses with restriction of the left and right atrial channels were assigned to group B, and 68 fetuses with premature contraction of the arterial catheter were assigned to group C. The ventricular transverse diameter, the right heart TAPSE value and the Tei index of fetuses in late pregnancy and 90 days after birth were measured in the three groups, and the diagnostic value of each index for the right heart function injury was evaluated. P < 0.05 indicates significant.ResultsThe P-value of the TAPSE value and Tei index of infants in BC and AC groups and postnatal infants were less than 0.05, which was significant. In the BC group, the RV/LV ratio of fetuses was compared when P > 0.05, which was not significant; however, P < 0.05 after birth was considered significant. For fetuses and postnatal infants in the BC group, the RV/LV ratio was negatively associated with the TAPSE value. However, it was positively associated with the Tei index; Diagnostic test results. To predict impaired right heart function after birth, TAPSE had low diagnostic value, RV/LV and Tei index had high diagnostic value.ConclusionsOval foramen restriction and premature contraction of the arterial catheter may affect the right heart function after birth and be related to the degree of the right heart enlargement. Although TAPSE prediction of the fetal and postnatal right heart function is limited, the RV/LV ratio and the Tei index can be used to predict impaired right heart function after birth. creator: Hongqiang Liu creator: Jinqiu Li creator: Xiaolong Cao creator: Yicheng Wang creator: Dehui Wen creator: Fengqun Dong creator: Jing Wang creator: Tian Li uri: https://doi.org/10.7717/peerj.14702 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Liu et al. title: Acute physiological outcomes of high-intensity functional training: a scoping review link: https://peerj.com/articles/14493 last-modified: 2023-01-03 description: BackgroundSystematic reviews and meta-analyses related to high-intensity functional training (HIFT) have been conducted. However, due to a restricted pool of available research, these investigations are often limited in scope. As such, a scoping review investigating the present literature surrounding the acute physiological response to HIFT-based exercise was chosen as a more appropriate structured review.MethodologyA scoping review was conducted following Arksey and O’Malley’s framework. Three large scale databases were searched to reveal any article pertaining to HIFT and related exercise terminology.ResultsA total of 2,241 articles were found during the initial search. Following this, titles, then abstracts, and full-texts were reviewed to determine inclusion eligibility. A total of 60 articles which investigated a combined total of 35 unique HIFT workouts were included within this review.ConclusionsA variety of physiological parameters and HIFT workouts have been examined. Markers of intensity (e.g., blood lactate concentrations, heart rate) have been most consistently assessed across all studies, and these support the idea that HIFT workouts are typically performed at high-intensity. In contrast, the inclusion of most other measures (e.g., hormonal, markers of inflammation and damage, energy expenditure, performance) has been inconsistent and has thus, limited the possibility for making generalized conclusions. Differences in study methodologies have further impacted conclusions, as different studies have varied in sample population characteristics, workouts assessed, and time points. Though it may be impossible to comprehensively research all possible HIFT workouts, consistent adoption of population definitions and workload quantification may overcome this challenge and assist with future comparisons. creator: Jacob M. McDougle creator: Gerald T. Mangine creator: Jeremy R. Townsend creator: Adam R. Jajtner creator: Yuri Feito uri: https://doi.org/10.7717/peerj.14493 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 McDougle et al. title: Phytoplankton diversity and chemotaxonomy in contrasting North Pacific ecosystems link: https://peerj.com/articles/14501 last-modified: 2023-01-03 description: BackgroundPhytoplankton is the base of majority of ocean ecosystems. It is responsible for half of the global primary production, and different phytoplankton taxa have a unique role in global biogeochemical cycles. In addition, phytoplankton abundance and diversity are highly susceptible to climate induced changes, hence monitoring of phytoplankton and its diversity is important and necessary.MethodsWater samples for phytoplankton and photosynthetic pigment analyses were collected in boreal winter 2017, along transect in the North Pacific Subtropical Gyre (NPSG) and the California Current System (CCS). Phytoplankton community was analyzed using light and scanning electron microscopy and photosynthetic pigments by high-performance liquid chromatography. To describe distinct ecosystems, monthly average satellite data of MODIS Aqua Sea Surface temperature and Chlorophyll a concentration, as well as Apparent Visible Wavelength were used.ResultsA total of 207 taxa have been determined, mostly comprised of coccolithophores (35.5%), diatoms (25.2%) and dinoflagellates (19.5%) while cryptophytes, phytoflagellates and silicoflagellates were included in the group “others” (19.8%). Phytoplankton spatial distribution was distinct, indicating variable planktonic dispersal rates and specific adaptation to ecosystems. Dinoflagellates, and nano-scale coccolithophores dominated NPSG, while micro-scale diatoms, and cryptophytes prevailed in CCS. A clear split between CCS and NPSG is evident in dendogram visualising LINKTREE constrained binary divisive clustering analysis done on phytoplankton counts and pigment concentrations. Of all pigments determined, alloxanthin, zeaxanthin, divinyl chlorophyll b and lutein have highest correlation to phytoplankton counts.ConclusionCombining chemotaxonomy and microscopy is an optimal method to determine phytoplankton diversity on a large-scale transect. Distinct communities between the two contrasting ecosystems of North Pacific reveal phytoplankton groups specific adaptations to trophic state, and support the hypothesis of shift from micro- to nano-scale taxa due to sea surface temperatures rising, favoring stratification and oligotrophic conditions. creator: Antonija Matek creator: Sunčica Bosak creator: Luka Šupraha creator: Aimee Neeley creator: Hrvoje Višić creator: Ivona Cetinić creator: Zrinka Ljubešić uri: https://doi.org/10.7717/peerj.14501 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Matek et al. title: Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota link: https://peerj.com/articles/14511 last-modified: 2023-01-03 description: BackgroundIntegrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation.MethodsHere we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes.ResultsAll the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30–50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover.ConclusionsThese results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards’ metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems. creator: Laura Baldo creator: Giacomo Tavecchia creator: Andreu Rotger creator: José Manuel Igual creator: Joan Lluís Riera uri: https://doi.org/10.7717/peerj.14511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Baldo et al. title: Influences of oxygen and temperature interaction on the antibacterial activity, antioxidant activity, serum biochemical indices, blood indices and growth performance of crucian carp link: https://peerj.com/articles/14530 last-modified: 2023-01-03 description: The well-being of fish used in aquaculture is of great interest. Oxygen and temperature are the main factors affecting the welfare of the crucian carp (carassius); however, there are few studies on the combined effects of these on the species. Therefore, this study investigated the impact of different temperatures (18 °C, 24 °C, 30 °C) and oxygen concentrations (2.1 mgL−1, 5.4 mgL−1, 9.3 mgL−1) on serum antibacterial activity, antioxidant activity, hematological parameters and growth performance of the crucian carp. The results showed that there were greater antibacterial properties under conditions of hypoxia at 18 °C (L18) and hyperoxia at 24 °C (H24). The activities of catalase, glutathione peroxidase and total superoxide dismutase were the highest at 24 °C under hypoxia and hyperoxia. In addition, the contents of glucose and total protein first increased and then decreased with the change of temperature; triglycerides were the lowest at 30 °C. The blood parameters of the carp were within a normal range at 24 °C; however, the growth rate was at its lowest under hypoxia treatment at 30 °C (L30). This study showed that high temperature impairs the antibacterial ability, antioxidant capacity and growth performance of the crucian carp, and high oxygen levels can alleviate these adverse reactions. This research provides a theoretical basis for subsequent aquaculture studies. creator: Bin Wang creator: Hanping Mao creator: Jian Zhao creator: Yong Liu creator: Yafei Wang creator: Xiaoxue Du uri: https://doi.org/10.7717/peerj.14530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Epigenetic regulation of dental-derived stem cells and their application in pulp and periodontal regeneration link: https://peerj.com/articles/14550 last-modified: 2023-01-03 description: Dental-derived stem cells have excellent proliferation ability and multi-directional differentiation potential, making them an important research target in tissue engineering. An increasing number of dental-derived stem cells have been discovered recently, including dental pulp stem cells (DPSCs), stem cells from exfoliated deciduous teeth (SHEDs), stem cells from apical papilla (SCAPs), dental follicle precursor cells (DFPCs), and periodontal ligament stem cells (PDLSCs). These stem cells have significant application prospects in tissue regeneration because they are found in an abundance of sources, and they have good biocompatibility and are highly effective. The biological functions of dental-derived stem cells are regulated in many ways. Epigenetic regulation means changing the expression level and function of a gene without changing its sequence. Epigenetic regulation is involved in many biological processes, such as embryonic development, bone homeostasis, and the fate of stem cells. Existing studies have shown that dental-derived stem cells are also regulated by epigenetic modifications. Pulp and periodontal regeneration refers to the practice of replacing damaged pulp and periodontal tissue and restoring the tissue structure and function under normal physiological conditions. This treatment has better therapeutic effects than traditional treatments. This article reviews the recent research on the mechanism of epigenetic regulation of dental-derived stem cells, and the core issues surrounding the practical application and future use of pulp and periodontal regeneration. creator: Yuyang Chen creator: Xiayi Wang creator: Zhuoxuan Wu creator: Shiyu Jia creator: Mian Wan uri: https://doi.org/10.7717/peerj.14550 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Agricultural water allocation with climate change based on gray wolf optimization in a semi-arid region of China link: https://peerj.com/articles/14577 last-modified: 2023-01-03 description: BackgroundWe quantified and evaluated the allocation of soil and water resources in the Aksu River Basin to measure the consequences of climate change on an agricultural irrigation system.MethodsWe first simulated future climate scenarios in the Aksu River Basin by using a statistical downscaling model (SDSM). We then formulated the optimal allocation scheme of agricultural water as a multiobjective optimization problem and obtained the Pareto optimal solution using the multi-objective grey wolf optimizer (MOGWO). Finally, optimal allocations of water and land resources in the basin at different times were obtained using an analytic hierarchy process (AHP).Results(1) The SDSM is able to simulate future climate change scenarios in the Aksu River Basin. Evapotranspiration (ET0) will increase significantly with variation as will the amount of available water albeit slightly. (2) To alleviate water pressure, the area of cropland should be reduced by 127.5 km2 under RCP4.5 and 377.2 km2 under RCP8.5 scenarios. (3) To be sustainable, the allocation ratio of forest land and water body should increase to 39% of the total water resource in the Aksu River Basin by 2050. creator: Zhidong Wang creator: Xining Zhao creator: Jinglei Wang creator: Ni Song creator: Qisheng Han uri: https://doi.org/10.7717/peerj.14577 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Two new temporary ectoparasitic isopods (Cymothoida: Cymothooidea) from Korean waters with a note on geographical distributions of Rocinela Leach, 1818 and Gnathia Leach, 1814 link: https://peerj.com/articles/14593 last-modified: 2023-01-03 description: Two new species of temporary ectoparasitic isopods, Rocinela excavatasp. nov. and Gnathia obtusispinasp. nov., are reported from the southern Islands of the Korean Peninsula. Rocinela excavatasp. nov. is distinguishable from its related species by the following characteristics: (1) laterally stepped rostrum; (2) separated eyes; (3) propodal blade having eight robust setae; and (4) merus having four or five blunt robust setae in pereopods 1–3. Gnathia obtusispinasp. nov. differs from its congeners by the combination of the following characteristics: (1) body covered with numerous tubercles and setae, (2) cephalon having tooth-like paraocular ornamentations; and (3) frontal border having two inferior frontolateral processes. These two new species are the 13thRocinela species and 19thGnathia species in the temperate Northern Pacific region, respectively. Discovery of these new species represents high species diversity of the genera Rocinela Leach, 1818 and Gnathia Leach, 1814 worldwide as well as in the Northern Pacific region. In addition, faunal diversity analysis on the members of both genera revealed that Rocinela species show high-latitude diversity whereas Gnathia species have low-latitude diversity. creator: Sung Hoon Kim creator: Jong Guk Kim creator: Seong Myeong Yoon uri: https://doi.org/10.7717/peerj.14593 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kim et al. title: Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines link: https://peerj.com/articles/14617 last-modified: 2023-01-03 description: BackgroundBud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. ‘Jinzao Wuhe’ is a bud sport of the elite cultivar ‘Himord Seedless’ with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear.MethodsWhole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for ‘Jinzao Wuhe’ and its maternal plant ‘Himord Seedless’ were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation.ResultsIn two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between ‘Himord Seedless’ and ‘Jinzao Wuhe’ harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine.ConclusionOur results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars. creator: Jianquan Huang creator: Guan Zhang creator: Yanhao Li creator: Mingjie Lyu creator: He Zhang creator: Na Zhang creator: Rui Chen uri: https://doi.org/10.7717/peerj.14617 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Huang et al.