title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2022-05 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: High gene flow in the silverlip pearl oyster Pinctada maxima between inshore and offshore sites near Eighty Mile Beach in Western Australia link: https://peerj.com/articles/13323 last-modified: 2022-05-31 description: An understanding of stock recruitment dynamics in fisheries is fundamental to successful management. Pinctada maxima is a bivalve mollusc widely distributed throughout the Indo-Pacific and is the main species targeted for cultured pearl and pearl shell production in Australia. Pearl production in Australia relies heavily on wild-caught individuals, the majority of which come from the Eighty Mile Beach region near Broome in Western Australia. In this study, we used a genotyping by sequencing approach to explore fine-scale patterns of genetic connectivity among inshore shallow and offshore deep populations of P. maxima near Eighty Mile Beach. Our results revealed high-levels of gene flow among inshore and offshore sites and no differences in genetic diversity between depths. Global estimates of genetic differentiation were low (FST = 0.006) but significantly different from zero, and pairwise estimates of genetic differentiation among sites were significant in only 3% of comparisons. Moreover, Bayesian clustering detected no separation of inshore and offshore sample sites, and instead showed all samples to be admixed among sites, locations and depths. Despite an absence of any clear spatial clustering among sites, we identified a significant pattern of isolation by distance. In a dynamic environment like Eighty Mile Beach, genetic structure can change from year-to-year and successive dispersal and recruitment events over generations likely act to homogenize the population. Although we cannot rule out the null hypothesis of panmixia, our data indicate high levels of dispersal and connectivity among inshore and offshore fishing grounds. creator: Luke Thomas creator: Karen J. Miller uri: https://doi.org/10.7717/peerj.13323 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Thomas and Miller title: Ferulic acid attenuates high glucose-induced apoptosis in retinal pigment epithelium cells and protects retina in db/db mice link: https://peerj.com/articles/13375 last-modified: 2022-05-31 description: BackgroundHerein, we aimed to present evidence that Ferulic acid (FA), a phenolic acid, can alleviate high glucose (HG)-induced retinal pigment epithelium (RPE) cell apoptosis and protect retina in db/db mice.MethodsARPE-19 cells (a human RPE cell line) were divided into four groups: control group; HG group (30 mmol/L glucose); HG+FA group (30 mmol/L glucose and 10 mmol/L FA). Cell viability and apoptosis were detected using CCK-8 and Annexin-5 staining, respectively. Apoptosis-related markers including P53, BAX and Bcl2 were examined by RT-qPCR, western blot and immunohistochemistry. Totally, 30 male db/db mice were randomly divided into db/db group (5 ml/kg saline) and FA group (0.05 g/kg FA). After treatment for 2 months, retinal samples were subjected to hematoxylin and eosin (H&E) and Masson staining. Moreover, immunofluorescence was used to detect apoptosis-related markers. Blood samples were collected for measuring cholesterol, triglyceride (TG), low-density lipoprotein (LDL) and high-density lipoprotein (HDL) levels.ResultsFA treatment markedly increased cell viability and suppressed cell apoptosis of ARPE-19 cells compared to the HG-exposed group. Furthermore, FA ameliorated the abnormal expression levels of P53, BAX and Bcl2 in HG-induced ARPE-19 cells. In animal models, FA attenuated pathological changes in the retina tissues of diabetic mice. Consistent with in vitro models, FA significantly ameliorated the expression of apoptosis-related markers in retina tissues. Biochemical test results showed that FA reduced hyperlipidemia in diabetic mice.ConclusionOur findings suggest that FA alleviates HG-induced apoptosis in RPE cells and protects retina in db/db mice, which can be associated with P53 and BAX inactivation and Bcl2 activation. creator: Dejun Zhu creator: Wenqing Zou creator: Xiangmei Cao creator: Weigang Xu creator: Zhaogang Lu creator: Yan Zhu creator: Xiaowen Hu creator: Jin Hu creator: Qing Zhu uri: https://doi.org/10.7717/peerj.13375 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu et al. title: The application of plant growth-promoting rhizobacteria in Solanum lycopersicum production in the agricultural system: a review link: https://peerj.com/articles/13405 last-modified: 2022-05-31 description: Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria’s structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere soil. These bacteria also help tomato plants acquire essential nutrients like potassium (K), magnesium (Mg), phosphorus (P), and nitrogen (N). Some rhizobacteria may offer a solution to low tomato production and help tackle food insecurity and farming problems. In this review, an overview of soil-inhabiting rhizobacteria focused on improving the sustainable production of Solanum lycopersicum. creator: Afeez Adesina Adedayo creator: Olubukola Oluranti Babalola creator: Claire Prigent-Combaret creator: Cristina Cruz creator: Marius Stefan creator: Funso Kutu creator: Bernard R. Glick uri: https://doi.org/10.7717/peerj.13405 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Adedayo et al. title: Epidemiology of Helicobacter pylori in Australia: a scoping review link: https://peerj.com/articles/13430 last-modified: 2022-05-31 description: BackgroundHelicobacter pylori (H. pylori), a bacterium implicated in the development of peptic ulcer and gastric cancer, is estimated to infect around half the world’s population. Its prevalence in Australia is unclear. This scoping review aimed to evaluate all Australian literature providing estimates of the prevalence of H. pylori.MethodsAustralian studies examining H. pylori prevalence from 1982 onwards were eligible for inclusion. Medline, Embase and Scopus databases, and grey literature sources, were searched. Two independent reviewers undertook a two-stage screening process. Data were extracted by two independent reviewers using a pre-specified template.ResultsOf 444 identified studies, 75 were included in the review. H. pylori prevalence in Australian population-based studies (n = 8) ranged from 38.0% in 1991 to 15.1% in 2002; however, estimated prevalence across all non-clinical population studies in diverse sub-groups (n = 29) has varied dramatically. Decreased prevalence has been more marked in populations with gastrointestinal symptoms and conditions compared to non-clinical populations. Data on H. pyloriprevalence in vulnerable populations are lacking.ConclusionsThis is the first scoping review of Australian studies reporting H. pylori prevalence. A wide range of study designs, population groups, geographic regions, and diagnostic methods was included, involving data collected over a 50-year period (1969 to 2018). The summary of H. pylori prevalence estimates over time in this review points to a decrease in prevalence in Australia, particularly among populations with gastrointestinal symptoms and illnesses; however, it is unknown whether there is inequity in prevalence trends across vulnerable sub-groups of the Australian population. Future research and interventions supporting the health and wellbeing of vulnerable populations is required to ensure equitable health gains are made for all. creator: Jillian Congedi creator: Craig Williams creator: Katherine L. Baldock uri: https://doi.org/10.7717/peerj.13430 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Congedi et al. title: Population genetics and demography of the coral-killing cyanobacteriosponge, Terpios hoshinota, in the Indo-West Pacific link: https://peerj.com/articles/13451 last-modified: 2022-05-31 description: The first occurrence of the cyanobacteriosponge Terpios hoshinota was reported from coral reefs in Guam in 1973, but was only formally described in 1993. Since then, the invasive behavior of this encrusting, coral-killing sponge has been observed in many coral reefs in the West Pacific. From 2015, its occurrence has expanded westward to the Indian Ocean. Although many studies have investigated the morphology, ecology, and symbiotic cyanobacteria of this sponge, little is known of its population genetics and demography. In this study, a mitochondrial cytochrome oxidase I (COI) fragment and nuclear ribosomal internal transcribed spacer 2 (ITS2) were sequenced to reveal the genetic variation of T. hoshinota collected from 11 marine ecoregions throughout the Indo-West Pacific. Both of the statistical parsimony networks based on the COI and nuclear ITS2 were dominated by a common haplotype. Pairwise FST and Isolation-by-distance by Mantel test of ITS2 showed moderate gene flow existed among most populations in the marine ecoregions of West Pacific, Coral Triangle, and Eastern Indian Ocean, but with a restricted gene flow between these regions and Maldives in the Central Indian Ocean. Demographic analyses of most T. hoshinota populations were consistent with the mutation-drift equilibrium, except for the Sulawesi Sea and Maldives, which showed bottlenecks following recent expansion. Our results suggest that while long-range dispersal might explain the capability of T. hoshinota to spread in the IWP, stable population demography might account for the long-term persistence of T. hoshinota outbreaks on local reefs. creator: Savanna Wenhua Chow creator: Shashank Keshavmurthy creator: James Davis Reimer creator: Nicole de Voogd creator: Hui Huang creator: Jih-Terng Wang creator: Sen-Lin Tang creator: Peter J. Schupp creator: Chun Hong Tan creator: Hock-Chark Liew creator: Keryea Soong creator: Beginer Subhan creator: Hawis Madduppa creator: Chaolun Allen Chen uri: https://doi.org/10.7717/peerj.13451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chow et al. title: Spain is not different: teaching quantitative courses can also be hazardous to one’s career (at least in undergraduate courses) link: https://peerj.com/articles/13456 last-modified: 2022-05-31 description: Student evaluations of teaching (SETs) have become a widely used tool for assessing teaching in higher education. However, numerous investigations have shown that SETs are subject to multiple biases, one of which is particularly relevant, namely, the area of knowledge to which the subject belongs. This article aims to replicate the article by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299) in a different educational context to verify whether the negative bias toward instructors who teach quantitative courses found by the authors in the US also appears in the Spanish university system. The study was conducted at the Business and Law School of the Universidad Pontificia Comillas, a private Spanish university, using two different samples. First, we analyzed undergraduate courses using a sample of 80,667 SETs in which 2,885 classes (defined as a single semester-long course taught by an individual instructor to a specific group of students), 488 instructors, and 322 different courses were evaluated over a time period of four academic years (2016/2017–2019/2020). Second, in the same period, 16,083 SETs corresponding to master’s degree courses were analyzed, which involved the study of 871 classes, 275 instructors, and 155 different courses. All the data included in the analysis were obtained from official university surveys developed by a team of professionals specialized in teaching quality responsible for ensuring the reliability of the information. At the degree level, the results show that despite the considerable cultural and temporal difference between the samples, the results are very similar to those obtained by Uttl & Smibert (2017, https://doi.org/10.7717/peerj.3299); i.e., professors teaching quantitative courses are far more likely to obtain worse SETs than instructors in other areas. There are hardly any differences at the master’s degree level, regardless of whether nearly 75% of master’s degree instructors also teach at the undergraduate level. This leads us to three different conclusions. (1) Evidence suggests that the reason for these differences is not due to faculty teaching quantitative courses being less effective than faculty teaching in some other fields. Our results indicate that the same instructor is evaluated very differently depending on whether he or she teaches at the undergraduate or master’s level. (2) It is essential to avoid comparisons of SETs between different areas of knowledge, at least at the undergraduate level. (3) A significant change in the use and interpretation of SETs is imperative, or its replacement by other evaluation mechanisms should be considered. If this does not occur, it is possible that in the future, there will be an adverse selection effect among professors of quantitative methods; i.e., only the worst professionals in quantitative methods will opt for teaching since the good professionals will prefer other jobs. creator: Jose Luis Arroyo-Barrigüete creator: Antonio Obregón creator: José María Ortiz-Lozano creator: Antonio Rua-Vieites uri: https://doi.org/10.7717/peerj.13456 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Arroyo-Barrigüete et al. title: Dramatic impact of future climate change on the genetic diversity and distribution of ecologically relevant Western Mediterranean Carex (Cyperaceae) link: https://peerj.com/articles/13464 last-modified: 2022-05-31 description: Anticipating the evolutionary responses of species to ongoing climate change is essential to propose effective management and conservation measures. The Western Mediterranean Basin constitutes one of the hotspots of biodiversity where the effects of climate change are expected to be more dramatic. Plant species with ecological relevance constitute ideal models to evaluate and predict the impact of climate change on ecosystems. Here we investigate these impacts through the spatio-temporal comparison of genetic diversity/structure (AFLPs), potential distribution under different future scenarios of climate change, and ecological space in two Western Mediterranean sister species of genus Carex. Both species are ecologically key in their riparian habitats, but display contrasting distribution patterns, with one widespread in the Iberian Peninsula and North Africa (C. reuteriana), while the other (C. panormitana) is a restricted, probably endangered, Central Mediterranean endemic. At present, we found a strong genetic structure driven by geography in both species, and lower values of genetic diversity and a narrower ecological space in C. panormitana than in C. reuteriana, while the allelic rarity was higher in the former than in C. reuteriana subspecies. Future projections predict an overall dramatic reduction of suitable areas for both species under all climate change scenarios, which could be almost total for C. panormitana. In addition, gene diversity was inferred to decrease in all taxa, with genetic structure reinforcing in C. reuteriana by the loss of admixture among populations. Our findings stress the need for a reassessment of C. panormitana conservation status under IUCN Red List criteria and the implementation of conservation measures. creator: Carmen Benítez-Benítez creator: María Sanz-Arnal creator: Malvina Urbani creator: Pedro Jiménez-Mejías creator: Santiago Martín-Bravo uri: https://doi.org/10.7717/peerj.13464 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Benítez-Benítez et al. title: A comparative metabolomics study of anthocyanins and taste components in Chinese bayberry (Morella rubra) with different flesh colors link: https://peerj.com/articles/13466 last-modified: 2022-05-31 description: The Chinese bayberry (Morella rubra Sieb. et Zucc.) is grown commercially in China and other Asian countries for its flavorful and appealing fruit. Here, two bayberry varieties differing in both color and flavor, namely, BDK (‘Baidongkui’) and DK (‘Dongkui’), in China were compared. A total of 18 anthocyanins, three proanthocyanidins, and 229 primary metabolites were identified in the pulp of the two varieties; these were analyzed and compared using ultra-performance liquid chromatography-tandem mass spectrometry. The DK pulp showed higher concentrations of all 18 anthocyanins compared with BDK, apart from peonidin-3,5-O-diglucoside which was not detected in BDK and which was responsible for the formation of pink pulp in BDK. Principal component analysis and cluster analysis of the primary metabolites indicated that the two bayberry varieties had distinct metabolite profiles with approximately 37% (85/229) of the primary metabolome being significantly different. Of these, 62 metabolites were down-regulated and 23 metabolites were up-regulated in BDK relative to DK. Our results suggested that the flavor of the BDK fruit was different from DK, which could be explained by the reduced saccharide, organic acid, amino acid, and proanthocyanidin contents. These findings enhance our understanding of the metabolites responsible for color and taste differences in the Chinese bayberry. creator: Qihua Lin creator: Qiuzhen Zhong creator: Zehuang Zhang uri: https://doi.org/10.7717/peerj.13466 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lin et al. title: Prospective quantitative gene expression analysis of kallikrein-related peptidase KLK10 as a diagnostic biomarker for childhood acute lymphoblastic leukemia link: https://peerj.com/articles/13489 last-modified: 2022-05-31 description: BackgroundThe most common malignancy in children is acute lymphoblastic leukemia (ALL). This study aimed to explore KLK10 mRNA expression as a potential diagnostic biomarker for ALL in children and to examine the effect of chemotherapy on KLK10 mRNA expression following the induction and after three months of receiving chemotherapy.MethodsIn this prospective study, total RNA was extracted from blood samples of 23 pediatric ALL patients on diagnosis, after one month and three months of receiving chemotherapy. Healthy pediatric volunteers (n = 12) were selected as control individuals. After cDNA synthesis, KLK10 mRNA gene expression levels were quantified using quantitative real-time PCR (qRT-PCR).ResultsKLK10 mRNA expression levels were significantly decreased in leukemic cells compared to their levels in cells of normal blood samples (p = 0.0001). KLK10 expression levels in ALL patients after one month and three months of receiving chemotherapy decreased compared to normal blood samples (p < 0.0001 and p = 0.0175 respectively). The expression level of KLK10 mRNA in ALL patients after one month of chemotherapy was decreased compared to their level on diagnosis (p = 0.4413). KLK10 mRNA expression levels in ALL patients after three months of chemotherapy were increased compared to their level on diagnosis (p = 0.0602). The ROC curve illustrated that KLK10 mRNA expression could very efficiently discriminate ALL patients from normal counterparts (AUC=0.886, 95% CI [0.7720–1.000], SE = 0.0582, p = 0.0004).ConclusionKLK10 mRNA expression could serve as a potential diagnostic molecular biomarker for ALL in children. creator: Shwan Majid Ahmad creator: Basima Sadq Ahmed creator: Karzan Ghafur Khidhir creator: Heshu Sulaiman Rahman uri: https://doi.org/10.7717/peerj.13489 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ahmad et al. title: Taxonomic and functional alterations in the salivary microbiota of children with and without severe early childhood caries (S-ECC) at the age of 3 link: https://peerj.com/articles/13529 last-modified: 2022-05-31 description: BackgroundPrimary dental caries is the most prevalent oral disease among preschool children, which can cause severe damage to teeth and even affect the mental well-being of children. Various studies have demonstrated that the oral microbiome plays a pivotal role in the onset and development of dental caries. However, it remains uncertain about the key microbial markers associated with caries, owing to the limited evidence.MethodsFifteen S-ECC children and fifteen healthy controls were selected from three-year-old children in this study. Their clinical data and oral saliva samples were collected. Shotgun sequencing was conducted to investigate the microbial differences and the relevant functions between the two groups.ResultsWe observed no apparent difference in oral microbial community diversity between the two groups. Still, at the genus/species levels, several characteristic genera/species such as Propionibacterium, Propionibacterium acidifaciens, Prevotella denticola, Streptococcus mutans and Actinomyces sp. oral taxon 448/414 increased significantly in S-ECC children, compared with the oral health group. Furthermore, we found that functional pathways involving glycolysis and acid production, such as starch and sucrose metabolism, fructose and mannose metabolism, glycolysis/gluconeogenesis, were prominently up-regulated in the high-caries group.ConclusionsOur study showed that dental caries in children were associated with the alterations in the oral microbiota at the composition and functional levels, which may potentially inspire the exploration of microbial diagnosis or therapeutic treatments. creator: Zhe Tang creator: Wenyi Xu creator: Zhifang Zhou creator: Yanchun Qiao creator: Shuguo Zheng creator: Wensheng Rong uri: https://doi.org/10.7717/peerj.13529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tang et al. title: Goal adjustment and well-being after an acquired brain injury: the role of cognitive flexibility and personality traits link: https://peerj.com/articles/13531 last-modified: 2022-05-31 description: ObjectiveThe tendency to flexibly adjust goals that are hindered by chronic illness is related to indicators of wellbeing. However, cognitive flexibility is often impaired in persons with an acquired brain injury (ABI), possibly affecting the ability to flexibly adjust goals. In this study we examined whether cognitive flexibility is positively related with the ability to disengage from goals to reengage with goals in persons with ABI. Second, we explored whether goal adjustment abilities are predictive of a unique proportion of the variance inabilities are predictive of quality of life and life satisfaction after controlling for personality traits.MethodSeventy-eight persons with an ABI completed a set of questionnaires. Goal disengagement and goal reengagement were assessed using the Wrosch Goal Adjustment Scale (GAS). Indicators of wellbeing were measured with the European Brain Injury Questionnaire (EBIQ) and the Satisfaction with Life Scale (SWLS). The percentage of perseverative errors on the Wisconsin Card Sorting Test (WCST) was used as an indicator of cognitive inflexibility. Big Five personality traits were assessed via the NEO Five Factor Inventory (NEO-FFI). Four hierarchical multiple regression analyses were then conducted. The first two analyses tested the effect of cognitive flexibility on goal adjustment tendencies. The second two analyses tested whether goal adjustment has a predictive value for life satisfaction and QOL beyond personality.ResultsCognitive flexibility was positively related to goal reengagement, but not to goal disengagement. Goal reengagement was positively associated with both quality of life and life satisfaction after controlling for demographic, illness characteristics and personality factors. Goal disengagement was negatively related to life satisfaction.ConclusionFlexible goal adjustment abilities have a unique explanatory value for indicators of wellbeing, beyond personality traits. The findings indicate that in persons with lower cognitive flexibility, goal reengagement ability might be negatively affected, and should be taking into account during rehabilitation. creator: Gunther Van Bost creator: Stefaan Van Damme creator: Geert Crombez uri: https://doi.org/10.7717/peerj.13531 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Van Bost et al. title: Seamens’ Sign: a novel electrocardiogram prediction tool for left ventricular hypertrophy link: https://peerj.com/articles/13548 last-modified: 2022-05-31 description: IntroductionPatients with left ventricular hypertrophy (LVH) diagnosed by electrocardiogram (ECG) have increased mortality and higher risk for life-threatening cardiovascular disease. ECGs offer an opportunity to identify patients with increased risk for potential risk-modifying therapy. We developed a novel, quick, easy to use ECG screening criterion (Seamens’ Sign) for LVH. This new criterion was defined as the presence of QRS complexes touching or overlapping in two contiguous precordial leads.MethodsThis study was a retrospective chart review of 2,184 patient records of patients who had an ECG performed in the emergency department and a transthoracic echocardiogram performed within 90 days. The primary outcome was whether Seamens’ Sign was noninferior in confirming LVH compared to other common diagnostic criteria. Test characteristics were calculated for each of the LVH criteria. Inter-rater agreement was assessed on a random sample using Cohen’s Kappa.ResultsMedian age was 63, 52% of patients were male and there was a 35% prevalence of LVH by transthoracic echocardiogram (TTE). Nine percent were positive for LVH on ECG based on Seamens’ Sign. Seamens’ Sign had a specificity of 0.92. Tests assessing noninferiority indicated Seamens’ Sign was non-inferior to all criteria (p < 0.001) except for Cornell criterion for women (p = 0.98). Seamens’ Sign had 90% (0.81–1.00) inter-rater agreement, the highest of all criteria in this study.ConclusionWhen compared to both the Sokolow-Lyon criteria and the Cornell criterion for men, Seamens’ Sign is noninferior in ruling in LVH on ECG. Additionally, Seamens’ Sign has higher inter-rater agreement compared to both Sokolow-Lyon criteria as well as the Cornell criteria for men and women, perhaps related to its ease of use. creator: Philip Walker creator: Cathy A. Jenkins creator: Jeremy Hatcher creator: Clifford Freeman creator: Nickolas Srica creator: Bryant Rosell creator: Eriny Hanna creator: Cooper March creator: Charles Seamens creator: Alan Storrow creator: Nicole McCoin uri: https://doi.org/10.7717/peerj.13548 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Walker et al. title: Glomerular filtration rate correlation and agreement between common predictive equations and standard 24-hour urinary creatinine clearance in medical critically ill patients link: https://peerj.com/articles/13556 last-modified: 2022-05-31 description: BackgroundDetermining kidney function in critically ill patients is paramount for the dose adjustment of several medications. When assessing kidney function, the glomerular filtration rate (GFR) is generally estimated either by calculating urine creatinine clearance (UCrCl) or using a predictive equation. Unfortunately, all predictive equations have been derived for medical outpatients. Therefore, the validity of predictive equations is of concern when compared with that of the UCrCl method, particularly in medical critically ill patients. Therefore, we conducted this study to assess the agreement of the estimated GFR (eGFR) using common predictive equations and UCrCl in medical critical care setting.MethodsThis was the secondary analysis of a nutrition therapy study. Urine was collected from participating patients over 24 h for urine creatinine, urine nitrogen, urine volume, and serum creatinine measurements on days 1, 3, 5, and 14 of the study. Subsequently, we calculated UCrCl and eGFR using four predictive equations, the Cockcroft–Gault (CG) formula, the four and six-variable Modification of Diet in Renal Disease Study (MDRD-4 and MDRD-6) equations, and the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. The correlation and agreement between eGFR and UCrCl were determined using the Spearman rank correlation coefficient and Bland–Altman plot with multiple measurements per subject, respectively. The performance of each predictive equation for estimating GFR was reported as bias, precision, and absolute percentage error (APE).ResultsA total of 49 patients with 170 urine samples were included in the final analysis. Of 49 patients, the median age was 74 (21–92) years-old and 49% was male. All patients were hemodynamically stable with mean arterial blood pressure of 82 (65–108) mmHg. Baseline serum creatinine was 0.93 (0.3–4.84) mg/dL and baseline UCrCl was 46.69 (3.40–165.53) mL/min. The eGFR from all the predictive equations showed modest correlation with UCrCl (r: 0.692 to 0.759). However, the performance of all the predictive equations in estimating GFR compared to that of UCrCl was poor, demonstrating bias ranged from −8.36 to −31.95 mL/min, precision ranged from 92.02 to 166.43 mL/min, and an unacceptable APE (23.01% to 47.18%). Nevertheless, the CG formula showed the best performance in estimating GFR, with a small bias (−2.30 (−9.46 to 4.86) mL/min) and an acceptable APE (14.72% (10.87% to 23.80%)), especially in patients with normal UCrCl.ConclusionFrom our finding, CG formula was the best eGFR formula in the medical critically ill patients, which demonstrated the least bias and acceptable APE, especially in normal UCrCl patients. However, the predictive equation commonly used to estimate GFR in critically ill patients must be cautiously applied due to its large bias, wide precision, and unacceptable error, particularly in renal function impairment. creator: Suwikran Wongpraphairot creator: Attamon Thongrueang creator: Rungsun Bhurayanontachai uri: https://doi.org/10.7717/peerj.13556 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wongpraphairot et al. title: Quality assessment of a serum and xenofree medium for the expansion of human GMP-grade mesenchymal stromal cells link: https://peerj.com/articles/13391 last-modified: 2022-05-30 description: BackgroundCell-based therapies are emerging as a viable modality to treat challenging diseases, resulting in an increasing demand for their large-scale, high-quality production. Production facilities face the issue of batch-to-batch consistency while producing a safe and efficient cell-based product. Controlling culture conditions and particularly media composition is a key factor of success in this challenge. Serum and Xeno-Free Media (SXFM) represent an interesting option to achieve this goal. By reducing batch to batch variability, they increase Good Manufacturing Practices (GMP)-compliance and safety regarding xenogenic transmission, as compared to fetal bovine serum (FBS) supplemented-media or human platelet lysate supplemented medium.MethodsIn this study, the isolation, expansion and characteristics including the anti-inflammatory function of human mesenchymal stromal cells (MSC) are compared after culture in MEMα supplemented with human Concentrate Platelet Lysate (hCPL, reference medium) or in MSC-Brew GMP Medium. The latter is a GMP SXFM manufactured in bags under strictly controlled conditions in volumes suitable for expansion to a clinical scale and does not require neither pre-coating of the cell culture units nor the addition of blood derivatives at the isolation step.ResultsWe showed that MSC derived from human bone-marrow and adipose tissue can be successfully isolated and expanded in this SXFM. Number and size of Colony-Forming Unit fibroblast (CFU-F) is increased compared to cells cultivated in hCPL medium. All cells retained a CD90+, CD73+, CD105+, HLADR−, CD34−, CD45− phenotype. Furthermore, the osteogenic and adipocyte potentials as well as the anti-inflammatory activity were comparable between culture conditions. All cells reached the release criteria established in our production facility to treat inflammatory pathologies.ConclusionsThe use of MSC-Brew GMP Medium can therefore be considered for clinical bioprocesses as a safe and efficient substitute for hCPL media. creator: Clotilde Aussel creator: Elodie Busson creator: Helene Vantomme creator: Juliette Peltzer creator: Christophe Martinaud uri: https://doi.org/10.7717/peerj.13391 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aussel et al. title: IL-4/IL-13 axis as therapeutic targets in allergic rhinitis and asthma link: https://peerj.com/articles/13444 last-modified: 2022-05-30 description: Allergic rhinitis (AR) is a common disorder of the upper airway, while asthma is a disease affecting the lower airway and both diseases are usually comorbid. Interleukin (IL)-4 and IL-13 are critical cytokines in the induction of the pathogenic Th2 responses in AR and asthma. Targeting the IL-4/IL-13 axis at various levels of its signaling pathway has emerged as promising targeted therapy in both AR and asthma patient populations. In this review, we discuss the biological characteristics of IL-4 and IL-13, their signaling pathways, and therapeutic antibodies against each cytokine as well as their receptors. In particular, the pleiotropic roles of IL-4 and IL-13 in orchestrating Th2 responses in AR and asthma patients indicate that dual IL-4/IL-13 blockade is a promising therapeutic strategy for both diseases. creator: Siti Muhamad Nur Husna creator: Norasnieda Md Shukri creator: Noor Suryani Mohd Ashari creator: Kah Keng Wong uri: https://doi.org/10.7717/peerj.13444 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nur Husna et al. title: Too perfect to be good? An investigation of magicians’ Too Perfect Theory link: https://peerj.com/articles/13449 last-modified: 2022-05-30 description: The “Too Perfect Theory” states that if a trick is too perfect, it might paradoxically become less impressive, or give away its secret method. This theory suggests that an increased impossibility results in a less magical effect. The Too Perfect Theory is often applied to magic effects, but it conflicts with recent scientific investigations showing that participants’ level of enjoyment of a magic performance is positively related to their perceived impossibility of the trick. The current article investigated whether an imperfect magic performance is more impressive than a perfect one. Across two experiments, we studied whether participants enjoy a performance more if the effect is not perfect. We also examined the different types of explanations people give to these two types of performances. The results showed that participants enjoyed a perfect performance more than an imperfect one. However, consistently with the Too Perfect Theory, participants watching the perfect performance also discovered the correct method behind the magic trick more frequently and believed the performance was staged more often. Moreover, participants’ method explanation significantly impacted their reports about the performance. creator: Alice Pailhès creator: Kole Lee creator: Gustav Kuhn uri: https://doi.org/10.7717/peerj.13449 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pailhès et al. title: UDP-glucose pyrophosphorylase: genome-wide identification, expression and functional analyses in Gossypium hirsutum link: https://peerj.com/articles/13460 last-modified: 2022-05-30 description: In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton. The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved. Collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure. The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses. Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis. The addition of low concentrations of IAA and GA3 to ovule cultures revealed that energy efficiency promoted the development of ovules and fiber clusters, and qRT-PCR showed that expression of these six UGP genes was differentially increased. These results suggest that the UGP gene may play an important role in fiber development, and provides the opportunity to plant researchers to explore the mechanisms involve in fiber development in cotton. creator: Zhongyang Xu creator: Jiasen He creator: Muhammad Tehseen Azhar creator: Zhen Zhang creator: Senmiao Fan creator: Xiao Jiang creator: Tingting Jia creator: Haihong Shang creator: Youlu Yuan uri: https://doi.org/10.7717/peerj.13460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Risk factors for falls in community-dwelling older people with mild cognitive impairment: a prospective one-year study link: https://peerj.com/articles/13484 last-modified: 2022-05-30 description: ObjectiveMild cognitive impairment (MCI) is considered an intermediate stage between normal cognitive function and dementia. Fall risk is increased in this group, but there is limited literature exploring specific fall risk factors that may be addressed in fall prevention strategies. The aim of this study was to examine risk factors for falls in older people with MCI, focusing on cognitive, psychological and physical factors.MethodsParticipants (n = 266, 45% women) were community-dwelling older people aged 70–90 years who met the criteria for MCI. Cognitive, psychological, sensorimotor and physical assessments, physical activity levels, medication use, general health and disability were ascertained at baseline. Falls were monitored prospectively for 12 months.ResultsDuring follow-up, 106 (40%) participants reported one or more falls. Poorer visual contrast sensitivity, increased postural sway, lower levels of weekly walking activity, higher levels of depressive symptoms and psychotropic medication use were significantly associated with faller status (≥1 falls) in univariable analyses. Of these factors, poor visual contrast sensitivity, increased postural sway and psychotropic medication use were found to be significant independent predictors of falls in multivariable analysis while controlling for age and sex. No measures of cognitive function were associated with falls.ConclusionsPoor visual contrast sensitivity, impaired balance and psychotropic medication use predicted falls in community-dwelling people with MCI. These risk factors may be amenable to intervention, so these factors could be carefully considered in fall prevention programs for this population. creator: Thanwarat Chantanachai creator: Morag E. Taylor creator: Stephen R. Lord creator: Jasmine Menant creator: Kim Delbaere creator: Perminder S. Sachdev creator: Nicole A. Kochan creator: Henry Brodaty creator: Daina L. Sturnieks uri: https://doi.org/10.7717/peerj.13484 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chantanachai et al. title: Virgin and UV-weathered polyamide microplastics posed no effect on the survival and reproduction of Daphnia magna link: https://peerj.com/articles/13533 last-modified: 2022-05-30 description: Although evidence suggests that microplastic (MP) particles pose a risk to organisms, the effects of virgin and weathered MP should be evaluated separately as their effects may be different. In this work, we provide new information on the toxic potential of virgin and UV-weathered polyamide, one of the commonly used plastics worldwide. Polyamide MP particles were subjected to UV-weathering in wet conditions over 26 days in a customized irradiation chamber equipped with UV-C light tubes (15 W each, max. wavelength 254 nm). The toxicity of virgin and UV-weathered polyamide MP (< 180 µm in one dimension, 100 and 300 mg L−1) was evaluated by studying Daphnia magna reproduction in natural lake water spiked with MP, following the 21-day OECD 211 test guideline. In parallel, a nonionic surfactant Tween 20 (7 mg L−1) was added to the test medium to improve the suspendability of the MP. The results of the tests showed no adverse effects of either virgin or UV-weathered polyamide MP on the reproduction of D. magna. In addition, presence of Tween 20 in the test medium had no effects on the test results. These results bring a new perspective on the potential long-term impact of polyamide particles on aquatic organisms, especially considering that the polyamide has received marginal attention in the ecotoxicological research. However, standard test endpoints (survival and reproduction) may still miss long-term adverse effects of insoluble e.g., plastic particles and additional studies may be necessary. creator: Alla Khosrovyan creator: Anne Kahru uri: https://doi.org/10.7717/peerj.13533 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Khosrovyan and Kahru title: Automatic detection of the parasite Trypanosoma cruzi in blood smears using a machine learning approach applied to mobile phone images link: https://peerj.com/articles/13470 last-modified: 2022-05-27 description: Chagas disease is a life-threatening illness caused by the parasite Trypanosoma cruzi. The diagnosis of the acute form of the disease is performed by trained microscopists who detect parasites in blood smear samples. Since this method requires a dedicated high-resolution camera system attached to the microscope, the diagnostic method is more expensive and often prohibitive for low-income settings. Here, we present a machine learning approach based on a random forest (RF) algorithm for the detection and counting of T. cruzi trypomastigotes in mobile phone images. We analyzed micrographs of blood smear samples that were acquired using a mobile device camera capable of capturing images in a resolution of 12 megapixels. We extracted a set of features that describe morphometric parameters (geometry and curvature), as well as color, and texture measurements of 1,314 parasites. The features were divided into train and test sets (4:1) and classified using the RF algorithm. The values of precision, sensitivity, and area under the receiver operating characteristic (ROC) curve of the proposed method were 87.6%, 90.5%, and 0.942, respectively. Automating image analysis acquired with a mobile device is a viable alternative for reducing costs and gaining efficiency in the use of the optical microscope. creator: Mauro César Cafundó Morais creator: Diogo Silva creator: Matheus Marques Milagre creator: Maykon Tavares de Oliveira creator: Thaís Pereira creator: João Santana Silva creator: Luciano da F. Costa creator: Paola Minoprio creator: Roberto Marcondes Cesar Junior creator: Ricardo Gazzinelli creator: Marta de Lana creator: Helder I. Nakaya uri: https://doi.org/10.7717/peerj.13470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Morais et al. title: Proteomic analysis of differential anther development from sterile/fertile lines in Capsicum annuum L. link: https://peerj.com/articles/13168 last-modified: 2022-05-27 description: BackgroundPepper (Capsicum annuum L.) is a major cash crop throughout the world. Male sterility is an important characteristic in crop species that leads to a failure to produce functional pollen, and it has crucial roles in agricultural breeding and the utilization of heterosis.ObjectivesIn this study, we identified many crucial factors and important components in metabolic pathways in anther and pollen development, and elucidated the molecular mechanism related to pollen abortion in pepper.MethodsPepper pollen was observed at different stages to detect the characteristics associated with male sterility and fertility. The phytohormone and oxidoreductase activities were detected in spectrophotometric and redox reaction assays, respectively. Proteins were extracted from male sterile and fertile pepper lines, and identified by TMT/iTRAQ (tandem mass tags/isobaric tags for relative and absolute quantitation) and LC-MS/MS (liquid chromatograph-mass spectrometer) analysis. Differentially abundant proteins (DAPs) were analyzed based on Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes database according to |fold change)| > 1.3 and P value < 0.05. DAPs were quantified in the meiosis, tetrad, and binucleate stages by parallel reaction monitoring (PRM).ResultsIn this study, we screened and identified one male sterile pepper line with abnormal cytological characteristics in terms of pollen development. The peroxidase and catalase enzyme activities were significantly reduced and increased, respectively, in the male sterile line compared with the male fertile line. Phytohormone analysis demonstrated that the gibberellin, jasmonic acid, and auxin contents changed by different extents in the male sterile pepper line. Proteome analysis screened 1,645 DAPs in six clusters, which were mainly associated with the chloroplast and cytoplasm based on their similar expression levels. According to proteome analysis, 45 DAPs were quantitatively identified in the meiosis, tetrad, and binucleate stages by PRM, which were related to monoterpenoid biosynthesis, and starch and sucrose metabolism pathways.ConclusionsWe screened 1,645 DAPs by proteomic analysis and 45 DAPs were related to anther and pollen development in a male sterile pepper line. In addition, the activities of peroxidase and catalase as well as the abundances of phytohormones such as gibberellin, jasmonic acid, and auxin were related to male sterility. The results obtained in this study provide insights into the molecular mechanism responsible for male sterility and fertility in pepper. creator: Hongxia Pei creator: Hua Xie creator: Xuemei Wang creator: Xiujuan Yan creator: Baike Wang creator: Haiping Feng creator: Yunxia Zhao creator: Jingxia Gao creator: Jie Gao uri: https://doi.org/10.7717/peerj.13168 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pei et al. title: Ability of functional performance assessments to discriminate athletes with and without chronic ankle instability : a case-control study link: https://peerj.com/articles/13390 last-modified: 2022-05-27 description: BackgroundThe decline in motor function associated with chronic ankle instability (CAI) can be assessed using Functional Performance tests. Ankle muscular strength, endurance and range of motion (ROM) has been assessed in previous studies but functional activities such as sprinting and change of direction are less well studied in athletes with CAI. Hence the aim of this study was to determine how sprint, change of direction, ankle isometric strength, endurance and ROM measures may be associated with discriminate athletes with and without CAI.MethodsOne hundred and six participants (CAI: n = 53 or no CAI: n = 53) provided informed consent to participate in this study. Participants performed three functional performance tests, (30-m sprint test, Modified Illinois change of direction test (MICODT)) and change of direction test. Range of motion for dorsiflexion was measured using weight bearing lunge test and inversion, eversion and plantarflexion using Saunders® digital inclinometer. Strength was assessed using Baseline® hand-held dynamometer for plantarflexors, dorsiflexors, invertors and evertors. Muscular endurance was assessed by single heel raise test and Modified single heel raise test. Between-group comparisons utilised Student’s t-test and Mann-Whitney U-tests, with a number of unique variable and multivariable binomial logistic regression performed to determine which performance measures may discriminate participants with CAI.ResultsThe CAI participants performed significantly worse in the three functional performance tests as well as multiple measures of ankle ROM, isometric strength and muscular endurance (p < 0.008). While several measures of ROM (plantarflexion and dorsiflexion), strength (inversion and eversion) and both muscular endurance tests were significantly associated with CAI in the univariable analysis, the strongest association was the functional performance tests, especially MICDOT time (odds ratio (95% CI): 0.06 [0.02–0.17], sensitivity 94.3%, specificity 88.7%). Multivariable regression analyses indicated that performance across the functional performance tests were more strongly associated with CAI than any ankle ROM, muscular strength or endurance test. Further, the inclusion of the best ankle range of motion, strength or muscular endurance tests did not significantly improve upon the association of the MICDOT with CAI.ConclusionsChronic ankle instability in athletic populations appears to be highly associated with declines in functional performance and to a somewhat lesser extent, ankle range of motion, strength and muscle endurance measures. This may suggest that optimal rehabilitation for athletes with CAI may require a greater focus on improving sprinting speed and change of direction ability in the mid to latter stages of rehabilitation, with regular assessments of these functional performance tests necessary to guide the progression and overload of this training. creator: Madhura S. Jamsandekar creator: Vivek Dineshbhai Patel creator: Ashish J. Prabhakar creator: Charu Eapen creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.13390 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 S. Jamsandekar et al. title: Challenges of sperm cryopreservation in transferring heat adaptation of corals across ocean basins link: https://peerj.com/articles/13395 last-modified: 2022-05-27 description: Reef-building corals live very close to their upper thermal limits and their persistence is imperiled by a rapidly warming climate. Human interventions may be used to increase the thermal limits of sensitive corals by cross-breeding with heat-adapted populations. However, the scope of breeding interventions is constrained by regional variation in the annual reproductive cycle of corals. Here we use cryopreservation technology to overcome this barrier and cross-breed conspecific coral populations across ocean basins for the first time. During regional spawning events, sperm samples were cryopreserved from populations of the widespread Indo-Pacific coral, Platygyra daedalea, from the southern Persian Gulf (maximum daily sea surface temperature of 36 °C), the Oman Sea (33 °C), and the central Great Barrier Reef (30 °C). These sperm samples were thawed during a later spawning event to test their ability to fertilize freshly spawned eggs of P. daedalea colonies from the central Great Barrier Reef. Average fertilization success for the Persian Gulf (9%) and Oman Sea (6%) sperm were 1.4–2.5 times lower than those for the native cryopreserved sperm from Great Barrier Reef (13–15%), potentially due to lower sperm quality of the Middle Eastern sperm and/or reproductive incompatibility between these distant populations. Overall, fertilization success with cryopreserved sperm was low compared with fresh sperm (>80%), likely due to the low motility of thawed sperm (≤5%, reduced from 50% to >90% in fresh sperm). To evaluate whether cross-bred offspring had enhanced thermal tolerance, the survival of larvae sired by Persian Gulf cryopreserved sperm, Great Barrier Reef cryopreserved sperm, and Great Barrier Reef fresh sperm was monitored for six days at ambient (27 °C) and elevated (33 °C) temperature. Against expectations of thermal tolerance enhancement, survival of larvae sired by Persian Gulf cryopreserved sperm was 2.6 times lower than larvae sired by Great Barrier Reef fresh sperm at 33 °C (27% versus 71%), but did not differ at 27 °C (77% versus 84%). This lack of enhanced thermal tolerance was unlikely due to outbreeding depression as survival was equally poor in larvae sired by Great Barrier Reef cryopreserved sperm. Rather, follow-up tests showed that cryoprotectant exposure during fertilization (0.1% DMSO) has a negative effect on the survival of P. daedalea larvae which is exacerbated at elevated temperature. Collectively, our findings highlight challenges of breeding corals for enhanced thermal tolerance using cryopreserved sperm, which may be overcome by methodological advances in the collection and preservation of high-quality motile sperm and minimizing the exposure time of eggs to cryoprotectants. creator: Emily J. Howells creator: Mary Hagedorn creator: Madeleine J.H. Van Oppen creator: John A. Burt uri: https://doi.org/10.7717/peerj.13395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Howells et al. title: Influence of DNA extraction kits on freshwater fungal DNA metabarcoding link: https://peerj.com/articles/13477 last-modified: 2022-05-27 description: BackgroundEnvironmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes.MethodsDNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples.ResultsNo PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals. creator: Shunsuke Matsuoka creator: Yoriko Sugiyama creator: Mariko Nagano creator: Hideyuki Doi uri: https://doi.org/10.7717/peerj.13477 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Matsuoka et al. title: Sexual dimorphism in shell size of the land snail Leptopoma perlucidum (Caenogastropoda: Cyclophoridae) link: https://peerj.com/articles/13501 last-modified: 2022-05-27 description: Sexual dimorphism in the shell size and shape of land snails has been less explored compared to that of other marine and freshwater snail taxa. This study examined the differences in shell size and shape across both sexes of Leptopoma perlucidum land snails. We collected 84 land snails of both sexes from two isolated populations on two islands off Borneo. A total of five shell size variables were measured: (1) shell height, (2) shell width, (3) shell spire height, (4) aperture height, and (5) aperture width. We performed frequentist and Bayesian t-tests to determine if there was a significant difference between the two sexes of L. perlucidum on each of the five shell measurements. Additionally, the shell shape was quantified based on nine landmark points using the geometric morphometric approach. We used generalised Procrustes and principal component analyses to test the effects of sex and location on shell shape. The results showed that female shells were larger than male shells across all five measurements (all with p-values < 0.05), but particularly in regards to shell height and shell width. Future taxonomic studies looking to resolve the Leptopoma species’ status should consider the variability of shell size caused by sexual dimorphism. creator: Chee-Chean Phung creator: Ming-Huei Choo creator: Thor-Seng Liew uri: https://doi.org/10.7717/peerj.13501 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Phung et al. title: Anticancer mechanism of 7-α-hydroxyfrullanolide on microtubules and computational prediction of its target binding in triple-negative breast cancer cells link: https://peerj.com/articles/13508 last-modified: 2022-05-27 description: BackgroundTriple-negative breast cancer (TNBC) responds poorly to the available drugs; thus, the mortality rate associated with TNBC remains high. 7-α-Hydroxyfrullanolide (7HF) possesses anticancer properties and arrests cells in the G2/M-phase via modulation of several proteins involved in the G2/M-phase transition, as well as the mitotic checkpoint in MDA-MB-468 (TNBC) cells. Microtubules (MTs) dynamically regulate cell division in the G2/M phase and are related to cancer cell stress response. However, antimitotic drug cytotoxicity to multiple cancer resistance developed in response to drugs are obstacles faced to date. Here, the activity and mechanism via which 7HF controls MTs dynamics was investigated in MDA-MB-468 cells.Methods7HF uptake by MDA-MB-468 cells was assessed using spectrophotometry. The drug-like properties of 7HF were predicted using the Swiss-absorption, distribution, metabolism, and excretion (ADME) webtool. Then, the effect of 7HF treatment (6, 12, and 24 µM) on the dynamic arrangement of MTs was assessed for 1, 12, and 24 h using indirect immunofluorescence. Polymerization of α- and β-tubulin was assessed using different 7HF concentrations in a cell-free system for 1 h. Cell proliferation assay with bromodeoxyuridine plus propidium iodide staining and flow cytometry was performed at different 7HF concentrations and time points. The mechanism of action was assessed by detecting the expression of proteins, including Bub3, cyclin B1, p-Cdk1 (Tyr15), Rb, p-Rb (Ser780), Chk1, p-Chk1 (Ser345), Chk2, p-Chk2 (Ser516), and p-H2AX (Ser139), using western blotting. Molecular docking was used to predict the molecular interactions between 7HF and tubulins in MTs.ResultsWe observed that 7HF was able to enter the MDA-MB-468 cells. The ADME webtool analysis predicted that it possesses the high passive permeation and gastrointestinal absorption properties of drugs. Various concentrations of 7HF disrupted the dynamic arrangement of spindle MTs by causing radial spindle array shrinkage and expansion of fibrous spindle density and radial array lengths in a time-dependent manner. 7HF reduced polymerization of α-, β-tubulin in dose-dependent manner. 7HF also triggered DNA damage response by inducing G2/M and G1 phase arrests in a concentration and time-dependent manner, which occurred due to the upregulation of Bub3, Chk1, p-Chk1 (Ser345), p-Cdk1 (Tyr15), and cyclin B1. According to molecular docking analysis, 7HF preferred to bind to β-tubulin over α-tubulin. The lactone, ketone, and hydroxyl groups of 7HF supported the 7HF-tubulin interactions. Hydrogen bonding with a hydrocarbon ring and salt bridge attractive forces were responsible for the binding versatility of 7HF.ConclusionsThis is the first study to investigate the molecular mechanism, MTs interacting sites, and the internalization and drug-like properties of 7HF in TNBC cells. The findings will be useful for developing 7HF-based treatment for patients with TNBC. creator: Siriphorn Chimplee creator: Carl Smythe creator: Varomyalin Tipmanee creator: Suchada Sukrong creator: Kanyanatt Kanokwiroon uri: https://doi.org/10.7717/peerj.13508 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chimplee et al. title: Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic link: https://peerj.com/articles/13509 last-modified: 2022-05-27 description: Species distribution models have become a valuable tool to predict the distribution of species across geographic space and time. In this study, maximum entropy models were constructed for two temperate shallow-water octocoral species, the pink sea fan (Eunicella verrucosa) and dead man’s fingers (Alcyonium digitatum), to investigate and compare habitat suitability. The study area covered the north-east Atlantic from the Bay of Biscay to the British Isles and southern Norway; this area includes both the northern range of E. verrucosa and the middle-northern range of A. digitatum. The optimal models for each species showed that, overall, slope, temperature at the seafloor and wave orbital velocity were important predictors of distribution in both species. Predictions of habitat suitability showed areas of present-day (1951–2000) suitable habitat where colonies have not yet been observed, particularly for E. verrucosa, where areas beyond its known northern range limit were identified. Moreover, analysis with future layers (2081–2100) of temperature and oxygen concentration predicted a sizable increase in habitat suitability for E. verrucosa beyond these current range limits under the Representative Concentration Pathway 8.5 scenario. This suggests that projected climate change may induce a potential range expansion northward for E. verrucosa, although successful colonisation would also be conditional on other factors such as dispersal and interspecific competition. For A. digitatum, this scenario of projected climate change may result in more suitable habitat in higher latitudes, but, as with E. verrucosa, there is a degree of uncertainty in the model predictions. Importantly, the results from this study highlight present-day areas of high habitat suitability which, if combined with knowledge on population density, could be used to identify priority areas to enhance protection and ensure the long-term survival of these octocoral species in the region. creator: Tom L. Jenkins creator: Jamie R. Stevens uri: https://doi.org/10.7717/peerj.13509 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jenkins and Stevens title: Animal reactivity to camera traps and its effects on abundance estimate using distance sampling in the Taï National Park, Côte d’Ivoire link: https://peerj.com/articles/13510 last-modified: 2022-05-27 description: The use of camera traps (CTs) has become an increasingly popular method of studying wildlife, as CTs are able to detect rare, nocturnal, and elusive species in remote and difficult-to-access areas. It thus makes them suited to estimate animal density and abundance, identify activity patterns and new behaviours of animals. However, animals can react when they see the CTs and this can lead to bias in the animal population estimates. While CTs may provide many advantages, an improved understanding of their impacts on individual’s behaviour is necessary to avoid erroneous density estimates. Yet, the impact of CTs on detected individuals, such as human odour near the device and the environment, or the infrared illumination, has received relatively little attention. To date, there is no clear procedure to remove this potential bias. Here, we use camera trap distance sampling (CTDS) to (1) quantify the bias resulting from the different animal responses to the CTs when determining animal density and abundance, and (2) test if olfactory, visual and auditory signals have an influence on the animals’ reaction to CTs. Between March 2019 and March 2020, we deployed CTs at 267 locations distributed systematically over the entire Taï National Park. We obtained 58,947 videos from which we analysed four medium- to-large-bodied species (Maxwell’s duiker (Philantomba maxwellii), Jentink’s duiker (Cephalophus jentinki), pygmy hippopotamus (Choeropsis liberiensis) and Western chimpanzee (Pan troglodytes verus)) displaying different behaviours towards the CTs. We then established species-specific ethograms describing the behavioural responses to the CTs. Using these species-specific responses, we observed that the Maxwell’s duiker reacted weakly to CTs (about 0.11% of the distance data), contrary to Jentink’s duiker, pygmy hippopotamus and Western chimpanzee which reacted with relatively high frequencies, representing 32.82%, 52.96% and 16.14% of the distance data, respectively. Not taking into account the species-specific responses to the CTs can lead to an artificial doubling or tripling of the populations’ sizes. All species reacted more to the CTs at close distances. Besides, the Jentink’s duiker and the pygmy hippopotamus reacted significantly more to the CTs at night than during the day. Finally, as for olfactory signals, the probability of reaction to the CTs during the first days after CTs installation was weak in Maxwell’s duiker, but concerned 18% of the video captures in Western chimpanzees which decreasing with time, but they remained high in pygmy hippopotamus and Jentink’s duiker (65% and 70% of the video captures respectively). Careful consideration should be given to animal’s response to CTs during the analysis and in the field, by reducing human’s impact around the CTs installation. creator: Noël Adiko Houa creator: Noémie Cappelle creator: Eloi Anderson Bitty creator: Emmanuelle Normand creator: Yves Aka Kablan creator: Christophe Boesch uri: https://doi.org/10.7717/peerj.13510 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Houa et al. title: Trajectory patterns and factors influencing perinatal fatigue among Chinese women from late pregnancy to 6 months after delivery link: https://peerj.com/articles/13387 last-modified: 2022-05-26 description: BackgroundPerinatal fatigue among women is related to the clinical outcomes of mothers and infants. Perinatal fatigue changes over time, and the trajectory varies according to the predictors and outcomes of the mothers. This, however, has not been documented in any study.ObjectivesThis study aimed to identify and characterize the trajectory patterns of perinatal fatigue among women from late pregnancy to 6 months after delivery.MethodsWe used growth mixture modeling to estimate the trajectory of perinatal fatigue at 28 gestational weeks (T0), 37 gestational weeks (T1), 3 days (T2), 1 week (T3), 6 weeks (T4), and 6 months (T5) after delivery with (n = 1,030). The Mann-Whitney U test and binary logistic regression were used to tie the selected trajectory classes to predictors and outcomes.ResultsThere were two distinct patterns of perinatal fatigue in women: “persistently high” (11.1%, n = 114) and “persistently low” (88.9%, n = 916). Levels of perinatal fatigue among women in the “persistently high” group were higher than those in the “persistently low” group across the six measurements. Complications, fatigue at T0, and employment status in late pregnancy were all significant predictors of trajectories. Additionally, the “persistently high” group had a greater prevalence of difficult baby care and weight retention and a lower prevalence of exclusive breastfeeding.ConclusionsOur study proved the heterogeneity and characteristics of perinatal fatigue among women. Future research should concentrate on developing intervention packages targeted at specific individuals in order to alleviate perinatal fatigue in women. creator: Xiaoxiao Zhu creator: Haiou Xia uri: https://doi.org/10.7717/peerj.13387 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu and Xia title: Development of a bead-based assay for detection of three banana-infecting viruses link: https://peerj.com/articles/13409 last-modified: 2022-05-26 description: BackgroundBanana bunchy top virus (BBTV), cucumber mosaic virus (CMV) and banana streak virus (BSV) are important banana viruses, there are possible infections frequently with several viruses in field. Since the viruses are readily trasmitted in vegetative propagules, which pose a threat to banana production in banana-growing areas.MethodsA multiplex polymerase chain reaction (PCR) protocol combined with LiquiChip analysis to identify BSV, BBTV, and CMV, with consistent amplification of plant ubiquitin (UBQ), the banana plant messenger RNA used as a procedural control. Multiplex reverse transcription (RT)-PCR amplicons were extended by allele-specific primers, followed by hybridization with carboxylated microspheres containing unique fluorescent oligonucleotides, which were detected using the LiquiChip 200 workstation.ResultsIn this study, we aimed to develop a rapid, sensitive, and simultaneous detection method for BSV, BBTV, and CMV using a bead-based multiplex assay that can be applied in routine diagnosis. We demonstrated that this detection system was extremely efficient and highly specialized for differentiating individual in a mixture of viruses while being ten times more sensitive than traditional RT-PCR. The development of this method makes it feasible to detect banana viruses in field collected leaf samples. creator: Cheng-Ping Kuan creator: Chia-Hsin Tsai creator: Ching-Shan Tseng creator: Tso-Chi Yang uri: https://doi.org/10.7717/peerj.13409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kuan et al. title: Dementia-related user-based collaborative filtering for imputing missing data and generating a reliability scale on clinical test scores link: https://peerj.com/articles/13425 last-modified: 2022-05-26 description: Medical doctors may struggle to diagnose dementia, particularly when clinical test scores are missing or incorrect. In case of any doubts, both morphometrics and demographics are crucial when examining dementia in medicine. This study aims to impute and verify clinical test scores with brain MRI analysis and additional demographics, thereby proposing a decision support system that improves diagnosis and prognosis in an easy-to-understand manner. Therefore, we impute the missing clinical test score values by unsupervised dementia-related user-based collaborative filtering to minimize errors. By analyzing succession rates, we propose a reliability scale that can be utilized for the consistency of existing clinical test scores. The complete base of 816 ADNI1-screening samples was processed, and a hybrid set of 603 features was handled. Moreover, the detailed parameters in use, such as the best neighborhood and input features were evaluated for further comparative analysis. Overall, certain collaborative filtering configurations outperformed alternative state-of-the-art imputation techniques. The imputation system and reliability scale based on the proposed methodology are promising for supporting the clinical tests. creator: Savas Okyay creator: Nihat Adar uri: https://doi.org/10.7717/peerj.13425 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Okyay and Adar title: Pachygenium laurense (Orchidaceae, Spiranthinae), a new orchid species from Argentina—morphological evidence and phylogenetic reconstruction link: https://peerj.com/articles/13433 last-modified: 2022-05-26 description: BackgroundPachygenium embraces a group of terrestrial species formerly placed in Pelexia sensu lato. The genus currently comprises some 60 species, most of which are known from the southern parts of Brazil and Paraguay, with few species distributed in the Andean countries—only four species have been recorded from Argentina so far. In Jujuy Province, Argentina a new species of Pachygenium was found during our fieldwork. The aim of this article was to provide morphological and molecular evidence for its membership in this genus.MethodsMaterials from specimens were collected in the field and examined by classical taxonomic and molecular biological techniques, e.g., PCR and sequencing DNA. Phylogenetic reconstruction was performed by maximum-likelihood and Bayesian inference.ResultsPachygenium laurense from Argentina is described and illustrated based on morphological evidence and its taxonomic position was confirmed by phylogenetic analyses. A new combination for Pachygenium gutturosa is also proposed. A key for identification is provided for the Pachygenium species occurring in Argentina.ConclusionPachygenium laurense is the fifth species of the genus recorded from Argentina. creator: Claudia M. Martin creator: Adriana Marisel Morales creator: Magdalena Dudek creator: Dariusz L. Szlachetko uri: https://doi.org/10.7717/peerj.13433 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 M. Martin et al. title: The impact of different feeds on DNA methylation, glycolysis/gluconeogenesis signaling pathway, and gene expression of sheep muscle link: https://peerj.com/articles/13455 last-modified: 2022-05-26 description: DNA methylation is an important epigenetic regulatory form that regulates gene expression and tissue development. This study compared the effects of high fiber, low protein (HFLP) and low fiber, high protein (LFHP) diets on the DNA methylation profile of twin lambs’ muscles, their effect on glycolysis/gluconeogenesis and related pathways by transcriptome and deep whole-genome bisulfite sequencing (WGBS). Results identified 1,945 differentially methylated regions (DMRs) and 1,471 differentially methylated genes (DMGs). Also, 487 differentially expressed transcripts belonging to 368 differentially expressed genes (DEGs) were discovered between the twin lambs under different diets. Eleven overlapped genes were detected between the DEGs and the DMGs. FKBP5 and FOXO1 were detected to be significantly different. The FOXO1 regulated cAMP and the glycolysis/gluconeogenesis pathways. The glycolysis/gluconeogenesis, and the FOXO pathways were significantly enriched. The expressions of HOMER1 and FOXO1 in the HFLP group were significantly higher than those in the LFHP group. There is a significant correlation between the upregulated gene expression and hypomethylation of HOMER1 and FOXO1 gene in HFLP group. The results showed that FOXO1 induces PDK4 expression in muscle while regulating FKBP5 activity, which stimulates glucose production by activating specific gluconeogenesis target genes. The FOXO1 was able to regulate the glucose metabolism, the cAMP and the occurrence of glycolysis/gluconeogenesis pathways. This study showed that feed type can affect the methylation levels of the glycolysis related gluconeogenesis genes and interaction pathways, providing new ideas for a better understanding of the regulation of muscle energy metabolism and feed development. creator: Feng Song creator: Zaccheaus Pazamilala Akonyani creator: Ying Li creator: Deqiqige Su creator: Lantuya Wu creator: Yue Pang creator: Sile Hu creator: Dubala Wu creator: Chun Li creator: Ding Yang creator: Jianghong Wu uri: https://doi.org/10.7717/peerj.13455 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Song et al. title: Application of hydrophilic polymers for the preparation of tadalafil solid dispersions: micromeritics properties, release and erectile dysfunction studies in male rats link: https://peerj.com/articles/13482 last-modified: 2022-05-26 description: The objective of the present study was to improve the dissolution rate and aphrodisiac activity of tadalafil by using hydrophilic polymers. Solid dispersions were prepared by solvent evaporation-Rota evaporator using Koliphore 188, Kollidon® VA64, and Kollidon® 30 polymers in a 1:1 ratio. Prepared tadalafil-solid dispersions (SDs) evaluated for yield, drug content, micromeritics properties, physicochemical characterizations, and aphrodisiac activity assessment. The optimized SDs TK188 showed size (2.175 ± 0.24 µm), percentage of content (98.89 ± 1.23%), yield (87.27 ± 3.13%), bulk density (0.496 ± 0.005 g/cm3), true density (0.646 ± 0.003 g/cm3), Carr’s index (23.25 ± 0.81), Hausner ratio (1.303 ± 0.003) and angle of repose (<25°). FTIR spectrums revealed tadalafil doesn’t chemically interact with used polymers. XRD and DSC analysis represents TK188 SDs were in the amorphous state. Drug release was 97.17 ± 2.43% for TK188, whereas it was 32.76 ± 2.65% for pure drug at the end of 2 h with 2.96-fold increase in dissolution and followed release kinetics of Korsmeyer Peppa’s model. MDT and DE were noted to be 17.48 minutes and 84.53%, respectively. Furthermore, TK188 SDs showed relative improvement in the sexual behavior of the male rats. Thus the developed SDs TK188 could be potential tadalafil carriers for the treatment of erectile dysfunction. creator: Mohammed Muqtader Ahmed creator: Md Khalid Anwer creator: Gamal A. Soliman creator: Mohammed F. Aldawsari creator: Abdul Aleem Mohammed creator: Sultan Alshehri creator: Mohammed M. Ghoneim creator: Amer S. Alali creator: Abdullah Alshetaili creator: Ahmed Alalaiwe creator: Sarah I. Bukhari creator: Ameeduzzafar Zafar uri: https://doi.org/10.7717/peerj.13482 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ahmed et al. title: Healthcare applications of single camera markerless motion capture: a scoping review link: https://peerj.com/articles/13517 last-modified: 2022-05-26 description: BackgroundSingle camera markerless motion capture has the potential to facilitate at home movement assessment due to the ease of setup, portability, and affordable cost of the technology. However, it is not clear what the current healthcare applications of single camera markerless motion capture are and what information is being collected that may be used to inform clinical decision making. This review aims to map the available literature to highlight potential use cases and identify the limitations of the technology for clinicians and researchers interested in the collection of movement data.Survey MethodologyStudies were collected up to 14 January 2022 using Pubmed, CINAHL and SPORTDiscus using a systematic search. Data recorded included the description of the markerless system, clinical outcome measures, and biomechanical data mapped to the International Classification of Functioning, Disability and Health Framework (ICF). Studies were grouped by patient population.ResultsA total of 50 studies were included for data collection. Use cases for single camera markerless motion capture technology were identified for Neurological Injury in Children and Adults; Hereditary/Genetic Neuromuscular Disorders; Frailty; and Orthopaedic or Musculoskeletal groups. Single camera markerless systems were found to perform well in studies involving single plane measurements, such as in the analysis of infant general movements or spatiotemporal parameters of gait, when evaluated against 3D marker-based systems and a variety of clinical outcome measures. However, they were less capable than marker-based systems in studies requiring the tracking of detailed 3D kinematics or fine movements such as finger tracking.ConclusionsSingle camera markerless motion capture offers great potential for extending the scope of movement analysis outside of laboratory settings in a practical way, but currently suffers from a lack of accuracy where detailed 3D kinematics are required for clinical decision making. Future work should therefore focus on improving tracking accuracy of movements that are out of plane relative to the camera orientation or affected by occlusion, such as supination and pronation of the forearm. creator: Bradley Scott creator: Martin Seyres creator: Fraser Philp creator: Edward K. Chadwick creator: Dimitra Blana uri: https://doi.org/10.7717/peerj.13517 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Scott et al. title: Prevalence of food addiction using the Yale-C scale in Mexican children with overweight and obesity link: https://peerj.com/articles/13500 last-modified: 2022-05-25 description: BackgroundThe prevalence of excess weight and obesity in children has increased significantly worldwide. The concept of food addiction (FA) has been associated with eating-related problems and obesity. Studies on this topic have primarily examined adult samples and little is known about addictive-like eating among Mexican children and adolescents.MethodsWe conducted this study to examinate the prevalence of FA in a group of 291 overweight and obese children and adolescents using YFAS scale for children (YFAS-C) in Mexico.ResultsAccording to the YFAS-C approximately 14.4% of participants met for FA diagnosis. Forty-two (14.4%) received a FA diagnosis: 14 children and 28 adolescents. The number of FA symptoms in participants who received an FA diagnosis (M = 4.35, SD = 1.07) compared to participants with no FA diagnosis (M = 1.70, SD = 1.53) was significantly higher (p ≤ 0.001). There were no statistically significant gender differences and the proportion of subjects with an FA diagnosis did not differ by age between children and adolescents. FA is a focus of interest in attempting to explain certain behaviors that may contribute to the development of obesity and explain the failure of the weight loose programs in children. creator: Idalia Cura-Esquivel creator: Juan Ramos-Álvarez creator: Edna Delgado creator: Airam Regalado-Ceballos uri: https://doi.org/10.7717/peerj.13500 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cura-Esquivel et al. title: Ageing- and AAA-associated differentially expressed proteins identified by proteomic analysis in mice link: https://peerj.com/articles/13129 last-modified: 2022-05-25 description: BackgroundAbdominal aortic aneurysm (AAA) is a disease of high prevalence in old age, and its incidence gradually increases with increasing age. There were few studies about differences in the circulatory system in the incidence of AAA, mainly because younger patients with AAA are fewer and more comorbid nonatherosclerotic factors.MethodWe induced AAA in ApoE−/− male mice of different ages (10 or 24 weeks) and obtained plasma samples. After the top 14 most abundant proteins were detected, the plasma was analyzed by a proteomic study using the data-dependent acquisition (DDA) technique. The proteomic results were compared between different groups to identify age-related differentially expressed proteins (DEPs) in the circulation that contribute to AAA formation. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses were performed by R software. The top 10 proteins were determined with the MCC method of Cytoscape, and transcription factor (TF) prediction of the DEPs was performed with iRegulon (Cytoscape).ResultsThe aortic diameter fold increase was higher in the aged group than in the youth group (p < 0.01). Overall, 92 DEPs related to age and involved in AAA formation were identified. GO analysis of the DEPs showed enrichment of the terms wounding healing, response to oxidative stress, regulation of body fluid levels, ribose phosphate metabolic process, and blood coagulation. The KEGG pathway analysis showed enrichment of the terms platelet activation, complement and coagulation cascades, glycolysis/gluconeogenesis, carbon metabolism, biosynthesis of amino acids, and ECM-receptor interaction. The top 10 proteins were Tpi1, Eno1, Prdx1, Ppia, Prdx6, Vwf, Prdx2, Fga, Fgg, and Fgb, and the predicted TFs of these proteins were Nfe2, Srf, Epas1, Tbp, and Hoxc8.ConclusionThe identified proteins related to age and involved in AAA formation were associated with the response to oxidative stress, coagulation and platelet activation, and complement and inflammation pathways, and the TFs of these proteins might be potential targets for AAA treatments. Further experimental and biological studies are needed to elucidate the role of these age-associated and AAA-related proteins in the progression of AAA. creator: Jinrui Ren creator: Jianqiang Wu creator: Xiaoyue Tang creator: Siliang Chen creator: Wei Wang creator: Yanze Lv creator: Lianglin Wu creator: Dan Yang creator: Yuehong Zheng uri: https://doi.org/10.7717/peerj.13129 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ren et al. title: Exploring the perception and readiness of Pharmacists towards telepharmacy implementation; a cross sectional analysis link: https://peerj.com/articles/13296 last-modified: 2022-05-25 description: BackgroundAmid the turbulent nature of the COVID-19 pandemic, telepharmacy has shifted the paradigm of patient care by leveraging digital medicine. Government mandated lockdowns and norms of social distancing have further underscored the need for telepharmacy. Many developed and developing countries implemented such initiatives where pharmacists have provided tele-pharmacy services via telecommunications. However, the implementation and utilization of tele-pharmacy services are quite negligible in resource limited settings due to financial and administrative constraints. This study was aimed to ascertain the perception and readiness of pharmacists working in various sectors of a resource limiting country.MethodologyA cross sectional study was carried out in all provinces of Pakistan to explore the perceptions of pharmacists towards telepharmacy implementation through a 35-items study instrument. The collected data was analyzed descriptively and scored accordingly. The chi-square test was used for inferential analysis on pharmacist’s perception regarding implementation of tele-pharmacy with their demographics.ResultsOf 380 pharmacists, the mean age is 27.67 ± 3.67 years with a preponderance of male pharmacists (n = 238, 62.6%). The pharmacists (n = 321, 84.5%) perceived that telepharmacy implementation improves patient’s quality of life and decreases patients’ visits (n = 291, 76.6%). Overall, pharmacists (n = 227, 59.7%) had negative perception towards benefits of telepharmacy implementation, but pharmacists had positive perception towards eligibility (n = 258, 67.9%), regulatory issues (n = 271, 71.3%) and telepharmacy during pandemic and beyond (n = 312, 82.1%). In chi-square testing gender (p = 0.03) and age (p = 0.03) had a significant association with perception regarding regulatory issues. Among perception regarding telepharmacy during COVID-19 pandemic and beyond age had a significant association (p = 0.03). Among perception regarding eligibility job location of pharmacists had significant association (p = 0.04).ConclusionThe majority of pharmacists had a positive perception regarding the eligibility of patients and regulatory issues/legal framework regarding the implementation of tele-pharmacy, as well as its use during the COVID-19 pandemic and beyond. The implementation of tele-pharmacy can play a major role in providing timely and better patient care to remote patient areas and may help in the prevention and treatment of different infectious diseases. creator: Khayal Muhammad creator: Mohamed A. Baraka creator: Syed Sikandar Shah creator: Muhammad Hammad Butt creator: Haytham Wali creator: Muhammad Saqlain creator: Tauqeer Hussain Mallhi creator: Khezar Hayat creator: Khairi Mustafa Fahelelbom creator: Royes Joseph creator: Yusra Habib Khan uri: https://doi.org/10.7717/peerj.13296 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Muhammad et al. title: Overexpression of AmCBF1 enhances drought and cold stress tolerance, and improves photosynthesis in transgenic cotton link: https://peerj.com/articles/13422 last-modified: 2022-05-25 description: China’s main cotton production area is located in the northwest where abiotic stresses, particularly cold and drought, have serious effects on cotton production. In this study, Ammopiptanthus mongolicus C-repeat-binding factor (AmCBF1) isolated from the shrub Ammopiptanthus mongolicus was inserted into upland cotton (Gossypium hirsutum L.) cultivar R15 to evaluate the potential benefits of this gene. Two transgenic lines were selected, and the transgene insertion site was identified using whole-genome sequencing. The results showed that AmCBF1 was incorporated into the cotton genome as a single copy. Transgenic plants had distinctly higher relative water content (RWC), chlorophyll content, soluble sugar content, and lower ion leakage than R15 after drought and cold stress. Some characteristics, such as the area of lower epidermal cells, stomatal density, and root to shoot ratio, varied significantly between transgenic cotton lines and R15. Although the photosynthetic ability of transgenic plants was inhibited after stress, the net photosynthetic rate, stomatal conductance, and transpiration rate in transgenic plants were significantly higher than in R15. This suggested that an enhanced stress tolerance and photosynthesis of transgenic cotton was achieved by overexpressing AmCBF1. All together, our results demonstrate that the new transgenic cotton germplasm has great application value against abiotic stresses, especially in the northwest inland area of China. creator: Guoqing Lu creator: Lihua Wang creator: Lili Zhou creator: Xiaofeng Su creator: Huiming Guo creator: Hongmei Cheng uri: https://doi.org/10.7717/peerj.13422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lu et al. title: Influence of hot air drying on capsaicinoids, phenolics, flavonoids and antioxidant activities of ‘Super Hot’ chilies link: https://peerj.com/articles/13423 last-modified: 2022-05-25 description: Hot air drying is an alternative technique to either maintain or increase bioactive compounds in agricultural products because temperatures can be controlled. The effects of different hot air oven drying temperatures and times on the physicochemical changes, bioactive compounds (capsaicinoids, phenolic and flavonoid profiles and contents) and antioxidant activities in dried ‘Super Hot’ chili fruits were evaluated. The chilies were dried in a hot air oven at low (60–100 °C) or high (120–160 °C) temperatures for 30, 60, 120 min and at 12–13% moisture content (MC). The main compounds presented in chili fruits were capsaicinoids, limonene, pinene, tocopherol and oleic acid, regardless of drying temperature and time. Although the total flavonoid contents decreased during the drying process, the total phenolic contents increased (38–51%), and capsaicinoids, the primary pungent compounds, increased six-times at 120–160 °C compared to the fresh chilies. The phenolic profiles showed that chlorogenic acid was the most stable and abundant amongst the nine quantified phenolic compounds. In the flavonoid profile, both rutin and quercetin can be detected at a high temperature of 160 °C, with a decreasing trend. The main pungent compounds, capsaicin and dihydrocapsaicin, were found to increase compared to the fresh chilies, especially at 12–13% wet basis (w.b.). Although the antioxidant activities (ABTS• + and DPPH•) of dried chilies at all temperatures decreased with increasing drying time, these activities were still detected. Therefore, drying chilies at 160 °C (120 min) can not only maintain the capsaicinoids, phenolics and flavonoids that can be utilized by the pharmaceutical and food industry, but can also reduce the production time. creator: Esther Shiau Ping Yap creator: Apiradee Uthairatanakij creator: Natta Laohakunjit creator: Pongphen Jitareerat uri: https://doi.org/10.7717/peerj.13423 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yap et al. title: Heat stress response in Chinese cabbage (Brassica rapa L.) revealed by transcriptome and physiological analysis link: https://peerj.com/articles/13427 last-modified: 2022-05-25 description: High temperatures have a serious impact on the quality and yield of cold-loving Chinese cabbage, which has evolved to have a unique set of stress mechanisms. To explore the relationship between these mechanisms and the heat-tolerance of Chinese cabbage, the physiological indicators of the heat-tolerant ‘268’ line and heat-sensitive ‘334’ line were measured. Under heat stress, the proline (Pro), soluble sugar (SS), and superoxide dismutase (SOD) indexes of the ‘268’ line increased significantly. When additionally using transcriptome analysis, we found that the identified 3,360 DEGs were abundantly enriched in many metabolic pathways including ‘plant hormone signal transduction’, ‘carbon metabolism’, and ‘glycolysis/gluconeogenesis’. Dynamic gene expression patterns showed that HKL1 in Cluster 15 may be a key factor in the regulation of sugar homeostasis. The interaction network screened four ABA-related genes in Cluster 15, suggesting that high temperatures lead to changes in hormonal signaling, especially an increase in ABA signaling. Compared with the ‘334’ line, the expressions of Prx50, Prx52, Prx54, SOD1, and SOD2 in the ‘268’ line were significantly upregulated, and these genes were actively involved in the reactive oxygen species (ROS) scavenging process. In summary, our results revealed the relationship between plant heat tolerance, physiology, and biochemistry and may also provide ideas for the future development of high-quality and heat-tolerant Chinese cabbage germplasm resources. creator: Lei Zhang creator: Yun Dai creator: Lixin Yue creator: Guohu Chen creator: Lingyun Yuan creator: Shifan Zhang creator: Fei Li creator: Hui Zhang creator: Guoliang Li creator: Shidong Zhu creator: Jinfeng Hou creator: Xiaoyan Tang creator: Shujiang Zhang creator: Chenggang Wang uri: https://doi.org/10.7717/peerj.13427 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Integrative analysis of transcriptome complexity in pig granulosa cells by long-read isoform sequencing link: https://peerj.com/articles/13446 last-modified: 2022-05-25 description: BackgroundIn intensive and large-scale farms, abnormal estradiol levels in sows can cause reproductive disorders. The high incidence rate of reproductive disturbance will induce the elimination of productive sows in large quantities, and the poor management will bring great losses to the pig farms. The change in estradiol level has an important effect on follicular development and estrus of sows. To solve this practical problem and improve the productive capacity of sows, it is significant to further clarify the regulatory mechanism of estradiol synthesis in porcine granulosa cells (GCs). The most important function of granulosa cells is to synthesize estradiol. Thus, the studies about the complex transcriptome in porcine GCs are significant. As for precursor-messenger RNAs (pre-mRNAs), their post-transcriptional modification, such as alternative polyadenylation (APA) and alternative splicing (AS), together with long non-coding RNAs (lncRNAs), may regulate the functions of granulosa cells. However, the above modification events and their function are unclear within pig granulosa cells.MethodsCombined PacBio long-read isoform sequencing (Iso-Seq) was conducted in this work for generating porcine granulosa cells’ transcriptomic data. We discovered new transcripts and possible gene loci via comparison against reference genome. Later, combined Iso-Seq data were adopted to uncover those post-transcriptional modifications such as APA or AS, together with lncRNA within porcine granulosa cells. For confirming that the Iso-Seq data were reliable, we chose four AS genes and analyzed them through RT-PCR.ResultsThe present article illustrated that pig GCs had a complex transcriptome, which gave rise to 8,793 APA, 3,465 AS events, 703 candidate new gene loci, as well as 92 lncRNAs. The results of this study revealed the complex transcriptome in pig GCs. It provided a basis for the interpretation of the molecular mechanism in GCs. creator: Shuxin Li creator: Jiarui Wang creator: Jiale Li creator: Meihong Yue creator: Chuncheng Liu creator: Libing Ma creator: Ying Liu uri: https://doi.org/10.7717/peerj.13446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Nutrient composition of Chenopodium formosanum Koidz. bran: Fractionation and bioactivity of its soluble active polysaccharides link: https://peerj.com/articles/13459 last-modified: 2022-05-25 description: BackgroundChenopodium formosanum Koidz. Amaranthaceae—also known as Djulis or red quinoa (RQ)—is a cereal plant indigenous to Taiwan, known for its high nutrient value. However, its bran is considered a waste product and the nutrient value has never been analyzed.MethodsIn this study, we examined the proximate composition of RQ bran, specifically its soluble polysaccharide fractions.ResultsRQ bran exhibited high contents of protein (16.56%), ash (7.10%), carbohydrate (60.45%), total polyphenolics (1.85%), betaxanthin (9.91 mg/100 g of RQ bran), and indicaxanthin (7.27 mg/100 g of RQ bran). Specifically, it was rich in polyunsaturated fatty acids (PUFAs; 39.24%)—with an n-6/n-3 and PUFA/saturated fatty acid (SFA) ratio of 18.137 and 0.743, respectively. Four soluble polysaccharide fractions were also obtained: CF-1, CF-2, CF-3, and CF-4, with yields of 3.90%, 6.74%, 22.28%, and 0.06%, respectively, and molecular weights of 32.54, 24.93, 72.39, and 55.45 kDa, respectively. CF-1, CF-2, CF-3, and CF-4 had respectively 15.67%, 42.41%, 5.44%, and 14.52% peptide moiety content and 38.92%, 50.70%, 93.76%, and 19.80% carbohydrate moiety. In CF-2, the glucose content was 95.86 mol% and that of leucine was 16.23%, implicating the presence of a typical leucinoglucan. All four polysaccharide fractions lacked glutamic acid and hydroxyproline. The IC50 of CF-1, CF-2, and CF-3 was respectively 12.05, 3.98, and 14.5 mg/mL for DPPH free radical–scavenging ability; 5.77, 4.10, and 7.03 mg/mL for hydrogen peroxide–scavenging capability; 0.26, 0.05, and 0.19 mg/mL for O2− free radical–scavenging capability; and 100.41, 28.12, and 29.73 mg/mL for Fe2+ chelation.ConclusionOur results indicated that RQ bran has a large amount of nutrient compounds, and a cost-efficient process for their extraction is needed. Their biomedical application as nutraceuticals also warrants further investigation. creator: Yaw-Bee Ker creator: Hui-Ling Wu creator: Kuan-Chou Chen creator: Robert Y. Peng uri: https://doi.org/10.7717/peerj.13459 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ker et al. title: Phytochemical content, especially spermidine derivatives, presenting antioxidant and antilipoxygenase activities in Thai bee pollens link: https://peerj.com/articles/13506 last-modified: 2022-05-25 description: BackgroundBee pollen (BP) is full of useful nutrients and phytochemicals.Its chemical components and bioactivities depend mainly on the type of floral pollen.MethodsMonofloral BP from Camellia sinensis L., Mimosa diplotricha, Helianthus annuus L., Nelumbo nucifera, Xyris complanata, and Ageratum conyzoides were harvested. Crude extraction and partition were performed to yield solvent-partitioned extracts of each BP. Total phenolic content (TPC) was assayed by the Folin-Ciocalteu method, while the flavonoid content (FC) was measured by the aluminium chloride colorimetric method. Antioxidant capacity was measured by the (i) 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity, (ii) 2,2’-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) scavenging activity and its Trolox equivalent antioxidant capacity (TEAC), and (iii) ferric reducing antioxidant power (FRAP). All samples were tested for lipoxygenase inhibitory (LOXI) activity. The most active sample was enriched by silica gel 60 column chromatography (SiG60-CC) and high performance liquid chromatography (HPLC), observing the chemical pattern of each fraction using thin layer chromatography. Chemical structure of the most active compound was analyzed by proton nuclear magnetic resonance and mass spectrometry.ResultsDichloromethane (DCM)-partitioned BP extracts of H. annuus L. and M. diplotricha (DCMMBP) showed a very high TPC, while DCMMBP had the highest FC. In addition, DCMMBP had the strongest DPPH and ABTS radical scavenging activities (as a TEAC value), as well as FRAP value. Also, DCMMBP (60 µg/mL) gave the highest LOXI activity (78.60 ± 2.81%). Hence, DCMMBP was chosen for further enrichment by SiG60-CC and HPLC. Following this, the most active fraction showed higher antioxidant andLOXI activities with an EC50 for DPPH and ABTS of 54.66 ± 3.45 µg/mL and 24.56 ± 2.99 µg/mL (with a TEAC value of 2,529.69 ± 142.16 µmole TE/g), respectively, and a FRAP value of 3,466.17 ± 81.30 µmole Fe2+/g and an IC50 for LOXI activity of 12.11 ± 0.36 µg/mL. Triferuloyl spermidines were revealed to be the likely main active components.ConclusionsTPC, FC, and spermidine derivatives played an important role in the antioxidant and antilipoxygenase activities in M. diplotricha bee pollen. creator: Phanthiwa Khongkarat creator: Preecha Phuwapraisirisan creator: Chanpen Chanchao uri: https://doi.org/10.7717/peerj.13506 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Khongkarat et al. title: Chromatin accessibility landscape of stromal subpopulations reveals distinct metabolic and inflammatory features of porcine subcutaneous and visceral adipose tissue link: https://peerj.com/articles/13250 last-modified: 2022-05-24 description: BackgroundFat accumulation in visceral adipose tissue (VAT) confers increased risk for metabolic disorders of obesity, whereas accumulation of subcutaneous adipose tissue (SAT) is associated with lower risk and may be protective. Previous studies have shed light on the gene expression profile differences between SAT and VAT; however, the chromatin accessibility landscape differences and how the cis-regulatory elements govern gene expression changes between SAT and VAT are unknown.MethodsPig were used to characterize the differences in chromatin accessibility between the two adipose depots-derived stromal vascular fractions (SVFs) using DNase-sequencing (DNase-seq). Using integrated data from DNase-seq, H3K27ac ChIP-sequencing (ChIP-seq), and RNA-sequencing (RNA-seq), we investigated how the regulatory locus complexity regulated gene expression changes between SAT and VAT and the possible impact that these changes may have on the different biological functions of these two adipose depots.ResultsSVFs form SAT and VAT (S-SVF and V-SVF) have differential chromatin accessibility landscapes. The differential DNase I hypersensitive site (DHS)-associated genes, which indicate dynamic chromatin accessibility, were mainly involved in metabolic processes and inflammatory responses. Additionally, the Krüppel-like factor family of transcription factors were enriched in the differential DHSs. Furthermore, the chromatin accessibility data were highly associated with differential gene expression as indicated using H3K27ac ChIP-seq and RNA-seq data, supporting the validity of the differential gene expression determined using DNase-seq. Moreover, by combining epigenetic and transcriptomic data, we identified two candidate genes, NR1D1 and CRYM, could be crucial to regulate distinct metabolic and inflammatory characteristics between SAT and VAT. Together, these results uncovered differences in the transcription regulatory network and enriched the mechanistic understanding of the different biological functions between SAT and VAT. creator: Wenyang Sun creator: Tinghuan Zhang creator: Silu Hu creator: Qianzi Tang creator: Xi Long creator: Xu Yang creator: Shuangbao Gun creator: Lei Chen uri: https://doi.org/10.7717/peerj.13250 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sun et al. title: Effect of a cover crop on the aphid incidence is not explained by increased top-down regulation link: https://peerj.com/articles/13299 last-modified: 2022-05-24 description: BackgroundCover crops can be used as a habitat management strategy to enhance the natural enemies and their temporal synchronization with a target pest. We examined the effect of winter oat intercropping within organic plum orchards on the natural enemy abundance and seasonal dynamics on the biological control of plum aphids in spring in Central Chile.MethodsWe compared the incidence and abundance of natural enemies and aphid pests from winter to the end of spring using two treatments: (1) plum trees with an oat cover crop (OCC) and (2) plum trees without a cover crop but with spontaneous vegetation (SV). We hypothesized that cover crops allow the development of winter cereal aphids, promoting the early arrival of natural enemies in spring, resulting in an earlier control of plum aphids.ResultsWinter cereal aphids developed well on the OCC, and as a result, a lower plum aphid incidence in spring was observed when compared to the SV. However, the abundance of natural enemies and the parasitism rates cannot explain the positive impacts of the oat cover crop on the aphid populations as there were no differences between treatments. A potential effect of the oat due to chemical and/or physical stimuli (bottom-up effects) could help to explain these results. creator: Jeniffer K. Alvarez-Baca creator: Xiomara Montealegre creator: Cécile Le Lann creator: Joan Van Baaren creator: Blas Lavandero uri: https://doi.org/10.7717/peerj.13299 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Alvarez-Baca et al. title: Down-regulated NEDD4L facilitates tumor progression through activating Notch signaling in lung adenocarcinoma link: https://peerj.com/articles/13402 last-modified: 2022-05-24 description: Neural precursor cell expressed developmentally down-regulated 4-like protein (NEDD4L), an E3 ubiquitin ligase, exerts an important role in diverse biological processes including development, tumorigenesis, and tumor progression. Although the role of NEDD4L in the pathogenesis of lung adenocarcinoma (LUAD) has been described, the mechanism by which NEDD4L promotes LUAD progression remains poorly understood. In the study, the correlation between NEDD4L level and clinical outcome in LUAD patients was analysed using the data from The Cancer Genome Atlas (TCGA) database. NEDD4L expression in LUAD cell lines and tissue samples was assessed through quantitative real-time PCR (qRT-PCR). The biological function of NEDD4L on regulating LUAD cell proliferation was tested with Cell Counting Kit-8 (CCK-8) assay in vitro, and mouse xenograft tumor model in vivo. We found that NEDD4L expression was significantly decreased in LUAD tissues and cell lines. Lower expression of NEDD4L exhibited a significantly poorer overall survival. Functionally, NEDD4L knockdown in H1299 cells accelerated cell growth, whereas NEDD4L overexpression in A549 cells repressed cell proliferation. NEDD4L overexpression also inhibited tumor xenograft growth in vivo. Mechanistically, NEDD4L decreased the protein stability of notch receptor 2 (Notch2) through facilitating its ubiquitination and degradation by ubiquitin-proteasome system. Consequently, NEDD4L negatively regulated Notch signaling activation in LUAD cells, and RO4929097 (a Notch inhibitor) treatment effectively repressed the effect of NEDD4L knockdown on LUAD cell proliferation. Taken together, these results demonstrate that down-regulated NEDD4L facilitates LUAD progression by activating Notch signaling, and NEDD4L may be a promising target to treat LUAD. creator: Liping Lin creator: Xuan Wu creator: Yuanxue Jiang creator: Caijiu Deng creator: Xi Luo creator: Jianjun Han creator: Jiazhu Hu creator: Xiaolong Cao uri: https://doi.org/10.7717/peerj.13402 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lin et al. title: Fisetin glycosides synthesized by cyclodextrin glycosyltransferase from Paenibacillus sp. RB01: characterization, molecular docking, and antioxidant activity link: https://peerj.com/articles/13467 last-modified: 2022-05-24 description: Fisetin is a flavonoid that exhibits high antioxidant activity and is widely employed in the pharmacological industries. However, the application of fisetin is limited due to its low water solubility. In this study, glycoside derivatives of fisetin were synthesized by an enzymatic reaction using cyclodextrin glycosyltransferase (CGTase) from Paenibacillus sp. RB01 in order to improve the water solubility of fisetin. Under optimal conditions, CGTase was able to convert more than 400 mg/L of fisetin to its glycoside derivatives, which is significantly higher than the previous biosynthesis using engineered E. coli. Product characterization by HPLC and LC-MS/MS revealed that the transglycosylated products consisted of at least five fisetin glycoside derivatives, including fisetin mono-, di- and triglucosides, as well as their isomers. Enzymatic analysis by glucoamylase and α-glucosidase showed that these fisetin glycosides were formed by α-1,4-glycosidic linkages. Molecular docking demonstrated that there are two possible binding modes of fisetin in the enzyme active site containing CGTase-glysosyl intermediate, in which O7 and O4’ atoms of fisetin positioned close to the C1 of glycoside donor, corresponding to the isomers of the obtained fisetin monoglucosides. In addition, the water solubility and the antioxidant activity of the fisetin monoglucosides were tested. It was found that their water solubility was increased at least 800 times when compared to that of their parent molecule while still maintaining the antioxidant activity. This study revealed the potential application of CGTase to improve the solubility of flavonoids. creator: Nattawadee Lorthongpanich creator: Panupong Mahalapbutr creator: Thanyada Rungrotmongkol creator: Thanapon Charoenwongpaiboon creator: Manchumas Hengsakul Prousoontorn uri: https://doi.org/10.7717/peerj.13467 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lorthongpanich et al. title: E161111 is an ultra-short-acting etomidate analogue with stable haemodynamics that elicits only slight adrenocortical suppression in rats link: https://peerj.com/articles/13492 last-modified: 2022-05-24 description: PurposeWe report on a novel ultra-short-acting etomidate analogue, E161111, which has the same primary metabolite as etomidate.MethodsThe metabolic rate of E161111 was determined in rat plasma and liver homogenate. Rats were infused for 30 or 60 min to maintain light sedation at Richmond Agitation-Sedation Scale (RASS) for −2 to 0 score. Mean arterial pressure (MAP) was monitored during 30 min infusion. The serum corticosterone was determined during and 3 h after infusion as a measure of adrenocortical function.ResultsE161111 was not detected in rat plasma at 1 min (t1/2 = 6.69 ± 0.07 s) and in rat liver homogenates at 5 min (t1/2 = 10.20 ± 3.76 s); its main metabolic product was etomidate acid. The recovery time from loss of righting reflex (LORR) was 4.3 ± 1.5 min after 1-h infusion of E161111. During 30 min infusion, E161111 did not cause MAP changes. The stimulated serum corticosterone levels after 1-h infusion of E161111 were significantly higher than that after 1-h infusion of etomidate at all time points tested for the 3 h study.ConclusionsE161111 was metabolised rapidly, the metabolites were same as etomidate, and the recovery time after 1-h infusion was short. It elicited haemodynamic stability and milder suppression of corticosterone than that elicited by etomidate. creator: Bin Wang creator: Deying Gong creator: Yi Kang creator: Jin Liu creator: Jun Yang creator: Wen-sheng Zhang uri: https://doi.org/10.7717/peerj.13492 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: The effects of isometric hand grip force on wrist kinematics and forearm muscle activity during radial and ulnar wrist joint perturbations link: https://peerj.com/articles/13495 last-modified: 2022-05-24 description: The purpose of this work was to investigate forearm muscle activity and wrist angular displacement during radial and ulnar wrist perturbations across various isometric hand grip demands. Surface electromyography (EMG) was recorded from eight muscles of the upper extremity. A robotic device delivered perturbations to the hand in the radial and ulnar directions across four pre-perturbation grip magnitudes. Angular displacement and time to peak displacement following perturbations were evaluated. Muscle activity was evaluated pre- and post-perturbation. Results showed an inverse relationship between grip force and angular displacement (p ≤ 0.001). Time to peak displacement decreased as grip force increased (p ≤ 0.001). There was an increase in muscle activity with higher grip forces across all muscles both pre-and post-perturbation (p ≤ 0.001) and a greater average muscle activity in ulnar as compared to radial deviation (p = 0.02). This work contributes to the wrist joint stiffness literature by relating wrist angular displacement to grip demands during novel radial/ulnar perturbations and provides insight into neuromuscular control strategies. creator: Kailynn Mannella creator: Garrick N. Forman creator: Maddalena Mugnosso creator: Jacopo Zenzeri creator: Michael W. R. Holmes uri: https://doi.org/10.7717/peerj.13495 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mannella et al. title: Indian nurses’ beliefs on physical activity promotion practices for cancer survivors in a tertiary care hospital—a cross-sectional survey link: https://peerj.com/articles/13348 last-modified: 2022-05-23 description: PurposeTo describe the physical activity (PA) promotion practices, beliefs, and barriers of Indian nurses working with cancer survivors, and to gain preliminary insights into how their educational qualification might affect PA promotion practices.MethodsA validated questionnaire was used to obtain the data (N = 388). Sub-group comparisons were performed based on nursing qualification i.e., Bachelor of Science in Nursing (BSc) and General Nursing and Midwifery (GNM) using Mann-Whitney U test and chi square analysis for continuous and categorical variables, respectively.ResultsThe nurses believed that oncologists (47%) followed by physiotherapists (28.9%) were primarily responsible for providing information regarding PA to cancer survivors. The most common period in which the nurses’ promoted PA was post treatment (31.7%), although very few nurses (13.3%) promoted PA across more than one of the three treatment periods. Nurses felt that PA had many benefits for cancer survivors; improved mental health (87.7%) and HRQoL (81.1%). Lack of knowledge (42.2%) and lack of time (41.6%) were the most frequently cited barriers. The comparisons based on educational qualification did not typically reveal many significant differences.ConclusionIndian nurses both BSc and GNM qualified, wish to promote PA to cancer survivors despite numerous barriers, across various stages of treatment and believe PA is beneficial to the survivors in the process of recovery. Overcoming these barriers might aid in better promotion of PA to cancer survivors.Implication for cancer survivorsNurses working in a tertiary care hospital in India are willing to promote PA amongst cancer survivors but require more training and support in this area of practice. creator: Hritika D. Pai creator: Stephen Rajan Samuel creator: K. Vijaya Kumar creator: Namrata S. Chauhan creator: Charu Eapen creator: Alicia Olsen creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.13348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pai et al. title: Does who I am and what I feel determine what I see (or say)? A meta-analytic systematic review exploring the influence of real and perceived bodily state on spatial perception of the external environment link: https://peerj.com/articles/13383 last-modified: 2022-05-23 description: BackgroundBodily state is theorised to play a role in perceptual scaling of the environment, whereby low bodily capacity shifts visuospatial perception, with distances appearing farther and hills steeper, and the opposite seen for high bodily capacity. This may play a protective role, where perceptual scaling discourages engaging with the environment when capacity is low.MethodologyOur protocol was pre-registered via Open Science Framework (https://osf.io/6zya5/) with all amendments to the protocol tracked. We performed a systematic review and meta-analysis examining the role of bodily state/capacity on spatial perception measures of the environment. Databases (Medline, PsychINFO, Scopus, Embase, and Emcare) and grey literature were searched systematically, inclusive to 26/8/21. All studies were assessed using a customised Risk of Bias form. Standard mean differences and 95% CIs were calculated via meta-analysis using a random-effects model.ResultsA total of 8,034 studies were identified from the systematic search. Of these, 68 experiments (3,195 participants) met eligibility and were included in the review. These were grouped into the following categories: fatigue; pain; age; embodiment; body size/body paty size; glucose levels; fitness; and interoception, and interoceptive accuracy. We found low level evidence (limited studies, high risk of bias) for the effect of bodily state on spatial perception. There was consistent evidence that both glucose manipulations and age influence spatial perception of distances and hills in a hypothesised direction (lower capacity associated with increased distance and hill steepness). Mixed evidence exists for the influence of external loads, embodiment, body/body-part size manipulations, pain, and interoceptive accuracy. Evidence for fitness and/or fatigue influencing spatial perception was conflicting; notably, methodological flaws with fitness and fatigue paradigms and heterogenous spatial perception measures may underlie null/conflicting results.ConclusionWe found limited evidence for bodily state influencing spatial perception of the environment. That all studies had high risk of bias makes conclusions about reported effects reflecting actual perceptual shifts (vs merely reflecting experimental demands or error due to inadequate study design) pre-emptive. Rigorous evaluation is needed to determine whether reported effects reflect more than bias (e.g., experimental demands, inadequate blinding). Future work using reliable measures of spatial perception, comprehensive evaluation of relevant confounders, and methodologically robust (and experimentally confirmed) bodily state experimental paradigms is warranted. creator: Erin MacIntyre creator: Felicity A. Braithwaite creator: Brendan Mouatt creator: Dianne Wilson creator: Tasha R. Stanton uri: https://doi.org/10.7717/peerj.13383 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 MacIntyre et al. title: Psychometric properties of the general self-efficacy scale among Thais with type 2 diabetes: a multicenter study link: https://peerj.com/articles/13398 last-modified: 2022-05-23 description: BackgroundType 2 diabetes (T2D) is one of the most common chronic diseases in the world. In recent decades the prevalence of this disease has increased alarmingly in lower to middle income countries, where their resource-limited health care systems have struggled to meet this increased burden. Improving patient self-care by improving diabetes knowledge and diabetes management self-efficacy represents a feasible way of ameliorating the impact of T2D on the patient, and the health care system. Unfortunately, the relationships between self-efficacy, diabetes self-management, and thereafter, patient outcomes, are still far from well understood. Although a domain-specific measure of diabetes management self-efficacy, the Diabetes Management Self-Efficacy Scale (DMSES), has been validated in the Thai T2D population, more general measures of self-efficacy, such as the General Self-Efficacy scale (GSE) have not been validated in this population. In this paper we translate and examine the psychometric properties of the GSE in Thais living with T2D.MethodsIn this nation-wide study we examined the psychometric properties of the GSE in 749 Thais diagnosed with T2D within the last five years, and evaluated its relationship with the DMSES along with other patient characteristics. Reliability of GSE was assessed using Cronbach’s alpha, and the construct validity was examined using confirmatory factor analysis, along with GSE’s convergence and discrimination from DMSES.ResultsThe Thai version of the GSE was shown to have good psychometric properties in Thais living with T2D. Cronbach’s alpha was shown to be 0.87 (95% CI [0.86, 0.88]). We also demonstrated the structural validity of the GSE (Tucker-Lewis Index = 0.994, Cumulative Fit Index = 0.995, Adjusted Goodness of Fit Index = 0.998, Root Mean Square Error of Approximations = 0.025, 95% CI [0.06–0.039]), and that this instrument has a similar structure in Thais as in other populations. GSE was also shown to have some overlap with the DMSES with correlations among GSE and the DMSES domains ranging from 0.18 to 0.26, but also the GSE has substantial discrimination from DMSES (Disattenuated correlation coefficient = 0.283, 95% CI [0.214–0.352], p < 0.001). This suggests that while general and diabetes management self-efficacy are somewhat associated, there are aspects of diabetes management self-efficacy not captured by the more stable general self-efficacy.ConclusionsWe demonstrate that the Thai GSE is a reliable and valid measure. We believe the GSE may represent a useful tool to examine the efficacy of proposed and existing diabetes self-management, and management self-efficacy interventions. creator: Cameron Hurst creator: Nitchamon Rakkapao creator: Eva Malacova creator: Sirima Mongkolsomlit creator: Pear Pongsachareonnont creator: Ram Rangsin creator: Yindee Promsiripaiboon creator: Gunter Hartel uri: https://doi.org/10.7717/peerj.13398 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hurst et al. title: Mental health problems among hotline callers during the early stage of COVID-19 pandemic link: https://peerj.com/articles/13419 last-modified: 2022-05-23 description: BackgroundThe study aims to explore the mental health of the hotline callers during the COVID-19 pandemic in China.MethodsCallers (N = 10,490) from the Beijing Psychological Support Hotline from January 21st to June 30th in 2019 and 2020 were enrolled and divided into two groups (during (2020) and before (2019) COVID-19 pandemic). The severity of depressive symptoms, psychological distress, hopefulness, and suicidal ideation (SI) was assessed. Demographic characteristics and major concerns were also collected. Mann-Whitney U and chi-square test were used to compare the differences in mental health conditions and major concerns between two years and between different age groups. The multivariable logistic regression was used to explore whether mental health conditions were associated with pandemic and demographic factors.ResultsResults from multivariable logistic regression analysis indicated that the change in suicidal ideation (OR = 1.52, 95% CI: 1.21–1.92) was significantly different across age groups. Callers during the pandemic reported a higher level of hopefulness (OR = 1.13, 95% CI [1.03–1.24]), a lower level of depressive symptoms (OR = 0.81, 95% CI [0.74–0.89]) and psychological distress (OR = 0.89, 95% CI [0.81–0.98]), and were less likely to report SI (OR = 0.69, 95% CI [0.61–0.77]) compared with callers before the pandemic.ConclusionsCompared with callers before the pandemic, hotline callers during the early stage of COVID-19 pandemic did not present significant mental health problems. Younger callers during the pandemic were more vulnerable for the presence of suicidal ideation. Hotline-based crisis interventions might provide specific psychological support to cope with troubles during the pandemic. creator: Jing An creator: Yi Yin creator: Liting Zhao creator: Yongsheng Tong creator: Nancy H. Liu uri: https://doi.org/10.7717/peerj.13419 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 An et al. title: Associations between lower limb eccentric muscle capability and change of direction speed in basketball and tennis players link: https://peerj.com/articles/13439 last-modified: 2022-05-23 description: BackgroundThe ability to perform a quick and rapid change of direction (CoD) is an important determinant of success in a variety of sports. Previous studies have already highlighted that eccentric strength is a dominant predictor of CoD. However, these studies evaluated eccentric strength through a limited number of outcome measures and used small sample sizes.MethodsA total of 196 athletes participated in the study. The aim of our study was to investigate: (1) the correlation between eccentric outcome measures derived from different tests (Nordic hamstring exercise (NHE), countermovement jump (CMJ) and flywheel (FW) squats), (2) the association between eccentric outcome measures and CoD 90°, CoD 180°; and (3) proportion of explained variance in CoD performance.ResultsVery large associations (r = 0.783, p < 0.001) were observed between peak torque during NHE (NHEPT) and force impulse during the eccentric phase of CMJ (CMJFI). Small to moderate correlations were calculated between peak eccentric force in flywheel squats and peak eccentric force in CMJ (r = 0.220–035, p < 0002). All eccentric CMJ outcome measures and NHEPT were reported as moderate negative associations with both CoD tests. Eccentric measures explained 25.1% of the variance in CoD 90° (CMJPF, NHEPT, F0.125 –peak eccentric force during FW squats with 0.125 kg m2 load), while the same outcome measures explained 37.4% of the variance for CoD 180°.ConclusionOur results suggest that different measures of eccentric strength specifically contribute to CoD performance. Therefore, for successful CoD performance, different aspects of eccentric strength training should be considered in testing and training (maximal eccentric strength, eccentric-concentric actions with fast execution). creator: Darjan Smajla creator: Žiga Kozinc creator: Nejc Šarabon uri: https://doi.org/10.7717/peerj.13439 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Smajla et al. title: Aflatoxin B1 exposure disrupts organelle distribution in mouse oocytes link: https://peerj.com/articles/13497 last-modified: 2022-05-23 description: Aflatoxin B1 (AFB1) is a secondary metabolite produced by the fungus Aspergillus, which is ubiquitous in moldy grain products. Aflatoxin B1 has been reported to possess hepatotoxicity, renal toxicity, and reproductive toxicity. Previous studies have shown that AFB1 is toxic to mammalian oocytes. However, the potential toxicity of AFB1 on the organelles of mouse oocytes is unknown. In this study, we found that exposure to AFB1 significantly reduced mouse oocyte development capacity. Further analysis showed that the endoplasmic reticulum (ER) failed to accumulate around the spindle, and scattered in the cytoplasm under AFB1 exposure. Similar to the ER, the Golgi apparatus showed a uniform localization pattern following AFB1 treatment. In addition, we found that AFB1 exposure caused the condensation of lysosomes in the cytoplasm, presenting as a clustered or spindle peripheral-localization pattern, which indicated that protein modification, transport, and degradation were affected. Mitochondrial distribution was also altered by AFB1 treatment. In summary, our study showed that AFB1 exposure had toxic effects on the distribution of mouse oocyte organelles, which further led to a decline in oocyte quality. creator: Yan-Zhe Zhang creator: Qian-Han Zhao creator: Hong-Wei Duan creator: Yuan-Jing Zou creator: Shao-Chen Sun creator: Lin-Lin Hu uri: https://doi.org/10.7717/peerj.13497 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Land use/land cover changes in the central part of the Chitwan Annapurna Landscape, Nepal link: https://peerj.com/articles/13435 last-modified: 2022-05-20 description: BackgroundLand use/land cover assessment and monitoring of the land cover dynamics are essential to know the ecological, physical and anthropogenic processes in the landscape. Previous studies have indicated changes in the landscape of mid-hills of Nepal in the past few decades. But there is a lack of study in the Chitwan Annapurna Landscape; hence, this study was carried out to fill in study gap that existed in the area.MethodsThis study evaluates land use/land cover dynamics between 2000 to 2020 in the central part of the Chitwan Annapurna Landscape, Nepal by using Landsat images. The Landsat images were classified into eight different classes using remote sensing and geographic information system (GIS). The accuracy assessment of classified images was evaluated by calculating actual accuracy, producer’s accuracy, user’s accuracy and kappa coefficient based on the ground-truthing points for 2020 and Google Earth and topographic maps for images of 2010 and 2000.ResultsThe results of land use/land cover analysis of Landsat image 2020 showed that the study area was composed of grassland (1.73%), barren area (1.76%), riverine forest (1.93%), water body (1.97%), developed area (4.13%), Sal dominated forest (15.4%), cropland (28.13%) and mixed forest (44.95%). The results of land cover change between 2000 to 2020 indicated an overall increase in Sal dominated forest (7.6%), developed area (31.34%), mixed forest (37.46%) and decrease in riverine forest (11.29%), barren area (20.03%), croplands (29.87%) and grasslands (49.71%). The classification of the images of 2000, 2010 and 2020 had 81%, 81.6% and 84.77% overall accuracy, respectively. This finding can be used as a baseline information for the development of a proper management plan to protect wildlife habitats and forecasting possible future changes, if needed. creator: Jagan Nath Adhikari creator: Bishnu Prasad Bhattarai creator: Maan Bahadur Rokaya creator: Tej Bahadur Thapa uri: https://doi.org/10.7717/peerj.13435 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Adhikari et al. title: Determining the optimal areas of effort in terms of force and force-velocity based on the functional state of the neuromuscular system in the training of elite female judokas link: https://peerj.com/articles/13468 last-modified: 2022-05-20 description: BackgroundThe evaluation of the functional state of the neuromuscular system (NMS) in elite female judokas according to the muscular activity indices is influenced by the force (F) and force-velocity (F-V) efforts. The implementation of the individual correction plan in the elite female judokas’ process of instruction and training must be based on the accurate determination of the force and force-velocity effort areas throughout the training and competitive periods.MethodsThe research involved 44 elite female judokas, divided in to two experimental groups (A, C) and two control groups (B, D). To diagnose the NMS, 21 elite female judokas were evaluated, belonging to different classification categories, divided into three groups: group I–category I (Cat. I), group II–candidates for Masters of Sports (CMS) and group III—Masters of Sports (MS).The evaluation of NMS was performed at the end of each two-week cycle, using 3 tests: Tmax—time to reach the maximum muscle contraction, (msec); Fy –examination of elasticity indices in different muscles, (Hz); J–explosive muscular strength, (kg/s). Measurements were made for six muscle groups and 9 indices of fitness tests: 5 force tests (F) and 4 force-velocity tests (F-V). The research was carried out during 24 cycles, each one lasting two weeks: 12 training cycles and 12 competitive ones. Each cycle lasted two weeks. During the research, the model plan of training for F and F-V was used, determining the optimal areas of F and F-V training efforts in the preparation and competitive periods. In the experimental groups (A and C), according to the data of judokas’ NMS functional state evaluation, the individual correction of the F and F-V efforts was performed every two weeks. As for the control groups (B, D), traditional methods of training were used.ResultsThe NMS evaluation of the female judokas was made every two weeks and the level of correlation of Tmax, Fy and J indices was determined. The value of the Fy index at F effort is 32% in group I, 30% - in group II, 27% - in group III, 28–30% at the effort of F-V. The total number of corrections in group A: 79 negative corrections and 59 positive corrections, while in group C: 65 negative corrections and 89 positive ones. Within the F-V effort, the number of effort corrections in group A was: 68 negative corrections and 92 positive; in group C - 81 positive and 78 negative corrections. The female judokas’ results in the final stage of EG–A were significantly improved in F indices by 52.15%, F-V by 6.22% and 6.18%. In the EG–C, the F increased considerably by 7.52%, F-V by 5.67% and 7.20%. These results characterize the level of physical training.ConclusionThe functional state of the NMS in elite judokas, determined according to the temporal indices of reaching the maximal muscular contraction, the muscle explosive strength and the muscles elasticity, is subjected to dynamics under the influence of force effort and force-velocity effort. creator: Veaceslav Manolachi creator: Vladimir Potop creator: Victor Manolachi creator: Irina Delipovici creator: Cristian Ştefan Liuşnea uri: https://doi.org/10.7717/peerj.13468 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Manolachi et al. title: The superior response speed of table tennis players is associated with proactive inhibitory control link: https://peerj.com/articles/13493 last-modified: 2022-05-20 description: ObjectiveTo explore the mechanism behind the faster volitional reaction time (RT) of open skill sports athletes from the perspective of proactive inhibitory control, with the hypothesis that the superior response speed of athletes from open skill sports is related to their enhanced capacity for releasing inhibition.MethodsParticipants were divided into two groups, an experimental group of 27 table tennis players and a control group of 27 non-athletes. By manipulating cue–target onset asynchrony (CTOA) in a simple cue-target detection task, the timing of target presentation occurred in different phases of the disinhibition process. The time needed for disinhibition were compared between groups.ResultsFor the experimental group, RT varied with CTOA at delays less than 200 ms; for CTOAs greater than 200 ms, RTs were not significantly different. For the control group, RT varied with CTOA for delays as long as 300 ms.ConclusionsTable tennis players took less time (200 ms) than non-athletes (300 ms) to complete the disinhibition process, which might partly explain their rapid response speed measured in unpredictable contexts.SignificanceThe study provided evidence for disinhibition speed as a new index to assess the capacity of proactive inhibitory control, and provided a new perspective to explore the superior RT of athletes from open skill sports. We also offered support for the fundamental cognitive benefits of table tennis training. creator: Mengyan Zhu creator: Yanling Pi creator: Jian Zhang creator: Nan Gu uri: https://doi.org/10.7717/peerj.13493 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu et al. title: The variability of emotions, physical complaints, intention, and self-efficacy: an ecological momentary assessment study in older adults link: https://peerj.com/articles/13234 last-modified: 2022-05-19 description: BackgroundMany theoretical frameworks have been used in order to understand health behaviors such as physical activity, sufficient sleep, healthy eating habits, etc. In most research studies, determinants within these frameworks are assessed only once and thus are considered as stable over time, which leads to rather ‘static’ health behavior change interventions. However, in real-life, individual-level determinants probably vary over time (within days and from day to day), but currently, not much is known about these time-dependent fluctuations in determinants. In order to personalize health behavior change interventions in a more dynamic manner, such information is urgently needed.ObjectiveThe purpose of this study was to explore the time-dependent variability of emotions, physical complaints, intention, and self-efficacy in older adults (65+) using Ecological Momentary Assessment (EMA).MethodsObservational data were collected in 64 healthy older adults (56.3% men; mean age 72.1 ± 5.6 years) using EMA. Participants answered questions regarding emotions (i.e., cheerfulness, relaxation, enthusiasm, satisfaction, insecurity, anxiousness, irritation, feeling down), physical complaints (i.e., fatigue, pain, dizziness, stiffness, shortness of breath), intention, and self-efficacy six times a day for seven consecutive days using a smartphone-based questionnaire. Generalized linear mixed models were used to assess the fluctuations of individual determinants within subjects and over days.ResultsA low variability is present for the negative emotions (i.e., insecurity, anxiousness, irritation, feeling down) and physical complaints of dizziness and shortness of breath. The majority of the variance for relaxation, satisfaction, insecurity, anxiousness, irritation, feeling down, fatigue, dizziness, intention, and self-efficacy is explained by the within subjects and within days variance (42.9% to 65.8%). Hence, these determinants mainly differed within the same subject and within the same day. The between subjects variance explained the majority of the variance for cheerfulness, enthusiasm, pain, stiffness, and shortness of breath (50.2% to 67.3%). Hence, these determinants mainly differed between different subjects.ConclusionsThis study reveals that multiple individual-level determinants are time-dependent, and are better considered as ‘dynamic’ or unstable behavior determinants. This study provides us with important insights concerning the development of dynamic health behavior change interventions, anticipating real-time dynamics of determinants instead of considering determinants as stable within individuals. creator: Iris Maes creator: Lieze Mertens creator: Louise Poppe creator: Geert Crombez creator: Tomas Vetrovsky creator: Delfien Van Dyck uri: https://doi.org/10.7717/peerj.13234 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Maes et al. title: Does the landscape functionality approach provide insight into rangeland conditions in the Tanqua Karoo region, South Africa? link: https://peerj.com/articles/13305 last-modified: 2022-05-19 description: The harsh environmental conditions coupled with a long history of overgrazing have altered the ecology of the arid Tanqua Karoo rangelands in South Africa, which necessitates rehabilitation. However, a suitable method for monitoring rangeland function over time is required for sustainable management. In this study, vegetation characteristics and landscape function indices were used to rate and compare rangeland conditions in 43 sites distributed among three vegetation types: Tanqua Karoo, Tanqua Wash Riviere, and Tanqua Escarpment Shrubland, which occupy different landscapes in the Tankwa Karoo National Park. The results showed low values of vegetation volume (mean of 10.1 m3 per 100 m−2) and low vegetated patches (mean of 29% patches vs 71% fetches). The overall landscape function indices (soil stability, water infiltration, and nutrient recycling) were low and amounted to 55%, 28%, and 17%, respectively. Amongst the various examined landscapes, the escarpment had the highest values of most of the measured landscape functionality parameters, and the open plains had the lowest values. This revealed high heterogeneity of soil properties and vegetation characteristics amongst the different vegetation types, mainly influenced by altitudinal gradients. The higher-lying landscapes on the escarpment are relatively more functional and more susceptible to improvement when compared to the lower-lying landscapes on the plains. The landscape functionality approach (LFA) approach demonstrated that some of the examined vegetation types had insignificant improvement in landscape functionality likely not to improve in the near term due to existing low patchiness, higher fetch space and low LFA indices coupled with the low annual rainfall of the region. The landscape functionality approach has provided a suitable benchmark for assessing and monitoring the diverse vegetation types in this arid part of the world. creator: Manam Saaed creator: Shayne Jacobs creator: Mmoto Leonard Masubelele creator: Lesego Khomo creator: Igshaan Samuels uri: https://doi.org/10.7717/peerj.13305 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Saaed et al. title: Influence of the COVID-19 pandemic on breastfeeding support for healthy mothers and the association between compliance with WHO recommendations for breastfeeding support and exclusive breastfeeding in Japan link: https://peerj.com/articles/13347 last-modified: 2022-05-19 description: BackgroundProfessional breastfeeding support contributes to maternal and child health. However, the influence of the current coronavirus disease 2019 (COVID-19) pandemic on breastfeeding support has not been carefully examined. Therefore, we assessed maternal breastfeeding intention and professional breastfeeding support before and during the pandemic. We further examined the association of compliance with World Health Organization (WHO) recommendations for professional breastfeeding support with exclusive breastfeeding during the pandemic.MethodsThis cross-sectional, internet-based, questionnaire study analyzed data from 484 healthy women with live singleton births between 15 October 2019 and 25 October 2020 in Japan. A delivery before 5 March 2020 was classified as a before-pandemic delivery (n = 135), and a delivery after 6 March 2020 was a during-pandemic delivery (n = 349). Among the ten breastfeeding support steps recommended by the WHO, we assessed the five steps that are measurable by maternal self-report and would likely exhibit variability. Receipt of a free formula sample or invitation to a free sample campaign by the time of survey was also asked. Infant feeding status at the time of the survey was measured among women with infants younger than 5 months, which was a subgroup of mothers who delivered during the pandemic. Mothers were asked what was given to infants during the 24 h before the survey and when nothing other than breast milk was given, the status was classified as exclusive breastfeeding.ResultsWhile 82.2% of women with a delivery before the pandemic intended to breastfeed, the rate was 75.6% during the pandemic (p = 0.120). The average number of breastfeeding support steps received was 3.24 before the pandemic but it was 3.01 during the pandemic (p = 0.069). In particular, rooming-in was less frequent (39.3% before vs. 27.8% during the pandemic, p = 0.014). Among mothers with infants younger than 5 months who had a delivery during the pandemic (n = 189), only 37.0% (n = 70) reported exclusively breastfeeding during the 24 h before completing the survey. Multiple logistic regression analysis indicated that receiving support for all five steps was positively associated with exclusive breastfeeding during the 24 h before the survey (adjusted odds ratio 4.51; 95% CI [1.50–13.61]). Receipt of a free formula sample or invitation to a free sample campaign was negatively associated with exclusive breastfeeding (adjusted odds ratio 0.43; 95% CI [0.19–0.98]). Other factors related to non-exclusive breastfeeding were older maternal age, lower education level, primiparity, and no breastfeeding intention.ConclusionsThe pandemic weakened breastfeeding support for healthy women in Japan; however, support practice that adhered to WHO recommendations appeared to be effective during the pandemic. creator: Keiko Nanishi creator: Sumiyo Okawa creator: Hiroko Hongo creator: Akira Shibanuma creator: Sarah K. Abe creator: Takahiro Tabuchi uri: https://doi.org/10.7717/peerj.13347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nanishi et al. title: Identification of vaccine targets & design of vaccine against SARS-CoV-2 coronavirus using computational and deep learning-based approaches link: https://peerj.com/articles/13380 last-modified: 2022-05-19 description: An unusual pneumonia infection, named COVID-19, was reported on December 2019 in China. It was reported to be caused by a novel coronavirus which has infected approximately 220 million people worldwide with a death toll of 4.5 million as of September 2021. This study is focused on finding potential vaccine candidates and designing an in-silico subunit multi-epitope vaccine candidates using a unique computational pipeline, integrating reverse vaccinology, molecular docking and simulation methods. A protein named spike protein of SARS-CoV-2 with the GenBank ID QHD43416.1 was shortlisted as a potential vaccine candidate and was examined for presence of B-cell and T-cell epitopes. We also investigated antigenicity and interaction with distinct polymorphic alleles of the epitopes. High ranking epitopes such as DLCFTNVY (B cell epitope), KIADYNKL (MHC Class-I) and VKNKCVNFN (MHC class-II) were shortlisted for subsequent analysis. Digestion analysis verified the safety and stability of the shortlisted peptides. Docking study reported a strong binding of proposed peptides with HLA-A*02 and HLA-B7 alleles. We used standard methods to construct vaccine model and this construct was evaluated further for its antigenicity, physicochemical properties, 2D and 3D structure prediction and validation. Further, molecular docking followed by molecular dynamics simulation was performed to evaluate the binding affinity and stability of TLR-4 and vaccine complex. Finally, the vaccine construct was reverse transcribed and adapted for E. coli strain K 12 prior to the insertion within the pET-28-a (+) vector for determining translational and microbial expression followed by conservancy analysis. Also, six multi-epitope subunit vaccines were constructed using different strategies containing immunogenic epitopes, appropriate adjuvants and linker sequences. We propose that our vaccine constructs can be used for downstream investigations using in-vitro and in-vivo studies to design effective and safe vaccine against different strains of COVID-19. creator: Bilal Ahmed Abbasi creator: Devansh Saraf creator: Trapti Sharma creator: Robin Sinha creator: Shachee Singh creator: Shriya Sood creator: Pranjay Gupta creator: Akshat Gupta creator: Kartik Mishra creator: Priya Kumari creator: Kamal Rawal uri: https://doi.org/10.7717/peerj.13380 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Abbasi et al. title: Potential and functional prediction of six circular RNAs as diagnostic markers for colorectal cancer link: https://peerj.com/articles/13420 last-modified: 2022-05-19 description: BackgroundCircular RNAs (circRNAs) have been discovered in colorectal cancer (CRC), but there are few reports on the expression distribution and functional mining analysis of circRNAs.MethodsDifferentially expressed circRNAs in CRC tissues and adjacent normal tissues were screened and identified by microarray and qRT-PCR. ROC curves of the six circRNAs were analyzed. A series of bioinformatics analyses on differentially expressed circRNAs were performed.ResultsA total of 207 up-regulated and 357 down-regulated circRNAs in CRC were screened, and three top up-regulated and down-regulated circRNAs were chosen to be verified in 33 pairs of CRCs by qRT-PCR. 6 circRNAs showed high diagnostic values (AUC = 0.6860, AUC = 0.8127, AUC = 0.7502, AUC = 0.9945, AUC = 0.9642, AUC = 0.9486 for hsa_circRNA_100833, hsa_circRNA_103828, hsa_circRNA_103831 and hsa_circRNA_103752, hsa_circRNA_071106, hsa_circRNA_102293). A circRNA-miRNA-mRNA regulatory network (cirReNET) including six candidate circRNAs, 19 miRNAs and 210 mRNA was constructed, and the functions of the cirReNET were predicted and displayed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on these mRNAs and protein-protein interaction (PPI) network of the hub genes acquired by string and CytoHubba.ConclusionA cirReNET containing potential diagnostic and predictive indicators of CRCs and several critical circRNA-miRNA-mRNA regulatory axes (cirReAXEs) in CRC were mined, and may provide a novel route to study the mechanism and clinical targets of CRC. creator: Li yuan Liu creator: Dan Jiang creator: Yuliang Qu creator: Hongxia Wang creator: Yanting Zhang creator: Shaoqi Yang creator: Xiaoliang Xie creator: Shan Wu creator: Haijin Zhou creator: Guangxian Xu uri: https://doi.org/10.7717/peerj.13420 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Differences in college students’ occupational dysfunction and mental health considering trait and state anxiety during the COVID-19 pandemic link: https://peerj.com/articles/13443 last-modified: 2022-05-19 description: BackgroundDue to the COVID-19 pandemic, university education has shifted from face-to-face classes to online and distance learning. Effects of exposure may manifest in terms of psychological, cognitive, or musculoskeletal impairments that affect an individual’s daily functioning and quality of life. There is a dearth of studies exploring anxiety states, occupational dysfunction, and mental health associated with the new standard of increased telecommunication. Accordingly, the present study aimed to identify the differences in occupational dysfunction, health literacy, positive and negative emotions, and stress response considering the anxiety states of college students during the COVID-19 pandemic. Another purpose is to identify relationships among the parameters such as occupational dysfunction and mental health.MethodsThis cross-sectional study included 358 students (average age: 18.5 years, age range: 18–29 years). Five tools were used: the State-Trait Anxiety Inventory (STAI), Classification and Assessment of Occupational Dysfunction (CAOD), European Health Literacy Survey Questionnaire (HLS-EU-Q47), Profile of Mood States 2nd Edition (POMS-2), and Stress Response Scale-18 (SRS-18). Based on the cutoff value of state and trait anxiety of the STAI, the participants were classified into four groups and compared using one-way analysis of variance and multiple comparison tests. The relationship between all parameters was analyzed using Pearson’s correlation coefficient.ResultsThe group with high trait anxiety and high state anxiety had the highest CAOD total score, Total Mood Disturbance score on the POMS-2, SRS-18 score, and scores on many sub-items of the three parameters. The prevalence of occupational dysfunction was 47% for university students, and there was a variation of from 19 to 61% in each group. The correlation coefficients of the state and trait anxiety scores of the STAI, Total Mood Disturbance score, and SRS-18 ranged from .64 to .75. Additionally, the correlation coefficient between the CAOD total score and these parameters ranged from .44 to .48.ConclusionThe prevalence of occupational dysfunction was highest in the group with high trait anxiety and high state anxiety, and occupational dysfunction, negative emotions, and stress responses were strongest in this group. Our findings point to potential areas for targeted support and interventions. creator: Yasuaki Kusumoto creator: Rieko Higo creator: Kanta Ohno uri: https://doi.org/10.7717/peerj.13443 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kusumoto et al. title: Prevalence and richness of malaria and malaria-like parasites in wild birds from different biomes in South America link: https://peerj.com/articles/13485 last-modified: 2022-05-19 description: South America has different biomes with a high richness of wild bird species and Diptera vectors, representing an ideal place to study the influence of habitat on vector-borne parasites. In order to better understand how different types of habitats do or do not influence the prevalence of haemosporidians, we performed a new analysis of two published datasets comprising wild birds from the Brazilian Savanna (Cerrado) as well as wild birds from the Venezuelan Arid Zone. We investigated the prevalence and genetic diversity of haemosporidian parasites belonging to two genera: Plasmodium and Haemoproteus. We evaluated data from 676 wild birds from the Cerrado and observed an overall prevalence of 49%, whereas, in the Venezuelan Arid Zone, we analyzed data from 527 birds and found a similar overall prevalence of 43%. We recovered 44 lineages, finding Plasmodium parasites more prevalent in the Cerrado (15 Plasmodium and 12 Haemoproteus lineages) and Haemoproteus in the Venezuelan Arid Zone (seven Plasmodium and 10 Haemoproteus lineages). No difference was observed on parasite richness between the two biomes. We observed seven out of 44 haemosporidian lineages that are shared between these two distinct South American biomes. This pattern of parasite composition and prevalence may be a consequence of multiple factors, such as host diversity and particular environmental conditions, especially precipitation that modulate the vector’s dynamics. The relationship of blood parasites with the community of hosts in large and distinct ecosystems can provide more information about what factors are responsible for the variation in the prevalence and diversity of these parasites in an environment. creator: Daniela de Angeli Dutra creator: Nayara Belo creator: Erika M. Braga uri: https://doi.org/10.7717/peerj.13485 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 de Angeli Dutra et al. title: Association of multiple tumor markers with newly diagnosed gastric cancer patients: a retrospective study link: https://peerj.com/articles/13488 last-modified: 2022-05-19 description: BackgroundThe purpose of this paper was to explore the correlation between multiple tumor markers and newly diagnosed gastric cancer.MethodsWe selected 268 newly diagnosed patients with gastric cancer and 209 healthy subjects for correlation research. The detection of multiple tumor markers was based on protein chips and the results were statistically analyzed using SPSS.ResultsWe concluded that gastric cancer was significantly related to gender, age, alpha fetoprotein (AFP), carcinoembryonic antigen (CEA), carbohydrate antigen 125 (CA125), carbohydrate antigen 199 (CA199), and carbohydrate antigen 242 (CA242) positive levels (P < 0.001). After CA199 and CA242 were stratified by gender, the male odds ratio (OR) was 30.400 and 31.242, respectively, while the female OR was 3.424. After CA125 was stratified by age in patients over 54 years old with gastric cancer, the risk of occurrence in the CA125-positive population was 16.673 times that of the CA125-negative patients. Among patients 54 years old and younger, being CA125-positive was not a risk factor for gastric cancer (P = 0.082). AFP, CEA, CA125, CA199, and CA242 positive levels during the M1 stage were statistically significant when compared with the M0 stage and control group (P < 0.001), but the AFP (P = 0.045) and CA125 (P = 0.752) positive levels were not statistically significant when compared with the M0 stage and control group. The combined detection sensitivity of multiple tumor markers was 44.78%.ConclusionOur research shows that gastric cancer is associated with age, gender, and the positive levels of AFP, CEA, CA125, CA199, and CA242. The positive levels of AFP and CA125 were related to the distant metastasis of gastric cancer. To a certain extent, the combined detection sensitivity can be used for the initial screening of gastric cancer. creator: Xiaoyang Li creator: Sifeng Li creator: Zhenqi Zhang creator: Dandan Huang uri: https://doi.org/10.7717/peerj.13488 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Seasonal and diel influences on bottlenose dolphin acoustic detection determined by whistles in a coastal lagoon in the southwestern Gulf of California link: https://peerj.com/articles/13246 last-modified: 2022-05-18 description: Marine mammals in subtropical coastal habitats are sentinels of the health of the ecosystem and offer important ecosystem services. They rely on prey that pursues feeding opportunities, while both avoid unfavorable conditions. In many cases, these predator-prey dynamics fluctuate seasonally and are regulated by lunar, tidal, and/or diel cycles (hour). However, these rhythmical patterns may vary under different seasonal conditions. Bottlenose dolphins (Tursiops truncatus) in the Ensenada de La Paz in Baja California Sur, Mexico, were detected acoustically over the course of an annual cycle on 21 separate occasions, covering 640 h from June 2017 to May 2019. The presence of bottlenose dolphins was examined using Generalized Additive Models (GAM) including variables that are related directly to their habitat (direct variables: hour, distance, depth) and to their prey (indirect variables: SST, moon phase and tides). Seasonal differences in the presence of bottlenose dolphins were influenced more by indirect variables (explained deviance: 34.8% vs. 37.7%). Hourly acoustic detections occurred less frequently when SST exceeded 27.4 °C (Aug–End of Nov.) and more frequently at moderate temperatures (22.7 °C to 26.3 °C) in May through July. Moreover, bottlenose dolphins were detected more frequently during waning and new moon phases, at the onset of flood and ebb tides, and during day (04:00 to 20:00). The seasonal differences in acoustic detections rates were highlighted by the global GAM and hierarchical clustering. The strong seasonal pattern indicated possible interactions with rhythmic pattern of bottlenose dolphins. Four candidate variables (SST, moon, tide, and hour) were tested for plausible interaction terms additional to their individual consideration, out of which only hour changed significantly between seasons. The patterns of presence likely increase feeding opportunities or may favor other behaviors such as socializing, resting, or nursing. These might prove responsible for the distinct occurrence and hourly patterns of bottlenose dolphins. creator: Marco F. W. Gauger creator: Eduardo Romero-Vivas creator: Myron A. Peck creator: Eduardo F. Balart creator: Javier Caraveo-Patiño uri: https://doi.org/10.7717/peerj.13246 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gauger et al. title: Growth of Lahontan cutthroat trout from multiple sources re-introduced into Sagehen Creek, CA link: https://peerj.com/articles/13322 last-modified: 2022-05-18 description: Lahontan cutthroat trout Oncorhynchus clarkii henshawi have experienced massive declines in their native range and are now a threatened species under the US Endangered Species Act. A key management goal for this species is re-establishing extirpated populations using translocations and conservation hatcheries. In California USA, two broodstocks (Pilot Peak and Independence Lake) are available for reintroduction, in addition to translocations from wild and naturalized sources. Pilot Peak and Independence Lake fish are hatchery stocks derived from native fish from the Truckee River basin and used for recovery activities in the western Geographic Management Unit Areas only, specifically within the Truckee River basin. Yet suitability of these sources for re-introduction in different ecosystem types remains an open and important topic. We conducted growth experiments using Lahontan cutthroat trout stocked into Sagehen Creek, CA, USA. Experiments evaluated both available broodstocks and a smaller sample of fish translocated representing a naturalized population of unknown origin from a nearby creek. Fish from the Independence Lake source had significantly higher growth in weight and length compared to the other sources. Further, Independence Lake fish were the only stock that gained weight on average over the duration of the experiment. Our experiments suggest fish from the Independence Lake brood stock should be considered in reintroduction efforts. creator: Jonathan E. Stead creator: Virginia L. Boucher creator: Peter B. Moyle creator: Andrew L. Rypel uri: https://doi.org/10.7717/peerj.13322 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Stead et al. title: Handcycling with concurrent lower body low-frequency electromyostimulation significantly increases acute oxygen uptake: implications for rehabilitation and prevention link: https://peerj.com/articles/13333 last-modified: 2022-05-18 description: BackgroundAcute increases in exercise-induced oxygen uptake (V̇O2) is crucial for aerobic training adaptations and depends on how much muscle mass is involved during exercising. Thus, handcycling is per se limited for higher maximal oxygen uptakes (V̇O2max) due to restricted muscle involvement. Handcycling with additional and simultaneous application of low-frequency electromyostimulation (EMS) to the lower extremities might be a promising stimulus to improve aerobic capacity in disabled and rehabilitative populations.MethodTwenty-six healthy young adults (13 female, age: 23.4 ± 4.5 years, height: 1.77 ± 0.09 m, mass: 71.7 ± 16.7 kg) completed 4 ×10 minutes of sitting (SIT), sitting with concurrent EMS (EMS_SIT), handcycling (60 rpm, 1/2 bodyweight as resistance in watts) (HANDCYCLE) and handcycling with concurrent EMS of the lower extremities (EMS_HANDCYCLE). During EMS_SIT and EMS_HANDCYCLE, low frequency EMS (impulse frequency: 4Hz, impulse width: 350 µs, continuous stimulation) was applied to gluteal, quadriceps and calf muscles. The stimulation intensity was selected so that the perceived pain could be sustained for a duration of 10 minutes (gluteus: 80.0 ± 22.7 mA, quadriceps: 94.5 ± 20.5 mA, calves: 77.5 ± 19.1 mA).ResultsSignificant mode-dependent changes of V̇O2 were found (p < 0.001, ηp2 = 0.852). Subsequent post-hoc testing indicated significant difference between SIT vs. EMS_SIT (4.70 ± 0.75 vs. 10.61 ± 4.28 ml min−1 kg−1, p < 0.001), EMS_SIT vs. HANDCYCLE (10.61 ± 4.28 vs. 13.52 ± 1.40 ml min−1 kg−1, p = 0.005), and between HANDCYCLE vs. EMS_HANDCYCLE (13.52 ± 1.40 vs. 18.98 ± 4.89 ml min−1 kg−1, p = 0.001).ConclusionHandcycling with simultaneous lower body low-frequency EMS application elicits notably higher oxygen uptake during rest and moderately loaded handcycling and may serve as an additional cardiocirculatory training stimuli for improvements in aerobic capacity in wheelchair and rehabilitation settings. creator: Ludwig Rappelt creator: Steffen Held creator: Lars Donath uri: https://doi.org/10.7717/peerj.13333 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rappelt et al. title: Embryonic development of the moon jellyfish Aurelia aurita (Cnidaria, Scyphozoa): another variant on the theme of invagination link: https://peerj.com/articles/13361 last-modified: 2022-05-18 description: BackgroundAurelia aurita (Scyphozoa, Cnidaria) is an emblematic species of the jellyfish. Currently, it is an emerging model of Evo-Devo for studying evolution and molecular regulation of metazoans’ complex life cycle, early development, and cell differentiation. For Aurelia, the genome was sequenced, the molecular cascades involved in the life cycle transitions were characterized, and embryogenesis was studied on the level of gross morphology. As a reliable representative of the class Scyphozoa, Aurelia can be used for comparative analysis of embryonic development within Cnidaria and between Cnidaria and Bilateria. One of the intriguing questions that can be posed is whether the invagination occurring during gastrulation of different cnidarians relies on the same cellular mechanisms. To answer this question, a detailed study of the cellular mechanisms underlying the early development of Aurelia is required.MethodsWe studied the embryogenesis of A. aurita using the modern methods of light microscopy, immunocytochemistry, confocal laser microscopy, scanning and transmission electron microscopy.ResultsIn this article, we report a comprehensive study of the early development of A. aurita from the White Sea population. We described in detail the embryonic development of A. aurita from early cleavage up to the planula larva. We focused mainly on the cell morphogenetic movements underlying gastrulation. The dynamics of cell shape changes and cell behavior during invagination of the archenteron (future endoderm) were characterized. That allowed comparing the gastrulation by invagination in two cnidarian species—scyphozoan A. aurita and anthozoan Nematostella vectensis. We described the successive stages of blastopore closure and found that segregation of the germ layers in A. aurita is linked to the ’healing’ of the blastopore lip. We followed the developmental origin of the planula body parts and characterized the planula cells’ ultrastructure. We also found that the planula endoderm consists of three morphologically distinct compartments along the oral-aboral axis.ConclusionsEpithelial invagination is a fundamental morphogenetic movement that is believed as highly conserved across metazoans. Our data on the cell shaping and behaviours driving invagination in A. aurita contribute to understanding of morphologically similar morphogenesis in different animals. By comparative analysis, we clearly show that invagination may differ at the cellular level between cnidarian species belonging to different classes (Anthozoa and Scyphozoa). The number of cells involved in invagination, the dynamics of the shape of the archenteron cells, the stage of epithelial-mesenchymal transition that these cells can reach, and the fate of blastopore lip cells may vary greatly between species. These results help to gain insight into the evolution of morphogenesis within the Cnidaria and within Metazoa in general. creator: Yulia Kraus creator: Boris Osadchenko creator: Igor Kosevich uri: https://doi.org/10.7717/peerj.13361 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kraus et al. title: Hospital-level characteristics of the standardised mortality ratio for ischemic heart disease: a retrospective observational study using Japanese administrative claim data from 2012 to 2019 link: https://peerj.com/articles/13424 last-modified: 2022-05-18 description: BackgroundIschemic heart disease (IHD) is one of the leading causes of mortality worldwide and imposes a heavy burden on patients. Previous studies have indicated that the optimal care for IHD during hospitalisation may reduce the risk of in-hospital mortality. The standardised mortality ratio (SMR) is an indicator for assessing the risk-adjusted in-hospital mortality ratio based on case-mix. This indicator can crucially identify hospitals that can be changed to improve patient safety and the quality of care. This study aimed to determine the hospital-level characteristics of the SMR for IHD in Japan.MethodsThis study was designed as a retrospective observational study using the Japanese administrative claim data from 2012 to 2019. The data of all hospital admissions with a primary diagnosis of IHD (ICD-10, I20-I25) were used. Patients with complete variables data were included in this study. Hospitals with less than 200 IHD inpatients in each 2-year period were excluded. The SMR was defined as the ratio of the observed number of in-hospital deaths to the expected number of in-hospital deaths multiplied by 100.The observed number of in-hospital deaths was the sum of the actual number of in-hospital deaths at that hospital, and the expected number of in-hospital deaths was the sum of the probabilities of in-hospital deaths. Ratios of in-hospital mortality was risk-adjusted using multivariable logistic regression analyses. The c-statistic and Hosmer-Lemeshow test were used to evaluate the predictive accuracy of the logistic models. Changes in SMRs in each consecutive period were assessed using Spearman’s correlation coefficient.ResultsA total of 64,831 were admitted patients with IHD in 27 hospitals as complete submission data. The SMRs showed wide variation among hospitals, ranging from 35.4 to 197.6, and analysis models indicated good predictive ability with a c-statistic of 0.93 (95% CI [0.92–0.94]) and Hosmer-Lemeshow test of 0.30. The results of chi-square tests and t-tests for all variables to assess the association with in-hospital mortality were P < 0.001. In the analysis of trends in each consecutive period, the SMRs showed positive correlations.ConclusionsThis study denoted that the SMRs for IHD could be calculated using Japanese administrative claim data. The SMR for IHD might contribute to the development of more appropriate benchmarking systems for hospitals to improve quality of care. creator: Ryo Onishi creator: Yosuke Hatakeyama creator: Kunichika Matsumoto creator: Kanako Seto creator: Koki Hirata creator: Yinghui Wu creator: Tomonori Hasegawa uri: https://doi.org/10.7717/peerj.13424 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Onishi et al. title: Melatonin increases growth properties in human dermal papilla spheroids by activating AKT/GSK3β/β-Catenin signaling pathway link: https://peerj.com/articles/13461 last-modified: 2022-05-18 description: BackgroundMelatonin, a neurohormone, maybe involved in physiological processes, such as antioxidation, anti-inflammation, and hair growth. In the present study, we investigated the effects of melatonin on proliferation and intracellular signaling in DP cells using a three-dimensional (3D) spheroid culture system that mimics the in vivo hair follicle system.MethodsDP cells were incubated in monolayer (2D) and 3D spheroid culture systems. The expression levels of melatonin receptors in DP cells were analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blotting. The effect of melatonin on the hair-inductive property of DP cells was analyzed using a WST-1-based proliferation assay, determination of DP spheroid size, expression analysis of DP signature genes, and determination of β-catenin stabilization in DP cells. The AKT/GSK3β/β-catenin signaling pathway associated with melatonin-induced β-catenin stabilization in DP cells was investigated by analyzing changes in upstream regulator proteins, including AKT, GSK3β, and their phosphorylated forms.ResultsThe expression levels of the melatonin receptors were higher in human DP cells than in human epidermal keratinocytes and human dermal fibroblast cells. Comparing the expression level according to the human DP cell culture condition, melatonin receptor expression was upregulated in the 3D culture system compared to the traditional two-dimensional monolayer culture system. Cell viability analysis showed that melatonin concentrations up to 1 mM did not affect cell viability. Moreover, melatonin increased the diameter of DP cell 3D spheroids in a dose-dependent manner. Immunoblotting and qRT-PCR analysis revealed that melatonin upregulated the expression of hair growth-related genes, including alkaline phosphatase, bone morphogenetic protein 2, versican, and wingless-int 5A, in a melatonin receptor-dependent manner. Cell fractionation analysis showed that melatonin increased the nuclear localization of β-catenin. This result correlated with the increased transcriptional activation of T-cell factor/lymphoid enhancer factor-responsive luciferase induced by melatonin treatment. Interestingly, melatonin induced the phosphorylation of protein kinase B/AKT at serine 473 residue and GSK-3β at serine 9 residue. To determine whether AKT phosphorylation at serine 473 induced β-catenin nuclear translocation through GSK3β phosphorylation at serine 9, the PI3K/AKT inhibitor LY294002 was cotreated with melatonin. Immunoblotting showed that LY294002 inhibited melatonin-induced phosphorylation of GSK3β at serine 9 residue and β-catenin activation.ConclusionCollectively, this report suggests that melatonin promotes growth properties by activating the AKT/GSK3β/β-catenin signaling pathway through melatonin receptors. creator: Sowon Bae creator: Yoo Gyeong Yoon creator: Ji Yea Kim creator: In-Chul Park creator: Sungkwan An creator: Jae Ho Lee creator: Seunghee Bae uri: https://doi.org/10.7717/peerj.13461 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bae et al. title: Bayesian estimation for the mean of delta-gamma distributions with application to rainfall data in Thailand link: https://peerj.com/articles/13465 last-modified: 2022-05-18 description: Precipitation and flood forecasting are difficult due to rainfall variability. The mean of a delta-gamma distribution can be used to analyze rainfall data for predicting future rainfall, thereby reducing the risks of future disasters due to excessive or too little rainfall. In this study, we construct credible and highest posterior density (HPD) intervals for the mean and the difference between the means of delta-gamma distributions by using Bayesian methods based on Jeffrey’s rule and uniform priors along with a confidence interval based on fiducial quantities. The results of a simulation study indicate that the Bayesian HPD interval based on Jeffrey’s rule prior performed well in terms of coverage probability and provided the shortest expected length. Rainfall data from Chiang Mai province, Thailand, are also used to illustrate the efficacies of the proposed methods. creator: Theerapong Kaewprasert creator: Sa-Aat Niwitpong creator: Suparat Niwitpong uri: https://doi.org/10.7717/peerj.13465 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kaewprasert et al. title: Inter-set rest configuration effect on acute physiological and performance-related responses to a resistance training session in terrestrial vs simulated hypoxia link: https://peerj.com/articles/13469 last-modified: 2022-05-18 description: BackgroundMetabolic stress is considered a key factor in the activation of hypertrophy mechanisms which seems to be potentiated under hypoxic conditions.This study aimed to analyze the combined effect of the type of acute hypoxia (terrestrial vs simulated) and of the inter-set rest configuration (60 vs 120 s) during a hypertrophic resistance training (RT) session on physiological, perceptual and muscle performance markers.MethodsSixteen active men were randomized into two groups based on the type of hypoxia (hypobaric hypoxia, HH: 2,320 m asl; vs normobaric hypoxia, NH: FiO2 of 15.9%). Each participant completed in a randomly counterbalanced order the same RT session in four separated occasions: two under normoxia and two under the corresponding hypoxia condition at each prescribed inter-set rest period. Volume-load (load × set × repetition) was calculated for each training session. Muscle oxygenation (SmO2) of the vastus lateralis was quantified during the back squat exercise. Heart rate (HR) was monitored during training and over the ensuing 30-min post-exercise period. Maximal blood lactate concentration (maxLac) and rating of perceived exertion (RPE) were determined after the exercise and at the end of the recovery period.ResultsVolume-load achieved was similar in all environmental conditions and inter-set rest period length did not appreciably affect it. Shorter inter-set rest periods displayed moderate increases in maxLac, HR and RPE responses in all conditions. Compared to HH, NH showed a moderate reduction in the inter-set rest-HR (ES > 0.80), maxLac (ES > 1.01) and SmO2 (ES > 0.79) at both rest intervals.ConclusionsResults suggest that the reduction in inter-set rest intervals from 120 s to 60 s provide a more potent perceptual, cardiovascular and metabolic stimulus in all environmental conditions, which could maximize hypertrophic adaptations in longer periods of training. The abrupt exposure to a reduced FiO2 at NH seems to reduce the inter-set recovery capacity during a traditional hypertrophy RT session, at least during a single acute exposition. These results cannot be extrapolated to longer training periods. creator: Cristina Benavente creator: Belén Feriche creator: Guillermo Olcina creator: Brad J. Schoenfeld creator: Alba Camacho-Cardenosa creator: Filipa Almeida creator: Ismael Martínez-Guardado creator: Rafael Timon creator: Paulino Padial uri: https://doi.org/10.7717/peerj.13469 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Benavente et al. title: Experimentally broadcast ocean surf and river noise alters birdsong link: https://peerj.com/articles/13297 last-modified: 2022-05-17 description: Anthropogenic noise and its effects on acoustic communication have received considerable attention in recent decades. Yet, the natural acoustic environment’s influence on communication and its role in shaping acoustic signals remains unclear. We used large-scale playbacks of ocean surf in coastal areas and whitewater river noise in riparian areas to investigate how natural sounds influences song structure in six songbird species. We recorded individuals defending territories in a variety of acoustic conditions across 19 study sites in California and 18 sites in Idaho. Acoustic characteristics across the sites included naturally quiet ‘control’ sites, ‘positive control’ sites that were adjacent to the ocean or a whitewater river and thus were naturally noisy, ‘phantom’ playback sites that were exposed to continuous broadcast of low-frequency ocean surf or whitewater noise, and ‘shifted’ playback sites with continuous broadcast of ocean surf or whitewater noise shifted up in frequency. We predicted that spectral and temporal song structure would generally correlate with background sound amplitude and that signal features would differ across site types based on the spectral profile of the acoustic environment. We found that the ways in which song structure varied with background acoustics were quite variable from species to species. For instance, in Idaho both the frequency bandwidth and duration of lazuli bunting (Passerina amoena) and song sparrow (Melospiza melodia) songs decreased with elevated background noise, but these song features were unrelated to background noise in the warbling vireo (Vireo gilvus), which tended to increase both the minimum and maximum frequency of songs with background noise amplitude. In California, the bandwidth of the trill of white-crowned sparrow (Zonotrichia leucophrys) song decreased with background noise amplitude, matching results of previous studies involving both natural and anthropogenic noise. In contrast, wrentit (Chamaea fasciata) song bandwidth was positively related to the amplitude of background noise. Although responses were quite heterogeneous, song features of all six species varied with amplitude and/or frequency of background noise. Collectively, these results provide strong evidence that natural soundscapes have long influenced vocal behavior. More broadly, the evolved behavioral responses to the long-standing challenges presented by natural sources of noise likely explain the many responses observed for species communicating in difficult signal conditions presented by human-made noise. creator: Veronica A. Reed creator: Cory A. Toth creator: Ryan N. Wardle creator: Dylan G.E. Gomes creator: Jesse R. Barber creator: Clinton D. Francis uri: https://doi.org/10.7717/peerj.13297 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Reed et al. title: Effects of three probiotics and their interactions on the growth performance of and nutrient absorption in broilers link: https://peerj.com/articles/13308 last-modified: 2022-05-17 description: The purpose of this study was to investigate the effects of three probiotics and their interactions on growth performance, intestinal digestion and absorption, and nutrient transporters in broilers. A total of 350 one-day-old male Arbor Acres broilers were randomly divided into seven groups: the control group (broilers receiving normal drinking water), groups P1, P2 and P3 (broilers receiving drinking water with 1% Lactobacillus casei, Lactobacillus acidophilus and Bifidobacterium lactis , respectively) and groups CP1, CP2 and CP3 (broilers receiving drinking water with a 1% compound probiotic mixture in 2:1:1, 1:2:1, 1:1:2 ratios, respectively). The feeding period was divided into two experimental periods: 1∼21 days and 22∼42 days. Compared to those in the control group, the broiler slaughter indexes and average daily feed intakes in the probiotics groups were not significantly different (P > 0.05), but the villus height in the small intestine increased significantly, and the crypt depth decreased significantly (P < 0.05). In the 1- to 21-day, experimental period, the broiler average daily gains in groups CP2 and CP3 were significantly greater than that in the control group. Amylase, lipase, and trypsin activities in the jejunum in groups CP and P3 increased significantly. GLUT2 mRNA expression in the probiotics group was significantly incresaed compared with that in the control group (P < 0.05). In the 22- to 42-day period, the average daily gain in the CP group was significantly greater than that in the control group. Amylase activity in the CP2 group, and lipase and trypsin activities in the CP, P1 and P3 groups increased significantly. The GLUT2 mRNA expression in the CP group increased significantly (P < 0.05). In summary, three probiotics and their interactions improved the digestibility and absorption of nutrients by increasing the activities of digestive enzymes, improving the morphology of the digestive tract, and upregulating the expression of GLUT2 mRNA in the intestinalcell membrane to improve the production performance in broilers. creator: Lihuan Zhang creator: Yanfei Wang creator: Ruonan Zhang creator: Hao Jia creator: Xuan Liu creator: Zhiwei Zhu uri: https://doi.org/10.7717/peerj.13308 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Transcriptome changes in ERGIC3-knockdown hepatocellular carcinoma cells: ERGIC3 is a novel immune function related gene link: https://peerj.com/articles/13369 last-modified: 2022-05-17 description: ObjectiveThe expression of ERGIC3 is increased in a variety of tumors and promotes the growth and metastasis of liver cancer, but the molecular mechanism needs to be further studied.In this study, we aimed to analyze the molecular mechanism of ERGIC3 regulating the proliferation of human hepatocellular carcinoma (HCC) SMMC-7721 cells using transcriptomics.MethodsERGIC3 was knocked down in SMMC-7721 cells by RNAi technique, and the expression of ERGIC3 was detected by Q-RT-PCR and Western Blot. RNA sequencing was performed in the Illumina HiSeq platform in the control group and the ERGIC3i group and bioinformatics methods were selected to analyze the data.ResultsThe expression of ERGIC3 was reduced to 10% in SMMC-7721 cells by RNAi technique, and 176 genes were up-regulated and 34 genes were down-regulated in ERGIC3i group compared with the control group. Analysis of the pathways and biological processes that enrich the function of differentially expressed genes showed thatthese differentially expressed genes were mainly involved in vesicular transport, growth factors, PI3K-Akt, NOD-like, Jak-STAT, NF-kappa B and other protein kinase-coupled receptors mediated signal transduction pathways, tumor immune response, collagen-integrin receptor-actin axis, and miRNA pathways. More importantly, most of the significantly altered pathways were related to immunity. ERGIC3 may be a key immune-related gene.ConclusionBased on the transcriptomic analysis, the mechanism of ERGIC3 promoting the growth of HCC is link with the transport of growth factor receptor, cytokine receptor and collagen. Then it is involved in signal transduction pathways mediated by protein kinase-coupled receptors, PI3K-Akt, NOD-like, Jak-STAT and NF-kappa B. In particular, the mechanism is also involved in the ERGIC3-dependent immune pathways. ERGIC3 is a potential target for prevention and treatment of HCC. creator: Mengyuan Liu creator: Qiurong Zhao creator: Xiang Zheng creator: Lei Yang creator: Yanyu Zhao creator: Xueying Li creator: Mingsong Wu uri: https://doi.org/10.7717/peerj.13369 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Different roles of urinary light chains and serum light chains as potential biomarkers for monitoring disease activity in systemic lupus erythematosus link: https://peerj.com/articles/13385 last-modified: 2022-05-17 description: ObjectiveThe assessment system for monitoring systemic lupus erythematosus (SLE) disease activity is complex and lacks reliable laboratory indicators. It is necessary to find rapid and noninvasive biomarkers. The aim of this study was to screen and identify the differentially expressed proteins in urine samples between active SLE and stable SLE and to further explore the expression of light chains.MethodsFirst, we used a label-free quantitative proteomics approach to establish the urine protein expression profile of SLE, and then screened differentially expressed proteins. Subsequently, the expression of overall light chains was examined by immunofixation electrophoresis and immunoturbidimetric methods, respectively.ResultsMass spectrometry data analysis found a total of 51 light chain peptides in the urinary protein expression spectrum, of which 27 light chain peptides were differentially expressed between the two groups. The largest difference was IGLV5-45 located in the variable region of the immunoglobulin Lambda light chain. The levels of urinary light chains and serum light chains were both significantly elevated in active SLE, and the levels of urinary light chains increased with the severity of disease activity.ConclusionsThe measurement of light chains would help to monitor SLE disease activity. Serum light chains had better discriminatory capacity than urinary light chains, while urine light chains were closely related to the severity of disease activity and could be used for dynamically monitoring the progress of disease activity. creator: Jun Jiang creator: Jin Zhao creator: Dan Liu creator: Man Zhang uri: https://doi.org/10.7717/peerj.13385 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jiang et al. title: Locally developed models improve the accuracy of remotely assessed metrics as a rapid tool to classify sandy beach morphodynamics link: https://peerj.com/articles/13413 last-modified: 2022-05-17 description: Classification of beaches into morphodynamic states is a common approach in sandy beach studies, due to the influence of natural variables in ecological patterns and processes. The use of remote sensing for identifying beach type and monitoring changes has been commonly applied through multiple methods, which often involve expensive equipment and software processing of images. A previous study on the South African Coast developed a method to classify beaches using conditional tree inferences, based on beach morphological features estimated from public available satellite images, without the need for remote sensing processing, which allowed for a large-scale characterization. However, since the validation of this method has not been tested in other regions, its potential uses as a trans-scalar tool or dependence from local calibrations has not been evaluated. Here, we tested the validity of this method using a 200-km stretch of the Brazilian coast, encompassing a wide gradient of morphodynamic conditions. We also compared this locally derived model with the results that would be generated using the cut-off values established in the previous study. To this end, 87 beach sites were remotely assessed using an accessible software (i.e., Google Earth) and sampled for an in-situ environmental characterization and beach type classification. These sites were used to derive the predictive model of beach morphodynamics from the remotely assessed metrics, using conditional inference trees. An additional 77 beach sites, with a previously known morphodynamic type, were also remotely evaluated to test the model accuracy. Intertidal width and exposure degree were the only variables selected in the model to classify beach type, with an accuracy higher than 90% through different metrics of model validation. The only limitation was the inability in separating beach types in the reflective end of the morphodynamic continuum. Our results corroborated the usefulness of this method, highlighting the importance of a locally developed model, which substantially increased the accuracy. Although the use of more sophisticated remote sensing approaches should be preferred to assess coastal dynamics or detailed morphodynamic features (e.g., nearshore bars), the method used here provides an accessible and accurate approach to classify beach into major states at large spatial scales. As beach type can be used as a surrogate for biodiversity, environmental sensitivity and touristic preferences, the method may aid management in the identification of priority areas for conservation. creator: Helio Herminio Checon creator: Yasmina Shah Esmaeili creator: Guilherme N. Corte creator: Nicole Malinconico creator: Alexander Turra uri: https://doi.org/10.7717/peerj.13413 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Checon et al. title: Genome-wide identification of xyloglucan endotransglucosylase/hydrolase gene family members in peanut and their expression profiles during seed germination link: https://peerj.com/articles/13428 last-modified: 2022-05-17 description: Seed germination marks the beginning of a new plant life cycle. Improving the germination rate of seeds and the consistency of seedling emergence in the field could improve crop yields. Many genes are involved in the regulation of seed germination. Our previous study found that some peanut XTHs (xyloglucan endotransglucosylases/hydrolases) were expressed at higher levels at the newly germinated stage. However, studies of the XTH gene family in peanut have not been reported. In this study, a total of 58 AhXTH genes were identified in the peanut genome. Phylogenetic analysis showed that these AhXTHs, along with 33 AtXTHs from Arabidopsis and 61 GmXTHs from soybean, were classified into three subgroups: the I/II, IIIA and IIIB subclades. All AhXTH genes were unevenly distributed on the 18 peanut chromosomes, with the exception of chr. 07 and 17, and they had relatively conserved exon-intron patterns, most with three to four introns. Through chromosomal distribution pattern and synteny analysis, it was found that the AhXTH family experienced many replication events, including 42 pairs of segmental duplications and 23 pairs of tandem duplications, during genome evolution. Conserved motif analysis indicated that their encoded proteins contained the conserved ExDxE domain and N-linked glycosylation sites and displayed the conserved secondary structural loops 1–3 in members of the same group. Expression profile analysis of freshly harvested seeds, dried seeds, and newly germinated seeds using transcriptome data revealed that 26 AhXTH genes, which account for 45% of the gene family, had relatively higher expression levels at the seed germination stage, implying the important roles of AhXTHs in regulating seed germination. The results of quantitative real-time PCR also confirmed that some AhXTHs were upregulated during seed germination. The results of GUS histochemical staining showed that AhXTH4 was mainly expressed in germinated seeds and etiolated seedlings and had higher expression levels in elongated hypocotyls. AhXTH4 was also verified to play a crucial role in the cell elongation of hypocotyls during seed germination. creator: Jieqiong Zhu creator: Guiying Tang creator: Pingli Xu creator: Guowei Li creator: Changle Ma creator: Pengxiang Li creator: Chunyu Jiang creator: Lei Shan creator: Shubo Wan uri: https://doi.org/10.7717/peerj.13428 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu et al. title: Fluoride effect indicators in Phaseolus vulgaris seeds and seedlings link: https://peerj.com/articles/13434 last-modified: 2022-05-17 description: BackgroundFluoride (F) is one of the main environmental pollutants, and high concentrations are commonly detected in the air and in both surface and groundwater. However, the effects of this pollutant on seed germination and on the initial growth of crop seedlings are still poorly understood. In this context, the aim of this study was to assess morphoanatomical, physiological and biochemical fluoride effect indicators in Phaseolus vulgaris L. seeds and seedlings.MethodsP. vulgaris seeds were exposed to a liquid potassium fluoride solution (KF, pH 6.0) at concentrations of 0 (control), 10, 20, 30 mg L−1 for 7 days. A completely randomized experimental design was applied, consisting of four treatments with four replications each. During the experimental period, physiological (7 days) anatomical and histochemical (2 days), biochemical and chemical (4 days) assessments. An analysis of variance was performed followed by Dunnett’s test. to determine significant differences between the KF-exposed groups and control seeds; and a multivariate analysis was performed.ResultsThe germination parameters, and anatomical, morphological, physiological, biochemical and nutritional characteristics of the seedlings did not show negative effects from exposure to KF at the lowest doses evaluated. On the other hand, treatment with the highest dose of KF (30 mg L−1) resulted in a lower germination rate index and increase in abnormal seedlings, and higher electrical conductivity. A lower root length, magnesium content and photochemical efficiency were also observed. The exposure of P. vulgaris to KF, regardless the dose did not affect seeds anatomy and the accumulation of starch and proteins, in relation to the control group.ConclusionsOur findings demonstrated that P. vulgaris seedlings were tolerant to KF solutions up to 20 mg L−1, and sensitive when exposed to 30 mg KF L−1. creator: Ingrid Maressa Hungria de Lima e Silva creator: Arthur Almeida Rodrigues creator: Juliana de Fátima Sales creator: Douglas Almeida Rodrigues creator: Sebastião Carvalho Vasconcelos Filho creator: Cássia Lino Rodrigues creator: Priscila Ferreira Batista creator: Alan Carlos Costa creator: Marisa Domingos creator: Caroline Müller creator: Adinan Alves da Silva uri: https://doi.org/10.7717/peerj.13434 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Maressa Hungria de Lima e Silva et al. title: A new perleidid neopterygian fish from the Early Triassic (Dienerian, Induan) of South China, with a reassessment of the relationships of Perleidiformes link: https://peerj.com/articles/13448 last-modified: 2022-05-17 description: Neopterygii is the largest clade of ray-finned fishes, including Teleostei, Holostei, and their closely related fossil taxa. This clade was first documented in the Early Carboniferous and underwent rapid evolutionary radiation during the Early to Middle Triassic. This article describes a new perleidid neopterygian species, Teffichthys elegans sp. nov., based on 13 well-preserved specimens from the lower Daye Formation (Dienerian, Induan) in Guizhou, China. The new species documents one of the oldest perleidids, providing insights into the early diversification of this family. The results of a phylogenetic analysis recover Teffichthys elegans sp. nov. as the sister taxon to Teffichthys madagascariensis within the Perleididae. T. elegans sp. nov. shares three derived features of Perleididae: the length of the anteroventral margin of the dermohyal nearly half the length of the anterodorsal margin of the preopercle; the anteroventral margin of the preopercle nearly equal to the anterior margin of the subopercle in length; and the anteroventral margin of the preopercle one to two times as long as the anterodorsal margin of the preopercle. It possesses diagnostic features of Teffichthys but differs from T. madagascariensis by the following features: presence of three supraorbitals; six pairs of branchiostegal rays; relatively deep anterodorsal process of subopercle; absence of spine on the posterior margin of the jugal; and pterygial formula of D26/P14, A22, C36/T39-41. The Perleidiformes are restricted to include only the Perleididae, and other previously alleged ‘perleidiform’ families (e.g., Hydropessidae and Gabanellidae) are excluded to maintain the monophyly of the order. Similar to many other perleidids, T. elegans sp. nov. was likely a durophagous predator with dentition combining grasping and crushing morphologies. The new finding also may indicate a relatively complex trophic structure of the Early Triassic marine ecosystem in South China. creator: Zhiwei Yuan creator: Guang-Hui Xu creator: Xu Dai creator: Fengyu Wang creator: Xiaokang Liu creator: Enhao Jia creator: Luyi Miao creator: Haijun Song uri: https://doi.org/10.7717/peerj.13448 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yuan et al. title: LncRNA OIP5-AS1 modulates the proliferation and apoptosis of Jurkat cells by sponging miR-181c-5p to regulate IL-7 expression in myasthenia gravis link: https://peerj.com/articles/13454 last-modified: 2022-05-17 description: BackgroundMyasthenia gravis (MG) is an antibody-mediated autoimmune disease. In recent years, accumulating evidence has indicated that long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs), contributing to the progression of various autoimmune diseases. Nevertheless, the regulatory roles of ceRNAs in MG pathogenesis remain unclear. In this study, we aimed to elucidate the role of lncRNA OIP5-AS1 as a ceRNA associated with MG progression.MethodsReal-time PCR was used to detect OIP5-AS1 levels in peripheral blood mononuclear cells (PBMCs) from patients with MG. Luciferase reporter assays were performed to validate the relationship between OIP5-AS1 and miR-181c-5p. CCK-8 and flow cytometry were performed to test the proliferation and apoptotic abilities of OIP5-AS1 in Jurkat cells. Furthermore, real-time PCR and Western blot assays were performed to explore the interactions between OIP5-AS1, miR-181c-5p, and IL-7.ResultsThe expression of OIP5-AS1 was up-regulated in patients with MG. Luciferase reporter assay indicated that OIP5-AS1 targeted the miR-181c-5p. Functional assays showed that OIP5-AS1 suppressed Jurkat cell apoptosis and promoted cell proliferation by sponging miR-181c-5p. Mechanistically, knockdown of OIP5-AS1 inhibited IL-7 expression at both the mRNA and protein levels in Jurkat cells, whereas the miR-181c-5p inhibitor blocked the reduction of IL-7 expression induced by OIP5-AS1 suppression.ConclusionsWe confirmed that OIP5-AS1 serves as an endogenous sponge for miR-181c-5p to regulate the expression of IL-7. Our findings provide novel insights into MG processes and suggests potential therapeutic targets for patients with MG. creator: Xu Wang creator: Huixue Zhang creator: Xiaoyu Lu creator: Shuang Li creator: Xiaotong Kong creator: Li Liu creator: Lifang Li creator: Si Xu creator: Tianfeng Wang creator: Jianjian Wang creator: Lihua Wang uri: https://doi.org/10.7717/peerj.13454 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Forecasting effects of transport infrastructure on endangered tigers: a tool for conservation planning link: https://peerj.com/articles/13472 last-modified: 2022-05-17 description: The rapid development of transport infrastructure is a major threat to endangered species worldwide. Roads and railways can increase animal mortality, fragment habitats, and exacerbate other threats to biodiversity. Predictive models that forecast the future impacts to endangered species can guide land-use planning in ways that proactively reduce the negative effects of transport infrastructure. Agent-based models are well suited for predictive scenario testing, yet their application to endangered species conservation is rare. Here, we developed a spatially explicit, agent-based model to forecast the effects of transport infrastructure on an isolated tiger (Panthera tigris) population in Nepal’s Chitwan National Park—a global biodiversity hotspot. Specifically, our model evaluated the independent and interactive effects of two mechanisms by which transport infrastructure may affect tigers: (a) increasing tiger mortality, e.g., via collisions with vehicles, and (b) depleting prey near infrastructure. We projected potential impacts on tiger population dynamics based on the: (i) existing transportation network in and near the park, and (ii) the inclusion of a proposed railway intersecting through the park’s buffer zone. Our model predicted that existing roads would kill 46 tigers over 20 years via increased mortality, and reduced the adult tiger population by 39% (133 to 81). Adding the proposed railway directly killed 10 more tigers over those 20 years; deaths that reduced the overall tiger population by 30 more individuals (81 to 51). Road-induced mortality also decreased the proportion of time a tiger occupied a given site by 5 years in the 20-year simulation. Interestingly, we found that transportation-induced depletion of prey decreased tiger occupancy by nearly 20% in sites close to roads and the railway, thereby reducing tiger exposure to transportation-induced mortality. The results of our model constitute a strong argument for taking into account prey distributions into the planning of roads and railways. Our model can promote tiger-friendly transportation development, for example, by improving Environmental Impact Assessments, identifying “no go” zones where transport infrastructure should be prohibited, and recommending alternative placement of roads and railways. creator: Neil H. Carter creator: Narendra Pradhan creator: Krishna Hengaju creator: Chinmay Sonawane creator: Abigail H. Sage creator: Volker Grimm uri: https://doi.org/10.7717/peerj.13472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Carter et al. title: The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma link: https://peerj.com/articles/13473 last-modified: 2022-05-17 description: BackgroundThe genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing.MethodsWe used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein–protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan–Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer.ResultsTargeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further analysis, four genes significantly related to the prognosis of liver cancer were identified.ConclusionIn this study, our findings indicate that ctDNA can be used for sequencing. Our results provide some molecular data for the mapping of genetic variation in Chinese patients with liver cancer, which enriches the understanding of HCC pathogenesis and provides new ideas for the diagnosis and prognosis of HCC patients. creator: Yubo Ding creator: Jingwei Yao creator: Meiling Wen creator: Xiong Liu creator: Jialu Huang creator: Minghui Zhang creator: Yu Zhang creator: Yufan Lv creator: Zhuoyi Xie creator: JianHong Zuo uri: https://doi.org/10.7717/peerj.13473 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ding et al. title: TFR1 expression in induced sputum is associated with asthma severity link: https://peerj.com/articles/13474 last-modified: 2022-05-17 description: BackgroundAsthma is characterized as a chronic inflammatory airway disease. Iron accumulation is related to asthma pathogenesis. Transferrin receptor 1(TFR1) expression is associated with intracellular iron overload in macrophages. In our study, we explored the association among TFR1 expression, the inflammatory macrophage phenotype, and asthma severity.MethodsInduced sputum was collected from 50 asthma patients. Real-time PCR was used to evaluate mRNA expression. The status of inflammatory macrophage phenotype was assessed using flow cytometry.ResultsTFR1 levels were inversely correlated with forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) and FEV1/vital capacity (VC). Among inflammatory cytokines, TFR1 expression was positively correlated with IL-1β, TNF-α, IL-6, IFN-γ, and IL-17A mRNA expression in induced sputum. Moreover, TFR1 expression was positively correlated with the number of proinflammatory M1 macrophages and iNOS expression in induced sputum. Neutrophil counts in induced sputum were significantly and positively related to TFR1 expression. Furthermore, TFR1 expression showed an increasing trend in asthma patients with no family history. Our findings indicated that TFR1 expression was consistent with the asthma severity index, especially the proinflammatory M1 macrophage phenotype. TFR1 expression may be a good marker to indicate asthma severity. creator: Yang Wang creator: li Feng Gu creator: Xincheng Zhao creator: Chengping Hu creator: Qiong Chen uri: https://doi.org/10.7717/peerj.13474 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: The sub-fossil diatom distribution in the Beibu Gulf (northwest South China Sea) and related environmental interpretation link: https://peerj.com/articles/13115 last-modified: 2022-05-16 description: Located in northwestern South China Sea (SCS), the Beibu Gulf constitutes an environmentally sensitive region shaped by land-ocean-atmosphere interactions in Asia between the western Pacific and eastern Indian Oceans. This study aims to provide a comprehensive view of the sub-fossil diatom biogeography, distribution pattern and oceanographic environmental controls with support of multivariate methods based on Beibu Gulf core-top samples. Cluster analysis of diatom assemblages divides the distribution pattern into four subclusters. Sea surface salinity (SSS), temperature (SST), trophic state (chlorophyll a concentration in this study) and water depth constrain the diatom distribution pattern through canonical redundancy analysis although only partly support an interpretation of the relationship between these various variables. Chlorophyll a has a strong correlation to diatom distribution, and responds to Paralia sulcata occurrence, while SSS and SST also have significant influence and indicate warm water invasion from the open SCS. Water depth is a subordinate factor in terms of Beibu Gulf diatom distribution. The ca. 25 m water-depth marks the upper extent of Paralia sulcata dominance in the northern Beibu Gulf. A strong mixing area with a complex diatom distribution exists below this water depth in the middle of Beibu Gulf. Coastal currents from north of SCS invade Beibu Gulf through Qiongzhou Strait and south of Hainan Island, as recorded by higher percentages of Paralia sulcata and Cyclotella striata at these sites. Our results provide a selection of evaluation method for a marine ecological red-line definition for sustainable development. This study highlights the perspective relationships between the spatial distribution of sub-fossil diatom assemblages in surface sediments and oceanographic variables, which could serve as a model for paleoenvironmental and paleoclimatic reconstruction in future marginal sea geoscience research for the Beibu Gulf, northwestern SCS. creator: Jinpeng Zhang creator: Andrzej Witkowski creator: Michał Tomczak creator: Chao Li creator: Kevin McCartney creator: Zhen Xia uri: https://doi.org/10.7717/peerj.13115 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna link: https://peerj.com/articles/13251 last-modified: 2022-05-16 description: The Swiss Upper Marine Molasse (OMM) documents a transgression event dated to around 21 to 17 million years in which dolphin and other vertebrate remains have been reported. We revised the whole cetacean (whales and dolphins) OMM assemblage available in main collections, focusing on the identification and interpretation of periotics (bone that contains the inner ear). Periotics are rare, but they provide the richest taxonomic information in the sample and hint to environmental associations. Micro-computerized tomography allowed the reconstruction of bony labyrinths for comparisons and environmental interpretations. Three families are represented by periotics: Kentriodontidae, Squalodelphinidae and Physeteridae. The cetacean taxonomic composition of the Swiss OMM reinforces biogeographical patterns reported for the Mediterranean and Paratethys during the Burdigalian at a regional scale and the Calvert cetacean fauna of the northwest Atlantic at oceanic scale. creator: Gabriel Aguirre-Fernández creator: Jürg Jost creator: Sarah Hilfiker uri: https://doi.org/10.7717/peerj.13251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aguirre-Fernández et al. title: Residency, movement patterns, behavior and demographics of reef manta rays in Komodo National Park link: https://peerj.com/articles/13302 last-modified: 2022-05-16 description: BackgroundThe reef manta ray (Mobula alfredi) is a globally threatened species and an iconic tourist attraction for visitors to Indonesia’s Komodo National Park (NP). In 2013, manta ray fishing was banned in Komodo NP and its surroundings, preceding the nationwide manta ray protection in 2014. Over a decade ago, a previous acoustic telemetry study demonstrated that reef manta rays had high fidelity to sites within the park, while more recent photo-identification data indicated that some individuals move up to 450 km elsewhere. Characterization of manta ray demographics, behavior, and a focused assessment on site use of popular tourism locations within the park is vital to assist the Komodo NP Management Authority formulate appropriate manta ray conservation and management policies.MethodsThis study uses a long-term library (MantaMatcher.org) of photo-identification data collected by researchers and citizen scientists to investigate manta ray demographics and habitat use within the park at four sites frequented by tour operators: Cauldron, Karang Makassar, Mawan, and Manta Alley. Residency and movements of manta rays were investigated with maximum likelihood analyses and Markov movement models.ResultsA total of 1,085 individual manta rays were identified from photographs dating from 2013 to 2018. In general, individual manta rays displayed a higher affinity to specific sites than others. The highest re-sighting probabilities came from the remote southern site, Manta Alley. Karang Makassar and Mawan are only ~5 km apart; however, manta rays displayed distinct site affinities. Exchange of individuals between Manta Alley and the two central sites (~35.5 km apart) occurred, particularly seasonally. More manta rays were recorded traveling from the south to the central area than vice versa. Female manta rays were more mobile than males. Similar demographic groups used Karang Makassar, Mawan, and Manta Alley for foraging, cleaning, cruising, or courtship activities. Conversely, a higher proportion of immature manta rays used the northern site, Cauldron, where foraging was commonly observed. Fishing gear-related injuries were noted on 56 individuals (~5%), and predatory injuries were present on 32 individuals (~3%). Tourism within the park increased from 2014 to 2017, with 34% more dive boats per survey at Karang Makassar and Mawan.DiscussionThe Komodo NP contains several distinct critical habitats for manta rays that encompass all demographics and accommodate seasonal manta ray movements. While the present study has not examined population trends, it does provide foundational data for such work. Continued research into manta ray abundance, long-range movements, and identifying and protecting other critical aggregation areas within the region is integral to securing the species’ recovery. We provide management recommendations to limit undue pressure on manta rays and their critical habitats from tourism. creator: Elitza S. Germanov creator: Simon J. Pierce creator: Andrea D. Marshall creator: I. Gede Hendrawan creator: Ande Kefi creator: Lars Bejder creator: Neil Loneragan uri: https://doi.org/10.7717/peerj.13302 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Germanov et al. title: Drivers and hazards of consumption of unpasteurised bovine milk and milk products in high-income countries link: https://peerj.com/articles/13426 last-modified: 2022-05-16 description: IntroductionThe consumption of dairy products contributes to health, nutrition, and livelihoods globally. However, dairy products do not come without microbiological food safety risks for consumers. Despite this risk, common hygiene measures in high-income countries, particularly pasteurisation, ensures that milk is safe, and is indeed frequently mandated by law. Nevertheless, over the past two decades, there has been a global increase in the number of consumers in high-income developed countries actively seeking out unpasteurised milk in liquid and product forms for perceived nutritional and health benefits, and improved taste. The often-anecdotal claims upon which consumers make such choices are not all supported by scientific evidence; however, some recent research studies have investigated (and in some cases demonstrated) the positive impact of unpasteurised milk consumption on the prevalence of asthma, atopy, rectal cancer and respiratory illness.MethodsTo investigate the significance of unpasteurised milk and milk product consumption for human health in high-income countries, outbreak data between the years 2000 and 2018 were obtained for the United States of America, Canada, the European Union, the United Kingdom, Japan, New Zealand and Australia, which were then categorized into three World Health Organisation subregions: AMR A, EUR A and WPR A. Outbreak dynamic variables such as pathogens, the place of consumption, numbers of outbreaks and deaths per million capita, the average number of cases per outbreak and regulations were described and analysed using R Studio. To provide an overview of unpasteurised milk-related disease outbreaks, a rapid evidence review was also undertaken to establish an overview of what is known in the current literature about hazards and drivers of consumption.ResultsFoodborne outbreaks associated with unpasteurised dairy consumption have risen in high-income countries over the period 2000 to 2018, with Campylobacter spp. being the most common aetiological agent responsible, followed by Escherichia coli and Salmonella spp. The most common places of consumption are on farms or in households, indicating individuals choose to drink unpasteurised milk, rather than a widespread distribution of the product, for example, at social events and in schools. Further study is needed to better understand contributing factors, such as cultural differences in the consumption of dairy products.ConclusionThere are several observable health benefits linked to consuming raw milk, but outbreaks associated with unpasteurised milk and milk products are on the rise. It cannot be definitively concluded whether the benefits outweigh the risks, and ultimately the decision lies with the individual consumer. Nevertheless, many countries have regulations in place to protect consumer health, acknowledging the definite risks to human health that unpasteurised dairy foods may pose, particularly from microbial hazards. creator: Joanna N. de Klerk creator: Philip A. Robinson uri: https://doi.org/10.7717/peerj.13426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 de Klerk and Robinson title: Search for morphological indicators that predict implantation by principal component analysis using images of blastocyst link: https://peerj.com/articles/13441 last-modified: 2022-05-16 description: BackgroundAlthough the current evaluation of human blastocysts is based on the Gardner criteria, there may be other notable parameters. The purpose of our study was to clarify whether the morphology of blastocysts has notable indicators other than the Gardner criteria.MethodsTo find such indicators, we compared blastocysts that showed elevated human chorionic gonadotropin (hCG) levels after transplantation (hCG-positive group; n = 129) and those that did not (hCG-negative group; n = 105) using principal component analysis of pixel brightness of the images.ResultsThe comparison revealed that the hCG-positive group had grainy morphology and the hCG-negative group had non-grainy morphology. Classification of the blastocysts by this indicator did not make a difference in Gardner score. Interestingly, all embryos with ≥20% fragmentation were non-grainy. The visual classification based on this analysis was significantly more accurate than the prediction of implantation using the Gardner score ≥3BB. As graininess can be used in combination with the Gardner score, this indicator will enhance current reproductive technologies. creator: Daisuke Mashiko creator: Mikiko Tokoro creator: Masae Kojima creator: Noritaka Fukunaga creator: Yoshimasa Asada creator: Kazuo Yamagata uri: https://doi.org/10.7717/peerj.13441 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mashiko et al. title: Malformations in Late Devonian brachiopods from the western Junggar, NW China and their potential causes link: https://peerj.com/articles/13447 last-modified: 2022-05-16 description: Although malformations are found in both extant organisms and the fossil record, they are more rarely reported in the fossil record than in living organisms, and the environmental factors causing the malformations are much more difficult to identify for the fossil record. Two athyrid brachiopod taxa from the Upper Devonian Hongguleleng Formation in western Junggar (Xinjiang, NW China) show distinctive shell malformation. Of 198 Cleiothyridina and 405 Crinisarina specimens, 18 and 39 individuals were malformed, respectively; an abnormality ratio of nearly 10%. Considering the preservation status and buried environment of the abnormal specimens, and analysis of trace elements and rare earth elements from whole-rock and brachiopod shells, we conclude that the appearance of malformed athyrids is likely related to epi/endoparasites, or less likely the slightly higher content of heavy metal in the sea. creator: Ruiwen Zong creator: Yiming Gong uri: https://doi.org/10.7717/peerj.13447 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zong and Gong title: Genome-wide identification and response stress expression analysis of the BES1 family in rubber tree (Hevea brasiliensis Muell. Arg.) link: https://peerj.com/articles/13189 last-modified: 2022-05-13 description: Brassinolide (BR) plays an important role in plant growth, development, and the adaptation adversity process. Moreover, BRI1-EMS-SUPPRESSOR 1 (BES1) genes are crucial transcription factors (TFs) in the BR signaling pathway. To realize the function of HbBES1 family is helpful to improve genetic resources for rubber tree breeding. Based on the rubber tree database, we used bioinformatics to characterize physicochemical properties, gene structure, cis-elements, and expression patterns. These results indicated that there were nine BES1 members in rubber tree, which we named HbBES1-1 to HbBES1-9 and divided into two groups (I and II) based on their genetic relationships. HbBES1 genes in the same group shared similar gene structures and motifs. Cis-acting element analysis showed that the promoter sequences of HbBES1 genes contained many regulator elements that were related to hormone and stress, indicating that HbBES1 genes might be involved in the regulation of hormone and stress signal pathways. Our analysis of tissue specificity revealed that all of the nine HbBES1 members expressed highly in branches. Gene expression profiles under different hormone treatments showed that the HbBES1 gene family was induced to varying degrees under different hormones, HbBES1-3 and HbBES1-9 were extremely induced by ethylene (ETH). These results lay the foundation for further exploration of the molecular mechanism of the BES1 gene family, especially HbBES1-3 and HbBES1-9, regulating plant stress tolerance in rubber tree. creator: Bingbing Guo creator: Hong Yang creator: Longjun Dai creator: Xizhu Zhao creator: Li-feng Wang uri: https://doi.org/10.7717/peerj.13189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Guo et al. title: Anatomical indicators of Eucalyptus spp. resistance to Glycaspis brimblecombei (Hemiptera: Aphalaridae) link: https://peerj.com/articles/13346 last-modified: 2022-05-13 description: The total area of forest crops in Brazil is 9.55 million hectares, of which 7.5 million hectares are Eucalyptus. These crops are the most productive in the world, but may suffer losses due to exotic pests, including Glycaspis brimblecombei Moore (Hemiptera: Aphalaridae) found in Brazil since 2003. Interactions between Eucalyptus plants and insect pests may led to the selection of resistant genotypes. Eucalyptus species are either susceptible or resistant to this pest group, but the damage they suffer needs to be evaluated. The objective was to determine possible leaf anatomy indicators of different Eucalyptus species associated with G. brimblecombei infestations, focusing on plant resistance to this pest. The study was carried out with Eucalyptus camaldulensis, Eucalyptus grandis, Eucalyptus saligna and Eucalyptus urophylla saplings infested or not by G. brimblecombei eggs and nymphs. Eighteen anatomical characteristics of the leaves of these plants were analyzed. The number of stomata on the adaxial and abaxial sides and the glandular area in the central leaf vein are associated with greater or lesser infestation by G. brimblecombei in the Eucalyptus genotypes. creator: Fernando Henrique Moreno de Oliveira Del Piero creator: Carlos Frederico Wilcken creator: Maurício Magalhães Domingues creator: Ana Laura Favoreto creator: Roberto Antonio Rodella creator: Alexandre Igor Azevedo Pereira creator: Wiane Meloni Silva creator: José Eduardo Serrão creator: José Cola Zanuncio uri: https://doi.org/10.7717/peerj.13346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Del Piero et al. title: Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L. link: https://peerj.com/articles/13372 last-modified: 2022-05-13 description: BackgroundCotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development.MethodsUsing genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum.ResultsChromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton. creator: Kun Liu creator: Nosheen Kabir creator: Zhenzhen Wei creator: Zhuojing Sun creator: Jian Wang creator: Jing Qi creator: Miaoyang Liu creator: Ji Liu creator: Kehai Zhou uri: https://doi.org/10.7717/peerj.13372 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Prevalence of hyperglycemia in masters athletes link: https://peerj.com/articles/13389 last-modified: 2022-05-13 description: BackgroundAgeing is associated with decreased physical activity, obesity and subsequently an increased risk of developing type 2 diabetes mellitus (T2dm). Master athletes (MA) have initiated exercise or sport later in life or pursued a physically active lifestyle for an extended period. Subsequently, MAs have been proposed as a model of successful ageing as this active lifestyle is associated with health benefits including decreased health risk of chronic diseases and a reduction in premature mortality. Given long-term physical activity/exercise has previously been shown to be protective against hyperglycemia, a risk factor for T2dm, it is plausible that MA may have protective benefit against developing hyperglycemia. Therefore, the aim of this study was to investigate the prevalence of hyperglycemia via fasting plasma glucose (FPG) in MAs competing at the World Masters Games (WMG).MethodsThis cross-sectional, observational survey utilized an online survey using open-source web-based software was used to investigate MAs physiological and medical-related parameters. Over 28,000 MAs competed in the WMG, of which 8,072 MAs completed the survey. Of these MAs, a total of 486 (males 277, females 209; range 27 to 91 years, mean age 55.1 ± 10.2 years) attained recent pathology results which included FPG which was subsequently analyzed for this study. FPG and other outcome variables were compared between genders and to the Australian and United States general population.ResultsMean FPG for MAs was 5.03 mmol (±1.2, 95% CI [4.9–5.1] mmol) with majority (75.5%) of MAs reporting a normal (<5.5 mmol) FPG, followed by pre-diabetes (20.2%, >5.51 to <5.99 mmol) and abnormal (4.3%, >7.0 mmol). There was no significant difference (P = 0.333) in FPG between genders however, males had a slightly higher (+2.1%) FPG as compared to females (5.08 ± 1.2 mmol (95% CI [4.9–5.22] mmol) versus 4.98 ± 1.1 mmol (95% CI 4.8-5.1 mmol)). The majority of males (71.8%) and females (80.3%) were classified with a normal FPG. With regard to an abnormal FPG level, only 4.0% of males and 4.9% of females were classified abnormal which was suggestive of undiagnosed T2dm. With regard to age by decade, there was no significant difference (P = 0.06–1.00) between age groups and no relationship between the MAs’ age and FPG (r = .054, P = 0.24). As a group, MAs had a significantly lower FPG as compared to the Australian (−3.2%, P = 0.005) and United States general populations (−13.9%, P < 0.001).ConclusionsMost, however not all, MAs were found to have normal glycaemia, with only a small percentage indicating a risk of developing T2dm (i.e., impaired fasting glucose) and a smaller percentage identified with an abnormal FPG, suggestive of T2dm. These findings suggest MAs appear to be at low metabolic risk for developing T2dm based upon FPG and the physical activity/exercise they complete as MAs may indeed be protective against hyperglycemia whilst maintaining an active lifestyle. creator: Mike Climstein creator: Joe Walsh creator: Kent Adams creator: Trish Sevene creator: Tim Heazlewood creator: Mark DeBeliso uri: https://doi.org/10.7717/peerj.13389 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Climstein et al. title: Comparative evaluation of the effect of two pulpal medicaments on pain and bleeding status of mandibular molars with irreversible pulpitis post-failure of inferior alveolar nerve block: a double-blind, randomized, clinical trial link: https://peerj.com/articles/13397 last-modified: 2022-05-13 description: BackgroundComplete relief of pain due to irreversible pulpitis is challenging to obtain with analgesic medications. The high incidence of an inferior alveolar nerve block (IANB) failure makes it difficult for practitioners to perform endodontic treatment without implementing other anesthetic techniques, especially mandibular molars. The aim of this study was to compare efficacies of two different quantities of paraformaldehyde based pulpal medicaments to relieve the pain and control hyperemic pulp post-failure of IANB and supplementary technique in patients experiencing this symptomatic irreversible pulpitis in the permanent mandibular tooth.MethodEighty-two participants with severe pain pre-operatively (Heft Parker Visual Analogue Scale, VAS > 114 mm) were enrolled, and pain responses were recorded at different time intervals using the Heft Parker visual analogue scale. To the patients experiencing pain even after the administration of the standard IANB and supplemental intraligamentary injection, one of the two paraformaldehyde based pulpal medicaments was placed in the pulp chamber and sealed. Participants were recalled after 24–48 h (second visit) to assess pain and bleeding reduction.ResultsResults showed a significant decrease in pain severity and bleeding score post medicament placement (p < .05). Hence judicious use within a recommended period, pulpal medicaments can be considered safe.ConclusionParaformaldehyde based pulpal medicament can be used as an alternative to manage pain in patients having severe irreversible pulpitis and hyperalgesia. creator: Naomi Ranjan Singh creator: Lora Mishra creator: Ajinkya M. Pawar creator: Nike Kurniawati creator: Dian Agustin Wahjuningrum uri: https://doi.org/10.7717/peerj.13397 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Singh et al. title: Tracing RNA viruses associated with Nudibranchia gastropods link: https://peerj.com/articles/13410 last-modified: 2022-05-13 description: BackgroundNudibranchia is an under-studied taxonomic group of gastropods, including more than 3,000 species with colourful and extravagant body shapes and peculiar predatory and defensive strategies. Although symbiosis with bacteria has been reported, no data are available for the nudibranch microbiome nor regarding viruses possibly associated with these geographically widespread species.MethodsBased on 47 available RNA sequencing datasets including more than two billion reads of 35 nudibranch species, a meta-transcriptome assembly was constructed. Taxonomic searches with DIAMOND, RNA-dependent-RNA-polymerase identification with palmscan and viral hallmark genes identification by VirSorter2 in combination with CheckV were applied to identify genuine viral genomes, which were then annotated using CAT.ResultsA total of 20 viral genomes were identified as bona fide viruses, among 552 putative viral contigs resembling both RNA viruses of the Negarnaviricota, Pisuviricota, Kitrinoviricota phyla and actively transcribing DNA viruses of the Cossaviricota and Nucleocytoviricota phyla. The 20 commonly identified viruses showed similarity with RNA viruses identified in other RNA-seq experiments and can be putatively associated with bacteria, plant and arthropod hosts by co-occurence analysis. The RNA samples having the highest viral abundances showed a heterogenous and mostly sample-specific distribution of the identified viruses, suggesting that nudibranchs possess diversified and mostly unknown viral communities. creator: Umberto Rosani uri: https://doi.org/10.7717/peerj.13410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rosani title: Exploring the spatiotemporal changes in carbon storage under different development scenarios in Jiangsu Province, China link: https://peerj.com/articles/13411 last-modified: 2022-05-13 description: Carbon storage (CS) is closely linked to the global challenge of climate change. Land use/cover (LULC) change is the main factor driving changes in CS, and evaluating the impact of LULC changes on CS is important for carbon balance. Taking Jiangsu Province as an example, we used the Integrated Valuation of Ecosystem Services and Trade-offs model to analyze the spatiotemporal changes in CS during 2000–2015. Then we coupled it with the patch-generating land use simulation model to simulate and predict LULC and CS in 2050 under four different development plans. The results showed that LULC change in Jiangsu Province was manifested mainly as transformation of cropland to construction land (3,485 km2) and cropland to water body (470 km2). The high value area for CS was concentrated mainly in forest land, water body and grassland, whereas the low value area was concentrated mainly in construction land. During 2000–2015, CS decreased by 0.23 Tg, and during 2015–2050, CS was predicted to decrease by 0.16, 1.69, 0.02, and 0.10 Tg under the baseline, fast, slow and harmonious development scenarios. The conversion of a large amount of cropland to construction land was the main cause of CS loss. In all scenarios, the carbon loss was the largest in southern Jiangsu and lowest in central Jiangsu. It is necessary to balance the conflict between economic development and ecological protection during the process of urbanization. This study can provide an important reference for decision makers during the formulation of regional development models and ecological management strategies. creator: Xiaomian Zhang creator: Jun Wang creator: Chunlei Yue creator: Shuai Ma creator: Liang-Jie Wang uri: https://doi.org/10.7717/peerj.13411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Identification of key differential genes in intimal hyperplasia induced by left carotid artery ligation link: https://peerj.com/articles/13436 last-modified: 2022-05-13 description: BackgroundIntimal hyperplasia is a common pathological process of restenosis following angioplasty, atherosclerosis, pulmonary hypertension, vein graft stenosis, and other proliferative diseases. This study aims to screen for potential novel gene targets and mechanisms related to vascular intimal hyperplasia through an integrated microarray analysis of the Gene Expression Omnibus Database (GEO) database.Material and MethodsThe gene expression profile of the GSE56143 dataset was downloaded from the Gene Expression Omnibus database. Functional enrichment analysis, protein-protein interaction (PPI) network analysis, and the transcription factor (TF)-target gene regulatory network were used to reveal the biological functions of differential genes (DEGs). Furthermore, the expression levels of the top 10 key DEGs were verified at the mRNA and protein level in the carotid artery 7 days after ligation.ResultsA total of 373 DEGs (199 upregulated DEGs and 174 downregulated DEGs) were screened. These DEGs were significantly enriched in biological processes, including immune system process, cell adhesion, and several pathways, which were mainly associated with cell adhesion molecules and the regulation of the actin cytoskeleton. The top 10 key DEGs (Ptprc, Fn1, Tyrobp, Emr1, Itgb2, Itgax, CD44, Ctss, Ly86, and Aif1) acted as key genes in the PPI network. The verification of these key DEGs at the mRNA and protein levels was consistent with the results of the above-mentioned bioinformatics analysis.ConclusionThe present study identified key genes and pathways involved in intimal hyperplasia induced by carotid artery ligation. These results improved our understanding of the mechanisms underlying the development of intimal hyperplasia and provided candidate targets. creator: Lina Zhang creator: Jianjun Gu creator: Sichuan Wang creator: Fuming He creator: Kaizheng Gong uri: https://doi.org/10.7717/peerj.13436 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: The Microphenotron: a novel method for screening plant growth-promoting rhizobacteria link: https://peerj.com/articles/13438 last-modified: 2022-05-13 description: BackgroundThe ‘Microphenotron’ is an automated screening platform that uses 96-well microtiter plates to test the response of seedlings to natural products. This system allows monitoring the phenotypic effect of a large number of small molecules. Here, this model system was used to study the effect of phytohormones produced by plant growth-promoting rhizobacteria (PGPR) on the growth of wild-type and mutant lines of Arabidopsis thaliana.MethodsIn the present study, high-throughput screening based on ‘Microphenotron’ was used to screen PGPRs. Rhizobacteria were isolated from the rhizosphere of Acacia Arabica, which was growing in saline habitats. The phylogeny of these rhizobacteria was determined by 16S rRNA gene sequencing. Strains were screened for plant growth-promoting traits such as auxin production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization. Ultra-Performance Liquid Chromatography (UPLC) was used to detect the presence of different indolic compounds. Finally, PGPR were evaluated to enhance the growth of A. thaliana in the ‘Microphenotron’ system and pot trials.ResultsSelected rhizobacteria strains showed positive results for multiple plant-growth promoting traits. For instance, strain (S-6) of Bacillus endophyticus exhibited the highest ACC-deaminase activity. UPLC analysis indicated the presence of different indolic compounds in bacterial extracts that included indole lactic acid (ILA), indole carboxylic acid (ICA), and indole-3-acetic acid (IAA). Two strains (S-7 and S-11) of Psychrobacter alimentarius produced the most IAA, ICA and ILA. A screening bioassay through 96-well microtiter plates with wild-type Col. N6000 showed an increase in root growth and proliferation. The highest twofold increase was recorded in root growth with B. thuringiensis S-26 and B. thuringiensis S-50. In pot trials, mutant lines of A. thaliana impaired for auxin signaling showed that B. endophyticus S-6, Psy. alimenterius S-11, Enterobacter asburiae S-24 and B. thuringiensis S-26 used auxin signaling for plant growth promotion. Similarly, for ethylene insensitive mutant lines (ein2.5 and etr1), Prolinoborus fasciculus S-3, B. endophyticus S-6, Psy. alimenterius S-7, E. asburiae S-24, and B. thuringiensis S-26 showed the involvement of ethylene signaling. However, the growth promotion pattern for most of the strains indicated the involvement of other mechanisms in enhancing plant growth. The result of Microphenotron assays generally agreed with pot trials with mutant and wild type A. thaliana varieties. Bacterial strains that induced the highest growth response by these cultivars in the ‘Microphenotron’ promoted plant growth in pot trials. This suggests that Microphenotron can accelerate the evaluation of PGPR for agricultural applications. creator: Asif Raheem creator: Basharat Ali uri: https://doi.org/10.7717/peerj.13438 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Raheem and Ali title: Lipopolysaccharide-activated macrophages regulate the osteogenic differentiation of bone marrow mesenchymal stem cells through exosomes link: https://peerj.com/articles/13442 last-modified: 2022-05-13 description: BackgroundPeriodontal tissue regeneration is the ultimate goal of periodontitis treatment. Exosomes are nanoscale vesicles secreted by cells that participate in and regulate the physiological activities between cells. However, the relationship between inflammatory macrophage-derived exosomes and osteoblast differentiation in periodontitis has not been thoroughly reported. Here, we attempt to explore the role of inflammatory macrophage-derived exosomes in crosstalk with osteoblasts.MethodsPorphyromonas gingivalis lipopolysaccharide was used to stimulate macrophages and inflate their inflammatory cellular state. Exosomes were extracted from inflammatory macrophages using supercentrifugation, and their characteristics were detected by transmission electron microscopy, particle size analysis, and Western blotting. Exosome uptake bybone marrow mesenchymal stem cells (BMSCs) was observed by fluorescence microscopy. The effects of exosomes on the BMSC inflammatory response and on osteogenic differentiation were detected by quantitative polymerase chain reaction and Western blot analysis. Alkaline phosphatase activity was tested for verification.ResultsWe successfully extracted and identified inflammatory macrophage-derived exosomes and observed that BMSCs successfully took up exosomes. Inflammatory macrophage-derived exosomes upregulated the expression levels of the inflammatory factors interleukin-6 and tumour necrosis factor-alpha in BMSCs and mediated inflammatory stimulation. Additionally, they inhibited the transcription levels of the osteogenic genes alkaline phosphatase, type I collagen, and Runt-related transcription factor 2 as well as the alkaline phosphatase activity, while the use of the exosome inhibitor GW4869 attenuated this effect.ConclusionOur study shows that macrophages in periodontitis can mediate inflammatory stimulation and inhibit the osteogenic differentiation of bone marrow mesenchymal stem cells through the exosome pathway. Interference with exosome secretion is likely to be a promising method for bone tissue regeneration in inflammatory states. creator: Xiao Song creator: Yiwen Xue creator: Siyu Fan creator: Jing Hao creator: Runzhi Deng uri: https://doi.org/10.7717/peerj.13442 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Song et al. title: A field test of forest canopy structure measurements with the CanopyCapture smartphone application link: https://peerj.com/articles/13450 last-modified: 2022-05-13 description: BackgroundSeveral smartphone applications have been developed for the purpose of low-cost and convenient assessments of vegetation canopy structure and understorey illumination. Like standard hemispherical photography, most of these applications require user decisions about image processing, posing challenges for repeatability of measurements. Here I report a test of CanopyCapture, an application that instantaneously estimates percentage canopy gap fraction without any input from the user, and has the added advantage of an intuitive levelling mechanism.MethodsGap fraction estimates by CanopyCapture were compared with gap fraction values computed by the LAI-2200C Canopy Analyzer, in two contrasting evergreen temperate forests in New Zealand: an even-aged southern beech (Nothofagus) stand and an old-growth podocarp/broadleaf forest. These comparisons were repeated using a wide-angle adapter to enhance the smartphone camera’s field of view from 45 to 65°. I also asked if CanopyCapture results depended on sky condition (sunny vs. overcast) and on the type of smartphone used.ResultsCanopyCapture output was significantly correlated with gap fraction computed by the LAI-2200C (R2 = 0.39), and use of the wide-angle adapter lifted this value to 0.56. However, CanopyCapture output was not significantly correlated with LAI-2200C output in the even-aged Nothofagus stand, where there was less spatial variation in canopy structure. Despite being much less sensitive to variation in gap fraction than the LAI-2200C, CanopyCapture was nevertheless able to detect differences in average gap fraction between the two forests studied. CanopyCapture results beneath intact canopies were not significantly affected by sky condition, but reflection of direct light off tree trunks in sunny weather caused slight overestimation of gap fraction beneath broken canopies and gaps. Uneven or patchy cloud cover can also cause erroneous readings beneath large canopy openings. Three different models of smartphone gave different results.ConclusionsCanopyCapture offers a rapid and repeatable proxy for comparisons of average canopy gap fraction in multiple stands/forests, provided large sample sizes are used. Measurement under even overcast skies is recommended, and studies involving multiple operators will need to standardize smartphones to ensure comparability of results. Although wide-angle adapters can improve performance, CanopyCapture’s low sensitivity prevents high-resolution comparisons of the light environments of individual understorey plants within a stand. creator: Christopher H. Lusk uri: https://doi.org/10.7717/peerj.13450 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lusk title: Soil properties and microbial communities of spring maize filed in response to tillage with straw incorporation and nitrogen fertilization in northeast China link: https://peerj.com/articles/13462 last-modified: 2022-05-13 description: Soil enzymes and microorganisms are both important to maintaining good soil quality and are also sensitive to changes in agricultural management. The individual effects of tillage, straw incorporation and nitrogen (N) fertilization on soil enzymes and microflora have been widely acknowledged, but their interactive effect remains largely unknown. In a 5–year in–situ field study, effects of rotary (RTS) and plow tillage (PTS) practices with straw incorporation combined with three N fertilization levels (0 kg N ha–1, CK; 187 kg N ha–1, MN; 337 kg N ha–1, HN) on soil enzyme activities and microbial communities were assessed. Our results showed that the activities of β–glucosidase (βG), N–acetylglucosaminidase (NAG) and acid phosphatase (APH) were improved in RTS+MN. The bacterial and fungal abundances in RTS+MN and RTS+HN were 1.27–27.51 times higher than those in other treatment groups. However, the bacterial and fungal alpha diversities were enhanced in PTS+MN and PTS+CK compared with other treatments, respectively. Proteobacteria and Basidiomycota were the predominant phylum for the respective bacterial and fungal communities. Moreover, significant interactive effects were found in the fungal community composition, but only minor impacts were observed on the bacterial community composition. Soil water content and penetration resistance contributed more to the soil enzyme activity and microbial community than other soil properties investigated, whereas there was a significant positive correlation between βG and APH activities and microbial abundance. These findings can provide new insights into tillage with straw incorporation and N fertilization on maize cultivation in northeast China. creator: Pengxiang Sui creator: Ping Tian creator: Zhengyu Wang creator: Hongli Lian creator: Yadong Yang creator: Ziqi Ma creator: Ying Jiang creator: Jinyu Zheng creator: Hua Qi uri: https://doi.org/10.7717/peerj.13462 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sui et al. title: Linking multi-level population dynamics: state, role, and population link: https://peerj.com/articles/13315 last-modified: 2022-05-12 description: The dynamics of an ecological community can be described at different focal scales of the species, such as individual states or the population level. More detailed descriptions of ecological dynamics offer more information, but produce more complex models that are difficult to analyze. Adequately controlling the model complexity and the availability of multiple descriptions of the concerned dynamics maximizes our understanding of ecological dynamics. One of the central goals of ecological studies is to develop links between multiple descriptions of an ecological community. In this article, starting from a nonlinear state-level description of an ecological community (generalized McKendrick–von Foerster model), role-level and population-level descriptions (Lotka–Volterra model) are derived in a consistent manner. The role-level description covers a wider range of situations than the population-level description. However, using the established connections, it is demonstrated that the population-level description can be used to predict the equilibrium status of the role-level description. This approach connects state-, role-, and population-level dynamics consistently, and offers a justification for the multiple choices of model description. creator: Nao Takashina uri: https://doi.org/10.7717/peerj.13315 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Takashina title: Non-destructive monitoring of 3D cell cultures: new technologies and applications link: https://peerj.com/articles/13338 last-modified: 2022-05-12 description: 3D cell cultures are becoming the new standard for cell-based in vitro research, due to their higher transferrability toward in vivo biology. The lack of established techniques for the non-destructive quantification of relevant variables, however, constitutes a major barrier to the adoption of these technologies, as it increases the resources needed for the experimentation and reduces its accuracy. In this review, we aim at addressing this limitation by providing an overview of different non-destructive approaches for the evaluation of biological features commonly quantified in a number of studies and applications. In this regard, we will cover cell viability, gene expression, population distribution, cell morphology and interactions between the cells and the environment. This analysis is expected to promote the use of the showcased technologies, together with the further development of these and other monitoring methods for 3D cell cultures. Overall, an extensive technology shift is required, in order for monolayer cultures to be superseded, but the potential benefit derived from an increased accuracy of in vitro studies, justifies the effort and the investment. creator: Marilisa Cortesi creator: Emanuele Giordano uri: https://doi.org/10.7717/peerj.13338 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cortesi and Giordano title: The choice of reference point for computing sagittal plane angular momentum affects inferences about dynamic balance link: https://peerj.com/articles/13371 last-modified: 2022-05-12 description: BackgroundMeasures of whole-body angular momentum in the sagittal plane are commonly used to characterize dynamic balance during human walking. To compute angular momentum, one must specify a reference point about which momentum is calculated. Although biomechanists primarily compute angular momentum about the center of mass (CoM), momentum-based controllers for humanoid robots often use the center of pressure. Here, we asked if the choice of the reference point influences interpretations of how dynamic balance is controlled in the sagittal plane during perturbed walking.MethodsEleven healthy young individuals walked on a dual-belt treadmill at their self-selected speed. Balance disturbances were generated by treadmill accelerations of varying magnitudes and directions. We computed angular momentum about two reference points: (1) the CoM or (2) the leading edge of the base of support and then projected it along the mediolateral axes that pass through either of the reference points as the sagittal plane angular momentum. We also performed principal component analysis to determine if the choice of reference point influences our interpretations of how intersegmental coordination patterns contribute to perturbation recovery.ResultsWe found that the peak angular momentum was correlated with perturbation amplitude and the slope of this relationship did not differ between reference points. One advantage of using a reference point at the CoM is that one can easily determine how the momenta from contralateral limbs, such as the left and right legs, offset one another to regulate the whole-body angular momentum. Alternatively, analysis of coordination patterns referenced to the leading edge of the base of support may provide more insight into the inverted-pendulum dynamics of walking during responses to sudden losses of balance. creator: Chang Liu creator: Sungwoo Park creator: James Finley uri: https://doi.org/10.7717/peerj.13371 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Curcumol alleviates liver fibrosis by inducing endoplasmic reticulum stress-mediated necroptosis of hepatic stellate cells through Sirt1/NICD pathway link: https://peerj.com/articles/13376 last-modified: 2022-05-12 description: Liver fibrosis is a repair response process after chronic liver injury. During this process, activated hepatic stellate cells (HSCs) will migrate to the injury site and secrete extracellular matrix (ECM) to produce fibrous scars. Clearing activated HSCs may be a major strategy for the treatment of liver fibrosis. Curcumol isolated from plants of the genus Curcuma can effectively induce apoptosis of many cancer cells, but whether it can clear activated HSCs remains to be clarified. In the present study, we found that the effect of curcumol in treating liver fibrosis was to clear activated HSCs by inducing necroptosis of HSCs. Receptor-interacting protein kinase 3 (RIP3) silencing could impair necroptosis induced by curcumol. Interestingly, endoplasmic reticulum (ER) stress-induced cellular dysfunction was associated with curcumol-induced cell death. The ER stress inhibitor 4-PBA prevented curcumol-induced ER stress and necroptosis. We proved that ER stress regulated curcumol-induced necroptosis in HSCs via Sirtuin-1(Sirt1)/Notch signaling pathway. Sirt1-mediated deacetylation of the intracellular domain of Notch (NICD) led to degradation of NICD, thereby inhibiting Notch signalling pathway to alleviate liver fibrosis. Specific knockdown of Sirt1 by HSCs in male ICR mice further exacerbated CCl4-induced liver fibrosis. Overall, our study elucidates the anti-fibrotic effect of curcumol and reveals the underlying mechanism between ER stress and necroptosis. creator: Sumin Sun creator: Sheng Huan creator: Zhanghao Li creator: Yue Yao creator: Ying Su creator: Siwei Xia creator: Shijun Wang creator: Xuefen Xu creator: Jiangjuan Shao creator: Zili Zhang creator: Feng Zhang creator: Jinbo Fu creator: Shizhong Zheng uri: https://doi.org/10.7717/peerj.13376 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sun et al. title: Impact of COVID-19 social distancing on medical research from the perspective of postgraduate students: a cross-sectional online survey link: https://peerj.com/articles/13384 last-modified: 2022-05-12 description: ObjectiveTo investigate the impact of COVID-19 social distancing on medical research from the perspective of postgraduate students.MethodsA cross-sectional study using an online survey was conducted from October 31 to November 1, 2021. A questionnaire was used to assess the impact of COVID-19 social distancing on medical research among postgraduate students. The questionnaire included basic information, medical research information, and information about social distancing measures. Participants also completed the self-made Research Work Affected Scale of Postgraduates (RWAS-P; qualitative evaluation: very mildly 0–10; mildly 11–20; moderately 21–30; severely 31–40; very severely 41–50). Logistic regression was used to identify factors related to the impact of COVID-19 social distancing.ResultsA total of 468 participants were analyzed; 95.2% of the participants adhered to social distancing measures. The median total RWAS-P score was 22. The median RWAS-P scores for earlier research data, current research projects, future research plans, paper publication, and graduation schedule were 2, 6, 6, 6, and 4, respectively (score range 0–10). The higher grade of students, experimental research, and existence of inappetence or sleeplessness were related to negative attitude towards COVID-19 social distancing (odd ratio = 6.35, 9.80, 2.31, 2.15, 1.95, respectively).ConclusionsParticipants reported that social distancing had a moderate overall impact on their medical research. Social distancing had the greatest impact on current research projects, future research plans, and paper publications among postgraduate students. Higher grade level, experimental research type, inappetence, and sleeplessness were related to the impact of social distancing on their medical research. creator: Chen Dong creator: Zhou Yu creator: Wei Liu creator: Yu Zhang creator: Zhe Zhang creator: Lei Zhang creator: Zhiwei Cui creator: Xiao Fan creator: Yuhan Zhu creator: Han Peng creator: Botao Gao creator: Xianjie Ma uri: https://doi.org/10.7717/peerj.13384 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Dong et al. title: Quantifying phenological diversity: a framework based on Hill numbers theory link: https://peerj.com/articles/13412 last-modified: 2022-05-12 description: BackgroundDespite the great concern triggered by the environmental crisis worldwide, the loss of temporal key functions and processes involved in biodiversity maintenance has received little attention. Species are restricted in their life cycles by environmental variables because of their physiological and behavioral properties; thus, the timing and duration of species’ presence and their activities vary greatly between species within a community. Despite the ecological relevance of such variation, there is currently no measure that summarizes the key temporal aspects of biological diversity and allows comparisons of community phenological patterns. Here, we propose a measure that synthesizes variability of phenological patterns using the Hill numbers-based attribute diversity framework.MethodsWe constructed a new phenological diversity measure based on the aforementioned framework through pairwise overlapping distances, which was supplemented with wavelet analysis. The Hill numbers approach was chosen as an adequate way to define a set of diversity values of different order q, a parameter that determines the sensitivity of the diversity measure to abundance. Wavelet transform analysis was used to model continuous variables from incomplete data sets for different phenophases. The new measure, which we call Phenological Hill numbers (PD), considers the decouplings of phenophases through an overlapping area value between pairs of species within the community. PD was first tested through simulations with varying overlap in phenophase magnitude and intensity and varying number of species, and then by using one real data set.ResultsPD maintains the diversity patterns of order q as in any other diversity measure encompassed by the Hill numbers framework. Minimum PD values in the simulated data sets reflect a lack of differentiation in the phenological curves of the community over time; by contrast, the maximum PD values reflected the most diverse simulations in which phenological curves were equally distributed over time. PD values were consistent with the homogeneous distribution of the intensity and concurrence of phenophases over time, both in the simulated and the real data set.DiscussionPD provides an efficient, readily interpretable and comparable measure that summarizes the variety of phenological patterns observed in ecological communities. PD retains the diversity patterns of order q characteristic of all diversity measures encompassed by the distance-based Hill numbers framework. In addition, wavelet transform analysis proved useful for constructing a continuous phenological curve. This methodological approach to quantify phenological diversity produces simple and intuitive values for the examination of phenological diversity and can be widely applied to any taxon or community’s phenological traits. creator: Daniel Sánchez-Ochoa creator: Edgar J. González creator: Maria del Coro Arizmendi creator: Patricia Koleff creator: Raúl Martell-Dubois creator: Jorge A. Meave creator: Hibraim Adán Pérez-Mendoza uri: https://doi.org/10.7717/peerj.13412 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sánchez-Ochoa et al. title: Genome-wide identification of CBF genes and their responses to cold acclimation in Taraxacum kok-saghyz link: https://peerj.com/articles/13429 last-modified: 2022-05-12 description: C-repeat binding factors (CBFs) are transcription factors that are known to play important roles in plant cold acclimation. They are highly conserved in most higher plants. Taraxacum kok-saghyz (TKS) is an herb native to China and Kazakhstan and is well-known for its production of rubber silk with industrial and economic value. To understand cold acclimation mechanisms, we conducted a genome-wide discovery of the CBF family genes in TKS and revealed ten CBF genes. A bioinformatic analysis of the CBF genes was carried out to analyze the phylogenetic relationship, protein conservative motifs, protein physicochemical properties, gene structure, promoter cis-acting elements, and the gene expression patterns under cold acclimation and control conditions. It was found that most of these genes were highly responsive at the late stage of cold acclimation, indicating that they play important roles in the cold acclimation processes of TKS. This study provides a theoretical basis for the study of the molecular functions of the CBF gene family in TKS, and a useful guidance for the genetic improvement of the cold tolerance traits of TKS and other plants, including crops. creator: Haifeng Zhang creator: Yongyong Gong creator: Peilin Sun creator: Sixue Chen creator: Chunquan Ma uri: https://doi.org/10.7717/peerj.13429 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Dental pathologies in lamniform and carcharhiniform sharks with comments on the classification and homology of double tooth pathologies in vertebrates link: https://peerj.com/articles/12775 last-modified: 2022-05-11 description: Double tooth pathologies are important indicators of trauma, disease, diet, and feeding biomechanics, and are widely documented in mammals. However, diagnosis of double tooth pathologies in extinct non-mammalian vertebrates is complicated by several compounding factors including: a lack of shared terminology reflecting shared etiology, inconsistencies in definitions and key features within and outside of mammals (e.g., gemination, fusion, twinning, concrescence); differences in tooth morphology, heterodonty, regeneration, and implantation between mammals and non-mammalian vertebrates; and the unmet need for diagnostic criteria that can be applied to isolated teeth, which are common in the fossil record. Here we report on double tooth pathologies in the lamniform and carcharhiniform Cenozoic sharks Otodus megalodon (NCSM 33639) and Carcharhinus leucas (NCSM 33640, 33641). All three teeth bear a singular bifid crown with mirrored halves and abnormal internal microstructure—a single, bifurcating pulp cavity in C. leucas and a more than tripling of vessels in O. megalodon (from two to seven main ascending canals). We identify these abnormalities as likely examples of gemination due to their symmetry, which rules out fusion of tooth buds in one tooth file in different developmental stages in polyphyodont taxa; however, we note that incomplete forms of mesiodistal tooth fusion can be morphologically indistinguishable from gemination, and thus fusion cannot be rejected. We further compile and recategorize, when possible, the diversity of tooth pathologies in sharks. The identification of double tooth pathologies in O. megalodon and C. leucas has paleobiological implications. Such pathologies in sharks are largely hypothesized to stem from trauma to developing tooth buds. Carcharhinus leucas is known to feed on prey documented to cause feeding-related oral traumas (e.g., rays, sawfish, spiny fish, and sea urchins). However, O. megalodon, is considered to have largely fed on marine mammals, and perhaps turtles and/or fish, raising the possibility that the dietary diversity of this species is, as of yet, underappreciated. The genetic underpinnings of tooth morphogenesis and regeneration is highly conserved throughout vertebrate evolution, suggesting a homologous framework can be established. However, more research is needed to link developmental, paleobiological, and/or paleoenvironmental factors to gemination/fusion in polyphyodont taxa. We argue that the definitions and diagnostic criteria for dental pathologies in vertebrates require standardization in order to advance macroevolutionary studies of feeding trauma in deep time. creator: Harrison S. Miller creator: Haviv M. Avrahami creator: Lindsay E. Zanno uri: https://doi.org/10.7717/peerj.12775 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Miller et al. title: DeepNC: a framework for drug-target interaction prediction with graph neural networks link: https://peerj.com/articles/13163 last-modified: 2022-05-11 description: The exploration of drug-target interactions (DTI) is an essential stage in the drug development pipeline. Thanks to the assistance of computational models, notably in the deep learning approach, scientists have been able to shorten the time spent on this stage. Widely practiced deep learning algorithms such as convolutional neural networks and recurrent neural networks are commonly employed in DTI prediction projects. However, they can hardly utilize the natural graph structure of molecular inputs. For that reason, a graph neural network (GNN) is an applicable choice for learning the chemical and structural characteristics of molecules when it represents molecular compounds as graphs and learns the compound features from those graphs. In an effort to construct an advanced deep learning-based model for DTI prediction, we propose Deep Neural Computation (DeepNC), which is a framework utilizing three GNN algorithms: Generalized Aggregation Networks (GENConv), Graph Convolutional Networks (GCNConv), and Hypergraph Convolution-Hypergraph Attention (HypergraphConv). In short, our framework learns the features of drugs and targets by the layers of GNN and 1-D convolution network, respectively. Then, representations of the drugs and targets are fed into fully-connected layers to predict the binding affinity values. The models of DeepNC were evaluated on two benchmarked datasets (Davis, Kiba) and one independently proposed dataset (Allergy) to confirm that they are suitable for predicting the binding affinity of drugs and targets. Moreover, compared to the results of baseline methods that worked on the same problem, DeepNC proves to improve the performance in terms of mean square error and concordance index. creator: Huu Ngoc Tran Tran creator: J. Joshua Thomas creator: Nurul Hashimah Ahamed Hassain Malim uri: https://doi.org/10.7717/peerj.13163 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tran et al. title: Comparative proteomic analysis between mature and germinating seeds in Paris polyphylla var. yunnanensis link: https://peerj.com/articles/13304 last-modified: 2022-05-11 description: The long dormancy period of Paris polyphylla var. yunnanensis seeds affects the supply of this scarce plant, which is used as an important traditional Chinese medicine. Mature seeds with a globular embryo and germinating seeds with developed embryo were used to explore the mechanisms of seed germination in this species. The protein profiles between the mature and germinating seeds were compared using the isobaric tags for relative and absolute quantification (iTRAQ) approach. Of the 4,488 proteins identified, a total of 1,305 differentially expressed proteins (DEPs) were detected. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these DEPs indicated that metabolic pathways and the biosynthesis of secondary metabolites were the two top pathways. Additionally, phytohormone quantification shows that the abscisic acid (ABA) level significantly decreased, whereas the GA3 level dramatically increased among nine endogenous gibberellins (GAs), resulting in a significant increase of the GA3/ABA ratio in germinating seeds. The biosynthesis pathways of carotenoid as a precursor for ABA production and GA were further analyzed, and showed that proteinic expressions of the candidate genes in the two pathways did not correlate with the transcriptional abundances. However, 9-cis-epoxycarotenoid dioxygenase (NCED), a rate limited enzyme for ABA biosynthesis, was significantly decreased in mRNA levels in germinating seeds. By contrast, gibberellin 20-oxidase (GA20ox), a key enzyme GA biosynthesis, exhibited the major increase in one copy and a slight decrease in three others at the protentional level in germinating seeds. Gibberellin 2-oxidase (GA2ox), an inactivate enzyme in bioactive GAs, has the tendency to down-regulate in mRNA or at the proteinic level in germinating seeds. Altogether, these results suggested that the analyses of ABA and GA levels, the GA3/ABA ratio, and the expressional patterns of their regulatory genes may provide a novel mechanistic understanding of how phytohormones regulate seed germination in P. polyphylla var. yunnanensis. creator: Li-Zhen Ling creator: Shu-Dong Zhang uri: https://doi.org/10.7717/peerj.13304 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ling and Zhang title: QTL mapping and candidate gene analysis of low temperature germination in rice (Oryza sativa L.) using a genome wide association study link: https://peerj.com/articles/13407 last-modified: 2022-05-11 description: Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding. creator: Feng Mao creator: Depeng Wu creator: Fangfang Lu creator: Xin Yi creator: Yujuan Gu creator: Bin Liu creator: Fuxia Liu creator: Tang Tang creator: Jianxin Shi creator: Xiangxiang Zhao creator: Lei Liu creator: Lilian Ji uri: https://doi.org/10.7717/peerj.13407 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mao et al. title: Combinations of action observation and motor imagery on golf putting’s performance link: https://peerj.com/articles/13432 last-modified: 2022-05-11 description: Motor imagery (MI) and action observation (AO) have been found to enhance motor performance, but recent research found that a combination of action observation and motor imagery (AOMI) together is even better. Despite this initial finding, the most effective way to combine them is unknown. The present study examined the effects of synchronized (i e., concurrently doing AO and MI), asynchronised (i.e., first doing AO then MI), and progressive (first asynchronised approach, then doing synchronized approach) AOMI on golf putting performance and learning. We recruited 45 university students (Mage = 20.18 + 1.32 years; males = 23, females = 22) and randomly assigned them into the following four groups: synchronized group (S-AOMI), asynchronised group (A-AOMI), progressive group (A-S-AOMI), and a control group with a pre-post research design. Participants engaged in a 6-week (three times/per-week) intervention, plus two retention tests. A two-way (group × time) mixed ANOVA statistical analysis found that the three experimental groups performed better than the control group after intervention. However, we found progressive and asynchronised had better golf putting scores than synchronized group and the control group on the retention tests. Our results advance knowledge in AOMI research, but it needs more research to reveal the best way of combining AOMI in the future. Theoretical implications, limitations, applications, and future suggestions are also discussed. creator: Chi-Hsian Lin creator: Frank J.H. Lu creator: Diane L. Gill creator: Ken Shih-Kuei Huang creator: Shu-Ching Wu creator: Yi-Hsiang Chiu uri: https://doi.org/10.7717/peerj.13432 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lin et al. title: Base water potential but not hydrotime predicts seedling emergence of Medicago sativa under water stress conditions link: https://peerj.com/articles/13206 last-modified: 2022-05-10 description: We determined the hydrotime model parameters of 10 alfalfa seed lots by incubating seeds at various water potentials in the laboratory. Meanwhile, seedling emergence under drought and salinity conditions in a greenhouse pot experiment, and seedling establishment in the field were determined. Correlation analysis was utilized to detect the relationship between hydrotime model parameters and seedling emergence under water stress conditions. The germination percentage did not differ significantly among seed lots when seeds were incubated at −0.1 MPa, while it differed significantly among seed lots at water potentials of −0.3 and −0.6 MPa. Compared to control conditions, drought and salinity decreased seedling emergence to different extents, depending on seed lots. Seedling emergence in the field differed significantly among seed lots and ranged from 30% to 80%. Ψb(50) showed a significant correlation with seedling emergence under various conditions and with seedling establishment in the field, while no correlation was observed between θH, σφb and seedling emergence and establishment. These results suggest that Ψb(50) can be used to rank the vigor of alfalfa seed lots and thus predict seedling emergence and establishment under water stress conditions. creator: Xianglai Chen creator: Zhichao Wei creator: Dali Chen creator: Xiaowen Hu uri: https://doi.org/10.7717/peerj.13206 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Contrasting patterns from two invasion fronts suggest a niche shift of an invasive predator of native bees link: https://peerj.com/articles/13269 last-modified: 2022-05-10 description: BackgroundThe accuracy of predictions of invasive species ranges is dependent on niche similarity between invasive and native populations and on our ability to identify the niche characteristics. With this work we aimed to compare the niche dynamics of two genetically related invasive populations of Vespa velutina (an effective predator of honeybees and wild pollinators), in two distinct climatic regions, one in central Europe and another one in the north-western Iberian Peninsula, and hence to identify uninvaded regions susceptible to invasion.MethodsNiche dynamics and shifts of V. velutina were assessed by comparing the environmental niches of the native and of the two invasive populations, using climatic, topographic and land use variables. We also ran reciprocal distribution models using different algorithms and records from both native and invasive ranges to compare model predictions and estimate which regions are at a greater risk of being invaded.ResultsAn apparent niche shift was detected in the population of the NW of Iberian Peninsula, where the species is living under environmental conditions different from the native niche. In central Europe, large suitable areas remain unoccupied. The fact that both invasive populations are well established, despite occupying environmentally distinct regions indicates that V. velutina has a high ability to successfully invade different environmental envelopes from those existing in its native range. For example, in north-western Iberian Peninsula the species is now thriving out of its native niche limits. Moreover, the large extent of still unoccupied environmental space with similar conditions to those used by the species in its native range suggests that there is still a large area of central and eastern Europe that can be potentially invaded by the species. creator: Maria João Verdasca creator: Luisa Carvalheiro creator: Jesus Aguirre Gutierrez creator: José Pedro Granadeiro creator: Quentin Rome creator: Sebastien J. Puechmaille creator: Rui Rebelo creator: Hugo Rebelo uri: https://doi.org/10.7717/peerj.13269 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Verdasca et al. title: Effects of fire disturbance on species and functional compositions vary with tree sizes in a tropical dry forest link: https://peerj.com/articles/13270 last-modified: 2022-05-10 description: BackgroundDisturbances are crucial in determining forest biodiversity, dynamics, and ecosystem functions. Surface fire is a significant disturbance in tropical forests, but research on the effect of surface fire on structuring species and functional composition in a community through time remains scarce. Using a 20-year dataset of tree demography in a seasonal evergreen tropical forest in Thailand, we specifically addressed two essential questions: (1) What is the pattern of temporal turnover in species and functional composition in a community with frequent fire disturbance? (2) How did the temporal turnover vary with tree size?MethodsWe analyzed species compositional and functional temporal turnovers in four different tree size classes among five tree censuses. We quantified species turnover by calculating Bray-Curtis dissimilarity, and investigated its underlying mechanisms by comparing pairwise dissimilarity of functional traits with simulations from null models. If fire disturbances contribute more to a stochastic process, the functional composition would display a random pattern. However, if they contribute more towards a deterministic process, the functional composition should reveal a non-random pattern.ResultsOver 20 years (1994–2014), we observed changes in species composition, whereas functional composition remained relatively stable. The temporal turnover patterns of species and functional compositions varied with tree sizes. In particular, temporal functional turnover shifted very little for large trees, suggesting that changes in species composition of larger trees are contributed by species with similar functional traits through time. The temporal functional composition turnovers of smaller trees (DBH ≤ 5 cm) were mostly at random. We detected a higher functional turnover than expected by null models in some quadrats throughout the 50-ha study plot, and their observed turnover varied with diameter classes.ConclusionsSpecies compositional changes were caused by changes in the abundance of species with similar functional traits through time. Temporal functional turnover in small trees was random in most quadrats, suggesting that the recruits came from the equal proportions of surviving trees and new individuals of fast-growing species, which increased rapidly after fires. On the other hand, functional composition in big trees was more likely determined by surviving trees which maintained higher functional similarities than small trees through time. Fire disturbance is important for ecosystem functions, as changing forest fire frequency may alter forest turnover, particularly in functional composition in the new recruits of this forest. creator: Kanokporn Kaewsong creator: Chia-Hao Chang-Yang creator: Sarayudh Bunyavejchewin creator: Ekaphan Kraichak creator: Jie Yang creator: Zhenhua Sun creator: Caicai Zhang creator: Wenfei Li creator: Luxiang Lin creator: I-Fang Sun uri: https://doi.org/10.7717/peerj.13270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kaewsong et al. title: An open source and convenient method for the wide-spread testing of COVID-19 using deep throat sputum samples link: https://peerj.com/articles/13277 last-modified: 2022-05-10 description: ImportanceThe rise of novel, more infectious SARS-CoV-2 variants has made clear the need to rapidly deploy large-scale testing for COVID-19 to protect public health. However, testing remains limited due to shortages of personal protective equipment (PPE), naso- and oropharyngeal swabs, and healthcare workers. Simple test methods are needed to enhance COVID-19 screening. Here, we describe a simple, and inexpensive spit-test for COVID-19 screening called Patient Self-Collection of Sample-CoV2 (PSCS-CoV2).ObjectiveTo evaluate an affordable and convenient test for COVID-19.MethodsThe collection method relies on deep throat sputum (DTS) self-collected by the subject without the use of swabs, and was hence termed the Self-Collection of Sample for SARS-CoV-2 (abbreviated PSCS-CoV2). We used a phenol-chloroform extraction method for the viral RNA. We then tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction with primers against at least two coding regions of the viral nucleocapsid protein (N1 and N2 or E) of SARS-CoV-2. We evaluted the sensitivity and specificity of our protocol. In addition we assess the limit of detection, and efficacy of our Viral Inactivating Solution. We also evaluated our protocol, and pooling strategy from volunteers on a local college campus.ResultsWe show that the PSCS-CoV2 method accurately identified 42 confirmed COVID-19 positives, which were confirmed through the nasopharyngeal swabbing method of an FDA approved testing facility. For samples negative for COVID-19, we show that the cycle threshold for N1, N2, and RP are similar between the PSCS-CoV2 and nasopharynx swab collection method (n = 30). We found a sensitivity of 100% (95% Confidence Interval [CI], 92-100) and specifity of 100% (95% CI, 89-100) for our PSCS-CoV2 method. We determined our protocol has a limit of detection of 1/10,000 for DTS from a COVID-19 patient. In addition, we show field data of the PSCS-CoV2 method on a college campus. Ten of the twelve volunteers (N1 < 30) that we tested as positive were subsequently tested positive by an independent laboratory. Finally, we show proof of concept of a pooling strategy to test for COVID-19, and recommend pool sizes of four if the positivity rate is less than 15%.Conclusion and RelevanceWe developed a DTS-based protocol for COVID-19 testing with high sensitivity and specificity. This protocol can be used by non-debilitated adults without the assistance of another adult, or by non-debilitated children with the assistance of a parent or guardian. We also discuss pooling strategies based on estimated positivity rates to help conserve resources, time, and increase throughput. The PSCS-CoV2 method can be a key component of community-wide efforts to slow the spread of COVID-19. creator: Sunny C. Huang creator: Thomas K. Pak creator: Cameron P. Graber creator: Charles C. Searby creator: Guanghao Liu creator: Jennifer Marcy creator: Alexandra K. Yaszemski creator: Kurt Bedell creator: Emily Bui creator: Stanley Perlman creator: Qihong Zhang creator: Kai Wang creator: Val C. Sheffield creator: Calvin S. Carter uri: https://doi.org/10.7717/peerj.13277 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Huang et al. title: Evaluating acoustic signals to reduce avian collision risk link: https://peerj.com/articles/13313 last-modified: 2022-05-10 description: Collisions with human-made structures are responsible for billions of bird deaths each year, resulting in ecological damage as well as regulatory and financial burdens to many industries. Acoustic signals can alert birds to obstacles in their flight paths in order to mitigate collisions, but these signals should be tailored to the sensory ecology of birds in flight as the effectiveness of various acoustic signals potentially depends on the influence of background noise and the relative ability of various sound types to propagate within a landscape. We measured changes in flight behaviors from zebra finches released into a flight corridor containing a physical obstacle, either in no-additional-sound control conditions or when exposed to one of four acoustic signals. We selected signals to test two frequency ranges (4–6 kHz or 6–8 kHz) and two temporal modulation patterns (broadband or frequency-modulated oscillating) to determine whether any particular combination of sound attributes elicited the strongest collision avoidance behaviors. We found that, relative to control flights, all sound treatments caused birds to maintain a greater distance from hazards and to adjust their flight trajectories before coming close to obstacles. There were no statistical differences among different sound treatments, but consistent trends within the data suggest that the 4–6 kHz frequency-modulated oscillating signal elicited the strongest avoidance behaviors. We conclude that a variety of acoustic signals can be effective as avian collision deterrents, at least in the context in which we tested these birds. These results may be most directly applicable in scenarios when birds are at risk of collisions with solid structures, such as wind turbines and communication towers, as opposed to window collisions or collisions involving artificial lighting. We recommend the incorporation of acoustic signals into multimodal collision deterrents and demonstrate the value of using behavioral data to assess collision risk. creator: Robin G. Thady creator: Lauren C. Emerson creator: John P. Swaddle uri: https://doi.org/10.7717/peerj.13313 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Thady et al. title: ESR2 gene variants (rs1256049, rs4986938, and rs1256030) and their association with breast cancer risk link: https://peerj.com/articles/13379 last-modified: 2022-05-10 description: BackgroundVariants of the estrogen receptor b (ESR2) gene have been associated with different types of cancer. However, these associations have been inconsistent. We genotyped the ESR2 variants (rs1256049, rs4986938, and rs1256030) in breast cancer (BC) patients and in healthy women.ResultsThe variants rs1256049 and rs4986938 in the ESR2 gene were not associated with risk susceptibility in BC patients. However, the rs1256030 variant had an association as a risk factor for BC patients when compared with controls and BC patients for the TT genotype (odds ratio (OR) 1.86, 95% confidence intervals (CI) [1.05–3.28], p = 0.042). In addition, differences were observed in patients and controls carrying the TT genotype under 50 years of age (OR 1.85, 95% CI [1.05–3.27], p = 0.043). Thus, evident differences showed the rs1256030 variant in patients with TT, TC, and TC+TT genotypes with: (1) Stage IV (OR 1.60, 95% CI [1.06–2.54], p = 0.033), and (2) Luminal A (OR 1.60, 95% CI [0.47–0.21], p = 0.041), as well as in BC carriers of the TT genotype with indices of cellular proliferative (Ki-67) elevated (>20%) and overweight (OR 1.67, 95% CI [0.85–3.28], p = 0.041), respectively. In BC HER2 with lymph node metastasis, the TT genotype was a protective factor (OR 0.38, 95% CI [0.18–0.78], p = 0.005). The identification of haplotypes included two common GAT as risk factors (OR 3.1, 95% CI [1.31–7.72], p = 0.011) and GGC as a protective factor (OR 0.7, 95% CI [0.60–0.97], p = 0.034). The haplogenotype GGGATC was a risk factor (OR 2.5, 95% CI [1.28–5.0], p = 0.008).ConclusionThe variant rs1256030 (TT) of the ESR2 gene and haplotype GAT were associated with susceptibility to BC as risk factors in this sample from the Mexican population. creator: Martha Patricia Gallegos-Arreola creator: Guillermo M. Zúñiga-González creator: Luis E. Figuera creator: Ana María Puebla-Pérez creator: María Guadalupe Márquez-Rosales creator: Belinda Claudia Gómez-Meda creator: Mónica Alejandra Rosales-Reynoso uri: https://doi.org/10.7717/peerj.13379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gallegos-Arreola et al. title: Different pruning level effects on flowering period and chlorophyll fluorescence parameters of Loropetalum chinense var. rubrum link: https://peerj.com/articles/13406 last-modified: 2022-05-10 description: “Pruning” is a simple and efficient way to control the flowering period, but it is rarely used in perennial woody ornamental plants. In this paper, Loropetalum chinense var. rubrum was pruned in different degrees, and the relationship between pruning intensity and flowering number, and flowering time and chlorophyll fluorescence parameters were compared. After statistics, it was found that pruning could advance blossoms of L. chinense var. rubrum; also, light and heavy cutting could both obtain a larger number of flowers. In addition, through correlation analysis, it was found that during the flowering period, the Rfd parameter of the unpruned treatment had a very significant positive correlation with the number of flowers FN, which was 0.81. In other pruning treatment groups, Rfd and FN also presented a certain positive correlation, indicating that the Rfd parameter can be used to predict the number of flowers during the flowering process of L. chinense var. rubrum. The research results provided a new idea for the regulation of the flowering period of L. chinense var. rubrum and other woody ornamental plants and laid the foundation for the diversified application of L. chinense var. rubrum. creator: Damao Zhang creator: Wenqi Cai creator: Xia Zhang creator: Weidong Li creator: Yi Zhou creator: Yaqian Chen creator: Qiulin Mi creator: Lanting Jin creator: Lu Xu creator: Xiaoying Yu creator: Yanlin Li uri: https://doi.org/10.7717/peerj.13406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: The impacts of bovine milk, soy beverage, or almond beverage on the growing rat microbiome link: https://peerj.com/articles/13415 last-modified: 2022-05-10 description: BackgroundMilk, the first food of mammals, helps to establish a baseline gut microbiota. In humans, milk and milk products are consumed beyond infancy, providing comprehensive nutritional value. Non-dairy beverages, produced from plant, are increasingly popular as alternatives to dairy milk. The nutritive value of some plant-based products continues to be debated, whilst investigations into impacts on the microbiome are rare. The aim of this study was to compare the impact of bovine milk, soy and almond beverages on the rat gut microbiome. We previously showed soy and milk supplemented rats had similar bone density whereas the almond supplemented group had compromised bone health. There is an established link between bone health and the microbiota, leading us to hypothesise that the microbiota of groups supplemented with soy and milk would be somewhat similar, whilst almond supplementation would be different.MethodsThree-week-old male Sprague Dawley rats were randomly assigned to five groups (n = 10/group) and fed ad libitum for four weeks. Two control groups were fed either standard diet (AIN-93G food) or AIN-93G amino acids (AA, containing amino acids equivalent to casein but with no intact protein) and with water provided ad libitum. Three treatment groups were fed AIN-93G AA and supplemented with either bovine ultra-heat treatment (UHT) milk or soy or almond UHT beverages as their sole liquid source. At trial end, DNA was extracted from caecum contents, and microbial abundance and diversity assessed using high throughput sequencing of the V3 to V4 variable regions of the 16S ribosomal RNA gene.ResultsAlmost all phyla (91%) differed significantly (FDR < 0.05) in relative abundance according to treatment and there were distinct differences seen in community structure between treatment groups at this level. At family level, forty taxa showed significantly different relative abundance (FDR < 0.05). Bacteroidetes (Bacteroidaceae) and Firmicutes populations (Lactobacillaceae, Clostridiaceae and Peptostreptococcaceae) increased in relative abundance in the AA almond supplemented group. Supplementation with milk resulted in increased abundance of Actinobacteria (Coriobacteriaceae and Bifidobacteriaceae) compared with other groups. Soy supplementation increased abundance of some Firmicutes (Lactobacilliaceae) but not Actinobacteria, as previously reported by others.ConclusionSupplementation with milk or plant-based drinks has broad impacts on the intestinal microbiome of young rats. Changes induced by cow milk were generally in line with previous reports showing increased relative abundance of Bifidobacteriacea, whilst soy and almond beverage did not. Changes induced by soy and almond drink supplementation were in taxa commonly associated with carbohydrate utilisation. This research provides new insight into effects on the microbiome of three commercially available products marketed for similar uses. creator: Julie Cakebread creator: Olivia A.M. Wallace creator: Harold Henderson creator: Ruy Jauregui creator: Wayne Young creator: Alison Hodgkinson uri: https://doi.org/10.7717/peerj.13415 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cakebread et al. title: Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem link: https://peerj.com/articles/13169 last-modified: 2022-05-09 description: Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove. creator: Anwesha Ghosh creator: Ratul Saha creator: Punyasloke Bhadury uri: https://doi.org/10.7717/peerj.13169 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ghosh et al. title: Continuous video capture, and pollinia tracking, in Platanthera (Orchidaceae) reveal new insect visitors and potential pollinators link: https://peerj.com/articles/13191 last-modified: 2022-05-09 description: Orchids often have specific pollinators, which should provide reproductive isolation, yet many produce natural hybrids. Platanthera dilatata and P. stricta differ in floral morphology but often co-occur, overlap in flowering, and are reputed parents of P. xestesii. We used motion-triggered video detection units to monitor floral visitors of P. dilatata and P. stricta on Vancouver Island, Canada. Pollinia removal in P. dilatata was observed using histochemical staining, and cross-pollinations were performed to determine compatibility. From 1,152 h, 753 videos were recorded; 655 contained insects and 91 contained arachnids. Bumblebees, butterflies, and moths removed pollinia from P. dilatata. No pollinia removal was observed from P. stricta. Five videos showed insects moving between Platanthera species. Pollinia removal rates were low. Hand-pollinations resulted in capsule development and seed production. This study adds to the known diversity of insects interacting with these orchids, and highlights regional differences in floral visitors. creator: Genevieve E. van der Voort creator: Scott R. Gilmore creator: Jamieson C. Gorrell creator: Jasmine K. Janes uri: https://doi.org/10.7717/peerj.13191 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 van der Voort et al. title: Effect of napping on a bean bag chair on sleep stage, muscle activity, and heart rate variability link: https://peerj.com/articles/13284 last-modified: 2022-05-09 description: BackgroundAlthough ample evidence has demonstrated that daytime napping is beneficial for health and cognitive performance, bedding for napping has not yet been scientifically investigated.ObjectivesTo explore the effect of a bean bag chair on daytime napping and physiological parameters related to sleep.MethodsFourteen healthy participants were enrolled within the context of a randomized, single-blind, crossover study to evaluate the effects of a bean bag chair in comparison with those of a urethane chair manufactured to have a similar shape. Electroencephalogram, electromyogram, and heart rate variability were recorded and compared between wakefulness and napping.ResultsElectroencephalogram analyses revealed no significant differences in sleep architecture or frequency components; however, a significant decrease was found in electromyogram recordings in the trapezius muscle, which represents the neck region (p = 0.019). Additionally, a significant main effect of bedding in the low-frequency/high-frequency ratio (F[1,20] = 4.314, p = 0.037) was revealed.ConclusionsThese results suggest that napping in a bean bag chair may provide a comfortable napping environment involving muscle relaxation and proper regulation of the autonomic nervous function. creator: Masaki Nishida creator: Atsushi Ichinose creator: Yusuke Murata creator: Kohei Shioda uri: https://doi.org/10.7717/peerj.13284 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Nishida et al. title: Soil type and fertilizer rate affect wheat (Triticum aestivum L.) yield, quality and nutrient use efficiency in Ayiba, northern Ethiopia link: https://peerj.com/articles/13344 last-modified: 2022-05-09 description: The blanket NP fertilizer recommendation over the past five decades in Ethiopia did not result in a significant increment of crop productivity. The main lack of success was highly linked to the extrapolating approach of one site success to others without considering the climate, soil, and ecological setting and variations. As a result, a new fertilization approach was desperately needed, and with this premise, new blended fertilizers are now being introduced to replace the conventional approach. Thus, the objective of this study was to examine the effect of NPSZnB blended fertilizer on bread wheat yield attributes, quality traits and use efficiency in two different soil types under rain-fed conditions in Ayiba, northern Ethiopia. Relevant agronomic data were evaluated and recorded from plots of each soil types for analysis. The analysis of variance revealed a significant (p < 0.001) variation on all the agronomic and grain quality traits due to the main and interaction effects of soil type and fertilizer treatment factors. Most agronomic and quality characteristics recorded the highest result in the highest treatment applications (175 and 150 kg NPSZnB ha−1) in both soils. Yield and grain quality traits of bread wheat was also found better under fertilized plots than unfertilized plots. In both soil types increasing application of the new blended fertilizer rate from 50–175 kg NPSZnB ha−1 showed an increasing trend in grain yield from 1.6 to 4.3 and 2.5 to 5.4 t ha−1 in Vertisol and Cambisol soils, respectively. The varied yield as a response of fertilizer treatments across soils signifies soil-specific fertilization approach is critically important for production increment. On the other hand, based on the partial budget analysis the highest net benefit with the highest marginal rate of return in both Vertisol and Cambisol soils were obtained when treated with 100 and 125 kg NPSZnB ha−1, respectively. Therefore, to produce optimum bread wheat yield under rainfed conditions in Ayiba (northern Ethiopia) fertilizing Vertisols with 100 kg NPSZnB ha−1 and fertilizing Cambisols with 125 kg NPSZnB ha−1 is recommended. creator: Weldemariam Seifu creator: Eyasu Elias creator: Girmay Gebresamuel creator: Wolde Tefera uri: https://doi.org/10.7717/peerj.13344 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gessesew et al. title: An assessment of sensory sensitivity in women suffering from depression using transcutaneous electrical nerve stimulation link: https://peerj.com/articles/13373 last-modified: 2022-05-09 description: BackgroundPerception is the process or result of the process arising from the mental interpretation of the phenomena occurring, therefore it depends not only on physiology, but is also psychologically and socially conditioned. The aim of this study was to assess if there is a difference in the sensory sensitivity to an electrical stimulus in women suffering from depression and what the hedonic rating is of the lived experience of transcutaneous electrical nerve stimulation.MethodsThe depression group: 44 women, who were inpatients treated for depression at the Psychiatric Ward in the Clinical Hospital, and the control group: 41 women, matched by the age, height and weight, with no mental illness. Measures: threshold for sensing current, type of sensation evoked, hedonic rating.ResultsMedian sensing threshold of electric current (depression vs. control: 7.75 mA vs. 8.35 mA; no significant), type of sensation evoked (depression vs. control: tingling 90.9% vs. 92.7%, no significant), hedonic rating (depression vs. control: unpleasant 11.4% vs. 2.4%; p = 0.003), hedonic rating (mildly ill vs. moderately ill vs. markedly ill: unpleasant 5.3% vs. 6.3% vs. 33.3%; p = 0.066).ConclusionsWomen suffering from depression exhibit a similar threshold of sensitivity to an electrical stimulus as mentally healthy women, however the hedonic rating of the stimulus acting on the skin in the group of clinically depressed women was more negative than in the mentally healthy subjects. The stimulus was described as ‘unpleasant’ for many of the mentally unhealthy women. The most negative sensations related to the electrical stimulus were experienced by women with the highest severity of mental illness according to The Clinical Global Impression - Severity Scale. creator: Joanna Witkoś creator: Agnieszka Fusińska-Korpik creator: Magdalena Hartman-Petrycka creator: Agnieszka Nowak uri: https://doi.org/10.7717/peerj.13373 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Witkoś et al. title: Discovery of protein-based natural hydrogel from the girdle of the ‘sea cockroach’ Chiton articulatus (Chitonida: Chitonidae) link: https://peerj.com/articles/13386 last-modified: 2022-05-09 description: Hydrogels are widely used materials in biomedical, pharmaceutical, cosmetic, and agricultural fields. However, these hydrogels are usually formed synthetically via a long and complicated process involving crosslinking natural polymers. Herein, we describe a natural hydrogel isolated using a ‘gentle’ acid treatment from the girdle of a chiton species (Chiton articulatus). This novel hydrogel is shown to have a proliferative effect on mouse fibroblast cells (cell line, L929). The swelling capacity of this natural hydrogel was recorded as approximately 1,200% in distilled water, which is within desired levels for hydrogels. Detailed characterizations reveal that the hydrogel consists predominantly (83.93%) of protein. Considering its non-toxicity, proliferative effect and swelling properties, this natural hydrogel is an important discovery for material sciences, with potential for further applications in industry. Whether the girdle has some hydrogel activity in the living animal is unknown, but we speculate that it may enable the animal to better survive extreme environmental conditions by preventing desiccation. creator: Emel Çakmak creator: Behlül Koc-Bilican creator: Omar Hernando Avila-Poveda creator: Tuğçe Karaduman creator: Demet Cansaran-Duman creator: Suzanne T. Williams creator: Murat Kaya uri: https://doi.org/10.7717/peerj.13386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Çakmak et al. title: Genome-wide identification and expression analysis of fibrillin (FBN) gene family in tomato (Solanum lycopersicum L.) link: https://peerj.com/articles/13414 last-modified: 2022-05-09 description: BackgroundFibrillin (FBN) proteins are widely distributed in the photosynthetic organs. The members of FBN gene family play important roles in plant growth and development, and response to hormone and stresses. Tomato is a vegetable crop with significantly economic value and model plant commonly used in research. However, the FBN family has not been systematical studied in tomato.MethodsIn this study, 14 FBN genes were identified in tomato genome by Pfam and Hmmer 3.0 software. ExPASy, MEGA 6.0, MEME, GSDS, TBtools, PlantCARE and so on were used for physical and chemical properties analysis, phylogenetic analysis, gene structure and conserved motifs analysis, collinearity analysis and cis-acting element analysis of FBN family genes in tomato. Expression characteristics of SlFBNs in different tissues, fruit shape near isogenic lines (NILs), Pst DC3000 and ABA treatments were analyzed based on transcriptome data and quantitative Real-time qPCR (qRT-PCR) analysis.ResultsThe SlFBN family was divided into 11 subgroups. There were 8 FBN homologous gene pairs between tomato and Arabidopsis. All the members of SlFBN family contained PAP conserved domain, but their gene structure and conserved motifs showed apparent differences. The cis-acting elements of light and hormone (especially ethylene, methyl jasmonate (MeJA) and abscisic acid (ABA)) were widely distributed in the SlFBN promoter regions. The expression analysis found that most of SlFBNs were predominantly expressed in leaves of Heinz and S. pimpinellifolium LA1589, and showed higher expressions in mature or senescent leaves than in young leaves. Expression analysis of different tissues and fruit shape NILs indicated SlFBN1, SlFBN2b and SlFBN7a might play important roles during tomato fruit differentiation. All of the SlFBNs responded to Pst DC3000 and ABA treatments. The results of this study contribute to exploring the functions and molecular mechanisms of SlFBNs in leaf development, fruit differentiation, stress and hormone responses. creator: Huiru Sun creator: Min Ren creator: Jianing Zhang uri: https://doi.org/10.7717/peerj.13414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sun et al. title: Perceived stress and resilience levels during the COVID-19 pandemic among critical care nurses in Saudi Arabia: a correlational cross-sectional study link: https://peerj.com/articles/13164 last-modified: 2022-05-06 description: BackgroundThe continuous spreading of the respiratory coronavirus disease, COVID-19, has been a threat to global health, especially among those fighting directly against it. Nurses who work in critical care have reported very high levels of stress during these extreme circumstances. It is very important to measure the level of stress and resilience among these nurses in order to diminish further psychological distress. This study aims to assess the levels of perceived stress and resilience among critical care nurses.MethodologyIn this correlational cross-sectional study, critical care nurses (n = 139) were recruited by gatekeepers in a governmental university hospital in Riyadh City between 12 March and 8 April 2021 to complete an online questionnaire. The measurement tools used in this study were the Connor-Davidson Resilience Scale 10 (CD-RISC-10) and the Perceived Stress Scale of COVID-19 (PSS-10 items). Data were analyzed using a descriptive and inferential analysis to calculate frequencies to determine the distribution of stress and resilience, and multiple regression was applied to assess the relationship between them.ResultsOne hundred and thirty-nine critical care nurse (64%) responded. The perceived levels of stress reported were: no stress (8%; n = 12), mild stress (14%; n = 21), moderate stress (38%; n = 55), high stress (22%; n = 32), and severe stress (18%; n = 26). The levels of resilience reported were: very low (8%; n = 11), low (18%; n = 26), moderate (42%; n = 62), and high (32%; n = 47). The level of stress and resilience reported by the majority of critical care nurses was moderate; there was no significant correlation between COVID-19-related stress and resilience among the critical care nurses. Severe levels of stress were mostly reported among critical care nurses working in the NICU and high levels of stress were reported among those working in the emergency department. The nurses reported being highly confident that they were able to handle personal epidemic related problems with a mean score of 2.36. This reflects having a high level of resilience (42%; n = 62) and was significantly associated with years of experience as a nurse (p < 0.0027).ConclusionAlthough COVID-19 cases had declined significantly during the study period in Saudi Arabia, the majority of nurses were still experiencing moderate to high levels of stress about the epidemic, but were, at the same time, moderately resilient. Continued monitoring of the stress levels of this high-risk group is highly essential. Conducting more research is needed to measure the effectiveness of psychosocial support interventions. creator: Wafa Almegewly creator: Albatoul Alhejji creator: Lama Alotaibi creator: Malak Almalki creator: Maha Alanezi creator: Amal Almotiri creator: Fai Alotaibi creator: Seham Alharbi creator: Atheer Albarakah uri: https://doi.org/10.7717/peerj.13164 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Almegewly et al. title: Three new Penicillium species isolated from the tidal flats of China link: https://peerj.com/articles/13224 last-modified: 2022-05-06 description: During a survey of culturable fungi in the coastal areas of China, three new species of Penicillium sect. Lanata-Divaricata were discovered and studied with a polyphasic taxonomic approach, and then named as P. donggangicum sp. nov. (ex-type AS3.15900T = LN5H1-4), P. hepuense sp. nov. (ex-type AS3.16039T = TT2-4X3, AS3.16040 = TT2-6X3) and P. jiaozhouwanicum sp. nov. (ex-type AS3.16038T = 0801H2-2, AS3.16207 = ZZ2-9-3). In morphology, P. donggangicum is unique in showing light yellow sclerotia and mycelium, sparse sporulation, restricted growth at 37 °C, irregular conidiophores, intercalary phialides and metulae, and pyriform to subspherical conidia. P. hepuense is distinguished by the fast growth on CYA and YES and slow growth on MEA at 25 °C, weak or absence of growth at 37 °C, biverticillate and monoverticillate penicilli, and ellipsoidal conidia. P. jiaozhouwanicum is characterized by abundant grayish-green conidia en masse and moderate growth at 37 °C, the appressed biverticillate penicilli and fusiform, smooth-walled conidia. These three novelties were further confirmed by the phylogenetic analyses based on either the combined BenA-CaM-Rpb2 or the individual BenA, CaM, Rpb2 and internal transcribed spacer (ITS) sequences. creator: Ke-Xin Xu creator: Xia-Nan Shan creator: Yongming Ruan creator: JianXin Deng creator: Long Wang uri: https://doi.org/10.7717/peerj.13224 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: COVID-19 mortality is associated with pre-existing impaired innate immunity in health conditions link: https://peerj.com/articles/13227 last-modified: 2022-05-06 description: COVID-19 can be life-threatening to individuals with chronic diseases. To prevent severe outcomes, it is critical that we comprehend pre-existing molecular abnormalities found in common health conditions that predispose patients to poor prognoses. In this study, we focused on 14 pre-existing health conditions for which increased hazard ratios of COVID-19 mortality have been documented. We hypothesized that dysregulated gene expression in these pre-existing health conditions were risk factors of COVID-19 related death, and the magnitude of dysregulation (measured by fold change) were correlated with the severity of COVID-19 outcome (measured by hazard ratio). To test this hypothesis, we analyzed transcriptomics data sets archived before the pandemic in which no sample had COVID-19. For a given pre-existing health condition, we identified differentially expressed genes by comparing individuals affected by this health condition with those unaffected. Among genes differentially expressed in multiple health conditions, the fold changes of 70 upregulated genes and 181 downregulated genes were correlated with hazard ratios of COVID-19 mortality. These pre-existing dysregulations were molecular risk factors of severe COVID-19 outcomes. These genes were enriched with endoplasmic reticulum and mitochondria function, proinflammatory reaction, interferon production, and programmed cell death that participate in viral replication and innate immune responses to viral infections. Our results suggest that impaired innate immunity in pre-existing health conditions is associated with increased hazard of COVID-19 mortality. The discovered molecular risk factors are potential prognostic biomarkers and targets for therapeutic intervention. creator: Matthew Lee creator: Yung Chang creator: Navid Ahmadinejad creator: Crista Johnson-Agbakwu creator: Celeste Bailey creator: Li Liu uri: https://doi.org/10.7717/peerj.13227 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Lee et al. title: Bacterial profile of bovine mastitis in Ethiopia: a systematic review and meta-analysis link: https://peerj.com/articles/13253 last-modified: 2022-05-06 description: BackgroundBovine mastitis is the commonest episode of infection in the dairy industry, which often occurs after damage of epithelial cells lining the teat duct. It is ranked as the second most important cause of milk production loss directly and a devastating disease with a higher incidence leading to the culling of dairy cows. Thus, this systematic review and meta-analysis is aimed to quantitatively estimate the current status of mastitis in general and bacterial mastitis particular in Ethiopia.MethodsA literature search was carried from major databases and indexing services including PubMed, Google Scholar, Science Direct. Also, local institution repositories were searched to retrieve unpublished MSc and PhD theses. All studies were included addressing the prevalence of mastitis and bacterial isolates conducted in Ethiopia. Microsoft Excel was used to extract data and was imported to R Studio for the analyses. The random-effects model at a 95% confidence level was used for pooled estimates of outcomes. The degree of heterogeneity was computed by Higgins’s I2 statistics. Publication bias was checked by using the funnel plots of standard error augmented by Begg’s and Egger’s tests.ResultsA total of 46 studies with 15,780 cows were included in this study. All studies have collected 18,478 suspected samples for bacterial isolation. While pooled prevalence estimate of mastitis was 47.6%, the bacterial isolates pooled prevalence was 33.1%. The bacterial mastitis was 6.5% in cows infected by clinical patients and was 28.3% subclinical patients. The common isolates were Staph aureus, Strep species, Staph epidermis, Escherchia coli, Corynebacterium bovis, Coagulase Negative Staphylococcus and Klebsiella species. A univariate meta-regression analysis evidenced that the type of mastitis and management system was a possible source of heterogeneity (P-value = 0.001).ConclusionThe pooled prevalence of bacterial mastitis in Ethiopian dairy cattle was high. The analysis showed bacterial pathogens like Staphylococcus aureus, Staph epidermis, Strep species and Coagulase Negative Staphylococcus are majorly accounted for bovine mastitis in Ethiopia. Therefore, the highly prevalent and commonly isolated pathogens cause contagious mastitis which require immediate attention by dairy producers to put under control by devising robust mastitis prevention and control interventions. creator: Ephrem Toma Tora creator: Nahom Belay Bekele creator: R. S. Suresh Kumar uri: https://doi.org/10.7717/peerj.13253 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Development of nitrogen efficiency screening system in alfalfa (Medicago sativa L.) and analysis of alfalfa nitrogen efficiency types link: https://peerj.com/articles/13343 last-modified: 2022-05-06 description: Screening high nitrogen (N) efficiency crops is crucial to utilize resources rationally and reduce N losses. In this research, the biomass, morphological and N-related parameters of 28 alfalfa (Medicago sativa L.) cultivars were assessed at seedling stage. Then, we selected representative materials to compare the changes in stem-leaf dry weight (SDW), total root length (RL) and plant N accumulation (PNA) during whole period. Lastly, we analyzed the expressions of NRT2 and AMT1 genes of alfalfa cultivars. The correlation coefficients between SDW, PDW, RL, RV, SNA, RNA, and PNA were all in the range of 0.522∼0.996. The coefficient of variations of SDW, PDW, RL, RV, SNA and PNA were all more than 20% under low and medium N levels. Though the comprehensive evaluation and cluster analysis, the comprehensive value of LW6010, Gannong NO.5, Longmu 806, Giant 2, Giant 601, Zhaodong, Crown were greater than 0.5 under low and medium N levels; the comprehensive value of Gannong NO.3, Gannong NO.4, Xinjiangdaye, Xinmu NO.1 were less than 0.5 under low N level, but were greater than 0.5 under medium N level. The comprehensive value of Gannong NO.7 Gannong NO.9, Longmu 801, Gongnong NO.3, Elite, Sadie 10, Giant 551 were greater than 0.5 under low N level, but were lesser than 0.5 under medium N level; and those of Longdong, Gannong NO.8, Gongnong NO.1, Reindee, Goldqueen, Weston, Tourists, Giant 6, Algonquin, Sadie 7 were lesser than 0.5 under low and medium N levels. Four N efficiency types of alfalfa cultivars were classified: (1) Very efficient; (2) Efficient; (3) Anti-efficient; and (4) Inefficient.The SDW, RL and PNA of LW6010 were higher than Longdong in each growth period. The expressions of NRT2 and AMT1 genes were highest for LW6010, and lowest for Longdong. So, N efficiency parameters assessed at seedling stage include: SDW, PDW, RL, RV, SNA and PNA. We developed new classification system of N efficiency types of alfalfa cultivars. It proved its effectiveness on 28 alfalfa in China. creator: Xiaojing Liu creator: Yajiao Zhao creator: Feng Hao uri: https://doi.org/10.7717/peerj.13343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Excessive alcohol consumption and binge drinking in college students link: https://peerj.com/articles/13368 last-modified: 2022-05-06 description: BackgroundBinge drinking (BD) refers to a pattern of alcohol consumption characterized by the consumption of large amounts of alcohol in a short period of time followed by periods of abstinence. This drinking pattern is prevalent worldwide, mainly among young people. Excessive alcohol consumption is the spectrum of consumption patterns that may have or have had health consequences, and includes the concepts of risky alcohol use, harmful alcohol use and alcohol dependence according to Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM-IV), the latter two are currently grouped into alcohol use disorder (AUD) according to the fifth edition of the DSM (DSM-5). Due to the high prevalence of BD among young people, especially university students, as well as the important consequences of its practice, a study was conducted to evaluate excessive alcohol consumption and its relationship with the practice of BD in university students.MethodsA cross-sectional study was conducted among students (aged 18–30 years) enrolled in the academic year 2018–2019 at the Faculty of Nursing at a university in northern Spain. Data collection included sociodemographic information, and alcohol use information, collected using a semi-structured questionnaire. To measure the excessive alcohol consumption, this study used the Alcohol Use Disorders Identification Test (AUDIT).ResultsA total of 142 participants were included, of which 88.03% were women. Up to 38.03% were classified as BD. Up to 14.77% of non-BD participants and 66.67% of BD participants were classified as risky drinkers (AUDIT Total geq 8 in men or geq 6 in women) (p < 0.001). Up to 3.41% of the non-BD and 24.07% of the BD were drinkers with harmful alcohol use and probable alcohol dependence (AUDIT Total geq 13) (p < 0.001). A total of 5.68% of non-BD and 42.59% of BD were AUD drinkers (AUDIT Total geq 9 in males or geq 8 in females) (p < 0.001). In addition, statistically significant differences were found between the BD and non-BD groups in the responses to each of the AUDIT items, as well as in the total score and also in the scores of the three domains of the questionnaire.ConclusionsExcessive alcohol consumption is frequent among university students, especially among those who practice BD. creator: Manuel Herrero-Montes creator: Cristina Alonso-Blanco creator: María Paz-Zulueta creator: Amada Pellico-López creator: Laura Ruiz-Azcona creator: Carmen Sarabia-Cobo creator: Ester Boixadera-Planas creator: Paula Parás-Bravo uri: https://doi.org/10.7717/peerj.13368 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Herrero-Montes et al. title: Temperature responsiveness of soil carbon fractions, microbes, extracellular enzymes and CO2 emission: mitigating role of texture link: https://peerj.com/articles/13151 last-modified: 2022-05-05 description: The interaction of warming and soil texture on responsiveness of the key soil processes i.e. organic carbon (C) fractions, soil microbes, extracellular enzymes and CO2 emissions remains largely unknown. Global warming raises the relevant question of how different soil processes will respond in near future, and what will be the likely regulatory role of texture? To bridge this gap, this work applied the laboratory incubation method to investigate the effects of temperature changes (10–50 °C) on dynamics of labile, recalcitrant and stable C fractions, soil microbes, microbial biomass, activities of extracellular enzymes and CO2 emissions in sandy and clayey textured soils. The role of texture (sandy and clayey) in the mitigation of temperature effect was also investigated. The results revealed that the temperature sensitivity of C fractions and extracellular enzymes was in the order recalcitrant C fractions > stable C fractions > labile C fractions and oxidative enzymes > hydrolytic enzymes. While temperature sensitivity of soil microbes and biomass was in the order bacteria > actinomycetes > fungi ≈ microbial biomass C (MBC) > microbial biomass N (MBN) > microbial biomass N (MBP). Conversely, the temperature effect and sensitivity of all key soil processes including CO2 emissions were significantly (P < 0.05) higher in sandy than clayey textured soil. Results confirmed that under the scenario of global warming and climate change, soils which are sandy in nature are more susceptible to temperature increase and prone to become the CO2-C sources. It was revealed that clayey texture played an important role in mitigating and easing off the undue temperature influence, hence, the sensitivity of key soil processes. creator: Waseem Hassan creator: Yu’e Li creator: Tahseen Saba creator: Jianshuang Wu creator: Safdar Bashir creator: Saqib Bashir creator: Mansour K. Gatasheh creator: Zeng-Hui Diao creator: Zhongbing Chen uri: https://doi.org/10.7717/peerj.13151 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hassan et al. title: Physical characteristics of elite youth male football players aged 13–15 are based upon biological maturity link: https://peerj.com/articles/13282 last-modified: 2022-05-05 description: BackgroundOlder and more mature football players have been reported to gain advantages in the selection process during adolescence. The aim of this study was to investigate the influence of skeletal age (SA) on the physical characteristics of elite male football players aged 13–15 years through a cross-sectional study.Methods and MaterialsWe enrolled 167 elite players aged 13–15 from three academic football schools in China, and measured height, body mass, thigh circumference, skinfold (triceps and calf), 10 m/30-m sprint, T-tests (left and right), 5 × 25-m repeated-sprint ability (5 × 25 RSA), standing long jump, and YoYo intermittent recovery test level 1 (YYIR1). Subjects were divided into early-, average-, and late-maturity levels according to their SA and chronological age (CA) based on the following criteria: SA-CA > +1 year, SA-CA = ±1 year, and SA-CA < −1 year, respectively. The differences in parameters among the groups were analyzed using one-way analysis of variance and Bonferroni’s post-hoc test, with statistical significance set at p < 0.05.ResultsRelative to the late-maturing players, the early- and average-maturing players aged 13–15 years were taller, heavier, had a larger thigh circumference, and scored higher on the standing long jump, 30 m sprint, and 5 × 25-RSA (p < 0.05). The physical (except for body-fat percentage) and athletic characteristics of players aged 13–15 were not only significantly influenced by biological maturity, but also increased significantly with CA. The influence of biological maturity on height, 30-m sprints, and 5 × 25-m RSA diminished with age and exerted no significant effect on body-fat percentage and on YYIR1. Late-maturing players exhibited the greatest increase in physical (except for body-fat percentage) and athletic performance (except for the 10-m sprint) compared to players of early and/or average maturity.ConclusionsAlthough early-maturing players aged 13–15 possessed better anthropometric and physical performance than late- and average-maturing players, the growth and development of physical function of late- and average-maturing players was significantly greater, particularly with respect to height, sprint speed, and muscular power. creator: Shidong Yang creator: Haichun Chen uri: https://doi.org/10.7717/peerj.13282 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang and Chen title: Identification, diversity and domain structure analysis of mucin and mucin-like genes in sea anemone Actinia tenebrosa link: https://peerj.com/articles/13292 last-modified: 2022-05-05 description: BackgroundMucins are part of the glycoprotein family and the main proteinaceous component of mucus. The sea anemone species, Actinia tenebrosa (Phylum Cnidaria) produce large amounts of mucus, which have not been studied in detail. Furthermore, there has only been limited investigation of mucin genes in phylum Cnidaria. Therefore, the aim of current study was to identify and analyse the repertoire mucin genes present in A. tenebrosa and range of other sea anemone species to document their diversity in this group.MethodsTo achieve this aim, we undertook transcriptome sequencing, assembly, and annotation to identify mucin genes in A. tenebrosa.ResultsThe results from this study demonstrated a diverse repertoire of mucin proteins, including mucin1-like, mucin4-like, and a range of mucin-like genes in the range of sea anemone species examined. The domain structure of the identified mucin genes was found to be consistent with the conserved domains found in the homologous proteins of vertebrate species. The discovery of a diverse range of mucin genes in sea anemone species provided a basic reference for future mucin studies in cnidarians and could lead to research into their application in the pharmacological, clinical, and cosmetic industries. creator: Alaa Haridi uri: https://doi.org/10.7717/peerj.13292 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Haridi title: Text mining for identification of biological entities related to antibiotic resistant organisms link: https://peerj.com/articles/13351 last-modified: 2022-05-05 description: Antimicrobial resistance is a significant public health problem worldwide. In recent years, the scientific community has been intensifying efforts to combat this problem; many experiments have been developed, and many articles are published in this area. However, the growing volume of biological literature increases the difficulty of the biocuration process due to the cost and time required. Modern text mining tools with the adoption of artificial intelligence technology are helpful to assist in the evolution of research. In this article, we propose a text mining model capable of identifying and ranking prioritizing scientific articles in the context of antimicrobial resistance. We retrieved scientific articles from the PubMed database, adopted machine learning techniques to generate the vector representation of the retrieved scientific articles, and identified their similarity with the context. As a result of this process, we obtained a dataset labeled “Relevant” and “Irrelevant” and used this dataset to implement one supervised learning algorithm to classify new records. The model’s overall performance reached 90% accuracy and the f-measure (harmonic mean between the metrics) reached 82% accuracy for positive class and 93% for negative class, showing quality in the identification of scientific articles relevant to the context. The dataset, scripts and models are available at https://github.com/engbiopct/TextMiningAMR. creator: Kelle Fortunato Costa creator: Fabrício Almeida Araújo creator: Jefferson Morais creator: Carlos Renato Lisboa Frances creator: Rommel T. J. Ramos uri: https://doi.org/10.7717/peerj.13351 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fortunato Costa et al. title: How training loads in the preparation and competitive period affect the biochemical indicators of training stress in youth soccer players? link: https://peerj.com/articles/13367 last-modified: 2022-05-05 description: BackgroundPhysical fitness optimization and injury risk-reducing require extensive monitoring of training loads and athletes’ fatigue status. This study aimed to investigate the effect of a 6-month training program on the training-related stress indicators (creatine kinase – CK; cortisol – COR; serotonin – SER; brain-derived neurotrophic factor – BDNF) in youth soccer players.MethodsEighteen players (17.8 ± 0.9 years old, body height 181.6 ± 6.9 cm, training experience 9.7 ± 1.7 years) were blood-tested four times: at the start of the preparation period (T0), immediately following the preparation period (T1), mid-competitive period (T2), and at the end of the competitive period (T3). CK activity as well as concentrations of serum COR, SER and BDNF were determined. Training loads were recorded using a session rating of perceived exertion (sRPE).ResultsStatistical analyzes revealed significant effects for all biochemical parameters in relation to their time measurements (T0, T1, T2, T3). The statistical analyzes of sRPE and differences of biochemical parameters in their subsequent measurements (T0–T1, T1–T2, T2–T3) also demonstrated significant effects observed for all variables: sRPE (HKW = 13.189 (df = 2); p = 0.00), COR (HKW = 9.261 (df = 2); p = 0.01), CK (HKW = 12.492 (df = 2); p = 0.00), SER (HKW = 7.781 (df = 2); p = 0.02) and BDNF (HKW = 15.160 (df = 2); p < 0.001).DiscussionIn conclusion, it should be stated that the most demanding training loads applied in the preparation period (highest sRPE values) resulted in a significant increase in all analyzed biochemical training stress indicators. The reduction in the training loads during a competitive period and the addition of recovery training sessions resulted in a systematic decrease in the values of the measured biochemical indicators. The results of the study showed that both subjective and objective markers, including training loads, are useful in monitoring training stress in youth soccer players. creator: Marcin Andrzejewski creator: Marek Konefał creator: Tomasz Podgórski creator: Beata Pluta creator: Paweł Chmura creator: Jan Chmura creator: Jakub Marynowicz creator: Kamil Melka creator: Marius Brazaitis creator: Jakub Kryściak uri: https://doi.org/10.7717/peerj.13367 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Andrzejewski et al. title: Early warning model construction and validation for urinary tract infection in patients with neurogenic lower urinary tract dysfunction (NLUTD): a retrospective study link: https://peerj.com/articles/13388 last-modified: 2022-05-05 description: BackgroundThis study was performed to construct and validate an early risk warning model of urinary tract infection in patients with neurogenic lower urinary tract dysfunction (NLUTD).MethodsEligible patients with NLUTD admitted to Shenzhen Longcheng hospital from January 2017 to June 2021 were recruited for model construction, internal validation and external validation. The first time point of data collection was within half a month of patients first diagnosed with NLUTD. The second time point was at the 6-month follow-up. The early warning model was constructed by logistic regression. The model prediction effects were validated using the area under the Receiver Operating Characteristic curve, the Boostrap experiment and the calibration plot of the combined data. The model was externally validated using sensitivity, specificity and accuracy.ResultsSix predictors were identified in the model, namely patients ≥65 years old (OR = 2.478, 95%CI [1.215– 5.050]), female (OR = 2.552, 95%CI [1.286–5.065]), diabetes (OR = 2.364, 95%CI) [1.182–4.731]), combined with urinary calculi (OR = 2.948, 95%CI [1.387–6.265]), indwelling catheterization (OR = 1.988, 95%CI [1.003 –3.940]) and bladder behavior training intervention time ≥2 weeks (OR = 2.489, 95%CI [1.233–5.022]); and the early warning model formula was Y = 0.907 ×  age+ 0.937 × sex + 0.860 × diabetes +1.081 × combined with urinary calculi+ 0.687 × indwelling catheterization+ 0.912 × bladder behavior training intervention time-2.570. The results show that the area under the ROC curve is 0.832, which is close to that of 1,000 Bootstrap internal validation (0.828). The calibration plot shows that the early warning model has good discrimination ability and consistency. The external validation shows the sensitivity is 62.5%, the specificity is 100%, and the accuracy is 90%.ConclusionThe early warning model for urinary tract infection in patients with NLUTD is suitable for clinical practice, which can provide targeted guidance for the evaluation of urinary tract infection in patients with NLUTD. creator: Liqiong Zhou creator: Surui Liang creator: Qin Shuai creator: Chunhua Fan creator: Linghong Gao creator: Wenzhi Cai uri: https://doi.org/10.7717/peerj.13388 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhou et al. title: Breaking the mold: telescoping drives the evolution of more integrated and heterogeneous skulls in cetaceans link: https://peerj.com/articles/13392 last-modified: 2022-05-05 description: BackgroundAlong with the transition to the aquatic environment, cetaceans experienced profound changes in their skeletal anatomy, especially in the skull, including the posterodorsal migration of the external bony nares, the reorganization of skull bones (= telescoping) and the development of an extreme cranial asymmetry (in odontocetes). Telescoping represents an important anatomical shift in the topological organization of cranial bones and their sutural contacts; however, the impact of these changes in the connectivity pattern and integration of the skull has never been addressed.MethodsHere, we apply the novel framework provided by the Anatomical Network Analysis to quantify the organization and integration of cetacean skulls, and the impact of the telescoping process in the connectivity pattern of the skull. We built anatomical networks for 21 cetacean skulls (three stem cetaceans, three extinct and 10 extant mysticetes, and three extinct and two extant odontocetes) and estimated network parameters related to their anatomical integration, complexity, heterogeneity, and modularity. This dataset was analyzed in the context of a broader tetrapod skull sample as well (43 species of 13 taxonomic groups).ResultsThe skulls of crown cetaceans (Neoceti) occupy a new tetrapod skull morphospace, with better integrated, more heterogeneous and simpler skulls in comparison to other tetrapods. Telescoping adds connections and improves the integration of those bones involved in the telescoping process (e.g., maxilla, supraoccipital) as well as other ones (e.g., vomer) not directly affected by telescoping. Other underlying evolutionary processes (such as basicranial specializations linked with hearing/breathing adaptations) could also be responsible for the changes in the connectivity and integration of palatal bones. We also find prograde telescoped skulls of mysticetes distinct from odontocetes by an increased heterogeneity and modularity, whereas retrograde telescoped skulls of odontocetes are characterized by higher complexity. In mysticetes, as expected, the supraoccipital gains importance and centrality in comparison to odontocetes, increasing the heterogeneity of the skull network. In odontocetes, an increase in the number of connections and complexity is probably linked with the dominant movement of paired bones, such as the maxilla, in retrograde telescoping. Crown mysticetes (Eubalaena, Caperea, Piscobalaena, and Balaenoptera)are distinguished by having more integrated skulls in comparison to stem mysticetes (Aetiocetus and Yamatocetus), whereas crown odontocetes (Waipatia, Notocetus, Physeter, and Tursiops) have more complex skulls than stem forms (Albertocetus). Telescoping along with feeding, hearing and echolocation specializations could have driven the evolution of the different connectivity patterns of living lineages. creator: Mónica R. Buono creator: Evangelos Vlachos uri: https://doi.org/10.7717/peerj.13392 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Buono and Vlachos title: Measuring inter-individual differences in behavioural types of gilthead seabreams in the laboratory using deep learning link: https://peerj.com/articles/13396 last-modified: 2022-05-05 description: Deep learning allows us to automatize the acquisition of large amounts of behavioural animal data with applications for fisheries and aquaculture. In this work, we have trained an image-based deep learning algorithm, the Faster R-CNN (Faster region-based convolutional neural network), to automatically detect and track the gilthead seabream, Sparus aurata, to search for individual differences in behaviour. We collected videos using a novel Raspberry Pi high throughput recording system attached to individual experimental behavioural arenas. From the continuous recording during behavioural assays, we acquired and labelled a total of 14,000 images and used them, along with data augmentation techniques, to train the network. Then, we evaluated the performance of our network at different training levels, increasing the number of images and applying data augmentation. For every validation step, we processed more than 52,000 images, with and without the presence of the gilthead seabream, in normal and altered (i.e., after the introduction of a non-familiar object to test for explorative behaviour) behavioural arenas. The final and best version of the neural network, trained with all the images and with data augmentation, reached an accuracy of 92,79% ± 6.78% [89.24–96.34] of correct classification and 10.25 ± 61.59 pixels [6.59-13.91] of fish positioning error. Our recording system based on a Raspberry Pi and a trained convolutional neural network provides a valuable non-invasive tool to automatically track fish movements in experimental arenas and, using the trajectories obtained during behavioural tests, to assay behavioural types. creator: Marco Signaroli creator: Arancha Lana creator: Martina Martorell-Barceló creator: Javier Sanllehi creator: Margarida Barcelo-Serra creator: Eneko Aspillaga creator: Júlia Mulet creator: Josep Alós uri: https://doi.org/10.7717/peerj.13396 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Signaroli et al. title: Unbalanced relationships: insights into the interaction between gut microbiota, geohelminths, and schistosomiasis link: https://peerj.com/articles/13401 last-modified: 2022-05-05 description: Hosts and their microbiota and parasites have co-evolved in an adaptative relationship since ancient times. The interaction between parasites and intestinal bacteria in terms of the hosts’ health is currently a subject of great research interest. Therapeutic interventions can include manipulations of the structure of the intestinal microbiota, which have immunological interactions important for modulating the host’s immune system and for reducing inflammation. Most helminths are intestinal parasites; the intestinal environment provides complex interactions with other microorganisms in which internal and external factors can influence the composition of the intestinal microbiota. Moreover, helminths and intestinal microorganisms can modulate the host’s immune system either beneficially or harmfully. The immune response can be reduced due to co-infection, and bacteria from the intestinal microbiota can translocate to other organs. In this way, the treatment can be compromised, which, together with drug resistance by the parasites makes healing even more difficult. Thus, this work aimed to understand interactions between the microbiota and parasitic diseases caused by the most important geohelminths and schistosomiasis and the consequences of these associations. creator: Matheus Pereira de Araújo creator: Marcello Otake Sato creator: Megumi Sato creator: Kasun M. Bandara WM creator: Luiz Felipe Leomil Coelho creator: Raquel Lopes Martins Souza creator: Satoru Kawai creator: Marcos José Marques uri: https://doi.org/10.7717/peerj.13401 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Pereira de Araújo et al. title: Transcriptomic signals of mitochondrial dysfunction and OXPHOS dynamics in fast-growth chicken link: https://peerj.com/articles/13364 last-modified: 2022-05-04 description: IntroductionBirds are equipped with unique evolutionary adaptations to counter oxidative stress. Studies suggest that lifespan is inversely correlated with oxidative damage in birds. Mitochondrial function and performance are critical for cellular homeostasis, but the age-related patterns of mitochondrial gene expression and oxidative phosphorylation (OXPHOS) in birds are not fully understood. The domestic chicken is an excellent model to understand aging in birds; modern chickens are selected for rapid growth and high fecundity and oxidative stress is a recurring feature in chicken. Comparing fast- and slow-growing chicken phenotypes provides us an opportunity to disentangle the nexus of oxidative homeostasis, growth rate, and age in birds.Methods and ResultsWe compared pectoralis muscle gene expression patterns between a fast and a slow-growing chicken breed at 11 and 42 days old. Using RNAseq analyses, we found that mitochondrial dysfunction and reduced oxidative phosphorylation are major features of fast-growth breast muscle, compared to the slow-growing heritage breed. We found transcriptomic evidence of reduced OXPHOS performance in young fast-growth broilers, which declined further by 42 days.DiscussionOXPHOS performance declines are a common feature of aging. Sirtuin signaling and NRF2 dependent oxidative stress responses support the progression of oxidative damage in fast-growth chicken. Our gene expression datasets showed that fast growth in early life places immense stress on oxidative performance, and rapid growth overwhelms the OXPHOS system. In summary, our study suggests constraints on oxidative capacity to sustain fast growth at high metabolic rates, such as those exhibited by modern broilers. creator: Shawna Hubert creator: Giridhar Athrey uri: https://doi.org/10.7717/peerj.13364 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hubert and Athrey title: Prevalence, awareness, and associated factors of high blood pressure among female migrant workers in Central South China link: https://peerj.com/articles/13365 last-modified: 2022-05-04 description: BackgroundAlthough many young Chinese women migrate to urban regions for better opportunities, little is known about the prevalence and awareness of having high blood pressure (HBP) in this population. This study investigated the prevalence, awareness, and factors associated with HBP among young female migrant workers in Central South China.MethodsWe conducted a cross-sectional study to identify HBP (2017 ACC/AHA guidelines) among female migrant workers aged 18–45 years in Central South China. Demographics, anthropometric measurements, hypertension-related lifestyle, awareness of HBP, and blood pressure were recorded. Logistic regression analysis was used to identify the factors associated with HBP (blood pressure ≥ 130/80 mmHg).ResultsOverall, 232 female migrants participated in the study (mean age 34.4; standard deviation: 6.4 years). The prevalence of HBP was 27.2% (95% CI [21.6–33.2]), and 88.9% of the participants were unaware of their HBP status. Having rural medical insurance (odds ratio [OR] = 20.7; 95% confidence interval 95% CI [2.1–204.8]), awareness of having HBP (OR = 5.1; 95% CI [1.4–18.5]), physical inactivity (OR = 2.9; 95% CI [1.1–7.9]), and being overweight/obese (OR = 2.7; 95% CI [1.3–6.1]) were independently associated with HBP.ConclusionsThis study revealed a high prevalence of HBP among young Chinese female migrant workers, as well as a high frequency of being unaware of their condition and some associated factors (rural medical insurance, awareness of having HBP, physical inactivity, and overweight/obesity). The uncontrolled HBP among young Chinese female migrant workers suggested that health education needs further promotion in such a population. creator: Hua Peng creator: Mei Sun creator: Xin Hu creator: Huiwu Han creator: Jing Su creator: Emin Peng creator: James Wiley creator: Lisa Lommel creator: Jyu-Lin Chen uri: https://doi.org/10.7717/peerj.13365 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Peng et al. title: Contrasting nursery habitats promote variations in the bioenergetic condition of juvenile female red squat lobsters (Pleuroncodes monodon) of the Southern Pacific Ocean link: https://peerj.com/articles/13393 last-modified: 2022-05-04 description: The red squat lobster Pleuroncodes monodon is an important fishery resource in the Humboldt Current System (HCS). This decapod is exploited in two fishing units: (a) the northern fishing unit (NFU, from 26°S to 30°S) and (b) the southern fishing unit (SFU, from 32°S to 37°S), each of which have an adjacent nursery area that is the source of recruits to replace the exploited adult populations (in the NFU: off the coast of Coquimbo (28°S) and in the SFU: off the coast of Concepción (36°S)). Marked spatial differences in the environmental conditions of the NFU and SFU, and the biogeographic break that exists between these nursery areas (30°S) may promote changes in the bioenergetic condition of new P. monodon juveniles. To evaluate this, we analyzed the bioenergetic condition (measured as: body mass, lipids, proteins, glucose, and energy) of new juvenile females in the main nursery areas off the Chilean coast. The juvenile females from the SFU showed a higher body mass than those from the NFU. Consistently, the juvenile females from the SFU had a higher content of lipids, proteins, and glucose than those from the NFU, indicative of higher energy contents and a higher lipid/protein ratio in the south compared to the north. Considering the current overexploitation of this fishery resource in the HCS, it is essential to understand how the bioenergetic condition of juvenile females of P. monodon may vary in nursery areas at different latitudes in order to generate sustainable fishery management policies with an ecological approach, designed specifically to each fishing unit. Furthermore, identifying the latitudinal variations of these biochemical compounds in P. monodon juveniles can elucidate the geographic origin of red squat lobsters that present a ”better bioenergetic condition” in the HCS, which may significantly benefit sustainable fishing certification processes. creator: Fabián Guzmán-Rivas creator: Marco Quispe creator: Ángel Urzúa uri: https://doi.org/10.7717/peerj.13393 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Guzmán-Rivas et al. title: The response of geophytes to continuous human foraging on the Cape south coast, South Africa and its implications for early hunter-gatherer mobility patterns link: https://peerj.com/articles/13066 last-modified: 2022-05-03 description: Current ecological understanding of plants with underground storage organs (USOs) suggests they have, in general, low rates of recruitment and thus as a resource it should be rapidly exhausted, which likely had implications for hunter-gatherer mobility patterns. We focus on the resilience (defined here as the ability of species to persist after being harvested) of USOs to human foraging. Human foragers harvested all visible USO material from 19 plots spread across six Cape south coast (South Africa) vegetation types for three consecutive years (2015–2017) during the period of peak USO apparency (September–October). We expected the plots to be depleted after the first year of harvesting since the entire storage organ of the USO is removed during foraging, i.e. immediate and substantial declines from the first to the second harvest. However, over 50% of the total weight harvested in 2015 was harvested in 2016 and 2017; only after two consecutive years of harvesting, was there evidence of significantly lower yield (p = 0.034) than the first (2015) harvest. Novel emergence of new species and new individuals in year two and three buffered the decline of harvested USOs. We use our findings to make predictions on hunter-gatherer mobility patterns in this region compared to the Hadza in East Africa and the Alyawara in North Australia. creator: M. Susan Botha creator: Richard M. Cowling creator: Jan C. De Vynck creator: Karen J. Esler creator: Alastair J. Potts uri: https://doi.org/10.7717/peerj.13066 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Botha et al. title: Network subgraph-based approach for analyzing and comparing molecular networks link: https://peerj.com/articles/13137 last-modified: 2022-05-03 description: Molecular networks are built up from genetic elements that exhibit feedback interactions. Here, we studied the problem of measuring the similarity of directed networks by proposing a novel alignment-free approach: the network subgraph-based approach. Our approach does not make use of randomized networks to determine modular patterns embedded in a network, and this method differs from the network motif and graphlet methods. Network similarity was quantified by gauging the difference between the subgraph frequency distributions of two networks using Jensen–Shannon entropy. We applied the subgraph approach to study three types of molecular networks, i.e., cancer networks, signal transduction networks, and cellular process networks, which exhibit diverse molecular functions. We compared the performance of our subgraph detection algorithm with other algorithms, and the results were consistent, but other algorithms could not address the issue of subgraphs/motifs embedded within a subgraph/motif. To evaluate the effectiveness of the subgraph-based method, we applied the method along with the Jensen–Shannon entropy to classify six network models, and it achieves a 100% accuracy of classification. The proposed information-theoretic approach allows us to determine the structural similarity of two networks regardless of node identity and network size. We demonstrated the effectiveness of the subgraph approach to cluster molecular networks that exhibit similar regulatory interaction topologies. As an illustration, our method can identify (i) common subgraph-mediated signal transduction and/or cellular processes in AML and pancreatic cancer, and (ii) scaffold proteins in gastric cancer and hepatocellular carcinoma; thus, the results suggested that there are common regulation modules for cancer formation. We also found that the underlying substructures of the molecular networks are dominated by irreducible subgraphs; this feature is valid for the three classes of molecular networks we studied. The subgraph-based approach provides a systematic scenario for analyzing, compare and classifying molecular networks with diverse functionalities. creator: Chien-Hung Huang creator: Efendi Zaenudin creator: Jeffrey J.P. Tsai creator: Nilubon Kurubanjerdjit creator: Ka-Lok Ng uri: https://doi.org/10.7717/peerj.13137 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Huang et al. title: Genome-wide identification of the SWEET gene family mediating the cold stress response in Prunus mume link: https://peerj.com/articles/13273 last-modified: 2022-05-03 description: The Sugars Will Eventually be Exported Transporter (SWEET) gene family encodes a family of sugar transporters that play essential roles in plant growth, reproduction, and biotic and abiotic stresses. Prunus mume is a considerable ornamental wood plant with high edible and medicinal values; however, its lack of tolerance to low temperature has severely limited its geographical distribution. To investigate whether this gene family mediates the response of P. mume to cold stress, we identified that the P. mume gene family consists of 17 members and divided the family members into four groups. Sixteen of these genes were anchored on six chromosomes, and one gene was anchored on the scaffold with four pairs of segmental gene duplications and two pairs of tandem gene duplications. Cis-acting regulatory element analysis indicated that the PmSWEET genes are potentially involved in P. mume development, including potentially regulating roles in procedure, such as circadian control, abscisic acid-response and light-response, and responses to numerous stresses, such as low-temperature and drought. We performed low-temperature treatment in the cold-tolerant cultivar ‘Songchun’ and cold-sensitive cultivar ‘Zaolve’ and found that the expression of four of 17 PmSWEETs was either upregulated or downregulated with prolonged treatment times. This finding indicates that these family members may potentially play a role in cold stress responses in P. mume. Our study provides a basis for further investigation of the role of SWEET proteins in the development of P. mume and its responses to cold stress. creator: Zhenying Wen creator: Mingyu Li creator: Juan Meng creator: Ping Li creator: Tangren Cheng creator: Qixiang Zhang creator: Lidan Sun uri: https://doi.org/10.7717/peerj.13273 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wen et al. title: Reassessment of Faxinalipterus minimus, a purported Triassic pterosaur from southern Brazil with the description of a new taxon link: https://peerj.com/articles/13276 last-modified: 2022-05-03 description: Faxinalipterus minimus was originally described as a purported pterosaur from the Late Triassic (early Norian) Caturrita Formation of southern Brazil. Its holotype comprises fragmentary postcranial elements, whereas a partial maxilla was referred to the species. The assignment of Faxinalipterus minimus to Pterosauria has been questioned by some studies, but the specimen has never been accessed in detail after its original description. Here we provide a reassessment of Faxinalipterus minimus after additional mechanical preparation of the holotype. Our interpretations on the identity of several bones differ from those of the original description, and we found no support favoring pterosaur affinities for the taxon. The maxilla previously referred to Faxinalipterus minimus is disassociated from this taxon and referred to a new putative pterosauromorph described here from a partial skull and fragmentary postcranial elements. Maehary bonapartei gen. et sp. nov. comes from the same fossiliferous site that yielded Faxinalipterus minimus, but the lack of overlapping bones hampers comparisons between the two taxa. Our phylogenetic analysis places Faxinalipterus minimus within Lagerpetidae and Maehary bonapartei gen. et sp. nov. as the earliest-diverging member of Pterosauromorpha. Furthermore, the peculiar morphology of the new taxon reveals a new dental morphotype for archosaurs, characterized by conical, unserrated crowns, with a pair of apicobasally oriented grooves. These two enigmatic archosaurs expand our knowledge on the Caturrita Formation fauna and reinforce the importance of its beds on the understanding of Late Triassic ecosystems. creator: Alexander W.A. Kellner creator: Borja Holgado creator: Orlando Grillo creator: Flávio Augusto Pretto creator: Leonardo Kerber creator: Felipe Lima Pinheiro creator: Marina Bento Soares creator: Cesar Leandro Schultz creator: Ricardo Tadeu Lopes creator: Olga Araújo creator: Rodrigo Temp Müller uri: https://doi.org/10.7717/peerj.13276 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Kellner et al. title: Climate change influences on the geographic distributional potential of the spotted fever vectors Amblyomma maculatum and Dermacentor andersoni link: https://peerj.com/articles/13279 last-modified: 2022-05-03 description: Amblyomma maculatum (Gulf Coast tick), and Dermacentor andersoni (Rocky Mountain wood tick) are two North American ticks that transmit spotted fevers associated Rickettsia. Amblyomma maculatum transmits Rickettsia parkeri and Francisella tularensis, while D. andersoni transmits R. rickettsii, Anaplasma marginale, Coltivirus (Colorado tick fever virus), and F. tularensis. Increases in temperature causes mild winters and more extreme dry periods during summers, which will affect tick populations in unknown ways. Here, we used ecological niche modeling (ENM) to assess the potential geographic distributions of these two medically important vector species in North America under current condition and then transfer those models to the future under different future climate scenarios with special interest in highlighting new potential expansion areas. Current model predictions for A. maculatum showed suitable areas across the southern and Midwest United States, and east coast, western and southern Mexico. For D. andersoni, our models showed broad suitable areas across northwestern United States. New potential for range expansions was anticipated for both tick species northward in response to climate change, extending across the Midwest and New England for A. maculatum, and still farther north into Canada for D. andersoni. creator: Abdelghafar Alkishe creator: A. Townsend Peterson uri: https://doi.org/10.7717/peerj.13279 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Alkishe and Peterson title: Spatial heterogeneity of soil nutrients in Yili River Valley link: https://peerj.com/articles/13311 last-modified: 2022-05-03 description: Soil nutrients are a vital reference index of soil fertility and are essential in studying spatial variability for the development of land resources. The traditional statistical methods including correlation analysis and geostatistical analysis, were used to explore the spatial variability of nutrients and its influencing factors in the Yili River Valley. The results showed that soil total potassium (STK) had a weak variation, soil organic carbon (SOC), soil total nitrogen (STN) and soil total phosphorus (STP) showed a moderate degree of variation. Correlation analysis showed that SOC had a significant correlation with STN, STP, STK, silt, soil water content (SWC), Cos a and altitude (p < 0.01). In contrast, negative correlations were found between the SOC and sand, soil bulk density (SBD) and pH (p < 0.01), the same as STN. STP had a significant correlation with STK, silt (p < 0.01) and Cos a (p < 0.05), whereas negative correlations were found between the STP, sand and SBD (p < 0.01). STK had a significant correlation with silt, whereas negative correlations were found between the STK, sand and SBD. Ordinary Kriging interpolation showed that the distribution of SOC and STN had a high value in the northeast, northwest and southeast, and a low value in the central and southwest. STP was high in the northwest and southeast and low in the northeast and southwest. STK was high in the northwest and northeast and low in the central and southeast regions. This is helpful for the rational exploitation of land resources in ecological economy development in the Yili River Basin. creator: Guojun Sun creator: Haijun Liu creator: Dong Cui creator: Chunmei Chai uri: https://doi.org/10.7717/peerj.13311 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sun et al. title: Glucocorticoids induce osteonecrosis of the femoral head in rats via PI3K/AKT/FOXO1 signaling pathway link: https://peerj.com/articles/13319 last-modified: 2022-05-03 description: BackgroundSteroid-induced osteonecrosis of the femoral head (SONFH) is a disorder that causes severe disability in patients and has a high incidence worldwide. Although glucocorticoid (GC)-induced apoptosis of osteoblasts is an important cytological basis of SONFH, the detailed mechanism underlying SONFH pathogenesis remains elusive. PI3K/AKT signaling pathway was reported to involve in cell survival and apoptosis.ObjectiveWe explored the role of PI3K/AKT/FOXO1 signaling pathway and its downstream targets during glucocorticoid -induced osteonecrosis of the femoral head.MethodsWe obtained gene expression profile of osteoblasts subjected to dexamethasone (Dex) treatment from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened out and functional enrichment analysis were conducted by bioinformatics analysis. In vitro, we analyzed Dex-induced apoptosis in MC3T3-E1 cells and explored the role of PI3K/AKT/FOXO1 signaling pathway in this phenomenon by employing siRNA-FOXO1 and IGF-1(PI3K/AKT agonist). Finally, we verified our results in a rat model of SONFH.ResultsIn Dex-treated osteoblasts, DEGs were mainly enriched in the FOXO signaling pathway. Dex inhibited MC3T3-E1 cell viability in a dose-dependent effect and induced apoptosis by increasing the expression levels of FOXO1, Bax, cleaved-Caspase-3, and cleaved-Caspase-9, while reducing the expression of Bcl-2. Notably, these results were reversed by siRNA-FOXO1 treatment. Dex inhibited PI3K/AKT signaling pathway, upregulated FOXO1 expression and increased FOXO1 nuclear translocation, which were reversed by IGF-1. Compared to normal rats, the femoral head of SONFH showed increased expression of FOXO1, increased number of apoptotic cells, and empty osteocytic lacunas, as well as decreased bone tissue content and femoral head integrity. Significantly, the effects of GC-induced SONFH were alleviated following IGF-1 treatment.ConclusionDex induces osteoblast apoptosis via the PI3K/AKT/FOXO1 signaling pathway. Our research offers new insights into the underlying molecular mechanisms of glucocorticoid-induced osteonecrosis in SONFH and proposes FOXO1 as a therapeutic target for this disease. creator: Fei Sun creator: Jian Lin Zhou creator: Si Xing Wei creator: Ze Wen Jiang creator: Hao Peng uri: https://doi.org/10.7717/peerj.13319 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sun et al. title: The association of plasma osteoprotegerin levels and functional outcomes post endovascular thrombectomy in acute ischemic stroke patients: a retrospective observational study link: https://peerj.com/articles/13327 last-modified: 2022-05-03 description: BackgroundOsteoprotegerin (OPG), also known as osteoclastogenesis inhibitory factor, is a tumor necrosis factor receptor superfamily component. There is an established relationship between OPG and cardiovascular disease. We hypothesized that plasma OPG levels are associated with functional outcomes in acute ischemic stroke patients who have undergone endovascular thrombectomy (EVT).MethodsFrom April 2014 through December 2020, a total of 360 acute ischemic stroke patients who underwent EVT were prospectively included in this retrospective observational study. Plasma OPG was measured after fasting for 12 postoperative hours after EVT. A modified Rankin Scale (mRS) was used to assess functional outcomes 3 months after index stroke occurrence. Univariate and multivariate binary logistic regression and ordinal logistic regression analyses were performed to investigate the association of plasma OPG levels with poor functional outcomes.ResultsOverall, 145 (40.2%) patients had poor (mRS > 2) outcomes. The mean ± standard deviation plasma OPG level was 200.2 ± 74.4 pg/mL. Multivariate analysis after adjusting for sex, body mass index, and variables with p < 0.1 in the preceding univariate analysis revealed high plasma OPG levels were independently associated with poor functional outcomes (highest tertile vs. lowest tertile of OPG; odds ratios (OR) 2.121, 95% confidence interval (CI) [1.089–4.191], p = 0.037 in binary logistic regression, OR 2.102, 95% CI [1.301–3.412], p = 0.002 in ordinal logistic regression analysis).ConclusionsThis study demonstrated that higher plasma OPG levels were associated with poor functional outcomes in acute ischemic stroke patients who underwent EVT. creator: Moo-Seok Park creator: Jin-Hee Park creator: Ahran Joo creator: Yoonkyung Chang creator: Tae-Jin Song uri: https://doi.org/10.7717/peerj.13327 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Park et al. title: Feature tuning improves MAXENT predictions of the potential distribution of Pedicularis longiflora Rudolph and its variant link: https://peerj.com/articles/13337 last-modified: 2022-05-03 description: Pedicularis longiflora Rudolph and its variant (P. longiflora var. tubiformis (Klotzsch) Tsoong) are alpine plants and traditional Chinese medicines with important medicinal value, and future climate changes may have an adverse impact on their geographic distribution. The maximum entropy (MAXENT) model has the outstanding ability to predict the potential distribution region of species under climate change. Therefore, given the importance of the parameter settings of feature classes (FCs) and the regularization multiplier (RM) of the MAXENT model and the importance of add indicators to evaluate model performance, we used ENMeval to improve the MAXENT niche model and conducted an in-depth study on the potential distributions of these two alpine medicinal plants. We adjusted the parameters of FC and RM in the MAXENT model, evaluated the adjusted MAXENT model using six indicators, determined the most important ecogeographical factors (EGFs) that affect the potential distributions of these plants, and compared their current potential distributions between the adjusted model and the default model. The adjusted model performed better; thus, we used the improved MAXENT model to predict their future potential distributions. The model predicted that P. longiflora Rudolph and its variant (P. longiflora var. tubiformis (Klotzsch) Tsoong) would move northward and showed a decrease in extent under future climate scenarios. This result is important to predict their potential distribution regions under changing climate scenarios to develop effective long-term resource conservation and management plans for these species. creator: Ru Bao creator: Xiaolong Li creator: Jianghua Zheng uri: https://doi.org/10.7717/peerj.13337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bao et al. title: miR-9-5p promotes myogenic differentiation via the Dlx3/Myf5 axis link: https://peerj.com/articles/13360 last-modified: 2022-05-03 description: MicroRNAs play an important role in myogenic differentiation, they bind to target genes and regulate muscle formation. We previously found that miR-9-5p, which is related to bone formation, was increased over time during the process of myogenic differentiation. However, the mechanism by which miR-9-5p regulates myogenic differentiation remains largely unknown. In the present study, we first examined myotube formation and miR-9-5p, myogenesis-related genes including Dlx3, Myod1, Mef2c, Desmin, MyoG and Myf5 expression under myogenic induction. Then, we detected the expression of myogenic transcription factors after overexpression or knockdown of miR-9-5p or Dlx3 in the mouse premyoblast cell line C2C12 by qPCR, western blot and myotube formation under myogenic induction. A luciferase assay was performed to confirm the regulatory relationships between not only miR-9-5p and Dlx3 but also Dlx3 and its downstream gene, Myf5, which is an essential transcription factor of myogenic differentiation. The results showed that miR-9-5p promoted myogenic differentiation by increasing myogenic transcription factor expression and promoting myotube formation, but Dlx3 exerted the opposite effect. Moreover, the luciferase assay showed that miR-9-5p bound to the 3’UTR of Dlx3 and downregulated Dlx3 expression. Dlx3 in turn suppressed Myf5 expression by binding to the Myf5 promoter, ultimately inhibiting the process of myogenic differentiation. In conclusion, the miR-9-5p/Dlx3/Myf5 axis is a novel pathway for the regulation of myogenic differentiation, and can be a potential target to treat the diseases related to muscle dysfunction. creator: Liying Dong creator: Meng Wang creator: Xiaolei Gao creator: Xuan Zheng creator: Yixin Zhang creator: Liangjie Sun creator: Na Zhao creator: Chong Ding creator: Zeyun Ma creator: Yixiang Wang uri: https://doi.org/10.7717/peerj.13360 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Dong et al. title: HIF1α is dispensable for oocyte development and female fertility in mice link: https://peerj.com/articles/13370 last-modified: 2022-05-03 description: BackgroundIt has been thought that oocyte may develop in a low oxygen environment, as changes in follicle structure and formation of a fluid-filled antrum. The survival of hypoxic tissues is controlled by hypoxia-inducible factors (HIFs) that are activated in a low oxygen state. HIF1α is expressed in mature mouse oocytes and continues to be expressed after fertilization, from the 2-cell to blastocyst stage. However, the physiological roles of HIF pathway during oogenesis and embryogenesis have still not been elucidated in detail.MethodsMutant mice with oocyte-specific HIF1α deletion were generated by crossing Hif1αfl/fl mice with transgenic mice expressing Gdf9-promoter-mediated Cre recombinase. Breeding assay was carried out to detect female fertility. In vitro fertilization and embryo culture were used to assess early embryo development. Oocyte meiotic progression was also examined. Quantitative RT-PCR was used for analyzing of candidate genes expression.ResultsWe successfully generated mutant mice with oocyte-specific deletion of HIF1α. Oocytes loss of HIF1α did not affect female fertility, ovulation and early embryo development. Moreover, oocytes can mature in vitro, and form well-organized spindle in the absence of HIF1α. In addition, pronounced differences in Hif2α and Hif3α mRNA expression were not observed in HIF1α-deleted oocytes. These results revealed that HIF pathway in oocytes is not essential for female fertility. creator: Yujia Chen creator: Siyu Du creator: Zhenyue Huang creator: Longsen Han creator: Qiang Wang uri: https://doi.org/10.7717/peerj.13370 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: A new comprehensive approach for regional drought monitoring link: https://peerj.com/articles/13377 last-modified: 2022-05-03 description: The Standardized Precipitation Index (SPI) is a vital component of meteorological drought. Several researchers have been using SPI in their studies to develop new methodologies for drought assessment, monitoring, and forecasting. However, it is challenging for SPI to provide quick and comprehensive information about precipitation deficits and drought probability in a homogenous environment. This study proposes a Regional Intensive Continuous Drought Probability Monitoring System (RICDPMS) for obtaining quick and comprehensive information regarding the drought probability and the temporal evolution of the droughts at the regional level. The RICDPMS is based on Monte Carlo Feature Selection (MCFS), steady-state probabilities, and copulas functions. The MCFS is used for selecting more important stations for the analysis. The main purpose of employing MCFS in certain stations is to minimize the time and resources. The use of MCSF makes RICDPMS efficient for drought monitoring in the selected region. Further, the steady-state probabilities are used to calculate regional precipitation thresholds for selected drought intensities, and bivariate copulas are used for modeling complicated dependence structures as persisting between precipitation at varying time intervals. The RICDPMS is validated on the data collected from six meteorological locations (stations) of the northern area of Pakistan. It is observed that the RICDPMS can monitor the regional drought and provide a better quantitative way to analyze deficits with varying drought intensities in the region. Further, the RICDPMS may be used for drought monitoring and mitigation policies. creator: Rizwan Niaz creator: Mohammed M. A. Almazah creator: Ijaz Hussain creator: Muhammad Faisal creator: A. Y. Al-Rezami creator: Mohammed A. Naser uri: https://doi.org/10.7717/peerj.13377 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Niaz et al. title: Solubilization, purification, and ligand binding characterization of G protein-coupled receptor SMO in native membrane bilayer using styrene maleic acid copolymer link: https://peerj.com/articles/13381 last-modified: 2022-05-03 description: Smoothened (SMO) protein is a member of the G protein-coupled receptor (GPCR) family that is involved in the Hedgehog (Hh) signaling pathway. It is a putative target for treating various cancers, including medulloblastoma and basal cell carcinoma (BCC). Characterizing membrane proteins such as SMO in their native state is highly beneficial for the development of effective pharmaceutical drugs, as their structures and functions are retained to the highest extent in this state. Therefore, although SMO protein is conventionally solubilized in detergent micelles, incorporating the protein in a lipid-based membrane mimic is still required. In this study, we used styrene maleic acid (SMA) copolymer that directly extracted membrane protein and surrounding lipids as well as formed the so-called polymer nanodiscs, to solubilize and purify the SMO transmembrane domain encapsulated by SMA-nanodiscs. The obtained SMA-nanodiscs showed high homogeneity and maintained the physiological activity of SMO protein, thereby enabling the measurement of the dissociation constant (Kd) for SMO ligands SMO-ligands Shh Signaling Antagonist V (SANT-1) and Smoothened Agonist (SAG) using ligand-based solution nuclear magnetic resonance spectroscopy. This work paves the way for investigating the structure, function, and drug development of SMO proteins in a native-like lipid environment. creator: Lina Zhu creator: Hongxin Zhao creator: Yizhuo Wang creator: Chuandi Yu creator: Juanjuan Liu creator: Ling Li creator: Zehua Li creator: Jin Zhang creator: Han Dai creator: Junfeng Wang creator: Lei Zhu uri: https://doi.org/10.7717/peerj.13381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu et al. title: Microbial communities in carbonate precipitates from drip waters in Nerja Cave, Spain link: https://peerj.com/articles/13399 last-modified: 2022-05-03 description: Research on cave microorganisms has mainly focused on the microbial communities thriving on speleothems, rocks and sediments; however, drip water bacteria and calcite precipitation has received less attention. In this study, microbial communities of carbonate precipitates from drip waters in Nerja, a show cave close to the sea in southeastern Spain, were investigated. We observed a pronounced difference in the bacterial composition of the precipitates, depending on the galleries and halls. The most abundant phylum in the precipitates of the halls close to the cave entrance was Proteobacteria, due to the low depth of this sector, the direct influence of a garden on the top soil and the infiltration of waters into the cave, as well as the abundance of members of the order Hyphomicrobiales, dispersing from plant roots, and other Betaproteobacteria and Gammaproteobacteria, common soil inhabitants. The influence of marine aerosols explained the presence of Marinobacter, Idiomarina, Thalassobaculum, Altererythrobacter and other bacteria due to the short distance from the cave to the sea. Nineteen out of forty six genera identified in the cave have been reported to precipitate carbonate and likely have a role in mineral deposition. creator: Valme Jurado creator: Yolanda Del Rosal creator: Concepcion Jimenez de Cisneros creator: Cristina Liñan creator: Tamara Martin-Pozas creator: Jose Luis Gonzalez-Pimentel creator: Bernardo Hermosin creator: Cesareo Saiz-Jimenez uri: https://doi.org/10.7717/peerj.13399 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jurado et al. title: Spatiotemporal changes of eutrophication and heavy metal pollution in the inflow river system of Baiyangdian after the establishment of Xiongan New Area link: https://peerj.com/articles/13400 last-modified: 2022-05-03 description: Pollution in inflow rivers seriously endangers the water environment in downstream lakes. In this study, an inflow river system of the Baiyangdian–Fuhe river system (FRS) was investigated to display timely pollution patterns of eutrophication and heavy metals after the establishment of Xiongan New Area, aiming to reveal the weak parts in current pollution treatments and guide the further water quality management. The results showed that the pollution of eutrophication was worse than the heavy metals in FRS, with serious eutrophic parameters of ammonia nitrogen (NH4+-N) and chemical oxygen demand (COD). There were greatly spatiotemporal variations of the pollution in FRS. (1) Concentrations of NH4+-N and total phosphorus were all higher in summer and autumn, whereas, COD contents were higher in spring; the water quality index (WQI) of eutrophication linearly increased along FRS in summer and autumn, with pollution hotspots around the estuary area. (2) The pollution levels of plumbum exceeded cadmium (Cd) and chromium (Cr) but without strongly spatiotemporal changes; however, Cd and Cr in the town area and Cd in spring showed higher concentrations; the WQI of heavy metals showed single peak curves along FRS, with significantly higher values around the town area. Additionally, the four potential pollution sources: domestic sewage, traffic pollution, agricultural wastewater and polluted sediments were identified based on the pollution patterns and pollutant associations. These findings demonstrated current treatments failed to eliminate the pollution in some hotspots and periods, and the in-depth understanding of the pollution spatiotemporal patterns in this study, especially the pollution hotspots, serious periods and potential sources, are crucial to furtherly develop spatiotemporally flexible pollution treatment strategies. creator: Yibing Wang creator: Yang Wang creator: Wenjie Zhang creator: Xu Yao creator: Bo Wang creator: Zheng Wang uri: https://doi.org/10.7717/peerj.13400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Impact of length and width of footwear on foot structure of preschool-aged children link: https://peerj.com/articles/13403 last-modified: 2022-05-03 description: BackgroundDue to the dynamics of developmental changes, the preschool age is of crucial importance for the later health and efficiency of the feet. The aim of this study was the analysis of the fitting of indoor footwear and its impact on the features of the foot structure in 6-year-old children.MethodsThe study group consisted of 100 children, including 50 girls and 50 boys at the age of 6 years. The applied device was the CQ-ST podoscope and the Clevermess. The data were analyzed based on Mann-Whitney U test, Chi-square test and regression analysis.ResultsAbout 60% of children wore correctly fitted shoes in terms of length and width. Multiple regression models with two variables explaining the variance of the Clarke’s angle were statistically significant for girls (right foot: p < 0.001 and left foot: p = 0.009), and boys (right foot: p < 0.001 and left foot: p < 0.001). The influence of predictive variables on the values of the heel angle (γ) was statistically significant for girls (right foot: p < 0.001 and left foot: p < 0.001) and boys (right foot p < 0.001 and left foot: p < 0.001).ConclusionsBoth in the case of girls and boys, the frequency of using too long and too wide shoes was higher in relation to the frequency of using too short and too narrow shoes. The length and width of the shoes affected the length and width of the footwear both in girls and boys. The longer and wider the shoes, the lower the height of the arch. Longer shoes are accompanied by a greater transverse arch, and wider ones with a lower transverse arch of the foot. creator: Ewa Puszczalowska-Lizis creator: Sabina Lizis creator: Magdalena Prusak creator: Jaroslaw Omorczyk uri: https://doi.org/10.7717/peerj.13403 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Puszczalowska-Lizis et al. title: Integrated lipidomics and RNA sequencing analysis reveal novel changes during 3T3-L1 cell adipogenesis link: https://peerj.com/articles/13417 last-modified: 2022-05-03 description: After adipogenic differentiation, key regulators of adipogenesis are stimulated and cells begin to accumulate lipids. To identify specific changes in lipid composition and gene expression patterns during 3T3-L1 cell adipogenesis, we carried out lipidomics and RNA sequencing analysis of undifferentiated and differentiated 3T3-L1 cells. The analysis revealed significant changes in lipid content and gene expression patterns during adipogenesis. Slc2a4 was up-regulated, which may enhance glucose transport; Gpat3, Agpat2, Lipin1 and Dgat were also up-regulated, potentially to enrich intracellular triacylglycerol (TG). Increased expression levels of Pnpla2, Lipe, Acsl1 and Lpl likely increase intracellular free fatty acids, which can then be used for subsequent synthesis of other lipids, such as sphingomyelin (SM) and ceramide (Cer). Enriched intracellular diacylglycerol (DG) can also provide more raw materials for the synthesis of phosphatidylinositol (PI), phosphatidylcholine (PC), phosphatidylethanolamine (PE), ether-PE, and ether-PC, whereas high expression of Pla3 may enhance the formation of lysophophatidylcholine (LPC) and lysophosphatidylethanolamine (LPE). Therefore, in the process of adipogenesis of 3T3-L1 cells, a series of genes are activated, resulting in large changes in the contents of various lipid metabolites in the cells, especially TG, DG, SM, Cer, PI, PC, PE, etherPE, etherPC, LPC and LPE. These findings provide a theoretical basis for our understanding the pathophysiology of obesity. creator: Yangli Pei creator: Yuxin Song creator: Bingyuan Wang creator: Chenghong Lin creator: Ying Yang creator: Hua Li creator: Zheng Feng uri: https://doi.org/10.7717/peerj.13417 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pei et al. title: Unified system describing factors related to the eradication of an alien plant species link: https://peerj.com/articles/13027 last-modified: 2022-05-02 description: BackgroundIn the field of biological invasions science, a problem of many overlapping terms arose among eradication assessment frameworks. Additionally there is a need to construct a universally applicable eradication evaluation system. To unify the terminology and propose an eradication feasibility assessment scale we created the Unified System for assessing Eradication Feasibility (USEF) as a complex tool of factors for the analysis of eradications of alien (both invasive and candidate) plant species. It compiles 24 factors related to eradication success probability reported earlier in the literature and arranges them in a hierarchical system (context/group/factor/component) with a possibility to score their influence on eradication success.MethodologyAfter a literature survey we analyzed, rearranged and defined each factor giving it an intuitive name along with the list of its synonyms and similar and/or related terms from the literature. Each factor influencing eradication feasibility is ascribed into one of four groups depending on the context that best matches the factor: location context (size and location of infestation, ease of access), species context (fitness and fecundity, detectability), human context (knowledge, cognition and resources to act) and reinvasion context (invasion pathways). We also devised a simple ordinal scale to assess each factor’s influence on eradication feasibility.ConclusionsThe system may be used to report and analyze eradication campaign data in order to (i) prioritize alien species for eradication, (ii) create the strategy for controlling invasive plants, (iii) compare efficiency of different eradication actions, (iv) find gaps in knowledge disabling a sound eradication campaign assessment. The main advantage of using our system is unification of reporting eradication experience data used by researchers performing different eradication actions in different systems. creator: Halina Galera creator: Agnieszka Rudak creator: Maciej Wódkiewicz uri: https://doi.org/10.7717/peerj.13027 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Galera et al. title: Alleviation of cadmium stress in rice by inoculation of Bacillus cereus link: https://peerj.com/articles/13131 last-modified: 2022-05-02 description: Heavy metal resistant bacteria are of great importance because they play a crucial role in bioremediation. In the present study, 11 bacterial strains isolated from industrial waste were screened under different concentrations of cadmium (Cd) (100 µM and 200 µM). Among 11 strains, the Cd tolerant Bacillus cereus (S6D1–105) strain was selected for in vitro and in vivo studies. B. cereus was able to solubilize potassium, and phosphate as well as produce protease and siderophores during plate essays. Moreover, we observed the response of hydroponically grown rice plants, inoculated with B. cereus which was able to promote plant growth, by increasing plant biomass, chlorophyll contents, relative water content, different antioxidant enzymatic activity such as catalase, superoxide dismutase, ascorbate peroxidase, polyphenol oxidase and phenylalanine ammonia-lyase and reducing malondialdehyde content in both roots and leaves of rice plants under Cd stress. Our results showed that the B. cereus can be used as a biofertilizer which might be beneficial for rice cultivation in Cd contaminated soils. creator: Zahra Jabeen creator: Faiza Irshad creator: Ayesha Habib creator: Nazim Hussain creator: Muhammad Sajjad creator: Saqib Mumtaz creator: Sidra Rehman creator: Waseem Haider creator: Muhammad Nadeem Hassan uri: https://doi.org/10.7717/peerj.13131 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jabeen et al. title: A new spatiotemporal two-stage standardized weighted procedure for regional drought analysis link: https://peerj.com/articles/13249 last-modified: 2022-05-02 description: Drought is a complex phenomenon that occurs due to insufficient precipitation. It does not have immediate effects, but sustained drought can affect the hydrological, agriculture, economic sectors of the country. Therefore, there is a need for efficient methods and techniques that properly determine drought and its effects. Considering the significance and importance of drought monitoring methodologies, a new drought assessment procedure is proposed in the current study, known as the Maximum Spatio-Temporal Two-Stage Standardized Weighted Index (MSTTSSWI). The proposed MSTTSSWI is based on the weighting scheme, known as the Spatio-Temporal Two-Stage Standardized Weighting Scheme (STTSSWS). The potential of the weighting scheme is based on the Standardized Precipitation Index (SPI), Standardized Precipitation Evapotranspiration Index (SPEI), and the steady-state probabilities. Further, the STTSSWS computes spatiotemporal weights in two stages for various drought categories and stations. In the first stage of the STTSSWS, the SPI, SPEI, and the steady-state probabilities are calculated for each station at a 1-month time scale to assign weights for varying drought categories. However, in the second stage, these weights are further propagated based on spatiotemporal characteristics to obtain new weights for the various drought categories in the selected region. The STTSSWS is applied to the six meteorological stations of the Northern area, Pakistan. Moreover, the spatiotemporal weights obtained from STTSSWS are used to calculate MSTTSSWI for regional drought characterization. The MSTTSSWI may accurately provide regional spatiotemporal characteristics for the drought in the selected region and motivates researchers and policymakers to use the more comprehensive and accurate spatiotemporal characterization of drought in the selected region. creator: Rizwan Niaz creator: Nouman Iqbal creator: Nadhir Al-Ansari creator: Ijaz Hussain creator: Elsayed Elsherbini Elashkar creator: Sadaf Shamshoddin Soudagar creator: Showkat Hussain Gani creator: Alaa Mohamd Shoukry creator: Saad Sh. Sammen uri: https://doi.org/10.7717/peerj.13249 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Niaz et al. title: Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions link: https://peerj.com/articles/13252 last-modified: 2022-05-02 description: Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting point to the study of the potential uses of agaves’ fungi as biotechnological tools. creator: Marina Püpke Marone creator: Maria Fernanda Zaneli Campanari creator: Fabio Trigo Raya creator: Gonçalo Amarante Guimarães Pereira creator: Marcelo Falsarella Carazzolle uri: https://doi.org/10.7717/peerj.13252 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Marone et al. title: Assessment of the readiness of restorations manufactured by CAD/CAM in terms of marginal fit (Part I) link: https://peerj.com/articles/13280 last-modified: 2022-05-02 description: BackgroundThe master cast is the gold standard for the control and eventual adjustment of restorations produced by conventional procedures. Some digital workflow bypasses the master cast and relies completely on the precision of the CAD/CAM restoration.AimTo examine the reproducibility of the margins of CAD/CAM restorations generated from a single digital scan. Also, to check the readiness of these restorations for delivery directly after fabrication without adjustment on a master cast and thereby eliminate the need for the master cast.MethodsA total of 18 metal substructures made from cobalt chrome alloy were fabricated utilizing a single STL file. The circumference was divided into eight zones. The vertical marginal discrepancy (VMD) was measured at each zone of each metal substructure, with optical microscopy at ×200 magnification.ResultsMeasurements of vertical marginal discrepancy were in a range of (−94: 300) with a mean of 62 ± 60 μm. A one-way ANOVA test revealed that the mean VMD is significantly different among the 18 substructures (F17, 1,134 = 63.948, p < 0.001).ConclusionAlthough all the received substructures were fabricated from the same scan file, they were not identical and varied widely, and they were going outside the acceptable range in some zones. Within the limitations of this study, the marginal fit can be improved by extraoral adjustments on the master cast. Thus, skipping the master cast deprives the dentist of delivering a restoration of higher quality. creator: Radek Mounajjed creator: Thomas Taylor creator: Omar Hamadah creator: Iva Voborná creator: Marwan Al-akkad uri: https://doi.org/10.7717/peerj.13280 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mounajjed et al. title: Stress coping strategies used by nurses during the COVID-19 pandemic link: https://peerj.com/articles/13288 last-modified: 2022-05-02 description: IntroductionThe risk of getting SARS-CoV-2 infection, worries about exposing loved ones, anxiety and frustration, emotional and physical exhaustion, burn out, a feeling of being overwhelmed, and struggles and challenges with parenting are a few among many factors that affect nurses’ personal lives and professional functioning. The aim of the research is to assess nurses’ level of stress during the COVID-19 pandemic and their sense of self-efficacy, and to learn what coping strategies they use.Methodology/MethodsThe study was carried out online and based on the diagnostic poll method, using an original survey questionnaire, the General Self-Efficacy Scale (GSES 10–40), the Mini-COPE questionnaire (0–3), and the Perceived Stress Scale PSS-10 (0–40). The respondent group was made up of nurses (n = 220) who provide health services in inpatient and outpatient health care institutions in the northeastern region of Poland. The statistical analysis was performed using the STATISTICA 13.0 package (StatSoft). The distribution of variables was checked with Shapiro-Wilk tests. The Mann–Whitney U test was used to compare two independent samples, while the Kruskal–Wallis test was used to compare more samples. The adopted statistical significance level was p < 0.05. Multivariate regression analysis was applied to determine which factors were related to the level of stress.ResultsThe mean age of the participants was 43.3 years. The vast majority were women (96.4). The mean work experience of the nurses was over 20 years (58.2%). A total of 62.3% worked directly with patients in hospitals, including 11.8% respondents working at COVID-19 units and 37.7% working at primary care institutions. The analyses show that the respondents represented a high level of stress (PSS-10 – 20.9), related to their work experience as a nurse (β −0.250, p = 0.014), the number of hours worked a month (β 0.156, p = 0.015), and self-assessed health status (β −0.145, p = 0.037). They declared an average sense of self-efficacy (GSES – 29.1), which significantly depended on the nurses’ places of employment (p = 0.044). Out of stress coping strategies (Mini-COPE), the younger nurses mentioned venting (p = 0.010), instrumental support (p = 0.011), sense of humour (p = 0.013) and self-blame (0.031). Practice nurses also chose the strategy of behavioral disengagement (p = 0.032), and nurse managers chose the strategy of planning (p = 0.018).ConclusionsThe experience of the COVID-19 pandemic highlights the need to implement some strategies to protect nurses’ mental health and to take extensive prevention measures in critical situations. Special attention should be given to nurses who are younger and have shorter work experience. It is also important to monitor nurses’ working time and health status, and those who work at outpatient health care institutions should be given more support and information. creator: Matylda Sierakowska creator: Halina Doroszkiewicz uri: https://doi.org/10.7717/peerj.13288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sierakowska and Doroszkiewicz title: Comparison between hydroxyapatite and polycaprolactone in inducing osteogenic differentiation and augmenting maxillary bone regeneration in rats link: https://peerj.com/articles/13356 last-modified: 2022-05-02 description: BackgroundThe selection of appropriate scaffold plays an important role in ensuring the success of bone regeneration. The use of scaffolds with different materials and their effect on the osteogenic performance of cells is not well studied and this can affect the selection of suitable scaffolds for transplantation. Hence, this study aimed to investigate the comparative ability of two different synthetic scaffolds, mainly hydroxyapatite (HA) and polycaprolactone (PCL) scaffolds in promoting in vitro and in vivo bone regeneration.MethodIn vitro cell viability, morphology, and alkaline phosphatase (ALP) activity of MC3T3-E1 cells on HA and PCL scaffolds were determined in comparison to the accepted model outlined for two-dimensional systems. An in vivo study involving the transplantation of MC3T3-E1 cells with scaffolds into an artificial bone defect of 4 mm length and 1.5 mm depth in the rat’s left maxilla was conducted. Three-dimensional analysis using micro-computed tomography (micro-CT), hematoxylin and eosin (H&E), and immunohistochemistry analyses evaluation were performed after six weeks of transplantation.ResultsMC3T3-E1 cells on the HA scaffold showed the highest cell viability. The cell viability on both scaffolds decreased after 14 days of culture, which reflects the dominant occurrence of osteoblast differentiation. An early sign of osteoblast differentiation can be detected on the PCL scaffold. However, cells on the HA scaffold showed more prominent results with intense mineralized nodules and significantly (p < 0.05) high levels of ALP activity with prolonged osteoblast induction. Micro-CT and H&E analyses confirmed the in vitro results with bone formation were significantly (p < 0.05) greater in HA scaffold and was supported by IHC analysis which confirmed stronger expression of osteogenic markers ALP and osteocalcin.ConclusionDifferent scaffold materials of HA and PCL might have influenced the bone regeneration ability of MC3T3-E1. Regardless, in vitro and in vivo bone regeneration was better in the HA scaffold which indicates its great potential for application in bone regeneration. creator: Nur Atmaliya Luchman creator: Rohaya Megat Abdul Wahab creator: Shahrul Hisham Zainal Ariffin creator: Nurrul Shaqinah Nasruddin creator: Seng Fong Lau creator: Farinawati Yazid uri: https://doi.org/10.7717/peerj.13356 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Luchman et al. title: Predicting surface abundance of federally threatened Jollyville Plateau Salamanders (Eurycea tonkawae) to inform management activities at a highly modified urban spring link: https://peerj.com/articles/13359 last-modified: 2022-05-02 description: Urban expansion has contributed to the loss of habitat for range restricted species across the globe. Managing wildlife populations within these urban settings presents the challenge of balancing human and wildlife needs. Jollyville Plateau Salamanders (Eurycea tonkawae) are a range restricted, federally threatened, species of neotenic brook salamander endemic to central Texas. Almost the entire geographic range of E. tonkawae is embedded in the Austin, Cedar Park, and Round Rock metropolitan areas of Travis and Williamson counties, Texas. Among E. tonkawae occupied sites, Brushy Creek Spring has experienced some of the most extensive anthropogenic disturbance. Today the site consists of small groundwater outlets that emerge in the seams within a concrete culvert underlying a highway. Salamanders persist within this system though they are rarely detected. Here, we model the occurrence of salamanders within the surface habitat of Brushy Creek Spring using generalized linear models. In the absence of available data regarding the amount of water that is discharged from the spring, we use accumulated rainfall as a proxy for discharge to estimate salamander abundance. Additionally, we present evidence of reproduction, recruitment, and subterranean movement by E. tonkawae throughout this site. Infrastructure maintenance is inevitable at Brushy Creek Spring. We intend for our results to inform when maintenance should occur, i.e., during environmental conditions when salamanders are less likely to be observed in the surface habitat, to avoid unnecessary impacts to this federally threatened species. creator: Zachary C. Adcock creator: Andrew R. MacLaren creator: Ryan M. Jones creator: Andrea Villamizar-Gomez creator: Ashley E. Wall creator: Kemble White IV creator: Michael R. J. Forstner uri: https://doi.org/10.7717/peerj.13359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Adcock et al. title: Scavenging vs hunting affects behavioral traits of an opportunistic carnivore link: https://peerj.com/articles/13366 last-modified: 2022-05-02 description: BackgroundHuman-induced changes to ecosystems transform the availability of resources to predators, including altering prey populations and increasing access to anthropogenic foods. Opportunistic predators are likely to respond to altered food resources by changing the proportion of food they hunt versus scavenge. These shifts in foraging behavior will affect species interactions through multiple pathways, including by changing other aspects of predator behavior such as boldness, innovation, and social structure.MethodsTo understand how foraging behavior impacts predator behavior, we conducted a controlled experiment to simulate hunting by introducing a prey model to captive coyotes (Canis latrans) and compared their behavior to coyotes that continued to scavenge over one year. We used focal observations to construct behavioral budgets, and conducted novel object, puzzle box, and conspecific tests to evaluate boldness, innovation, and response to conspecifics.ResultsWe documented increased time spent resting by hunting coyotes paired with decreased time spent active. Hunting coyotes increased boldness and persistence but there were no changes in innovation. Our results illustrate how foraging behavior can impact other aspects of behavior, with potential ecological consequences to predator ecology, predator-prey dynamics, and human-wildlife conflict; however, the captive nature of our study limits specific conclusions related to wild predators. We conclude that human-induced behavioral changes could have cascading ecological implications that are not fully understood. creator: Mitchell A. Parsons creator: Andrew Garcia creator: Julie K. Young uri: https://doi.org/10.7717/peerj.13366 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Parsons et al.