title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2022-04 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: How beavers affect riverine aquatic macroinvertebrates: a review link: https://peerj.com/articles/13180 last-modified: 2022-04-29 description: BackgroundAs ecosystem engineers, the construction of dams by beavers alters stream habitat physically and biologically, making them a species of interest for habitat restoration. Beaver-created habitat changes affect a wide range of aquatic invertebrate species. However, despite numerous individual studies of how beavers affect aquatic macroinvertebrate assemblages, there has been no evaluation of the consensus of these effects across studies.MethodologyWe collated and examined studies comparing beaver-created ponds to nearby lotic reaches to determine general trends in aquatic macroinvertebrate richness, density, biomass, and functional composition between habitats. From this evidence, we highight knowledge gaps in how beaver activity affects aquatic macroinvertebrates.ResultsOverall, in the majority of studies, aquatic macroinvertebrate richness was higher in nearby lotic reaches compared to beaver-created ponds, but richness at coarser scales (gamma diversity) increased with the addition of beaver ponds due to increased habitat heterogeneity. Functional feeding group (FFG) patterns were highly context-dependent, though predator taxa were generally more abundant in beaver ponds than adjacent lotic reaches. Site-specific geomorphological changes, coupled with dam or riparian zone characteristics and resulting differences in basal food resources likely shape other FFG responses.ConclusionsWe identify a lack of long-term studies at single or multiple sites and conclude that fine-scale approaches may improve our understanding of the dynamics of macroinvertebrates within the freshwater realm and beyond. Due to the context-dependent nature of each study, further systematic studies of beaver engineering effects across a wider variety of environmental conditions and wetland types will also help inform land and species management decisions, such as where to prioritize protection of beaver habitats in the face of a global freshwater biodiversity crisis, or where to restore beaver populations to deliver maximum benefit. creator: Susan Washko creator: Nigel Willby creator: Alan Law uri: https://doi.org/10.7717/peerj.13180 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Washko et al. title: The influencing factors for distribution patterns of resident and migrant bird species richness along elevational gradients link: https://peerj.com/articles/13258 last-modified: 2022-04-29 description: The latitudinal and elevational patterns of species richness of resident and migrant birds have been of interest to researchers over the past few decades, and various hypotheses have been proposed to explain the factors that may affect these patterns. This study aimed to shed light on the elevational distribution patterns of resident and migrant bird species richness by examining biotic and abiotic factors such as climate, and habitat heterogeneity using a piecewise structural equation model (pSEM). The overall pattern of resident species richness showed a decreasing trend with increasing elevation, whereas that of migrant species richness showed an increasing trend. The mid-peak pattern of species richness was affected by a combination of resident and migrant species and not by either resident or migrant species. Our results showed that resident species were distributed in lower elevation regions with higher mean spring temperatures, whereas migrant species were found in higher elevation regions with lower mean spring temperatures and higher overstory vegetation coverage. Although high elevation conditions might adversely affect the reproduction of migrant birds, higher overstory vegetation coverage at high elevations seemed to compensate for this by providing a better nesting and roosting environment. Despite the significance of habitat diversity and understory vegetation coverage in univariate linear regression models, multiple regression models of the interconnection of ecological processes demonstrated that mean spring temperature and overstory vegetation coverage were more explanatory than other variables. creator: Jin-Yong Kim creator: Jongmin Yoon creator: Yu-Seong Choi creator: Soo Hyung Eo uri: https://doi.org/10.7717/peerj.13258 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kim et al. title: Chronic psychological stress alters gene expression in rat colon epithelial cells promoting chromatin remodeling, barrier dysfunction and inflammation link: https://peerj.com/articles/13287 last-modified: 2022-04-29 description: Chronic stress is commonly associated with enhanced abdominal pain (visceral hypersensitivity), but the cellular mechanisms underlying how chronic stress induces visceral hypersensitivity are poorly understood. In this study, we examined changes in gene expression in colon epithelial cells from a rat model using RNA-sequencing to examine stress-induced changes to the transcriptome. Following chronic stress, the most significantly up-regulated genes included Atg16l1, Coq10b, Dcaf13, Nat2, Ptbp2, Rras2, Spink4 and down-regulated genes including Abat, Cited2, Cnnm2, Dab2ip, Plekhm1, Scd2, and Tab2. The primary altered biological processes revealed by network enrichment analysis were inflammation/immune response, tissue morphogenesis and development, and nucleosome/chromatin assembly. The most significantly down-regulated process was the digestive system development/function, whereas the most significantly up-regulated processes were inflammatory response, organismal injury, and chromatin remodeling mediated by H3K9 methylation. Furthermore, a subpopulation of stressed rats demonstrated very significantly altered gene expression and transcript isoforms, enriched for the differential expression of genes involved in the inflammatory response, including upregulation of cytokine and chemokine receptor gene expression coupled with downregulation of epithelial adherens and tight junction mRNAs. In summary, these findings support that chronic stress is associated with increased levels of cytokines and chemokines, their downstream signaling pathways coupled to dysregulation of intestinal cell development and function. Epigenetic regulation of chromatin remodeling likely plays a prominent role in this process. Results also suggest that super enhancers play a primary role in chronic stress-associated intestinal barrier dysfunction. creator: John W. Wiley creator: Gerald A. Higgins creator: Shuangsong Hong uri: https://doi.org/10.7717/peerj.13287 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wiley et al. title: Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China link: https://peerj.com/articles/13345 last-modified: 2022-04-29 description: Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable. creator: Lin Zhang creator: Fangfang Sun creator: Songmei Ma creator: Chuncheng Wang creator: Bo Wei creator: Yunling Zhang uri: https://doi.org/10.7717/peerj.13345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Acidity and availability of aluminum, iron and manganese as factors affecting germination in European acidic dry and alkaline xerothermic grasslands link: https://peerj.com/articles/13255 last-modified: 2022-04-28 description: Germination ecology of 10 species from acidic dry grasslands and 10 species from alkaline xerothermic grasslands was studied. The seeds were subjected to different pH, iron (Fe), manganese (Mn) and aluminum (Al) treatments under controlled conditions. Effects of ionic (chlorides) and chelated forms (HBED chelates) of Fe and Mn were also compared. Final germination percentage (FGP) and index of germination velocity (IGV) were calculated. The results indicate that pH and extremely high availability of Al are the major edaphic filters regulating germination-based revegetation, while availability of Fe and Mn is of the secondary importance. Both chelates and ionic forms of Fe and Mn exerted similar effects on the ability of seeds to complete germination. It suggests that both chelates are not hazardous for early ontogenetic stages of plants. Neither group has group-specific adaptations pertaining to germination characteristics in the context of the studied chemical stimuli, which indicates a diversity of germination strategies and individual species-specific reactions to the tested factors. creator: Mateusz Wala creator: Jeremi Kołodziejek creator: Tomasz Wilk uri: https://doi.org/10.7717/peerj.13255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wala et al. title: Soil characteristic changes and quality evaluation of degraded desert steppe in arid windy sandy areas link: https://peerj.com/articles/13100 last-modified: 2022-04-28 description: Grassland degradation has become a serious problem in some areas, making it necessary to quantitatively evaluate this process and its related factors. The study area was the arid windy sandy area in eastern Ningxia. The purpose of this study was to explore how soil properties and quality change during the process of grassland degradation in arid windy sandy areas. We looked at undegraded, lightly degraded, moderately degraded, and severely degraded desert steppe to study the physical, chemical, and biological changes at 0–5 cm, 5–15 cm, and 15–30 cm soil depths at different degradation degrees. We also analyzed the correlations across soil factors, established the minimum data set, and used the soil quality index (SQI) to evaluate the soil quality of grassland at different degradation degrees. The results showed that with grassland degradation, the soil bulk density increased; the soil clay, moisture, organic matter, total nitrogen, and available potassium content decreased; and the number of soil bacteria, actinomycetes, and fungi, as well as the activity of urease, polyphenol oxidase, protease, phosphatase, and sucrase, decreased. As soil depth increased, soil bulk density increased; the soil moisture, organic matter, available potassium, and available phosphorus content decreased; and soil microorganisms accumulated in the upper soil of undegraded, lightly, and moderately degraded grassland. There was also a positive correlation among the soil clay content, moisture content, organic matter content, total nitrogen content, available potassium content, microorganism quantity, and enzyme activity, while soil bulk density was negatively correlated with the above factors. The minimum data set for the soil quality evaluation of the degraded desert steppe was comprised of soil organic matter content, soil total nitrogen content, soil available phosphorus content, and phosphatase activity. Based on the minimum data set, we calculated the SQI of the grassland at different degradation degrees and found that the ranking based on overall soil quality was undegraded >lightly degraded >moderately degraded >severely degraded grassland. The results showed that the degradation of desert steppe in arid windy sandy areas had relatively consistent effects on the physical, chemical, and biological traits of the soil. The minimum data set can be used to replace the total data set when evaluating the soil quality of the desert steppe at different degrees of degradation. creator: Jing Ma creator: Jianrong Qin creator: Hongbin Ma creator: Yao Zhou creator: Yan Shen creator: Yingzhong Xie creator: Dongmei Xu uri: https://doi.org/10.7717/peerj.13100 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ma et al. title: Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan link: https://peerj.com/articles/13202 last-modified: 2022-04-28 description: BackgroundThe climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands.MethodsHere, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space.ResultsOur result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island. creator: Keita Niwa creator: Dung Van Tran creator: Kanto Nishikawa uri: https://doi.org/10.7717/peerj.13202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Niwa et al. title: Point prevalence of non-melanoma and melanoma skin cancers in Australian surfers and swimmers in Southeast Queensland and Northern New South Wales link: https://peerj.com/articles/13243 last-modified: 2022-04-28 description: BackgroundSurfing and swimming are two popular outdoor aquatic activities in Australia with an estimated 2.7 million surfers and three million swimmers; however, these activities are associated with intermittent exposure to ultraviolet radiation. Our aim was to determine the point prevalence of pre-skin cancer (actinic keratosis (PSC)), non-melanoma (NMSC) and melanoma skin cancers (MSC) in Australian surfers and swimmers.MethodsThis cross-sectional study involved Australian surfers who completed a survey that included physiological demographics, aquatic activity-specific demographics, history of skin cancer followed by screening.ResultsA total of 171 surfers (n = 116) and swimmers (n = 55) participated in the study. Both groups were identified as having a history of skin cancer (surfers 41.4%, swimmers 36.4%) and a family history of skin cancer (surfers 52.6%, swimmers 43.6%). The majority of both groups reported using a high percentage of a chemical or physical skin cancer prevention strategy (surfers 100%, Swimmers 92.7%, P = 0.003). Significantly more surfers were identified with a skin cancer of any type vs. swimmers (50% vs. 27.3%; OR 2.67; P = 0.005) with most the common skin cancer being PSC (44.7% vs. 11.3%, P = 0.076) followed by basal cell carcinoma (BCC) (24.2% vs. 7.6%, P = 0.068). There was a total of seven MSC identified in surfers and swimmers (4.6% vs. 0.8%, respectively, P = 0.137). Most skin cancers in surfers were located on the face (28.0%) followed by the arm and back (12.1% each), whereas in swimmers, the majority of skin cancers were identified on the face (17.3%), followed by the arm and lower leg (15.4% each). The highest number of melanomas were identified in surfers (n = 6) and mainly located on the face (n = 2) and back (n = 2). There was a single melanoma identified on the back in a swimmer. With the groups combined, the majority (42.9%) of melanomas were identified on the back in participants, followed by the face (28.6%). Rates per 100,000 of NMSC and MSC in surfers and swimmers (respectively) were BCC (11,206 vs. 14,545), squamous cell carcinoma (SCC) in situ (13,793 vs. 12,727), SCC (1,724 vs. 3,636) and MSC (5,172 vs. 1,818). When compared to the general Australian population, surfers and swimmers had higher odds ratios (OR), which included BCCs (OR 7.3 and 9.4, respectively), SCCs (OR 1.7 and 3.5, respectively) and MSC (OR 96.7 and 18.8, respectively).ConclusionSurfers and swimmers had consistently higher rates of PSC, NMSC and MSC than the general Australian population. Point prevalence of MSC (groups combined) was 76-fold higher than the general Australian population. These findings highlight the clinical importance of regular skin cancer screenings in individuals who surf or swim for early detection and treatment of skin cancer. Additionally, these aquatic enthusiasts should be advised of the benefits of sun protection strategies such as chemical and physical barriers to reduce the likelihood of developing skin cancer. creator: Mike Climstein creator: Brendan Doyle creator: Michael Stapelberg creator: Nedeljka Rosic creator: Isolde Hertess creator: James Furness creator: Vini Simas creator: Joe Walsh uri: https://doi.org/10.7717/peerj.13243 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Climstein et al. title: Transcranial direct current stimulation combined with trunk-targeted, proprioceptive neuromuscular facilitation in subacute stroke: a randomized controlled trial link: https://peerj.com/articles/13329 last-modified: 2022-04-28 description: BackgroundStroke is the foremost cause of death and disability worldwide. Improving upper extremity function and quality of life are two paramount therapeutic targets during rehabilitation.Aim of the studyTo investigate the effects of transcranial direct current stimulation (tDCS) combined with trunk-targeted proprioceptive neuromuscular facilitation (PNF) on impairments, activity limitations, and participation restrictions of subjects with subacute stroke.MethodologyFifty-four subjects with subacute stroke were divided into three groups using block randomization. All three groups received rehabilitation sessions lasting 90 min in duration, four times per week, for 6 weeks. Group 1 (n = 18) received conventional physical therapy (CPT); group 2 (n = 18) received CPT, trunk-targeted PNF, and sham tDCS; and group 3 (n = 18) received CPT, trunk-targeted PNF, and bihemispheric motor cortex stimulation with tDCS. Changes in motor impairment, motor activity, and health-related quality of life assessments were outcome measures.ResultsA two-way linear mixed model analysis revealed interaction effects (group × time) for all outcome measurements (Trunk Impairment Scale, Fugl-Meyer Assessment of Motor Recovery after stroke upper extremity subsection, Wolf Motor Function Test, 10-Meter Walk Test, and the Stroke-Specific Quality of Life scale; all p < 0.01 or lower). Overall, post–pre mean differences demonstrate more substantial improvement in the active tDCS group, followed by sham stimulation associated with the PNF group and the group that received CPT alone.ConclusionTrunk-targeted PNF combined with bihemispheric tDCS along with CPT engender larger improvements in upper extremity and trunk impairment, upper limb function, gait speed, and quality of life in the subacute stroke population. creator: Jaya Shanker Tedla creator: Erika Rodrigues creator: Arthur S. Ferreira creator: Jose Vicente creator: Ravi Shankar Reddy creator: Kumar Gular creator: Devika Rani Sangadala creator: Venkata Nagaraj Kakaraparthi creator: Faisal Asiri creator: Ajaya Kumar Midde creator: Snehil Dixit uri: https://doi.org/10.7717/peerj.13329 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tedla et al. title: Effectiveness of agricultural waste in the enhancement of biological denitrification of aquaculture wastewater link: https://peerj.com/articles/13339 last-modified: 2022-04-28 description: Nitrogen pollution in aquaculture wastewater can pose a significant health and environmental risk if not removed before wastewater is discharged. Biological denitrification uses external carbon sources to remove nitrogen from wastewater; however, these carbon sources are often expensive and require significant energy. In this study, we investigated how six types of agricultural waste can be used as solid carbon sources in biological denitrification. Banana stalk (BS), loofah sponge (LS), sorghum stalk (SS), sweet potato stalk (SPS), watermelon skins (WS) and wheat husk (WH) were studied to determine their capacity to release carbon and improve denitrification efficiency. The results of batch experiments showed that all six agricultural wastes had excellent carbon release capacities, with cumulative chemical oxygen demands of 37.74–535.68 mg/g. During the 168-h reaction, the carbon release process followed the second-order kinetic equation and Ritger-Peppas equation, while carbon release occurred via diffusion. The kinetic equation fitting, scanning electron microscopy, and Fourier transform infrared spectroscopy results showed that LS had the lowest cm and the maximum t1/2 values and only suffered a moderate degree of hydrolysis. It also had the lowest pollutant release rate and cumulative chemical oxygen demand, as well as the most efficient removal of total phosphorous (TP) and total nitrogen (TN). Therefore, we concluded that LS has the lowest potential risk of excess carbon release and capacity for long-lasting and stable carbon release. The WS leachate had the highest TN contents, while the SPS leachate had the highest TP content. In the 181-h denitrification reaction, all six agricultural wastes completely removed nitrate and nitrite; however, SS had the highest denitrification rate, followed by LS, WH, BS, SPS, and WS (2.16, 1.35, 1.35, 1.34, 1.34, and 1.01 mg/(L·h), respectively). The denitrification process followed a zero-order and first-order kinetic equation. These results provide theoretical guidance for effectively selecting agricultural waste as a solid carbon source and improving the denitrification efficiency of aquaculture wastewater treatment. creator: Shuwei Gao creator: Wangbao Gong creator: Kai Zhang creator: Zhifei Li creator: Guangjun Wang creator: Ermeng Yu creator: Yun Xia creator: Jingjing Tian creator: Hongyan Li creator: Jun Xie uri: https://doi.org/10.7717/peerj.13339 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gao et al. title: Effect of strip clear-cutting on the natural regeneration of Pinus tabuliformis plantations in northeastern China link: https://peerj.com/articles/13341 last-modified: 2022-04-28 description: In this study, the effect of strip clear-cutting on the natural regeneration performance of mature Pinus tabuliformis plantations in the three locations in western part of the Liaoning Province was analyzed. Strip clear-cutting, with clear-cut and uncut strip widths of 15, 20, 25 m, and 10 and 18 m, respectively, was conducted in spring 2014, and control, in each study location. Field investigations were conducted in 2017. Fifteen sample plots with sizes of 4 m2 (2 m × 2 m) were established in each clear-cut strip, uncut strip, and control. One to four saplings were randomly selected to measure the current year increment, and the lengths and numbers for branch of the first whorl. Three saplings were randomly selected from the center of the strip to measure the photosynthetic rate. Three sample plots with sizes of 4 m2 (2 m × 2 m) and 1 m2 (1 m × 1 m) were developed in each strip and control to determine the biodiversity of shrubs and herbs as well as the water content of the decomposition and semi-decomposition layer. The results show that the current year increment and branch length of the first whorl can be ordered as follows: clear-cut strips > control > uncut strips. Number of the branches of the first whorl can be ordered as follows: clear-cut strips > uncut strips > control. Strip clear-cutting was a statistically significant treatment for the current year increment and length and number of branches of the first whorl. The saplings from the clear-cut strip with a width of 25 m have the largest photosynthetic capacity compared with those from the other strips and control. The transpiration rates of the large, medium, and small saplings from clear-cut strips are the largest and those of saplings from the control are the smallest. The water content of the decomposition and semi-decomposition layer in the control is the highest, but no significant difference was confirmed between the strip clear-cutting approaches. creator: Yunxia Sun creator: Jian Feng creator: Huilin Gao creator: Wanjin Hu creator: Yang Qu creator: Hongtao Zou creator: You Yin creator: Yuan Li creator: Meiyan Xin uri: https://doi.org/10.7717/peerj.13341 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sun et al. title: Genetic polymorphisms in the IFNL4, MxA, and MxB genes were associated with biochemical index of chronic HBV patients from Yunnan, China link: https://peerj.com/articles/13353 last-modified: 2022-04-28 description: Hepatitis B virus (HBV) infection causes Hepatitis B, which is one of the most common causes of hepatocellular carcinoma (HCC). The single nucleotide polymorphisms (SNPs) of the host immune genes could impact HBV infection, viral clearance, and treatment effect. However, the contradictory roles of several studies suggest further analysis of various populations. The whole blood and biochemical indexes of 448 HBV patients and matched controls were collected from the Yunnan population to investigate the genetic roles of IFNL4 and the downstream genes (MxA and MxB). The genotypes, alleles, and haplotypes frequencies of the seven SNPs (rs11322783, rs117648444, rs2071430, rs17000900, rs9982944, rs408825, and rs2838029) from the HBV patients and controls were analyzed. However, no association was identified between the SNPs and HBV infection. Then, biochemical index levels were evaluated among the HBV patients with different genotypes of the seven SNPs. The results indicated that the liver function index levels (including alanine transaminase (ALT), aspartate transaminase (AST), total bilirubin (TBIL), direct bilirubin (DBIL), indirect bilirubin (IBIL), and albumin (ALB)) were influenced by the genotypes of the SNPs in HBV patients. Moreover, when the HBV patients were divided into HBsAg-positive and -negative groups, the association between the SNP genotypes and the biochemical indexes still existed. In addition, although the genetic polymorphisms in the IFNL4, MxA, and MxB genes were not significantly associated with HBV infection in the Yunnan population, these genes could indirectly influence disease progression by associating with the biochemical index levels of Yunnan HBV patients. creator: Kexi Zheng creator: Yunsong Shen creator: Xueshan Xia creator: Yuzhu Song creator: A-Mei Zhang uri: https://doi.org/10.7717/peerj.13353 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zheng et al. title: Quantitative analysis of vegetation restoration and potential driving factors in a typical subalpine region of the Eastern Tibet Plateau link: https://peerj.com/articles/13358 last-modified: 2022-04-28 description: Vegetation restoration is an essential approach to re-establish the ecological balance in subalpine areas. Changes in vegetation cover represent, to some extent, vegetation growth trends and are the consequence of a complex of different natural factors and human activities. Microtopography influences vegetation growth by affecting the amount of heat and moisture reaching the ground, a role that is more pronounced in subalpine areas. However, little research is concerned with the characteristics and dynamics of vegetation restoration in different microtopography types. The respective importance of the factors driving vegetation changes in subalpine areas is also not clear yet. We used linear regression and the Hurst exponent to analyze the trends in vegetation restoration and sustainability in different microtopography types since 2000, based on Fractional Vegetation Cover (FVC) and identified potential driving factors of vegetation change and their importance by using Geographical Detector. The results show that: (1) The FVC in the region under study has shown an up-trend since 2000, and the rate of increase is 0.26/year (P = 0.028). It would be going from improvement to degradation, continuous decrease or continuous significant decrease in 47.48% of the region, in the future. (2) The mean FVC is in the following order: lower slope (cool), lower slope, lower slope (warm), valley, upper slope (warm), upper slope, valley (narrow), upper slope (cool), cliff, mountain/divide, peak/ridge (warm), peak/ridge, peak/ridge (cool). The lower slope is the microtopographic type with the best vegetation cover, and ridge peak is the most difficult to be afforested. (3) The main factors affecting vegetation restoration in subalpine areas are aspect, microtopographic type, and soil taxonomy great groups. The interaction between multiple factors has a much stronger effect on vegetation cover than single factors, with the effect of temperatures and aspects having the most significant impact on the vegetation cover changes. Natural factors have a greater impact on vegetation restoration than human factors in the study area. The results of this research can contribute a better understanding of the influence of different drivers on the change of vegetation cover, and provide appropriate references and recommendations for vegetation restoration and sustainable development in typical logging areas in subalpine areas. creator: Yu Feng creator: Juan Wang creator: Qin Zhou creator: Maoyang Bai creator: Peihao Peng creator: Dan Zhao creator: Zengyan Guan creator: Xian’an Liu uri: https://doi.org/10.7717/peerj.13358 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Feng et al. title: Predicting crown width using nonlinear mixed-effects models accounting for competition in multi-species secondary forests link: https://peerj.com/articles/13105 last-modified: 2022-04-27 description: Crown width (CW) is an important tree variable and is often used as a covariate predictor in forest growth models. The precise measurement and prediction of CW is therefore critical for forest management. In this study, we introduced tree species as a random effect to develop nonlinear mixed-effects CW models for individual trees in multi-species secondary forests, accounting for the effects of competition. We identified a simple power function for the basic CW model. In addition to diameter at breast height (DBH), other significant predictor variables including height to crown base (HCB), tree height (TH), and competition indices (CI) were selected for the mixed-effects CW model. The sum of relative DBH (SRD) was identified the optimal distance-independent CI and as a covariate predictor for spatially non-explicit CW models, whereas the sum of the Hegyi index for fixed number competitors (SHGN) was the optimal distance-dependent CI for spatially explicit CW models, with significant linear correlation (R2 = 0.943, P < 0.001). Both spatially non-explicit and spatially explicit mixed-effects CW models were developed for studied secondary forests. We found that these models can describe more than 50% of the variation in CW without significant residual trends. Spatially explicit models exhibited a significantly larger effect on CW than spatially non-explicit ones; however, spatially explicit models are computationally complex and difficult and can be replaced by corresponding spatially non-explicit models due to the small differences in the fit statistics. The models we present may be useful for forestry inventory practices and have the potential to aid the evaluation and management of secondary forests in the region. creator: Rui Hou creator: Zongzheng Chai uri: https://doi.org/10.7717/peerj.13105 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hou and Chai title: Skeletal variation in bird domestication: limb proportions and sternum in chicken, with comparisons to mallard ducks and Muscovy ducks link: https://peerj.com/articles/13229 last-modified: 2022-04-27 description: BackgroundDomestication, including selective breeding, can lead to morphological changes of biomechanical relevance. In birds, limb proportions and sternum characteristics are of great importance and have been studied in the past for their relation with flight, terrestrial locomotion and animal welfare. In this work we studied the effects of domestication and breed formation in limb proportions and sternum characteristics in chicken (Gallus gallus), mallard ducks (Anas plathyrhynchos) and Muscovy ducks (Cairina moschata).MethodsFirst, we quantified the proportional length of three long bones of the forelimb (humerus, radius, and carpometacarpus) and the hind limb (femur, tibiotarsus, and tarsometatarsus) in domestic chickens, mallard ducks, and Muscovy ducks and their wild counterparts. For this, we took linear measurements of these bones and compared their proportions in the wild vs. the domestic group in each species. In chicken, these comparisons could also be conducted among different breeds. We then evaluated the proportional differences in the context of static and ontogenetic allometry. Further, we compared discrete sternum characteristics in red jungle fowl and chicken breeds. In total, we examined limb bones of 287 specimens and keel bones of 63 specimens.ResultsWe found a lack of significant change in the proportions of limb bones of chicken and Muscovy duck due to domestication, but significant differences in the case of mallard ducks. Variation of evolvability, allometric scaling, and heterochrony may serve to describe some of the patterns of change we report. Flight capacity loss in mallard ducks resulting from domestication may have a relation with the difference in limb proportions. The lack of variation in proportions that could distinguish domestic from wild forms of chicken and Muscovy ducks may reflect no selection for flight capacity during the domestication process in these groups. In chicken, some of the differences identified in the traits discussed are breed-dependent. The study of the sternum revealed that the condition of crooked keel was not unique to domestic chicken, that some sternal characteristics were more frequent in certain chicken breeds than in others, and that overall there were no keel characteristics that are unique for certain chicken breeds. Despite some similar morphological changes identified across species, this study highlights the lack of universal patterns in domestication and breed formation. creator: Carlos Manuel Herrera-Castillo creator: Madeleine Geiger creator: Daniel Núñez-León creator: Hiroshi Nagashima creator: Sabine Gebhardt-Henrich creator: Michael Toscano creator: Marcelo R. Sanchez-Villagra uri: https://doi.org/10.7717/peerj.13229 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Herrera-Castillo et al. title: Lipids associated with plant-bacteria interaction identified using a metabolomics approach in an Arabidopsis thaliana model link: https://peerj.com/articles/13293 last-modified: 2022-04-27 description: BackgroundSystemic acquired resistance (SAR) protects plants against a wide variety of pathogens. In recent decades, numerous studies have focused on the induction of SAR, but its molecular mechanisms remain largely unknown.MethodsWe used a metabolomics approach based on ultra-high-performance liquid chromatographic (UPLC) and mass spectrometric (MS) techniques to identify SAR-related lipid metabolites in an Arabidopsis thaliana model. Multiple statistical analyses were used to identify the differentially regulated metabolites.ResultsNumerous lipids were implicated as potential factors in both plant basal resistance and SAR; these include species of phosphatidic acid (PA), monogalactosyldiacylglycerol (MGDG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), and triacylglycerol (TG).ConclusionsOur findings indicate that lipids accumulated in both local and systemic leaves, while other lipids only accumulated in local leaves or in systemic leaves. PA (16:0_18:2), PE (34:5) and PE (16:0_18:2) had higher levels in both local leaves inoculated with Psm ES4326 or Psm avrRpm1 and systemic leaves of the plants locally infected with Psm avrRpm1 or Psm ES4326. PC (32:5) had high levels in leaves inoculated with Psm ES4326. Other differentially regulated metabolites, including PA (18:2_18:2), PA (16:0_18:3), PA (18:3_18:2), PE (16:0_18:3), PE (16:1_16:1), PE (34:4) and TGs showed higher levels in systemic leaves of the plants locally infected with Psm avrRpm1 or Psm ES4326. These findings will help direct future studies on the molecular mechanisms of SAR. creator: Jian-Bo Song creator: Rui-Ke Huang creator: Miao-Jie Guo creator: Qian Zhou creator: Rui Guo creator: Shu-Yuan Zhang creator: Jing-Wen Yao creator: Ya-Ni Bai creator: Xuan Huang uri: https://doi.org/10.7717/peerj.13293 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Song et al. title: Winter diet of Burrowing Owls in the Llano La Soledad, Galeana, Nuevo León, México link: https://peerj.com/articles/13324 last-modified: 2022-04-27 description: The dietary niche breadth of the Burrowing Owl was determined (Athene cunicularia Molina, 1782) in Llano La Soledad, Galeana, Nuevo Leon in northern Mexico, by considering prey type, numerical percentage, weight, weight percentage, frequency of occurrence percentage, and IRI percentage. The study compared data from three winters (2002–2003, 2003–2004, 2004–2005) by analyzing 358 pellets, identifying 850 prey items. Invertebrates constituted 90% of prey items, which mostly included insects (85%); beetles were the most common insects found in pellets (70%). Vertebrates made up 84% of consumed weight, of which 83% were mammals. Most of the mammals were cricetid rodents (41%). Niche breadth based on the numerical and weight percentage confirmed the Burrowing Owl as a generalist species with mean values per year ranging between 0.65 and 0.82. Additionally, there was a strong association between the weight of rodent species in winter. This association was mainly driven by changes in composition and frequency of these prey species during the second winter, probably caused by high annual rainfall. The second season also showed a statistically significant narrower niche (Ro = 0.96) and the smallest overlap (0.45 vs. 0.76) among the three winters. creator: Jose I. Gonzalez Rojas creator: Miguel Angel Cruz Nieto creator: Antonio Guzmán Velasco creator: Irene Ruvalcaba-Ortega creator: Alina Olalla-Kerstupp creator: Gabriel Ruiz-Ayma uri: https://doi.org/10.7717/peerj.13324 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gonzalez Rojas et al. title: Polyphenolic extract from Punica granatum peel causes cytoskeleton-related damage on Giardia lamblia trophozoites in vitro link: https://peerj.com/articles/13350 last-modified: 2022-04-27 description: BackgroundDiarrheal diseases caused by protozoa have a great impact on human health around the world. Giardia lamblia is one of the most common flagellates in the intestinal tract. Factors such as adverse effects to first-line drugs or the appearance of drug-resistant strains, make it necessary to identify new treatment alternatives. Agroindustry waste, like pomegranate peel, are a source of phenolic compounds, which possess antiparasitic activities. In vivo studies demonstrated antigiardiasic potential by reducing cyst shedding and protecting intestinal cells; however, they did not identify the compounds or elucidate any mechanism of action in the parasite. The objective of this study is to identify potential molecular targets and to test the in vitro effects of polyphenols from Punica granatum on Giardia lamblia.MethodsThe in vitro antigiardial potential of polyphenolic extract from pomegranate peel (Punica granatum L.) obtained using microwave-ultrasound methodology was evaluated on Giardia lamblia trophozoites. Extract phytochemical identification was performed by HPLC/MS analysis. The effect of polyphenolic extract on growth and adhesion capacity was determined by parasite kinetics; morphological damage was evaluated by SEM, alteration on α-tubulin expression and distribution were analyzed by western blot and immunofluorescence, respectively.ResultsThe pomegranate peel extract showed the presence of ellagitannins (punicalin and punicalagin, galloyl-dihexahydroxydiphenoyl-hexoside), flavones (luteolin), and ellagic acid, that caused an inhibitory effect on growth and adhesion capacity, particularly on cells treated with 200 µg/mL, where growth inhibition of 74.36%, trophozoite adherence inhibition of 46.8% and IC50 of 179 µg/mL at 48 h were demonstrated. The most important findings were that the extract alters α-tubulin expression and distribution in Giardia trophozoites in a concentration-independent manner. Also, an increase in α-tubulin expression at 200 µg/mL was observed in western blot and diffuse or incomplete immunolabeling pattern, especially in ventral disk. In addition, the extract caused elongation, disturbance of normal shape, irregularities in the membrane, and flagella abnormalities.DiscussionThe pomegranate peel extract affects Giardia trophozoites in vitro. The damage is related to the cytoskeleton, due to expression and distribution alterations in α-tubulin, particularly in the ventral disk, a primordial structure for adhesion and pathogenesis. Microtubule impairment could explain morphological changes, and inhibition of adhesion capacity and growth. Besides, this is the first report that suggests that ellagic acid, punicalin, punicalagin and luteolin could be interactioning with the rich-tubulin cytoskeleton of Giardia. Further investigations are needed in order to elucidate the mechanisms of action of the isolated compounds and propose a potential drug alternative for the giardiasis treatment. creator: Lissethe Palomo-Ligas creator: Job Estrada-Camacho creator: Mariana Garza-Ontiveros creator: José Roberto Vargas-Villanueva creator: Filiberto Gutiérrez-Gutiérrez creator: Sendar Daniel Nery-Flores creator: Jorge Arturo Cañas Montoya creator: Juan Ascacio-Valdés creator: Lizeth Guadalupe Campos-Muzquiz creator: Raul Rodriguez-Herrera uri: https://doi.org/10.7717/peerj.13350 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Palomo-Ligas et al. title: Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules link: https://peerj.com/articles/13354 last-modified: 2022-04-27 description: The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it. creator: Stepan Nersisyan creator: Anton Zhiyanov creator: Maria Zakharova creator: Irina Ishina creator: Inna Kurbatskaia creator: Azad Mamedov creator: Alexei Galatenko creator: Maxim Shkurnikov creator: Alexander Gabibov creator: Alexander Tonevitsky uri: https://doi.org/10.7717/peerj.13354 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Nersisyan et al. title: Dynamics of human take and animal predation on sea turtle nests in Northwest Costa Rica link: https://peerj.com/articles/12925 last-modified: 2022-04-26 description: Many conservation projects relocate sea turtle eggs to hatcheries to protect the sea turtle nests from the anthropogenic and natural threats they face in the early stages of development. The Rescue Center for Endangered Marine Species (CREMA) manages four sea turtle conservation projects on the nesting beaches of the Southern Nicoya Peninsula in Costa Rica, where the predominant nesting activity is from olive ridley turtles (Lepidochelys olivacea). Two of these nesting projects are based in Costa de Oro and San Miguel, which are adjacent beaches divided by an estuary. In this study, we compared the dynamics and rates of human and animal predation of nests prior to being relocated to the hatchery on both nesting beaches from 2012 to 2018. We hypothesized that human take and animal predation were compensatory threats, meaning that lower human take may result in higher animal predation, and vice versa, resulting in a similar number of nests lost to predation overall. We discuss the community-based conservation programs on both beaches, one of which has been monitored since 1998 (San Miguel) and the other of which has been monitored since 2012 (Costa de Oro). We found that Costa de Oro exhibited high rates of human take with up to 51% of nests being extracted per season, which has decreased since the conservation project was established. Human take was significantly higher than animal predation on both beaches and human take was significantly higher in Costa de Oro. While San Miguel exhibited higher animal predation, the difference was not statistically significant. Higher depredation by animals corresponded to higher overall nest abundance on both beaches. We were unable to find evidence that human take or animal predation increased in the absence of the other threat, suggesting a lack of compensatory effects of predation. Our findings support further analysis of animal predation and a continuation of patrol-based conservation efforts as well as community outreach to attempt to merge cultural values with sea turtle conservation. creator: Janie L. Reavis creator: Daniela Rojas-Cañizales creator: Carmen Mejías-Balsalobre creator: Isabel Naranjo creator: Randall Arauz creator: Jesse F. Senko uri: https://doi.org/10.7717/peerj.12925 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Reavis et al. title: Exosomes and ferroptosis: roles in tumour regulation and new cancer therapies link: https://peerj.com/articles/13238 last-modified: 2022-04-26 description: Research on the biological role of exosomes is rapidly developing, and recent evidence suggests that exosomal effects involve ferroptosis. Exosomes derived from different tissues inhibit ferroptosis, which increases tumour cell chemoresistance. Therefore, exosome-mediated regulation of ferroptosis may be leveraged to design anticancer drugs. This review discusses three pathways of exosome-mediated inhibition of ferroptosis: (1) the Fenton reaction; (2) the ferroptosis defence system, including the Xc-GSH-GPX4 axis and the FSP1/CoQ10/NAD(P)H axis; and (3) lipid peroxidation. We also summarize three recent approaches for combining exosomes and ferroptosis in oncology therapy: (1) promoting exosome-inhibited ferroptosis to enhance chemotherapy; (2) encapsulating exosomes with ferroptosis inducers to inhibit cancers; and (3) developing therapies that combine exosomal inhibitors and ferroptosis inducers. This review will contribute toward establishing effective cancer therapies. creator: Yixin Shi creator: Bingrun Qiu creator: Linyang Huang creator: Jie Lin creator: Yiling Li creator: Yiting Ze creator: Chenglong Huang creator: Yang Yao uri: https://doi.org/10.7717/peerj.13238 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Shi et al. title: Need for split: integrative taxonomy reveals unnoticed diversity in the subaquatic species of Pseudohygrohypnum (Pylaisiaceae, Bryophyta) link: https://peerj.com/articles/13260 last-modified: 2022-04-26 description: We present an integrative molecular and morphological study of subaquatic representatives of the genus Pseudohygrohypnum (Pylaisiaceae, Bryophyta), supplemented by distribution modelling of the revealed phylogenetic lineages. Phylogenetic analyses of nuclear and plastid datasets combined with the assemble species by automatic partitioning (ASAP) algorithm revealed eight distinct species within the traditionally circumscribed P. eugyrium and P. subeugyrium. These species are therefore yet another example of seemingly widely distributed taxa that harbour molecularly well-differentiated lineages with narrower distribution ranges. Studied accessions that were previously assigned to P. eugyrium form three clearly allopatric lineages, associated with temperate regions of Europe, eastern North America and eastern Asia. Remarkably, accessions falling under the current morphological concept of P. subeugyrium were shown to be even more diverse, containing five phylogenetic lineages. Three of these lineages occur under harsh Asian continental climates from cool-temperate to Arctic regions, while the remaining two, referred to P. subeugyrium s.str. and P. purpurascens, have more oceanic North Atlantic and East Asian distributions. Niche identity and similarity tests suggested no similarity in the distributions of the phylogenetically related lineages but revealed the identity of two East Asian species and the similarity of two pairs of unrelated species. A morphological survey confirmed the distinctness of all eight phylogenetic lineages, requiring the description of five new species. Pseudohygrohypnum appalachianum and P. orientale are described for North American and East Asian plants of P. eugyrium s.l., while P. sibiricum, P. subarcticum and P. neglectum are described for the three continental, predominantly Asian lineages of P. subeugyrium s.l. Our results highlight the importance of nontropical Asia as a center of bryophyte diversity. Phylogenic dating suggests that the diversification of subaquatic Pseudohygrohypnum lineages appeared in late Miocene, while mesophilous species of the genus split before Miocene cooling, in climatic conditions close to those where the ancestor of Pseudohygrohypnum appeared. We speculate that radiation of the P. subeugyrium complex in temperate Asia might have been driven by progressive cooling, aridification, and increases in seasonality, temperature and humidity gradients. Our results parallel those of several integrative taxonomic studies of North Asian mosses, which have resulted in a number of newly revealed species. These include various endemics from continental areas of Asia suggesting that the so-called Rapoport’s rule of low diversity and wide distribution range in subpolar regions might not be applicable to bryophytes. Rather, the strong climatic oscillations in these regions may have served as a driving force of speciation and niche divergence. creator: Vladimir E. Fedosov creator: Anna V. Shkurko creator: Alina V. Fedorova creator: Elena A. Ignatova creator: Evgeniya N. Solovyeva creator: John C. Brinda creator: Michael S. Ignatov creator: Jan Kučera uri: https://doi.org/10.7717/peerj.13260 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fedosov et al. title: Taxonomic revision of the Pheidole megacephala species-group (Hymenoptera, Formicidae) from the Malagasy Region link: https://peerj.com/articles/13263 last-modified: 2022-04-26 description: BackgroundThe Malagasy Region, one of the top megadiversity regions, hosts one of the highest numbers of endemic and threatened organisms on earth. One of the most spectacular examples of ant radiation on the island has occurred in the hyperdiverse genus Pheidole. To this date, there are 135 described Madagascan Pheidole divided into 16 species-groups, and 97% of Malagasy species are endemic to the island. This study is a taxonomic revision of the Pheidole megacephala group, one of only two species-groups comprising a combination of native, endemic taxa and widely distributed introduced species.MethodsThe diversity of the Malagasy members of the megacephala group was assessed via application of qualitative morphological and DNA sequence data. Qualitative, external morphological characteristics (e.g., head shape, gaster sculpture, body colouration) were evaluated in order to create a priori grouping hypotheses, and confirm and improve species delimitation. Mitochondrial DNA sequences from cytochrome oxidase I (COI) gene fragments were analyzed to test the putative species previously delimited by morphological analyses.ResultsWe recognize three species belonging to the megacephala group: P. megacephala (Fabricius, 1793), P. megatronFischer & Fisher, 2013 and P. spinosaForel, 1891stat. nov.Pheidole spinosa is redescribed and elevated to the species level. The following names are recognized as junior synonyms of P. spinosa: P. megacephala scabriorForel, 1891syn. nov., P. picataForel, 1891syn. nov., P. picata gietleniForel, 1905syn. nov., P. picata bernhardaeEmery, 1915syn. nov., and P. decepticonFischer & Fisher, 2013syn. nov. The results are supplemented with an identification key to species for major workers of the megacephala group, high-resolution images for major and minor workers, and comments on the distribution and biology of all Malagasy members of the group. Our study revealed that Pheidole megacephala, a species listed among the 100 worst invasive species worldwide, occurs in both natural and disturbed sites in the Malagasy region. The two remaining members of the megacephala group, most likely endemic to this region, are also present in anthropogenic habitats and often co-occur with P. megacephala. It appears that the Malagasy members of the group are generalists and dominant in anthropogenic habitats. Additionally, we documented the presence of supermajors in colonies of P. spinosa—a phenomenon previously not known for this group. creator: Sebastian Salata creator: Brian L. Fisher uri: https://doi.org/10.7717/peerj.13263 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Salata and Fisher title: Radar remote sensing-based inversion model of soil salt content at different depths under vegetation link: https://peerj.com/articles/13306 last-modified: 2022-04-26 description: Excessive soil salt content (SSC) seriously affects the crop growth and economic benefits in the agricultural production area. Prior research mainly focused on estimating the salinity in the top bare soil rather than in deep soil that is vital to crop growth. For this end, an experiment was carried out in the Hetao Irrigation District, Inner Mongolia, China. In the experiment, the SSC at different depths under vegetation was measured, and the Sentinel-1 radar images were obtained synchronously. The radar backscattering coefficients (VV and VH) were combined to construct multiple indices, whose sensitivity was then analyzed using the best subset selection (BSS). Meanwhile, four most commonly used algorithms, partial least squares regression (PLSR), quantile regression (QR), support vector machine (SVM), and extreme learning machine (ELM), were utilized to construct estimation models of salinity at the depths of 0–10, 10–20, 0–20, 20–40, 0–40, 40–60 and 0–60 cm before and after BSS, respectively. The results showed: (a) radar remote sensing can be used to estimate the salinity in the root zone of vegetation (0-30 cm); (b) after BSS, the correlation coefficients and estimation accuracy of the four monitoring models were all improved significantly; (c) the estimation accuracy of the four regression models was: SVM > QR > ELM > PLSR; and (d) among the seven sampling depths, 10–20 cm was the optimal inversion depth for all the four models, followed by 20–40 and 0–40 cm. Among the four models, SVM was higher in accuracy than the other three at 10–20 cm (RP2 = 0.67, RMSEP = 0.12%). These findings can provide valuable guidance for soil salinity monitoring and agricultural production in the arid or semi-arid areas under vegetation. creator: Yinwen Chen creator: Yuyan Du creator: Haoyuan Yin creator: Huiyun Wang creator: Haiying Chen creator: Xianwen Li creator: Zhitao Zhang creator: Junying Chen uri: https://doi.org/10.7717/peerj.13306 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Analysis of professional soccer players in competitive match play based on submaximum intensity periods link: https://peerj.com/articles/13309 last-modified: 2022-04-26 description: The main objective of this study is to analyse sub-maximum intensity periods (SubMIP’s) manifested by professional soccer players during official matches (number of events and time spent in each event), according to the player position, match halve and match, and also to group the players according to their SubMip values during the competition.MethodsWe collected a total of 247 individual records of 14 players using Global Positioning System (GPS) during 15 official league matches (Azerbaijan Premier League 2019–2020). We calculated both the number of SubMIPs events and the time each player spent in the SubMIPs zone (threshold of 85% MIP). We analysed the possible independence of the variables with the Kruskal–Wallis test and the possible specific relationships between the groups using a post-hoc analysis with Dunn’s test. In order to explore the possible distribution of physical demands in homogeneous groups, a cluster analysis was performed.ResultsThe statistical analysis showed significant differences between the individual variables in the number of events and in the time spent by the player above the threshold in distance covered at speed >19.8 km/h (HSR), distance covered at speed >25.2 km/h (Sprint), acceleration density (AccDens), mean metabolic power (MetPow), metres per minute (Mmin) and high metabolic load distance >25.5 W/kg (HMLD). Differences were also found according to the playing position in MetPow, Mmin and between halves in AccDens, MetPow, Mmin. In the clustering based on the time spent by the player in SubMIPs, three main groups were described: (1) the centroid was located in lower values in each of the variables; (2) there were an accentuation of the AccDens variable; (3) all the variables, except AccDens, were accentuated.ConclusionsThe main differences with regard to SubMIPs were related to the player’s individual physical performance and not to position. However, the player’s position could act as an attractor and show significant differences during matches. creator: Eduardo Caro creator: Miguel Ángel Campos-Vázquez creator: Manuel Lapuente-Sagarra creator: Toni Caparrós uri: https://doi.org/10.7717/peerj.13309 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Caro et al. title: Integrated bioinformatics analysis for the identification of hub genes and signaling pathways related to circANRIL link: https://peerj.com/articles/13135 last-modified: 2022-04-25 description: BackgroundAntisense noncoding RNA in the INK4 locus (ANRIL) is located on human chromosome 9p21, and modulation of ANRIL expression mediates susceptibility to some important human disease, including atherosclerosis (AS) and tumors, by affecting the cell cycle circANRIL and linear ANRIL are isoforms of ANRIL. However, it remains unclear whether these isoforms have distinct functions. In our research, we constructed a circANRIL overexpression plasmid, transfected it into HEK-293T cell line, and explored potential core genes and signaling pathways related to the important differential mechanisms between the circANRIL-overexpressing cell line and control cells through bioinformatics analysis.MethodsStable circANRIL-overexpressing (circANRIL-OE) HEK-293T cells and control cells were generated by infection with the circANRIL-OE lentiviral vector or a negative control vector, and successful transfection was confirmed by conventional flurescence microscopy and quantitative real-time PCR (qRT-PCR). Next, differentially expressed genes (DEGs) between circANRIL-OE cells and control cells were detected. Subsequently, Gene Ontology (GO) biological process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to explore the principal functions of the significant DEGs. A protein–protein interaction (PPI) network and competing endogenous RNA (ceRNA) network were constructed in Cytoscape to determine circularRNA (circRNA)- microRNA(miRNA)-messenger RNA (mRNA) interactions and hub genes, and qRT-PCR was used to verify changes in the expression of these identified target genes.ResultsThe successful construction of circANRIL-OE cells was confirmed by plasmid sequencing, visualization with fluorescence microscopy and qRT-PCR. A total of 1745 DEGs between the circANRIL-OE group and control were identified, GO BP analysis showed that these genes were mostly related to RNA biosynthesis and processing, regulation of transcription and signal transduction. The KEGG pathway analysis showed that the up regulated DEGs were mainly enriched in the MAPK signaling pathway. Five associated target genes were identified in the ceRNA network and biological function analyses. The mRNA levels of these five genes and ANRIL were detected by qRT-PCR, but only COL5A2 and WDR3 showed significantly different expression in circANRIL-OE cells. creator: Qiuyan Qin creator: Pengfei Zheng creator: Ronghui Tu creator: Jiegang Huang creator: Xiaoli Cao uri: https://doi.org/10.7717/peerj.13135 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Qin et al. title: Effect of steady-state aerobic exercise intensity and duration on the relationship between reserves of heart rate and oxygen uptake link: https://peerj.com/articles/13190 last-modified: 2022-04-25 description: BackgroundThe percentages of heart rate (%HRR) or oxygen uptake (%V̇O2R) reserve are used interchangeably for prescribing aerobic exercise intensity due to their assumed 1:1 relationship, although its validity is debated. This study aimed to assess if %HRR and %V̇O2R show a 1:1 relationship during steady-state exercise (SSE) and if exercise intensity and duration affect their relationship.MethodsEight physically active males (age 22.6 ± 1.2 years) were enrolled. Pre-exercise and maximal HR and V̇O2 were assessed on the first day. In the following 4 days, different SSEs were performed (running) combining the following randomly assigned durations and intensities: 15 min, 45 min, 60% HRR, 80% HRR. Post-exercise maximal HR and V̇O2 were assessed after each SSE. Using pre-exercise and post-exercise maximal values, the average HR and V̇O2 of the last 5 min of each SSE were converted into percentages of the reserves (%RES), which were computed in a 3-way RM-ANOVA (α = 0.05) to assess if they were affected by the prescription parameter (HRR or V̇O2R), exercise intensity (60% or 80% HRR), and duration (15 or 45 min).ResultsThe %RES values were not affected by the prescription parameter (p = 0.056) or its interactions with intensity (p = 0.319) or duration and intensity (p = 0.117), while parameter and duration interaction was significant (p = 0.009). %HRRs and %V̇O2Rs did not differ in the 15-min SSEs (mean difference [MD] = 0.7 percentage points, p = 0.717), whereas %HRR was higher than %V̇O2R in the 45-min SSEs (MD = 6.7 percentage points, p = 0.009).ConclusionSSE duration affects the %HRR-%V̇O2R relationship, with %HRRs higher than %V̇O2Rs in SSEs of longer duration. creator: Carlo Ferri Marini creator: Ario Federici creator: James S. Skinner creator: Giovanni Piccoli creator: Vilberto Stocchi creator: Luca Zoffoli creator: Luca Correale creator: Stefano Dell’Anna creator: Carlo Alberto Naldini creator: Matteo Vandoni creator: Francesco Lucertini uri: https://doi.org/10.7717/peerj.13190 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ferri Marini et al. title: Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods link: https://peerj.com/articles/13205 last-modified: 2022-04-25 description: The tremendous boost in next generation sequencing and in the “omics” technologies makes it possible to characterize the human gut microbiome—the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn’s disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the gut microbiome in IBD patients is far from being complete. Due to the complexity of metagenomic studies, the applications of the state-of-the-art machine learning techniques became popular to address a wide range of questions in the field of metagenomic data analysis. In this regard, using IBD associated metagenomics dataset, this study utilizes both supervised and unsupervised machine learning algorithms, (i) to generate a classification model that aids IBD diagnosis, (ii) to discover IBD-associated biomarkers, (iii) to discover subgroups of IBD patients using k-means and hierarchical clustering approaches. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy max relevance (mRMR), Select K Best (SKB), Information Gain (IG) and Extreme Gradient Boosting (XGBoost). In our experiments with 100-fold Monte Carlo cross-validation (MCCV), XGBoost, IG, and SKB methods showed a considerable effect in terms of minimizing the microbiota used for the diagnosis of IBD and thus reducing the cost and time. We observed that compared to Decision Tree, Support Vector Machine, Logitboost, Adaboost, and stacking ensemble classifiers, our Random Forest classifier resulted in better performance measures for the classification of IBD. Our findings revealed potential microbiome-mediated mechanisms of IBD and these findings might be useful for the development of microbiome-based diagnostics. creator: Burcu Bakir-Gungor creator: Hilal Hacılar creator: Amhar Jabeer creator: Ozkan Ufuk Nalbantoglu creator: Oya Aran creator: Malik Yousef uri: https://doi.org/10.7717/peerj.13205 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bakir-Gungor et al. title: A DNA barcode survey of insect biodiversity in Pakistan link: https://peerj.com/articles/13267 last-modified: 2022-04-25 description: Although Pakistan has rich biodiversity, many groups are poorly known, particularly insects. To address this gap, we employed DNA barcoding to survey its insect diversity. Specimens obtained through diverse collecting methods at 1,858 sites across Pakistan from 2010–2019 were examined for sequence variation in the 658 bp barcode region of the cytochrome c oxidase 1 (COI) gene. Sequences from nearly 49,000 specimens were assigned to 6,590 Barcode Index Numbers (BINs), a proxy for species, and most (88%) also possessed a representative image on the Barcode of Life Data System (BOLD). By coupling morphological inspections with barcode matches on BOLD, every BIN was assigned to an order (19) and most (99.8%) were placed to a family (362). However, just 40% of the BINs were assigned to a genus (1,375) and 21% to a species (1,364). Five orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) accounted for 92% of the specimens and BINs. More than half of the BINs (59%) are so far only known from Pakistan, but others have also been reported from Bangladesh (13%), India (12%), and China (8%). Representing the first DNA barcode survey of the insect fauna in any South Asian country, this study provides the foundation for a complete inventory of the insect fauna in Pakistan while also contributing to the global DNA barcode reference library. creator: Muhammad Ashfaq creator: Arif M. Khan creator: Akhtar Rasool creator: Saleem Akhtar creator: Naila Nazir creator: Nazeer Ahmed creator: Farkhanda Manzoor creator: Jayme Sones creator: Kate Perez creator: Ghulam Sarwar creator: Azhar A. Khan creator: Muhammad Akhter creator: Shafqat Saeed creator: Riffat Sultana creator: Hafiz Muhammad Tahir creator: Muhammad A. Rafi creator: Romana Iftikhar creator: Muhammad Tayyib Naseem creator: Mariyam Masood creator: Muhammad Tufail creator: Santosh Kumar creator: Sabila Afzal creator: Jaclyn McKeown creator: Ahmed Ali Samejo creator: Imran Khaliq creator: Michelle L. D’Souza creator: Shahid Mansoor creator: Paul D. N. Hebert uri: https://doi.org/10.7717/peerj.13267 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ashfaq et al. title: Spatial variability of microzooplankton grazing on phytoplankton in coastal southern Florida, USA link: https://peerj.com/articles/13291 last-modified: 2022-04-25 description: Microzooplankton are considered the primary consumers of phytoplankton in marine environments. Microzooplankton grazing rates on phytoplankton have been studied across the globe, but there are still large regions of the ocean that are understudied, such as sub-tropical coastal oceans. One of these regions is the coastal area around south Florida, USA. We measured microzooplankton grazing rates in two distinct environments around south Florida; the oligotrophic Florida Keys and the mesotrophic outflow from the Everglades. For 2-years from January 2018 to January 2020, we set up 55 dilution and light-dark bottle experiments at five stations to estimate the microzooplankton community grazing rate, instantaneous phytoplankton growth rate, and primary production. Our results suggest that microzooplankton are consuming a higher proportion of the primary production near the Everglades outflow compared to the Florida Keys. We also found that changes in phytoplankton growth rates are disconnected from changes in the microzooplankton grazing rates in the Florida Keys. Overall, the data from the Everglades outflow is what would be expected based on global patterns, but factors other than microzooplankton grazing are more important in controlling phytoplankton biomass in the Florida Keys. creator: Nicole Millette creator: Christopher Kelble creator: Ian Smith creator: Kelly Montenero creator: Elizabeth Harvey uri: https://doi.org/10.7717/peerj.13291 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Millette et al. title: Association between laryngopharyngeal reflux and obstructive sleep apnea in adults link: https://peerj.com/articles/13303 last-modified: 2022-04-25 description: BackgroundObstructive sleep apnea syndrome (OSAS) and laryngopharyngeal reflux (LPR) have been found to coexist in the population. OSAS and LPR also share obesity as an important risk factor. However, the relationship between LPR and OSAS remains unclear. This study aimed to correlate LPR as measured by the Reflux Symptom Index (RSI) and the Reflux Finding Score (RFS) with OSAS.MethodsThis cross-sectional study included sixty-four subjects who underwent anamnesis to complete the RSI and the Epworth Sleeping Scale (ESS). The subjects were then divided into the OSAS and non-OSAS groups based on the Apnea-Hypopnea Index (AHI) obtained through a polysomnography examination. Both groups underwent a flexible fiberoptic nasopharyngolaryngoscopy examination to determine the RFS. LPR was identified based on the RSI and RFS.ResultsThe mean BMI of the OSAS group significantly was higher than the non-OSAS group (p < 0.05). Most of the subjects in the OSAS group exhibited mild-moderate OSAS (AHI 10–29), and severe OSAS occurred in only seven subjects. The mean RSI and RFS values in the OSAS group did not differ significantly from the non-OSAS group (p = 0.34 and p = 0.36, respectively). The proportion of LPR between the mild-moderate OSAS group, the severe OSAS group, and the non-OSAS group did not differ significantly (p = 1.00). RSI and RFS did not significantly correlate with AHI. Based on RSI, the proportion of LPR between the ESS (+) and ESS (-) groups did not significantly differ (adjusted p = 0.062). The proportion of LPR based on RFS was almost equal between the ESS (+) and ESS (-) groups (p = 0.817).ConclusionsThe BMI of the OSAS group was significantly higher than the non-OSAS group. There was no significant difference in RSI and RFS between the OSAS and non-OSAS groups. There was no significant correlation between RSI and AHI, or between RFS and AHI. There was no significant difference in the proportion of RSI between the ESS (+) and the ESS (-) groups. creator: Susyana Tamin creator: Dumasari Siregar creator: Syahrial Marsinta Hutauruk creator: Ratna Dwi Restuti creator: Elvie Zulka Kautzia Rachmawati creator: Saptawati Bardosono uri: https://doi.org/10.7717/peerj.13303 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Tamin et al. title: Do patterns of insect mortality in temperate and tropical zones have broader implications for insect ecology and pest management? link: https://peerj.com/articles/13340 last-modified: 2022-04-25 description: BackgroundUnderstanding how biotic and abiotic factors affect insect mortality is crucial for both fundamental knowledge of population ecology and for successful pest management. However, because these factors are difficult to quantify and interpret, patterns and dynamics of insect mortality remain unclear, especially comparative mortality across climate zones. Life table analysis provides robust information for quantifying population mortality and population parameters.MethodsIn this study, we estimated cause-of-death probabilities and irreplaceable mortality (the portion of mortality that cannot be replaced by another cause or combination of causes) using a Multiple Decrement Life Table (MDLT) analysis of 268 insect life tables from 107 peer-reviewed journal articles. In particular, we analyzed insect mortality between temperate and tropical climate zones.ResultsSurprisingly, our results suggest that non-natural enemy factors (abiotic) were the major source of insect mortality in both temperate and tropical zones. In addition, we observed that irreplaceable mortality from predators in tropical zones was 3.7-fold greater than in temperate zones. In contrast, irreplaceable mortality from parasitoids and pathogens was low and not different between temperate and tropical zones. Surprisingly, we did not observe differences in natural enemy and non-natural enemy factors based on whether the insect species was native or non-native. We suggest that characterizing predation should be a high priority in tropical conditions. Furthermore, because mortality from parasitoids was low in both tropical and temperate zones, this mortality needs to be better understood, especially as it relates to biological control and integrated pest management. creator: José R. L. Pinto creator: Odair A. Fernandes creator: Leon G. Higley creator: Robert K. D. Peterson uri: https://doi.org/10.7717/peerj.13340 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pinto et al. title: Effects of cigarette smoking on metabolic activity of lung cancer on baseline 18F-FDG PET/CT link: https://peerj.com/articles/13352 last-modified: 2022-04-25 description: BackgroundNever-smokers with lung cancer usually have a higher survival rate than that of smokers. The high metabolic activity of lung cancer on 18F-2-Fluoro-2-deoxyglucose (18F-FDG) PET/CT generally indicates a poor outcome. However, there is a lack of reports on the association between cigarette smoking and 18F-FDG metabolic activity in patients with lung cancer. In this study, we aimed to investigate the effects of cigarette smoking on metabolic activity of lung cancer on 18F-FDG PET/CT.Materials and MethodsA total of 338 patients (230 males, 108 females; mean age: 66.3, range 34–86) with pathologically diagnosed lung cancer were enrolled from September 2019 to April 2021. All patients underwent baseline 18F-FDG PET/CT and the maximum standard uptake value (SUVmax) of the primary tumor (pSUVmax), lymph node (nSUVmax) and distant metastasis (mSUVmax) were measured. The associations between cigarette smoking status, clinical stage, pathological subtypes and metabolic parameters on 18F-FDG PET/CT were analyzed.ResultsOf the 338 patients, cigarette smoking was identified in 153 patients (45.3%) and the remaining 185 (54.7%) were never-smokers. Smoking was found more frequently in males, squamous cell carcinoma (SCC) and stage III–IV diseases. The pSUVmax in smokers was significantly higher than that in never-smokers (t = 3.386, P < 0.001), but the nSUVmax and mSUVmax revealed no statistically significant differences (t = 0.399, P = 0.690 and t = 0.057, P = 0.955; respectively). With the increase of cumulative smoking dose, pSUVmax increased significantly (r = 0.217, P < 0.001). In addition, the pSUVmax in patients with stage III–IV was significantly higher than that in stage I–II (t = 8.509, P < 0.001). Smokers showed a higher pSUVmax than never-smokers for patients with stage I–II (t = 3.106, P = 0.002), but not in stage III–IV (t = 0.493, P = 0.622). The pSUVmax was significantly different among patients with different pathological subtypes of lung cancer (F = 11.45, P < 0.001), while only the adenocarcinoma (ADC) and SCC groups showed a difference in pSUVmax (t = 6.667, P < 0.001). Smokers with ADC showed a higher pSUVmax when compared to never-smokers, but not in SCC. There were no significant differences of pSUVmax between smokers and never-smokers at stage I–II ADC or SCC and stage III–IV ADC or SCC.ConclusionsThis study demonstrated a close association between cigarette smoking and the metabolic activity of lung cancer and suggests that smoking may be a potential risk factor of higher pSUVmax in early lung cancer on 18F-FDG PET/CT. creator: Maoqing Jiang creator: Xiuyu Guo creator: Xiaohui Zhang creator: Qiaoling Gao creator: Weiqi Mei creator: Jingfeng Zhang creator: Jianjun Zheng uri: https://doi.org/10.7717/peerj.13352 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jiang et al. title: Excito-repellency of Myristica fragrans Houtt. and Curcuma longa L. extracts from Southern Thailand against Aedes aegypti (L.) link: https://peerj.com/articles/13357 last-modified: 2022-04-25 description: The development of local plant extracts as a mosquito repellent is environmentally safe, inexpensive, and easily accessible for residents. In this study, three extracts from two local plants, Myristica fragrans Houtt. (flesh and mace) and Curcuma longa L. (rhizome) from southern Thailand, were investigated for their inherent repellent activity using the excito-repellency (ER) assay system against insectary-colonized Aedes aegypti (L.) (Diptera: Culicidae). The escape responses of mosquitoes exposed to concentrations of 0.5% to 5.0% (w/v) were measured to determine the contact irritant and non-contact repellent properties of each extract. Both the flesh and mace extracts of M. fragrans had relatively limited contact irritants (28.1% and 34.6% escape) and non-contact repellent (16.7% and 18.3% escape) activities against Ae. aegypti, respectively. The C. longa rhizome extract produced higher escape responses in the non-contact (42.6% escape) and contact (41.4% escape) trials at concentrations of 5.0% and 1.0%, respectively. GC-MS analysis found diethyl malate (56.5%) and elemicin (11.7%) to be the main components of the flesh and mace extracts, respectively, while ar-turmerone (24.6%), β-turmerone (15.2%), α-turmerone (10.5%) were the primary constituents of the rhizome extract. Overall, our results indicate that both M. fragrans extracts primarily caused Ae. aegypti escape through contact irritation. For C. longa, lower concentrations (0.5% and 1.0%) exhibited contact irritancy, but higher concentrations (2.5% and 5.0%) exhibited non-contact repellency against Ae. aegypti. Although they had limited efficacy, further experiments (e.g., mixing with other plant-based compounds) could enhance the ER of both local plant extracts. Additional evaluation of these extracts against other mosquito species and the ER of their chemical components, either alone or in combination, would also be beneficial for the development of green repellents. Our findings emphasize the possibility of utilizing plant-based mosquito repellent as an alternative personal protection method for future mosquito control programs. creator: Phuangthip Bhoopong creator: Theeraphap Chareonviriyaphap creator: Chutipong Sukkanon uri: https://doi.org/10.7717/peerj.13357 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bhoopong et al. title: RFPDR: a random forest approach for plant disease resistance protein prediction link: https://peerj.com/articles/11683 last-modified: 2022-04-22 description: BackgroundPlant innate immunity relies on a broad repertoire of receptor proteins that can detect pathogens and trigger an effective defense response. Bioinformatic tools based on conserved domain and sequence similarity are within the most popular strategies for protein identification and characterization. However, the multi-domain nature, high sequence diversity and complex evolutionary history of disease resistance (DR) proteins make their prediction a real challenge. Here we present RFPDR, which pioneers the application of Random Forest (RF) for Plant DR protein prediction.MethodsA recently published collection of experimentally validated DR proteins was used as a positive dataset, while 10x10 nested datasets, ranging from 400-4,000 non-DR proteins, were used as negative datasets. A total of 9,631 features were extracted from each protein sequence, and included in a full dimension (FD) RFPDR model. Sequence selection was performed, to generate a reduced-dimension (RD) RFPDR model. Model performances were evaluated using an 80/20 (training/testing) partition, with 10-cross fold validation, and compared to baseline, sequence-based and state-of-the-art strategies. To gain some insights into the underlying biology, the most discriminatory sequence-based features in the RF classifier were identified.Results and DiscussionRD-RFPDR showed to be sensitive (86.4 ± 4.0%) and specific (96.9 ± 1.5%) for identifying DR proteins, while robust to data imbalance. Its high performance and robustness, added to the fact that RD-RFPDR provides valuable information related to DR proteins underlying properties, make RD-RFPDR an interesting approach for DR protein prediction, complementing the state-of-the-art strategies. creator: Diego Simón creator: Omar Borsani creator: Carla Valeria Filippi uri: https://doi.org/10.7717/peerj.11683 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Simón et al. title: Species limits and recent diversification of Cerradomys (Sigmodontinae: Oryzomyini) during the Pleistocene link: https://peerj.com/articles/13011 last-modified: 2022-04-22 description: Cerradomys is a genus of the tribe Oryzomyini with eight species currently recognized, and a controversial taxonomy. These species are mainly distributed in the South America dry diagonal, but some species extend into Atlantic Forest, reaching the coastal sandy plains known as Restingas. This study aimed to address species limits and patterns of diversification of Cerradomys species. For this purpose, we performed cytogenetic and molecular analyses (phylogeny, coalescent species delimitation, barcoding, and divergence times estimation) using multiple mitochondrial and nuclear markers on a comprehensive sampling, representing all nominal taxa reported so far. Chromosomal information was a robust marker recognizing eight Cerradomys species. Reciprocal monophyly was recovered for all the species, except for C. subflavus. These results together with coalescent analyses recovered eight species as the most congruent species delimitation scenario for the genus (mean Ctax: 0.72). Divergence time estimates revealed that Cerradomys’ diversification occurred about 1.32 million years ago (Mya) during the Pleistocene. Although our results conservatively support the eight Cerradomys species described so far, different lines of evidence suggest that C. langguthi and C. subflavus could potentially be species-complexes. We discussed this scenario in the light of multiple evolutionary processes within and between species and populations, since Cerradomys comprises a species group with recent diversification affected by Pleistocene climatic changes and by the complex biogeographic history of South America dry diagonal. This work supports that the diversity of Cerradomys is underestimated and reiterates that interdisciplinary approaches are mandatory to identify small rodent species properly, and to unhide cryptic species. creator: Camilla B. Di-Nizo creator: Elkin Y. Suárez-Villota creator: Maria José J. Silva uri: https://doi.org/10.7717/peerj.13011 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Di-Nizo et al. title: Species identification of introduced veronicellid slugs in Japan link: https://peerj.com/articles/13197 last-modified: 2022-04-22 description: Reliable identification of species is important for protecting native ecosystems against the invasion of non-native species. DNA barcoding using molecular markers, such as the mitochondrial cytochrome oxidase subunit 1 (COI) gene, helps researchers distinguish species. In this study, we focused on introduced veronicellid slugs in the Ryukyu Islands and some greenhouses on mainland Japan. Some veronicellids are medium-to-high risk pest species for humans. Identifying veronicellid species by their external morphology is difficult and unreliable because there is substantial overlap between intraspecific variation and interspecific differentiation. Therefore, internal morphologies such as male genitalia have been the primary traits used to distinguish veronicellids. To identify introduced veronicellid slugs in Japan to the species level, we used morphological assessment of male genitalia and DNA barcoding of the standard COI gene fragment. We also conducted species-delimitation analyses based on the genetic data. The results showed that five evolutionarily significant units, corresponding to four nominal species inhabit the Ryukyu Islands, of which two species were also found in the greenhouses of mainland Japan, including the first record of Sarasinula plebeia in Japan. The presence of non-native slug species could increase the transmission of parasites in Japan. creator: Takahiro Hirano creator: Osamu Kagawa creator: Masanori Fujimoto creator: Takumi Saito creator: Shota Uchida creator: Daishi Yamazaki creator: Shun Ito creator: Shovon Mohammad Shariar creator: Takuo Sawahata creator: Satoshi Chiba uri: https://doi.org/10.7717/peerj.13197 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hirano et al. title: Zonula occludens-1 expression is reduced in nasal epithelial cells of allergic rhinitis patients link: https://peerj.com/articles/13314 last-modified: 2022-04-22 description: Allergic rhinitis (AR) is a common allergic disease characterized by disruption of nasal epithelial barrier. In this study, we investigated the mRNA expression of zonula occludens-1 (ZO-1), ZO-2 and ZO-3 and histone deacetylase 1 (HDAC1) and HDAC2 in AR patients compared to healthy controls. RNA samples were extracted from nasal epithelial cells of house dust mites (HDMs)-sensitized AR patients and healthy controls (n = 28 in each group). The RNAs were reverse transcribed into cDNAs for measurement of ZO-1, ZO-2, ZO-3, HDAC1 and HDAC2 expression levels by quantitative PCR. The mRNA expression of ZO-1 was significantly decreased in AR patients compared to healthy controls (p = 0.010). No significant difference was observed in the expression levels of ZO-2, ZO-3, HDAC1 and HDAC2 in AR patients compared to healthy controls. We found significant associations of higher HDAC2 levels in AR patients with lower frequency of changing bedsheet (p = 0.043) and with AR patients sensitized to Dermatophagoides farinae (p = 0.041). Higher expression of ZO-2 was observed in AR patients who had pets (p = 0.007). In conclusion, our data indicated that ZO-1 expression was lower in AR patients contributing to decreased integrity of nasal epithelial barrier integrity, and HDAC2 may be involved in the pathogenesis of the disease. creator: Che Othman Siti Sarah creator: Siti Muhamad Nur Husna creator: Norasnieda Md. Shukri creator: Kah Keng Wong creator: Noor Suryani Mohd Ashari uri: https://doi.org/10.7717/peerj.13314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Siti Sarah et al. title: Biological control potential of entomopathogenic fungal strains against peach Fruit fly, Bactrocera zonata (Saunders) (Diptera: Tephritidae) link: https://peerj.com/articles/13316 last-modified: 2022-04-22 description: The peachfruit fly, Bactrocera zonata (Saunders) is a polyphagous pest in nature, belonging to order, Diptera and their respective family is Tephritidae. It mostly feeds on different crops, vegetables and fruits. Different traditional chemical insecticides have been used to control this notorious pest. Excessive consumption of pesticides has become a major threat to the fresh fruits trade since many importing countries refused to accept the shipments due to public health and environmental concerns. There is a growing trend to control these pests using the most effective biological control methods and other preventive measures have been adopted for reducing their attacks. Fungal agents have been used as biological agents to manage the attack of different insects pest through biological means. The present study was conducted to assess the virulence of three entomopathogenic fungi, Metarhizium anisopliae, Beauveria bassiana and Verticillium lecanii, against Bactrocera zonata stages under different laboratory conditions. The results showed that B. bassiana and M. anisopliae were more effective in pathogenicity and potentially kill at all stages of B. zonata as compared to V. lecanii. The highest mortality rate for the third larval instar and the pupal stage were recorded after exposure to the 1 × 1010 conidia/ml concentrations, B. bassiana, with 68.67% and 89.67%, respectively. Adult B. zonata flies were the most susceptible to all entomopathogenic fungi. However, M. anisopliae was more virulent against B. zonata adult flies than B. bassiana and V. lecanii at 1 × 1010 conidial concentration. Therefore, the entomopathogenic fungi B. bassiana and M. anisopliae can be used as an cost effective bio-insecticide in the integrated pest management programs to control B. zonata. This study will be helpful to overcome this pest through biological control means. creator: Ghulam Murtaza creator: Muhammad Naeem creator: Saba Manzoor creator: Hammad Ahmad Khan creator: Emad M. Eed creator: Waqar Majeed creator: Hussain Ahmed Makki creator: Uzma Ramzan creator: Umm E. Ummara uri: https://doi.org/10.7717/peerj.13316 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Murtaza et al. title: Prevalence and incidence of sarcopenia and low physical activity among community-dwelling older Thai people: a preliminary prospective cohort study 2-year follow-up link: https://peerj.com/articles/13320 last-modified: 2022-04-22 description: BackgroundSarcopenia, defined as a loss of muscle mass, has become a major health problem in older people. Few prospective studies report the incidence and risk of sarcopenia. Therefore, this study aimed to explore the prevalence of sarcopenia at the baseline and follow-up after 2 years in community-dwelling older Thai individuals.MethodsIn 2019, 330 older people were recruited from a community-dwelling population, and these participants were requested to present again in 2021. Sarcopenia was diagnosed using the criteria for the Asia Working Group for Sarcopenia (AWGS). All participants were asked to perform a 6-meter walk test, handgrip strength test, and bioelectric impedance assessment, and complete the Global Physical Activity Questionnaire.ResultsThe study found that the prevalence of sarcopenia was 65 (19.70%) in 330 older people in 2019, and 44 of 205 participants (21.46%) were reported to have sarcopenia after 2 years. The incidence of sarcopenia was noted to be 2.44% in 2021. Analysis with ANOVA and pairwise comparisons showed that the reversibility of sarcopenia was attributed to high level of physical activity in the 2-year follow-up group (p = 0.014, 95% CI [−1753.25–−195.49]). Further, participants with moderate and high physical activity had a reduced incidence of sarcopenia (odds ratio = 9.00 and 14.47, respectively). Therefore, low physical activity in older people led to the development of sarcopenia from the baseline to the 2-year follow-up, indicating that increased physical activity may be useful in reversing sarcopenia, as suggested in the 2-year follow-up study. Low physical activity could be a risk factor for the incidence of sarcopenia. Hence, the prevention of sarcopenia could promote health improvement through moderate to high physical activity. creator: Kornanong Yuenyongchaiwat creator: Chareeporn Akekawatchai uri: https://doi.org/10.7717/peerj.13320 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yuenyongchaiwat et al. title: An earliest Triassic age for Tasmaniolimulus and comments on synchrotron tomography of Gondwanan horseshoe crabs link: https://peerj.com/articles/13326 last-modified: 2022-04-22 description: Constraining the timing of morphological innovations within xiphosurid evolution is central for understanding when and how such a long-lived group exploited vacant ecological niches over the majority of the Phanerozoic. To expand the knowledge on the evolution of select xiphosurid forms, we reconsider the four Australian taxa: Austrolimulus fletcheri, Dubbolimulus peetae, Tasmaniolimulus patersoni, and Victalimulus mcqueeni. In revisiting these taxa, we determine that, contrary to previous suggestion, T. patersoni arose after the Permian and the origin of over-developed genal spine structures within Austrolimulidae is exclusive to the Triassic. To increase the availability of morphological data pertaining to these unique forms, we also examined the holotypes of the four xiphosurids using synchrotron radiation X-ray tomography (SRXT). Such non-destructive, in situ imaging of palaeontological specimens can aid in the identification of novel morphological data by obviating the need for potentially extensive preparation of fossils from the surrounding rock matrix. This is particularly important for rare and/or delicate holotypes. Here, SRXT was used to emphasize A. fletcheri and T. patersoni cardiac lobe morphologies and illustrate aspects of the V. mcqueeni thoracetronic doublure, appendage impressions, and moveable spine notches. Unfortunately, the strongly compacted D. peetae precluded the identification of any internal structures, but appendage impressions were observed. The application of computational fluid dynamics to high-resolution 3D reconstructions are proposed to understand the hydrodynamic properties of divergent genal spine morphologies of austrolimulid xiphosurids. creator: Russell D.C. Bicknell creator: Patrick M. Smith creator: Sienna A Birch creator: Joseph J. Bevitt uri: https://doi.org/10.7717/peerj.13326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bicknell et al. title: The effects of music on cardiorespiratory endurance and muscular fitness in recreationally active individuals: a narrative review link: https://peerj.com/articles/13332 last-modified: 2022-04-22 description: Music is made up of several features (e.g., melody and rhythm) and it accompanies our life in different daily activities. During the last years, there was a growing interest in research about the music-related effects in the exercise domain. Music stimuli could act as an ergogenic effect leading to improvements in health-related and physical fitness components like cardiorespiratory endurance and muscular fitness. Moreover, listening to music may positively affect individuals’ psychological state which could lead to increased exercise adherence. Conflicting data exist regarding the effects of music on cardiorespiratory and muscle-strengthening exercises indicating that music’s characteristics (i.e., rhythm and musicality), studied samples (i.e., athletes and amateur) and methodology (i.e., self-selected music and research-selected music) might influence the results. Listening to music while exercising is becoming more frequent also in recreationally active individuals. While literature mainly focused on the effects of music in elite and amateur athletes, little data are available regarding recreationally active participants. Therefore, this review aims to summarize evidence regarding the effects of music on health-related physical fitness components in recreationally active individuals, specifically referring to cardiorespiratory endurance and muscular fitness. These outcomes will be helpful to all recreationally active participants to optimize the exercise protocol with the use of music. creator: Francesca Greco creator: Elisa Grazioli creator: Loretta Francesca Cosco creator: Attilio Parisi creator: Maurizio Bertollo creator: Gian Pietro Emerenziani uri: https://doi.org/10.7717/peerj.13332 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Greco et al. title: lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p link: https://peerj.com/articles/13355 last-modified: 2022-04-22 description: BackgroundBone mesenchymal stem cells (BMSCs) have good osteogenic differentiation potential and have become ideal seed cells in bone tissue engineering. However, the osteogenic differentiation ability of BMSCs gradually weakens with age, and the regulatory mechanism is unclear.MethodWe conducted a bioinformatics analysis, dual-luciferase reporter (DLR) experiment, and RNA binding protein immunoprecipitation (RIP) to explore the hub genes that may affect BMSC functions.ResultsThe expression level of long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (Malat1) was significantly higher in the BMSCs from elderly than younger mice, while miR-129-5p showed the opposite trend. The results of alkaline phosphatase staining, quantitative reverse transcription PCR and western blot experiments indicated that inhibiting the expression of Malat1 inhibits the osteogenic differentiation of BMSCs. This effect can be reversed by reducing the expression of miR-129-5p. Additionally, DLR and RIP experiments confirmed that Malat1 acts as a sponge for miR-129-5p.ConclusionOverall, our study findings indicated that lncRNA Malat1 may play a critical role in maintaining the osteoblast differentiation potential of BMSCs by sponging miR-129-5p. creator: Junhao Yin creator: Zhanglong Zheng creator: Xiaoli Zeng creator: Yijie Zhao creator: Zexin Ai creator: Miao Yu creator: Yang’ou Wu creator: Jirui Jiang creator: Jia Li creator: Shengjiao Li uri: https://doi.org/10.7717/peerj.13355 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yin et al. title: Foliar nutrient concentrations of six northern hardwood species responded to nitrogen and phosphorus fertilization but did not predict tree growth link: https://peerj.com/articles/13193 last-modified: 2022-04-21 description: Foliar chemistry can be useful for diagnosing soil nutrient availability and plant nutrient limitation. In northern hardwood forests, foliar responses to nitrogen (N) addition have been more often studied than phosphorus (P) addition, and the interactive effects of N and P addition have rarely been described. In the White Mountains of central New Hampshire, plots in ten forest stands of three age classes across three sites were treated annually beginning in 2011 with 30 kg N ha−1 y−1 or 10 kg P ha−1 y−1 or both or neither–a full factorial design. Green leaves of American beech (Fagus grandifolia Ehrh.), pin cherry (Prunus pensylvanica L.f.), red maple (Acer rubrum L.), sugar maple (A. saccharum Marsh.), white birch (Betula papyrifera Marsh.), and yellow birch (B. alleghaniensis Britton) were sampled pre-treatment and 4–6 years post-treatment in two young stands (last cut between 1988–1990), four mid-aged stands (last cut between 1971–1985) and four mature stands (last cut between 1883–1910). In a factorial analysis of species, stand age class, and nutrient addition, foliar N was 12% higher with N addition (p < 0.001) and foliar P was 45% higher with P addition (p < 0.001). Notably, P addition reduced foliar N concentration by 3% (p = 0.05), and N addition reduced foliar P concentration by 7% (p = 0.002). When both nutrients were added together, foliar P was lower than predicted by the main effects of N and P additions (p = 0.08 for N × P interaction), presumably because addition of N allowed greater use of P for growth. Foliar nutrients did not differ consistently with stand age class (p ≥ 0.11), but tree species differed (p ≤ 0.01), with the pioneer species pin cherry having the highest foliar nutrient concentrations and the greatest responses to nutrient addition. Foliar calcium (Ca) and magnesium (Mg) concentrations, on average, were 10% (p < 0.001) and 5% lower (p = 0.01), respectively, with N addition, but were not affected by P addition (p = 0.35 for Ca and p = 0.93 for Mg). Additions of N and P did not affect foliar potassium (K) concentrations (p = 0.58 for N addition and p = 0.88 for P addition). Pre-treatment foliar N:P ratios were high enough to suggest P limitation, but trees receiving N (p = 0.01), not P (p = 0.64), had higher radial growth rates from 2011 to 2015. The growth response of trees to N or P addition was not explained by pre-treatment foliar N, P, N:P, Ca, Mg, or K. creator: Daniel S. Hong creator: Kara E. Gonzales creator: Timothy J. Fahey creator: Ruth D. Yanai uri: https://doi.org/10.7717/peerj.13193 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hong et al. title: Nickel mine soil is a potential source for soybean plant growth promoting and heavy metal tolerant rhizobia link: https://peerj.com/articles/13215 last-modified: 2022-04-21 description: Mine soil is not only barren but also contaminated by some heavy metals. It is unclear whether some rhizobia survived under extreme conditions in the nickel mine soil. Therefore, this study tries to isolate some effective soybean plant growth promoting and heavy metal resistant rhizobia from nickel mine soil, and to analyze their diversity. Soybean plants were used to trap rhizobia from the nickel mine soil. A total of 21 isolates were preliminarily identified as rhizobia, which were clustered into eight groups at 87% similarity level using BOXA1R-PCR fingerprinting technique. Four out of the eight representative isolates formed nodules on soybean roots with effectively symbiotic nitrogen-fixing and plant growth promoting abilities in the soybean pot experiment. Phylogenetic analysis of 16S rRNA, four housekeeping genes (atpD-recA-glnII-rpoB) and nifH genes assigned the symbiotic isolates YN5, YN8 and YN10 into Ensifer xinjiangense and YN11 into Rhizobium radiobacter, respectively. They also showed different tolerance levels to the heavy metals including cadmium, chromium, copper, nickel, and zinc. It was concluded that there were some plant growth promoting and heavy metal resistant rhizobia with the potential to facilitate phytoremediation and alleviate the effects of heavy metals on soybean cultivation in nickel mine soil, indicating a novel evidence for further exploring more functional microbes from the nickel mine soil. creator: Han Liu creator: Yongliang Cui creator: Jie Zhou creator: Petri Penttinen creator: Jiahao Liu creator: Lan Zeng creator: Qiang Chen creator: Yunfu Gu creator: Likou Zou creator: Ke Zhao creator: Quanju Xiang creator: Xiumei Yu uri: https://doi.org/10.7717/peerj.13215 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Strategic decision making and prediction differences in autism link: https://peerj.com/articles/13328 last-modified: 2022-04-21 description: BackgroundSeveral theories in autism posit that common aspects of the autism phenotype may be manifestations of an underlying differentiation in predictive abilities. The present study investigates this hypothesis in the context of strategic decision making in autistic participants compared to a control group.MethodAutistic individuals (43 adults, 35 male) and a comparison group (42 adults, 35 male) of age and gender matched individuals, played a modified version of the prisoner’s dilemma (PD) task where they were asked, if capable, to predict their opponents’ move. The predictive performance of the two groups was assessed.ResultsOverall, participants in the autism group had a significantly lower number of correct predictions. Moreover, autistic participants stated, significantly more frequently than the comparison group, that they were unable to make a prediction. When attempting a prediction however, the success ratio did not differ between the two groups.ConclusionsThese findings indicate that there is a difference in prediction performance between the two groups. Although our task design does not allow us to identify whether this difference is due to difficulty to form a prediction or a reluctance in registering one, these findings could justify a role for prediction in strategic decision making during the PD task. creator: Vasileios Mantas creator: Artemios Pehlivanidis creator: Katerina Papanikolaou creator: Vasileia Kotoula creator: Charalambos Papageorgiou uri: https://doi.org/10.7717/peerj.13328 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mantas et al. title: Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis link: https://peerj.com/articles/13336 last-modified: 2022-04-21 description: In the area of climate change, nanotechnology provides handy tools for improving crop production and assuring sustainability in global agricultural system. Due to excellent physiological and biochemical properties, silver nanoparticles (AgNPs) have been widely studied for potential use in agriculture. However, there are concerns about the mechanism of the toxic effects of the accumulation of AgNPs on crop growth and development. In this study, the impacts of AgNPs on cotton (Gossypium hirsutum) seedlings were evaluated by integrating physiological and comprehensive metabolomic analyses. Potting-soil-grown, two-week-old cotton seedlings were foliar-exposed to 5 mg/plant AgNP or 0.02 mg/plant Ag+ (equivalent to the free Ag+ released from AgNPs). Primary metabolites and volatile organic compounds (VOCs) were identified by gas chromatography–mass spectrometry (GC-MS) and solid-phase microextraction (SPME) GC-MS, respectively. AgNPs inhibited the photosynthetic capacity of the cotton leaves. The metabolic spectrum analysis identified and quantified 73 primary metabolites and 45 VOCs in cotton leaves. Both treatments significantly changed the metabolite profiles of plant leaves. Among the primary metabolites, AgNPs induced marked changes in amino acids, sugars and sugar alcohols. Among the VOCs, 13 volatiles, mainly aldehydes, alkanes and terpenoids, were specifically altered only in response to AgNPs. In summary, our study showed that the comprehensive influence of AgNPs on primary metabolites and VOCs was not merely attributed to the released Ag+ but was caused by AgNP-specific effects on cotton leaves. These results provide important knowledge about the physiological and chemical changes in cotton leaves upon exposure to AgNPs and offer a new insight for supporting the sustainable use of AgNPs in agriculture. creator: Yong Yang creator: PengMeng Du creator: Wenjie Lai creator: Liyan Yin creator: Yuanhao Ding creator: Zhonghua Li creator: Haiyan Hu uri: https://doi.org/10.7717/peerj.13336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera) link: https://peerj.com/articles/13213 last-modified: 2022-04-20 description: BackgroundThe hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy.MethodsA morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies.ResultsSequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally. creator: Dora Hlebec creator: Ignac Sivec creator: Martina Podnar creator: Mladen Kučinić uri: https://doi.org/10.7717/peerj.13213 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hlebec et al. title: Changes in serum amino acid levels in non-small cell lung cancer: a case-control study in Chinese population link: https://peerj.com/articles/13272 last-modified: 2022-04-20 description: BackgroundPrevious studies have shown the alteration of amino acid (AA) profile in patients with non-small cell lung cancer (NSCLC). However, there is little data regarding AA profile in NSCLC in Chinese population. The aim of this study was to evaluate AA profile in Chinese NSCLC patients, explore its utility in sample classification and further discuss its related metabolic pathways.MethodsThe concentrations of 22 AAs in serum samples from 200 patients with NSCLC and 202 healthy controls were determined by liquid chromatography-tandem mass spectrometer (LC-MS/MS). AA levels in different tumor stages and histological types were also discussed. The performance of AA panel in classifying the cases and controls was evaluated in the training data set and validation data set based on the receiver operating characteristic (ROC) curve, and the important metabolic pathways were identified.ResultsThe concentrations of tryptophan (Trp), phenylalanine (Phe), isoleucine (Ile), glycine (Gly), serine (Ser), aspartic acid (Asp), asparagine (Asn), cystein (Cys), glutamic acid (Glu), ornithine (Orn) and citrulline (Cit) were significantly altered in NSCLC patients compared with controls (all P-FDR < 0.05). Among these, four AAs including Asp, Cys, Glu and Orn were substantially up-regulated in NSCLC patients (FC ≥ 1.2). AA levels were significantly altered in patients with late-stage NSCLC, but not in those with early-stage when comparing with healthy controls. In terms of histological type, these AAs were altered in both adenocarcinoma and squamous cell carcinoma. For discrimination of NSCLC from controls, the area under the ROC curve (AUC) was 0.80 (95% CI [0.74–0.85]) in the training data set and 0.79 (95%CI [0.71–0.87]) in the validation data set. The AUCs for early-stage and late-stage NSCLC were 0.75 (95% CI [0.68–0.81]) and 0.86 (95% CI [0.82–0.91]), respectively. Moreover, the model showed a better performance in the classification of squamous cell carcinoma (AUC = 0.90, 95% CI [0.85–0.95]) than adenocarcinoma (AUC = 0.77, 95% CI [0.71–0.82]) from controls. Three important metabolic pathways were involved in the alteration of AA profile, including Gly, Ser and Thr metabolism; Ala, Asp and Glu metabolism; and Arg biosynthesis.ConclusionsThe levels of several AAs in serum were altered in Chinese NSCLC patients. These altered AAs may be utilized to classify the cases from the controls. Gly, Ser and Thr metabolism; Ala, Asp and Glu metabolism and Arg biosynthesis pathways may play roles in metabolism of the NSCLC patient. creator: Ke Liu creator: Jiaoyuan Li creator: Tingting Long creator: Yi Wang creator: Tongxin Yin creator: Jieyi Long creator: Ying Shen creator: Liming Cheng uri: https://doi.org/10.7717/peerj.13272 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Population biological traits of Periophthalmus chrysospilos Bleeker, 1853 in the Vietnamese Mekong Delta link: https://peerj.com/articles/13289 last-modified: 2022-04-20 description: Periophthalmus chrysospilos is an amphibious fish living in mudflats from eastern India to Indonesia, including the Vietnamese Mekong Delta. Population biological traits play an important role in fishery assessment, but understanding is limited for this species. In total 1,031 specimens were caught in two regions covering four provinces, including the TVST (Duyen Hai, Tra Vinh and Tran De, Soc Trang) and BLCM (Dong Hai, Bac Lieu and Dam Doi, Ca Mau). Results found that the sex ratio was close to 1:1. The parameters of the von Bertalanffy in TVST were L∞ = 12.8 cm, K = 0.41 yr−1, t0 = −0.10 yr and in BLCM were 12.7 cm, 0.38 yr−1 and −0.08 yr, respectively. Although the growth coefficient (Φ′) in BLCM (1.79), was lower than that in TVST (1.83), the species shared a similar size at first capture (7.9 cm in TVST and 7.9 cm in BLCM). The species suffered from heavy pressure of fishing in TVST as fishing mortality in TVST (2.32 yr−1) was higher than that in BLCM (1.38 yr−1), leading to the higher total mortality (Z = 3.60 yr−1) in TVST compared to BLCM (Z = 2.59 yr−1). By contrast, the species showed similar natural mortality over both sites (1.20 yr−1 in TVST and 1.22 yr−1 in BLCM). The Periophthalmus chrysospilos population was reasonably exploited because E values (0.64 in TVST and 0.53 in BLCM) were lower than E10 (0.706 in BTTV and 0.705 in STBL). Nonetheless, to avoid the consequences of overfishing, some sustainable fisheries practices should be implemented, such as protecting mangrove forests, restricting fishing during the recruitment period, using appropriate fishing tools and increasing mesh size. creator: Quang Minh Dinh creator: Ton Huu Duc Nguyen creator: Tien Thi Kieu Nguyen creator: Tran Thi Huyen Lam creator: Ngon Trong Truong creator: Dinh Dac Tran uri: https://doi.org/10.7717/peerj.13289 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Dinh et al. title: Change of intestinal microbiota in mice model of bronchopulmonary dysplasia link: https://peerj.com/articles/13295 last-modified: 2022-04-20 description: BackgroundGut microbiota has been proposed to be related to the pathogenesis of pulmonary diseases such as asthma and lung cancer, according to the gut-lung axis. However, little is known about the roles of gut microbiota in the pathogenesis of bronchopulmonary dysplasia (BPD). This study was designed to investigate the changes of gut microbiota in neonatal mice with BPD.MethodsBPD model was induced through exposure to high concentration of oxygen. Hematoxylin and eosin (H&E) staining was utilized to determine the modeling efficiency. Stool samples were collected from the distal colon for the sequencing of V3–V4 regions of 16S rRNA, in order to analyze the gut microbiota diversity.ResultsAlpha diversity indicated that there were no statistical differences in the richness of gut microbiota between BPD model group and control group on day 7, 14 and 21. Beta diversity analysis showed that there were statistical differences in the gut microbiota on day 14 (R = 0.368, p = 0.021). Linear discriminant analysis effect size (LEfSe) showed that there were 22 markers with statistical differences on day 14 (p < 0.05), while those on day 7 and 21 were 3 and 4, respectively. Functional prediction analysis showed that the top three metabolic pathways were signal transduction (PFDR = 0.037), glycan biosynthesis and metabolism (PFDR = 0.032), and metabolism of terpenoids and polyketides (PFDR = 0.049).ConclusionsBPD mice showed disorder of gut microbiota, which may involve specific metabolic pathways in the early stage. With the progression of neonatal maturity, the differences of the gut microbiota between the two groups would gradually disappear. creator: Tianqun Fan creator: Ling Lu creator: Rong Jin creator: Aihua Sui creator: Renzheng Guan creator: Fengjing Cui creator: Zhenghai Qu creator: Dongyun Liu uri: https://doi.org/10.7717/peerj.13295 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fan et al. title: Modification of the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes by availability of emergency cash reserves: findings from a nationally-representative survey in Thailand link: https://peerj.com/articles/13307 last-modified: 2022-04-20 description: BackgroundStudies have suggested that economic distress is associated with behavioral health outcomes, while availability of cash reserves for emergencies is associated with a reduction in economic distress. The objective of this study was to assess the extent that the availability of emergency cash reserves modified the association between experience of economic distress during the COVID-19 pandemic and behavioral health outcomes in the general adult population of Thailand.MethodsWe conducted a nationally-representative phone-based survey in late April 2021. Survey questions included questions on experience of economic distress, and a question on what participants would do to cover a 5,000 Thai Bahts (THB) emergency expense within one week, anxiety and depression screening questions, and questions regarding sleep, exercise, gambling, smoking, and drinking behaviors. We analyzed data using descriptive statistics and multivariate logistic regression analyses with adjustment for complex survey designs, and stratified analyses with assessment of heterogeneity of odds ratios between strata and assessment of additive and multiplicative interactions.ResultsA total of 1,555 individuals from 15 provinces participated in the survey (participation rate = 68.3%). Approximately 19.6% ± 1.0% of the participants reported that they would cover the 5,000 THB emergency expense only with cash or cash equivalent without resorting to other means. Experience of economic distress was associated with anxiety disorder after adjusting for covariables (Adjusted Odds Ratio (OR) = 2.47; 95% CI [1.45–4.19]). There was no evidence that availability of emergency cash reserves significantly modified the stated association, nor the association between experience of economic distress and other outcomes. However, with regard to anxiety disorder, depressive symptoms and history of gambling in past 30 days, the p-for-trend values (p-for-trend < 0.001) suggested that those with emergency cash reserves had lower prevalence of these outcomes than those without emergency cash reserves.ConclusionsThe study findings did not support our hypothesis that availability of emergency cash reserves modified the association between experience of economic distress and behavioral health outcomes. Nonetheless, the study findings can serve as potentially useful basic information for relevant stakeholders. Future studies should consider qualitative data collection and longitudinal study design in order to explore these associations at greater depths. creator: Wit Wichaidit creator: Chayapisika Prommanee creator: Sasira Choocham creator: Rassamee Chotipanvithayakul creator: Sawitri Assanangkornchai uri: https://doi.org/10.7717/peerj.13307 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wichaidit et al. title: Knowledge of acute stroke management and the predictors among Malaysian healthcare professionals link: https://peerj.com/articles/13310 last-modified: 2022-04-20 description: BackgroundDespite rapid advances in acute ischaemic stroke (AIS) management, many healthcare professionals (HCPs) might not be aware of the latest recommended management of AIS patients. Therefore, we aimed to determine the level and factors associated with AIS management knowledge among Malaysian HCPs.MethodsThis cross-sectional online questionnaire study was conducted nationwide among 627 HCPs in Malaysia using the Acute Stroke Management Questionnaire (ASMaQ). Multiple logistic regression was used to predict the relationship between the independent variables (age, gender, years of service, profession, work setting, work sector, seeing stroke patients in daily practice, and working with specialists) and the outcome variable (good vs poor knowledge).ResultsApproximately 76% (95% CI [73–79%]) of HCPs had good overall knowledge of stroke. The highest proportion of HCPs with good knowledge was noted for General Stroke Knowledge (GSK) [88.5% (95% CI [86–91%])], followed by Advanced Stroke Management (ASM) [61.2% (95% CI [57–65%])] and Hyperacute Stroke Management (HSM) [58.1% (95% CI [54–62%])]. The odds of having poor knowledge of stroke were significantly higher among non-doctor HCPs [adjusted OR = 3.46 (95% CI [1.49–8.03]), P = 0.004]; among those not seeing stroke patients in daily practice [adjusted OR = 2.67 (95% CI [1.73–4.10]), P < 0.001]; and among those working without specialists [adjusted OR = 2.41 (95% CI [1.38–4.18]), P = 0.002].ConclusionsStroke education should be prioritised for HCPs with limited experience and guidance. All HCPs need to be up-to-date on the latest AIS management and be able to make a prompt referral to an appropriate facility. Therefore, more stroke patients will benefit from advanced stroke care. creator: Stephenie Ann Albart creator: Abdul Hanif Khan Yusof Khan creator: Aneesa Abdul Rashid creator: Wan Asyraf Wan Zaidi creator: Mohammad Zulkarnain Bidin creator: Irene Looi creator: Fan Kee Hoo uri: https://doi.org/10.7717/peerj.13310 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Albart et al. title: The fecal microbiota of Thai school-aged children associated with demographic factors and diet link: https://peerj.com/articles/13325 last-modified: 2022-04-20 description: BackgroundBirth delivery method and breastfeeding practices contribute to microbiota colonization. Other factors including diet and demographic factors structure the gut microbiome assembly and diversity through childhood development. The exploration of these factors, especially in Southeast Asian children, remains limited.MethodsWe investigated the fecal microbiota of 127 school-aged children in Thailand using quantitative PCR (qPCR) to assess the influence of diet and demographic factors on the gut microbiota. Multivariate analysis (multiple factor analysis (MFA) and Partial Least Squares Discriminant Analysis (PLS-DA)) were used to link particular gut microbes to diet and demographic factors.ResultsDiet and demographic factors were associated with variation among gut microbiota. The abundance of Gammaproteobacteria increased in children with infrequent intake of high fat foods. Obese children possessed a lower level of Firmicutes and Ruminococcus. Bifidobacterium was enriched in pre-teen aged children and detected at lower levels among formula-fed children. Prevotella was more abundant in children who were delivered vaginally. While ethnicity explained a small amount of variation in the gut microbiota, it nonetheless was found to be significantly associated with microbiome composition.ConclusionsExogenous and demographic factors associate with, and possibly drive, the assembly of the gut microbiome of an understudied population of school-aged children in Thailand. creator: Lucsame Gruneck creator: Eleni Gentekaki creator: Kongkiat Kespechara creator: Justin Denny creator: Thomas J. Sharpton creator: Lisa K. Marriott creator: Jackilen Shannon creator: Siam Popluechai uri: https://doi.org/10.7717/peerj.13325 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Gruneck et al. title: Analysis of serum and gene expression profile of cytokines (IL-6, TNF-α and TGF-β1) in chronic hepatitis C virus infection link: https://peerj.com/articles/13330 last-modified: 2022-04-20 description: BackgroundChronic hepatitis C virus (HCV) infection is one of the major causes of liver cirrhosis and liver carcinoma. Studies have indicated that an imbalance of cytokine activities could contribute to the pathogenesis of chronic HCV infection. This study aimed to investigate serum levels and gene expression of cytokines (IL-6, TNF-α and TGF-β1) in chronic HCV infection among Malay male subjects.MethodsThirty-nine subjects were enrolled from various health clinics in Kelantan, Malaysia, and divided into two groups: patients with chronic HCV infection (HP) and healthy control (HS). The serum cytokines IL-6, TNF-a—were measured using Luminex assay, and serum TGF-β1 was measured by ELISA. The mRNA gene expression for IL-6, TNF-α and TGF-β1 was measured by real-time reverse transcriptase polymerase chain reaction (RT-PCR).ResultsThere were statistically significant differences in the mean serum levels of IL-6, and TGF-β1 in HP compared to HS group (p = 0.0180 and p = 0.0005, respectively). There was no significant difference in the mean serum level of TNF-α in HP compared to HS group. The gene expression for the studied cytokines showed no significant differences in HP compared to HS group.ConclusionSerum IL-6 was significantly associated with chronic HCV infection. creator: Ismail Che Noh creator: Richard Avoi creator: Asma Abdullah Nurul creator: Imran Ahmad creator: Ruzilawati Abu Bakar uri: https://doi.org/10.7717/peerj.13330 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Che Noh et al. title: Genetic relatedness and morphology as drivers of interspecific dominance hierarchy in hummingbirds link: https://peerj.com/articles/13331 last-modified: 2022-04-20 description: A dominance hierarchy is the set of ranks occupied by species within an assemblage. Species with a high position within the dominance hierarchy tend to dominate subordinate species in contests for access to resources. In hummingbirds, greater weight and wing disc loading have been associated with highest ranks within the dominance hierarchy. Nevertheless, the limit to which the difference between the weight of contending species represents a competitive advantage has not yet been determined. Here, we determined the dominance hierarchy of a hummingbird assemblage exploiting the most abundant floral resource (Palicourea padifolia, Rubiaceae) in a cloud forest of central Veracruz, Mexico. Specifically, we tested whether species weight and wing disc loading influence the dominance hierarchy. Additionally, we tested whether the flowers visited per foraging bout increases with species weight and dominance. We further tested whether weight, wing disc loading, and the genetic relatedness between contenders influenced the dominance relationships in species-pair interactions. Our results indicate that the hierarchy is positively influenced by weight. Hummingbirds visited similar number of flowers regardless their weight or their dominance. Nevertheless, the probability that the heaviest contender won contests was positively associated with the differences of weight and genetic relatedness between contenders. Contrarily, the probability that the contender with greatest wing disc loading won contests was positively associated with differences of weight and negatively associated with the relatedness between contenders. However, these models only explained between 22% and 34% of the variation, respectively. Our results demonstrate that the weight was the major contributor to high dominance values. However, future studies should include (1) the temporal variability of the weight and (2) experimental predictor variables such the burst power of the hummingbirds to evaluate its effects on the dynamics of dominance hierarchies in hummingbird assemblages. All the hummingbird species present in the studied assemblage have developed wide behavioral mechanisms that compensate their morphological differences, which allow them to coexist, even when they compete for the access to the same resource. creator: Ubaldo Márquez-Luna creator: Carlos Lara creator: Pablo Corcuera creator: Pedro Luis Valverde uri: https://doi.org/10.7717/peerj.13331 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Márquez-Luna et al. title: Serum expression of Vascular Endothelial-Cadherin, CD44, Human High mobility group B1, Kallikrein 6 proteins in different stages of laryngeal intraepithelial lesions and early glottis cancer link: https://peerj.com/articles/13104 last-modified: 2022-04-19 description: BackgroundThe study was designed to evaluate the potential validity and utility of selected molecular markers in serum samples from patients with specific stages of laryngeal intraepithelial lesions that could serve as diagnostic tools in differentiation of benign and dysplastic lesions from invasive pathologies.MethodsProspective study included 80 consecutive patients with vocal fold lesions treated at the single otorhinolaryngology centre. All participants had surgical resection of the lesion. Blood samples were collected from each patient before the surgery. Final diagnosis was confirmed on histopathological examination and included 39 (48.75%) non-dysplastic lesions, eight (10%) low-grade dysplasia, six (7.5%) high-grade dysplasia and 27 (33.75%) invasive cancers. The ELISA procedures were performed according to the manufacturer’s instruction. Individual serum concentration of selected proteins was reported in ng/ml: Vascular Endothelial-Cadherin Complex (VE-cad), CD44, Human High mobility group protein B1(HMGB1), Kallikrein 6.ResultsThe highest mean levels of HMGB1, KLK6 and VE-cad were detected in sera of patients with low-grade dysplasia (81.14, 24.33, 14.17 respectively). Soluble CD44 was the most elevated in patients with non-dysplastic lesions (2.49). The HMGB1, KLK6 and VE-cad serum levels were increasing from non-dysplastic to low-grade dysplasia and followed by the decrease for high-grade dysplasia and invasive cancer, however the differences were not significant (p-values 0.897, 0.354, 0.1 respectively). Patients’ serum had the highest CD44 concentration in non-dysplastic and low-grade dysplasia with the following decrease through high-grade dysplasia and invasive cancer. GERD symptomatic patients had higher levels of KLK6 and CD44 than other patients (p-value 0.06 and 0.084 respectively). There were no significant differences of biomarkers levels related to patients’ gender (p-value from 0.243 to 1) or smoking status (p-value from 0.22 to 0.706).ConclusionsVE-cad, HMGB1, CD44 and KLK6 did not prove to be reliable biomarkers implicating malignant potential within vocal fold hypertrophic intraepithelial lesions. creator: Michał Żurek creator: Anna Rzepakowska creator: Iwona Kotuła creator: Urszula Demkow creator: Kazimierz Niemczyk uri: https://doi.org/10.7717/peerj.13104 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Żurek et al. title: Morphological, functional, and phylogenetic aspects of the head capsule of the cockroach Ergaula capucina (Insecta/Blattodea) link: https://peerj.com/articles/12470 last-modified: 2022-04-19 description: BackgroundCockroaches are usually typical omnivorous detritivores and their cephalic morphology is considered to be ancestral in various aspects. Thus, several studies addressed the morphology and function of the blattodean head, and the cockroach usually serves as a model for standard mouthparts in text books. However, so far only two of the three major lineages of Blattodea have been studied and no detailed information for the head of any Corydioidea was available. The present study closes this gap by providing a detailed morphological description of the head of Ergaula capucina, studying some important functional parameters of the mandible and discussing it in a phylogenetic framework.MethodsThe cephalic morphology of Ergaula studied in detail using a broad set of different techniques including digital microscopy, µ-computed tomography, and 3-dimensional reconstructions. Concerning the functional morphology of the mandible, we compared the volume and effective cross sections of the eight compartments of the primary mandibular adductor muscle for Ergaula, Blattella germanica, and Salganea rossi and measured the mechanical advantage, i.e., the force transmission ratio for all teeth of the mandible of Ergaula.ResultsThe head capsule of Ergaula is characterized by a strong sexual dimorphism and typical orthopteran mouthparts. It resembles the head capsule of other roaches in several respects and confirms oesotendons, the reduction of the mesal occelus, and bipartite M. verticopharyngealis and M. hypopharyngosalivaris as blattodean apomorphies. But it also shows some unique adaptations. It is the first described cockroach that lacks the dorsal tentorial arms which has various consequences for the cephalic musculature. On the maxillary lacinia, Ergaula is the first described blattodean to show strong and blunt setae instead of a lacinula, which might be homologues to the dentisetae of dragonflies and mayflies. Like other corydiid roaches that inhabit xeric areas, Ergaula has an atmospheric water-vapor absorption mechanism that includes a gland and a ductus on the epipharnyx and bladders on the hypopharynx. The mandibular adductor is in cockroaches asymmetric, a pattern not found in termites, mantids, or other closely related insects. creator: Benjamin Wipfler creator: Felix Triesch creator: Dominic Evangelista creator: Tom Weihmann uri: https://doi.org/10.7717/peerj.12470 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wipfler et al. title: The management success of the invasive late goldenrod (Solidago gigantea Aiton.) in a nature conservation area is strongly related to site, control measures and environmental factors link: https://peerj.com/articles/13161 last-modified: 2022-04-19 description: The late goldenrod (Soldiago gigantea Aiton; Asteraceae) is one of the most abundant invasive species in various types of habitats. Its long-creeping plagiotropic rhizomes enable the plant to build up dense, monospecific stands within a short time. Particularly in nature conservation areas, the invasion of goldenrod can cause severe disruptions in the naturally occuring mutualims between plants, insects and higher trophic levels, subsequently impeding the achievement of nature conservation goals. As management options of goldenrod in nature conservation areas are limited, this three-year study aimed to test the effectiveness of three management treatments (two-time mowing, triticale cultivation, and reverse rotary cutting) on four different sites in the Austrian Donau-Auen National Park. The number and height of goldenrod shoots were recorded three times a year on twelve permanent trial plots on each site to test for the effectiveness of the treatments. In addition, vegetation surveys were performed to observe the recovery potential of native plant species. Even though the three-years mowing and the triticale cultivation reduced goldenrod by 95.6% and 97.2% resp., we could find no relation between the effectiveness of the treatment and the intensity of disturbance created by the control option. On the contrary, with a reduction of only 5.4% in goldenrod density the most intensive treatment, the rotary cutting, showed the lowest efficiency. The highest positive effect on the re-establishment of native plant species was recorded with two mowing events per year. Even though the study revealed that certain management options have the potential to effectively reduce goldenrod and to simultaneously increase the establishment success of native species, results can only be seen as so-called snapshots. For example, as shown on site EJW one unforeseeable wild boar digging event transformed a 84.5% reduction into a 4.7% increase in goldenrod density. Therefore, a proper and regular monitoring is essential to be able to react to the effects of unpredictable events that can have severe impact on vegetation dynamics. creator: Rea Maria Hall creator: Bernhard Urban creator: Hans-Peter Kaul uri: https://doi.org/10.7717/peerj.13161 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Hall et al. title: Microplastic ingestion by commercial marine fish from the seawater of Northwest Peninsular Malaysia link: https://peerj.com/articles/13181 last-modified: 2022-04-19 description: Over the past decade, concerns over microplastic pollution in the marine ecosystem has increasingly gained more attention, but research investigating the ingestion of microplastics by marine fish in Malaysia is still regrettably lacking. This study investigated the microplastic presence, abundance, and morphological types within the guts of four species of commercial marine fish (Atule mate, Crenimugil seheli, Sardinella fimbriata and Rastrelliger brachysoma) caught in seawater off the coast of Malaysia’s Northwest Peninsular. A total of 72 individual commercial marine fish guts from four species (fish per species n = 18) were examined. Remarkably, this study found that 100% of the samples contained microplastics. A total number of 432 microplastics (size < 5 mm) from the four species were found in the excised marine fish guts. The most common type of microplastic discovered was fragment, which accounted for 49.5% of all microplastics present. The gut microplastic content differed between species. Sardinella fimbriata recorded the greatest amount of microplastic ingestion, with an average microplastic count of 6.5 (±4.3) items per individual fish. However, there were no statistically significant differences found when comparing study species and different locations. SEM-EDX analysis confirmed the presence of microplastic particles by identifying the chemical elements found in the samples. Since the four studied species of commercial marine fish are popular protein sources in Malaysians’ daily diet, this study suggests potential microplastic exposure to humans via contaminated fish consumption in Malaysia, which was previously unknown. Based on previous scientific evidence, this study also demonstrates the high probability of microplastic ingestion in marine fish in the Malaysian seawater, which could have an adverse effect on fish health as well as marine biota. creator: Yuen Hwei Foo creator: Sharnietha Ratnam creator: Er Vin Lim creator: Masthurah Abdullah creator: Vincent J. Molenaar creator: Aileen Tan Shau Hwai creator: Shoufeng Zhang creator: Hongjun Li creator: Norlaila Binti Mohd Zanuri uri: https://doi.org/10.7717/peerj.13181 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Foo et al. title: Unlocking Andean sigmodontine diversity: five new species of Chilomys (Rodentia: Cricetidae) from the montane forests of Ecuador link: https://peerj.com/articles/13211 last-modified: 2022-04-19 description: The Andean cloud forests of Ecuador are home to several endemic mammals. Members of the Thomasomyini rodents are well represented in the Andes, with Thomasomys being the largest genus (47 species) of the subfamily Sigmodontinae. Within this tribe, however, there are genera that have escaped a taxonomic revision, and Chilomys Thomas, 1897, constitutes a paradigmatic example of these “forgotten” Andean cricetids. Described more than a century ago, current knowledge of this externally unmistakable montane rodent is very limited, and doubts persist as to whether or not it is monotypic. After several years of field efforts in Ecuador, a considerable quantity of specimens of Chilomys were collected from various localities representing both Andean chains. Based on an extensive genetic survey of the obtained material, we can demonstrate that what is currently treated as C. instans in Ecuador is a complex comprising at least five new species which are described in this paper. In addition, based on these noteworthy new evidence, we amend the generic diagnosis in detail, adding several key craniodental traits such as incisor procumbency and microdonty. These results indicate that Chilomys probably has a hidden additional diversity in large parts of the Colombian and Peruvian territories, inviting a necessary revision of the entire genus. creator: Jorge Brito creator: Nicolás Tinoco creator: C. Miguel Pinto creator: Rubí García creator: Claudia Koch creator: Vincent Fernandez creator: Santiago Burneo creator: Ulyses F. J. Pardiñas uri: https://doi.org/10.7717/peerj.13211 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Brito et al. title: Genome-wide identification, molecular characterization, and gene expression analyses of honeysuckle NHX antiporters suggest their involvement in salt stress adaptation link: https://peerj.com/articles/13214 last-modified: 2022-04-19 description: BackgroundIon homeostasis is an essential process for the survival of plants under salt stress. Na+/H+ antiporters (NHXs) are secondary ion transporters that regulate Na+ compartmentalization or efflux reduce Na+ toxicity and play a critical role during plant development and stress responses.Methods and ResultsTo gain insight into the functional divergence of NHX genes in honeysuckle, a total of seven LjNHX genes were identified on the whole genome level and were renamed according to their chromosomal positions. All LjNHXs possessed the Na+/H+ exchanger domain and the amiloride-binding site was presented in all NHX proteins except LjNHX4. The phylogenetic analysis divided the seven NHX genes into Vac-clade (LjNHX1/2/3/4/5/7) and PM-clade (LjNHX6) based on their subcellular localization and validated by the distribution of conserved protein motifs and exon/intron organization analysis. The protein-protein interaction network showed that LjNHX4/5/6/7 shared the same putatively interactive proteins, including SOS2, SOS3, HKT1, and AVP1. Cis-acting elements and gene ontology (GO) analysis suggested that most LjNHXs involve in the response to salt stress through ion transmembrane transport. The expression profile analysis revealed that the expression levels of LjNHX3/7 were remarkably affected by salinity. These results suggested that LjNHXs play significant roles in honeysuckle development and response to salt stresses.ConclusionsThe theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in honeysuckle. creator: Luyao Huang creator: Zhuangzhuang Li creator: Chunyong Sun creator: Shijie Yin creator: Bin Wang creator: Tongyao Duan creator: Yang Liu creator: Jia Li creator: Gaobin Pu uri: https://doi.org/10.7717/peerj.13214 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Huang et al. title: Association of heat shock protein 8 with atopic march in a murine experimental model link: https://peerj.com/articles/13247 last-modified: 2022-04-19 description: BackgroundAtopic march (AM), a unique characteristic of allergic diseases, refers to the sequential progression of atopic dermatitis (AD) in infants to allergic asthma and allergic rhinitis in children and young adults, respectively. Although there are several studies on AM, the establishment of an AM murine model to expand our understanding of the underlying mechanism and to identify the potential biomarkers is yet to be achieved. In this study, an improved murine model was established by applying a method to minimize skin irritation in inducing AD, and it was used to perform integrated analyses to discover candidate biomarkers.MethodsTo induce atopic dermatitis, 2,4-dinitrochlorobenzene (DNCB) was applied to the ear skin once a week, and this was continued for 5 weeks. From the second application of DNCB, Dermatophagoides pteronyssinus (Dp) extract was applied topically 2 days after each DNCB application; this was continued for 4 weeks. Dp sensitization and intranasal challenges were then performed for 4 weeks to develop conditions mimicking AM.ResultsExacerbated airway inflammation and allergic responses observed in the AM-induced group suggested successful AM development in our model. Two-dimensional gel electrophoresis (2-DE) and mass spectrometry analysis identified 753 candidate proteins from 124 2-DE spots differentially expressed among the experimental groups. Functional analyses, such as Gene Ontology (GO) annotation and protein–protein interaction (PPI) analysis were conducted to investigate the relationship among the candidate proteins. Seventy-two GO terms were significant between the two groups; heat shock protein 8 (Hspa8) was found to be included in six of the top 10 GO terms. Hspa8 scored high on the PPI parameters as well.ConclusionWe established an improved murine model for AM and proposed Hspa8 as a candidate biomarker for AM. creator: Kyu-Tae Jeong creator: Ji-Hye Do creator: Sung-Hee Lee creator: Jeom-Kyu Lee creator: Woo-Sung Chang uri: https://doi.org/10.7717/peerj.13247 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2022 Jeong et al. title: Phosphorus flow analysis of different crops in Dongying District, Shandong Province, China, 1995–2016 link: https://peerj.com/articles/13274 last-modified: 2022-04-19 description: Investigating the phosphorus (P) sources, pathways, and final sinks are important to reduce P pollution and improve P management. In this study, substance flow analysis (SFA) was performed for P flow analysis from 1995 to 2016 in different crops of Dongying District, a core region of the alluvial delta at the estuary of the Yellow River. The results showed that P input steadily increased from 1.48 × 104 t in 1995 to 2.16 × 104 t in 2007, and then decreased from 1.90 × 104 t in 2010 to 1.78 × 104 t in 2016. Chemical fertilizers made the highest contribution to P input. The cotton with the highest P load was on the top of P load risk ranks. More importantly, this study applied the Partial Least Squares Path Modeling (PLS-PM) model for P flow analysis and established the numerical relationship between the variables (including fertilizers, straws return-to-field, harvested grains, discarded straw, and P erosion and runoff), P use efficiency (PUE) and P load. The analysis revealed that fertilizer and crop production are the key factors affecting the PUE. Therefore, optimizing the use of P-fertilizer whilst maintaining yields can be an effective strategy to improve the local region PUE. creator: Huan He creator: Lvqing Zhang creator: Hongwei Zang creator: Mingxing Sun creator: Cheng Lv creator: Shuangshuang Li creator: Liyong Bai creator: Wenyuan Han creator: Jiulan Dai uri: https://doi.org/10.7717/peerj.13274 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 He et al. title: Analysis of fungal dynamic changes in the natural fermentation broth of ‘Hongyang’ kiwifruit link: https://peerj.com/articles/13286 last-modified: 2022-04-19 description: ‘Hongyang’ kiwifruit (Actinidia chinensis Planch.) is an ideal kiwifruit wine variety. At present, there is no research on the dynamic changes of yeast during the natural fermentation of kiwifruit wine. In this study, a high-throughput was employed to analyze the fungal population composition and diversity in the samples cultured in yeast extract peptone dextrose (YPD) medium and enriched in the natural fermentation process of ‘Hongyang’ kiwifruit at four time points, day one (D1T), day three (D3T), day five (D5T), and day fifteen (D15T). Five hundred and eighty-two operational taxonomic units (OTUs) were obtained from 131 genera and 178 species samples. The diversity analysis results showed that in the early natural fermentation stage, the dominant species was Aureobasidium pullulans, and as natural fermentation proceeded, the genus Pichia became the dominant species. Pichia kluyveri was an important species at the later stages of natural fermentation. An analysis of the metabolic pathways shows that P. kluyveri plays an aromatic-producing role in the natural fermentation of ‘Hongyang’ kiwifruit. These results could provide a theoretical basis for the studies of kiwifruit fungal diversity and fungal changes during fermentation. The findings could fix a major deficiency in the production of kiwifruit fruit wine, which lacks a specific flavor-producing yeast species or strain. creator: Zhiming Zhang creator: Yuhong Gao creator: Wenjuan Zhao creator: Zhuo Wei creator: Xiaozhen Liu creator: Hanyao Zhang uri: https://doi.org/10.7717/peerj.13286 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Exposure of adult sea urchin Strongylocentrotus intermedius to stranded heavy fuel oil causes developmental toxicity on larval offspring link: https://peerj.com/articles/13298 last-modified: 2022-04-19 description: Heavy fuel oil (HFO) spills pose serious threat to coastlines and sensitive resources. Stranded HFO that occurs along the coastline could cause long-term and massive damage to the marine environment and indirectly affect the survival of parental marine invertebrates. However, our understanding of the complex associations within invertebrates is primarily limited, particularly in terms of the toxicity effects on the offspring when parents are exposed to stranded HFO. Here, we investigated the persistent effects on the early development stage of the offspring following stranded HFO exposure on the sea urchin Strongylocentrotus intermedius. After 21 d exposure, sea urchins exhibited a significant decrease in the reproductive capacity; while the reactive oxygen species level, 3-nitrotyrosine protein level, protein carbonyl level, and heat shock proteins 70 expression in the gonadal tissues and gametes significantly increased as compared to the controls, indicating that HFO exposure could cause development toxicity on offspring in most traits of larval size. These results suggested that the stranded HFO exposure could increase oxidative stress of gonadal tissues, impair reproductive functions in parental sea urchins, and subsequently impact on development of their offspring. This study provides valuable information regarding the persistent toxicity effects on the offspring following stranded HFO exposure on sea urchins. creator: Xuanbo Wang creator: Xishan Li creator: Deqi Xiong creator: Hang Ren creator: Huishu Chen creator: Zhonglei Ju uri: https://doi.org/10.7717/peerj.13298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Unconscious priming shares a common resource pool with the manipulation subsystem link: https://peerj.com/articles/13312 last-modified: 2022-04-19 description: BackgroundWorking memory can be subdivided into two relatively independent subordinate systems, the maintenance subsystem and the manipulation subsystem. Although the two subsystems are quite heterogeneous, research thus far has not adequately distinguished the resource pools of the two subsystems. Additionally, previous research on the relationship between working memory and unconscious priming is paradoxical. Different subsystems leading to different effects on unconscious priming might be the reason for the paradoxical research. Therefore, the current article aimed to distinguish the resource pools among two working-memory subsystems and to investigate the relationship between the two subsystems and unconscious priming.MethodsTo address these issues, a maintenance dual-task and a manipulation dual-task program were developed. Each participant had to separately perform the two dual tasks in a balanced order. In each dual task, participants first completed a masked priming task accompanied by working-memory load. As a control, participants completed a prime identification test to confirm that the processing of the masked prime was at the unconscious level. The maintenance dual task comprised sandwich masking trials accompanied by Sternberg trials, while the manipulation dual task comprised sandwich masking trials accompanied by N-back trials.ResultsThe results of the prime identification test indicated that the participants could not consciously perceive the masked prime of both dual tasks. The results of the working-memory task of both dual tasks indicated that the load manipulation was successful for both dual tasks. Most importantly, the results of the masking task of both dual tasks showed that an increase in working-memory load decreased the magnitude of unconscious priming in the manipulation dual task, whereas an increase in working-memory load did not decrease unconscious priming in the maintenance dual task. These observations demonstrate that the manipulation subsystem, rather than the maintenance subsystem, interferes with unconscious priming. Together with previous research, we propose a two-pool attention resource model to explain the modulation of working memory on unconscious priming by dissociating the executive resource pool of the manipulation system from the retention resource pool of the maintenance system. Thus, the current work confirms and extends the extant literature about the dependence of unconscious processing on attention resources by suggesting that unconscious priming shares a common resource pool with the manipulation subsystem. creator: Xuechen Mao creator: Anmin Li uri: https://doi.org/10.7717/peerj.13312 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mao and Li title: Association of toll-like receptors single nucleotide polymorphisms with HBV and HCV infection: research status link: https://peerj.com/articles/13335 last-modified: 2022-04-19 description: BackgroundHepatitis B virus (HBV) and hepatitis C virus (HCV) infections have become increasingly severe worldwide and are a threat to public health. There have been a number of studies conducted recently on the relationship of single nucleotide polymorphisms (SNPs) to innate immune receptor genes such as toll-like receptors (TLRs). Some literature suggests that SNPs of TLRs are associated with HBV and HCV infection. We summarized the role of TLRs gene polymorphisms associated with HBV and HCV infections and explored their possible mechanisms of action.MethodologyPubMed and Web of Science were used to perform the literature review. Related articles and references were identified and used to analyze the role of TLRs gene polymorphism in HBV and HCV infection.ResultsTLRs gene polymorphisms may have beneficial or detrimental effects in HBV and HCV infection, and some SNPs can affect disease progression or prognosis. They affect the disease state by altering gene expression or protein synthesis; however, the mechanism of action is not clearly understood.ConclusionsSingle nucleotide polymorphisms of TLRs play a role in HBV and HCV infection, but the mechanism of action still needs to be explored in future studies. creator: Yaxin Xu creator: Wentao Xue creator: Hongwei Gao creator: Jiabo Cui creator: Lingzhi Zhao creator: Chongge You uri: https://doi.org/10.7717/peerj.13335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Water stress and nitrogen supply affect floral traits and pollination of the white mustard, Sinapis alba (Brassicaceae) link: https://peerj.com/articles/13009 last-modified: 2022-04-18 description: Changes in environmental conditions are likely to have a complex effect on the growth of plants, their phenology, plant-pollinator interactions, and reproductive success. The current world is facing an ongoing climate change along with other human-induced environmental changes. Most research has focused on the impact of increasing temperature as a major driving force for climate change, but other factors may have important impacts on plant traits and pollination too and these effects may vary from season to season. In addition, it is likely that the effects of multiple environmental factors, such as increasing temperature, water availability, and nitrogen enrichment are not independent. Therefore, we tested the impact of two key factors—water, and nitrogen supply—on plant traits, pollination, and seed production in Sinapis alba (Brassicaceae) in three seasons defined as three temperature conditions with two levels of water and nitrogen supply in a factorial design. We collected data on multiple vegetative and floral traits and assessed the response of pollinators in the field. Additionally, we evaluated the effect of growing conditions on seed set in plants exposed to pollinators and in hand-pollinated plants. Our results show that water stress impaired vegetative growth, decreased flower production, and reduced visitation by pollinators and seed set, while high amount of nitrogen increased nectar production under low water availability in plants grown in the spring. Temperature modulated the effect of water and nitrogen availability on vegetative and floral traits and strongly affected flowering phenology and flower production. We demonstrated that changes in water and nitrogen availability alter plant vegetative and floral traits, which impacts flower visitation and consequently plant reproduction. We conclude that ongoing environmental changes such as increasing temperature, altered precipitation regimes and nitrogen enrichment may thus affect plant-pollinator interactions with negative consequences for the reproduction of wild plants and insect-pollinated crops. creator: Asma Akter creator: Jan Klečka uri: https://doi.org/10.7717/peerj.13009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Akter and Klečka title: Concentration and quantification of Tilapia tilapinevirus from water using a simple iron flocculation coupled with probe-based RT-qPCR link: https://peerj.com/articles/13157 last-modified: 2022-04-18 description: BackgroundTilapia tilapinevirus, also known as tilapia lake virus (TiLV), is a significant virus that is responsible for the die-off of farmed tilapia across the globe. The detection and quantification of the virus using environmental RNA (eRNA) from pond water samples represents a potentially non-invasive and routine strategy for monitoring pathogens and early disease forecasting in aquaculture systems.MethodsHere, we report a simple iron flocculation method for concentrating viruses in water, together with a newly-developed hydrolysis probe quantitative RT-qPCR method for the detection and quantification of TiLV.ResultsThe RT-qPCR method designed to target a conserved region of the TiLV genome segment 9 has a detection limit of 10 viral copies per µL of template. The method had a 100% analytical specificity and sensitivity for TiLV. The optimized iron flocculation method was able to recover 16.11 ± 3.3% of the virus from water samples spiked with viral cultures. Tilapia and water samples were collected for use in the detection and quantification of TiLV disease during outbreaks in an open-caged river farming system and two earthen fish farms. TiLV was detected from both clinically sick and asymptomatic fish. Most importantly, the virus was successfully detected from water samples collected from different locations in the affected farms (i.e., river water samples from affected cages (8.50 × 103 to 2.79 × 105 copies/L) and fish-rearing water samples, sewage, and reservoir (4.29 × 103 to 3.53 × 104 copies/L)). By contrast, TiLV was not detected in fish or water samples collected from two farms that had previously experienced TiLV outbreaks and from one farm that had never experienced a TiLV outbreak. In summary, this study suggests that the eRNA detection system using iron flocculation, coupled with probe based-RT-qPCR, is feasible for use in the concentration and quantification of TiLV from water. This approach may be useful for the non-invasive monitoring of TiLV in tilapia aquaculture systems and may support evidence-based decisions on biosecurity interventions needed. creator: Suwimon Taengphu creator: Pattanapon Kayansamruaj creator: Yasuhiko Kawato creator: Jerome Delamare-Deboutteville creator: Chadag Vishnumurthy Mohan creator: Ha Thanh Dong creator: Saengchan Senapin uri: https://doi.org/10.7717/peerj.13157 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Taengphu et al. title: Differentiation patterns of emperor moths (Lepidoptera: Saturniidae: Saturniinae) of a continental island: divergent evolutionary history driven by Pleistocene glaciations link: https://peerj.com/articles/13240 last-modified: 2022-04-18 description: BackgroundOn the basis of molecular dating, Pleistocene glaciations have been proposed as the major driving force of biota speciation in the Palearctic and the pre-Quaternary origin of Amazonian taxa. However, the major driving factors in East Asia remain unclear. All 16 saturniine species inhabiting Taiwan with congeners of populations, subspecies, or species in East Asia constitute research objects for addressing the mode of speciation because of the repeated formation and disappearance of a landbridge from the Asian mainland to Taiwan during glacial cycles.MethodsThe genetic divergences of mitochondrial cytochrome c oxidase subunit I (COI) and 16S rDNA and the nuclear 28S rDNA of the saturniine species from Taiwan and the Asian mainland were assessed to determine the monophyly of each genus and species of Saturniinae. Moreover, 519 saturniine COI sequences of 114 taxa from adjacent East and Southeast Asian populations and closely related species were retrieved from GenBank and analyzed. The differentiation timing and possible origination of the insular saturniines were elucidated based on phylogenetic relationships, haplotype networks, and lineage calibrations.ResultsApproximately 90% of intraspecific COI divergence was <2%; all divergences exceeding 2% originated from comparisons between allopatric populations or subspecies. Relationship analyses revealed that multiple introductions likely occurred in insular saturniines and that some East Asian saturniines were paraphyletic as deduced by analyzing endemic insular species. Calibration dating revealed that Taiwanese endemic saturniines split from sibling Asian species 0.2–2.7 million years ago (Mya), whereas subspecific-level and population-level splitting events occurred 0.1–1.7 Mya and 0.2–1.2 Mya, respectively. Moreover, phylogenetic patterns combined with geographical distributions revealed that hill-distributed Taiwanese saturniines are closely related to those from southern China and Southeast Asia, whereas saturniines inhabiting altitudes higher than 1,500 m in Taiwan have siblings distributed in temperate Northeast Asia.DiscussionThe Global DNA Barcoding Initiative was successfully applied to study the population genetic structure in species. Most Formosan saturniines are distinct and monophyletic, reflecting the vicariant barrier of the Taiwan Strait; Pleistocene glacial cycles provided opportunities for insular saturniines to experience repeated isolation from and secondary contact with the continental mainland. Each insular saturniine may have evolved with a unique differentiation timing pattern that possibly emerged in the Early, Middle, or Late Pleistocene with these patterns differing from the consistent pattern that occurred in the temperate Palearctic and tropical Amazonian regions. Moreover, multiple migrations or artificial genetic admixtures may have also occurred, as suggested by the coexistence of two divergent lineages in a few Taiwanese saturniines. creator: Wen-Bin Yeh creator: Cheng-Lung Tsai creator: Thai-Hong Pham creator: Shipher Wu creator: Chia-Wei Chang creator: Hong-Minh Bui uri: https://doi.org/10.7717/peerj.13240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yeh et al. title: Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris link: https://peerj.com/articles/13268 last-modified: 2022-04-18 description: BackgroundThe genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved.MethodsSamples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses.ResultsWe sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T–). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris. creator: Wan Chen creator: Keer Miao creator: Junqi Wang creator: Hao Wang creator: Wan Sun creator: Sijia Yuan creator: Site Luo creator: Chaochao Hu creator: Qing Chang uri: https://doi.org/10.7717/peerj.13268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera) link: https://peerj.com/articles/13275 last-modified: 2022-04-18 description: African Saturniidae (Lepidoptera) include numerous species consumed at the caterpillar stage throughout the continent, and their importance to local communities as a source of nutrition and seasonal income cannot be overestimated. However, baseline genetic data with utility for the characterization of their diversity, phylogeography and phylogenetic relationships have remained scarce compared to their Asian counterparts. To bridge this gap, we sequenced the mitochondrial genomes of 12 species found in southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family, including the first representatives of the tribes Eochroini and Micragonini. Mitochondrial gene content and organization were conserved across all Saturniidae included in the analyses. The phylogenetic positions of the 12 species were assessed in the context of publicly available mitogenomes using Bayesian inference and maximum likelihood (ML) methods. The monophyly of the tribes Saturniini, Attacini, Bunaeini and Micragonini, the sister relationship between Saturniini and Attacini, and the placement of Eochroa trimenii and Rhodinia fugax in the tribes Eochroini and Attacini, respectively, were strongly supported. These results contribute to significantly expanding genetic data available for African Saturniidae and allow for the development of new mitochondrial markers in future studies. creator: Zwannda Nethavhani creator: Rieze Straeuli creator: Kayleigh Hiscock creator: Ruan Veldtman creator: Andrew Morton creator: Rolf G. Oberprieler creator: Barbara van Asch uri: https://doi.org/10.7717/peerj.13275 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nethavhani et al. title: How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships? link: https://peerj.com/articles/13285 last-modified: 2022-04-18 description: The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny. creator: Zeyuan Chen creator: Michael Schrödl uri: https://doi.org/10.7717/peerj.13285 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen and Schrödl title: Phenotypic variation of Chitala chitala (Hamilton, 1822) from Indian rivers using truss network and geometric morphometrics link: https://peerj.com/articles/13290 last-modified: 2022-04-18 description: Chitala chitala (Hamilton, 1822) is an economically important food fish species occurring throughout Indian rivers, which also has ornamental value. This study focuses on morphological variations in C. chitala from seven river basins across India namely; Son, Tons, Ken, Brahmaputra, Ganga, Gomti and Gandak. A truss network was constructed by interconnecting nine landmarks to generate 36 morphometric variables extracted from digital images of specimens sampled from the study locations. Transformed truss measurements were subjected to principal component analysis (PCA), canonical discriminant function analysis (CDFA) and discriminant analyses of principal components (DAPC). DAPC function coefficients performed much better in capturing the variation pattern and discrimination between the rivers which was not achieved using CDFA. Eight truss variables were identified with significant and highest loading for truss variables on principal components and coefficients on discriminant function from DAPC contributing to maximum variation between the rivers. Performance graph and functional distribution of identified truss variables clearly indicated distinction between the rivers. Thin plate spline analysis and procrustes shape analysis further showed the variation in morphology between specimens across the rivers. The significant parameters differentiating specimens from different rivers were linked to dorsal fin origin, the base of the pectoral fin and the perpendicular point on the anal fin from the dorsal fin origin. Variation in the hydrodynamics of the rivers studied might be possibly affecting the fin kinematics and consequently leading to adaption seen as phenotypic variation in C. chitala. The results showcased in the present study shall help in better understanding of intra-specific diversity which is significant for management and conservation of a species. creator: Rejani Chandran creator: Achal Singh creator: Rajeev K. Singh creator: Sangeeta Mandal creator: Kantharajan Ganesan creator: Priyanka Sah creator: Pradipta Paul creator: Abhinav Pathak creator: Nimisha Dutta creator: Ramashankar Sah creator: Kuldeep K. Lal creator: Vindhya Mohindra uri: https://doi.org/10.7717/peerj.13290 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chandran et al. title: The sterile insect technique is protected from evolution of mate discrimination link: https://peerj.com/articles/13301 last-modified: 2022-04-18 description: BackgroundThe sterile insect technique (SIT) has been used to suppress and even extinguish pest insect populations. The method involves releasing artificially reared insects (usually males) that, when mating with wild individuals, sterilize the broods. If administered on a large enough scale, the sterility can collapse the population. Precedents from other forms of population suppression, especially chemicals, raise the possibility of resistance evolving against the SIT. Here, we consider resistance in the form of evolution of female discrimination to avoid mating with sterile males. Is resistance evolution expected?MethodsWe offer mathematical models to consider the dynamics of this process. Most of our models assume a constant-release protocol, in which the same density of males is released every generation, regardless of wild male density. A few models instead assume proportional release, in which sterile releases are adjusted to be a constant proportion of wild males.ResultsWe generally find that the evolution of female discrimination, although favored by selection, will often be too slow to halt population collapse when a constant-release implementation of the SIT is applied appropriately and continually. The accelerating efficacy of sterile males in dominating matings as the population collapses works equally against discriminating females as against non-discriminating females, and rare genes for discrimination are too slow to ascend to prevent the loss of females that discriminate. Even when migration from source populations sustains the treated population, continued application of the SIT can prevent evolution of discrimination. However, periodic premature cessation of the SIT does allow discrimination to evolve. Likewise, use of a ‘proportional-release’ protocol is also prone to escape from extinction if discriminating genotypes exist in the population, even if those genotypes are initially rare. Overall, the SIT is robust against the evolution of mate discrimination provided care is taken to avoid some basic pitfalls. The models here provide insight for designing programs to avoid those pitfalls. creator: James J. Bull creator: Richard Gomulkiewicz uri: https://doi.org/10.7717/peerj.13301 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bull and Gomulkiewicz title: Differences in lower limb muscle activation between global and selective instability devices in single-leg stance in healthy active subjects link: https://peerj.com/articles/13317 last-modified: 2022-04-18 description: BackgroundBalance and strength training are frequent strategies to address lower limb injuries, including ankle injuries, which are usually performed in single-leg stance on global instability devices, producing generalized muscular activation of the lower limb. In this context, new specific instability devices arise from the need to selectively work the ankle, specifically the peroneus longus. This study aimed to compare the EMG muscle activation of the peroneus longus, as well as other lower limbs muscles, in a single-leg stance on different balance training devices (BOSU, wobble board, power board, and Blackboard) in standing or squatting positions.MethodsTwenty healthy recreationally trained subjects participated in the study. Subjects performed three repetitions of 15 s (one for familiarization and two for measurement) in standing and squatting positions on the floor, BOSU, wobble board, power board, and Blackboard. Surface electromyography (EMG) was used to record activity of the peroneus longus, soleus, gastrocnemius medialis, tibialis anterior, rectus femoris, and gluteus maximus.ResultsThe main outcome was that no differences were found for the peroneus longus normalized EMG, neither between devices (p = 0.09) nor between conditions (p = 0.11), nor in the interaction between them (p = 0.16). For the normalized EMG of the other muscles, there were multiple differences between devices and conditions. Of the devices studied, the Blackboard was the one that implied a lower activation of the lower limb muscles and a lower degree of instability, activating the peroneus longus similarly to global instability devices. The BOSU and wobble board achieved high levels of EMG muscle activation for most muscles of the lower limbs. Therefore, they should be considered as potential devices for work in highly unstable conditions or when high activation levels are sought. creator: Mariana Sánchez-Barbadora creator: Alba Cuerda-Del Pino creator: Javier González-Rosalén creator: Noemi Moreno-Segura creator: Adrian Escriche-Escuder creator: Rodrigo Martín-San Agustín uri: https://doi.org/10.7717/peerj.13317 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sánchez-Barbadora et al. title: miR-34a-5p inhibits the malignant progression of KSHV-infected SH-SY5Y cells by targeting c-fos link: https://peerj.com/articles/13233 last-modified: 2022-04-15 description: BackgroundWe aimed to investigate the effects of miR-34a-5p on c-fos regulation mediating the malignant behaviors of SH-SY5Y cells infected with Kaposi’s sarcoma-associated herpesvirus (KSHV).MethodsThe KSHV-infected (SK-RG) and uninfected SH-SY5Y parent cells were compared for differentially expressed miRNAs using transcriptome sequencing. Then miR-34a-5p was upregulated in SK-RG cells by the miRNA mimics transfection. Cell proliferation ability was determined by MTT and plate clone assays. The cell cycle was assessed by flow cytometry analysis, and CDK4, CDK6, cyclin D1 levels were determined by Western blot analysis. The migration behavior was detected by wound healing and transwell assays. The protein levels of MMP2 and MMP9 were measured by Western blot analysis. The regulation of c-fos by miR-34a-5p was detected by the dual-luciferase reporter gene assay. Rescue assays were carried out by upregulating c-fos in miR-34a-5p-overexpressing SK-RG cells. KSHV DNA copy numbers and relative virus gene expressions were detected. Xenograft tumor experiments and immunohistochemistry assays were further used to detect the effects of miR-34a-5p.ResultsmiR-34a-5p was lower in SK-RG cells. Restoration of miR-34a-5p decreased cell proliferation and migration, leading to a G1 cell cycle arrest and down-regulation of CDK4/6, cyclin D1, MMP2, MMP9. KSHV copy number and expression of virus gene including latency-associated nuclear antigen (LANA), replication and transcription activator (RTA), open reading frame (K8.1), and KSHV G protein-coupled receptor (v-GPCR) were also reduced. Furthermore, c-fos is the target of miR-34a-5p, while enhanced c-fos weakened cellular behaviors of miR-34a-5p-overexpressing cells. Xenograft experiments and immunohistochemistry assays showed that miR-34a-5p inhibited tumor growth and virus gene expression.ConclusionUpregulated miR-34a-5p in KSHV-infected SH-SY5Y cells suppressed cell proliferation and migration through down-regulating c-fos. miR-34a-5p was a candidate molecular drug for KSHV-infected neuronal cells. creator: Shuyuan Wu creator: Zhaofu Wu creator: Huiling Xu creator: Jinli Zhang creator: Wenyi Gu creator: Xiaohua Tan creator: Zemin Pan creator: Dongdong Cao creator: Dongmei Li creator: Lei Yang creator: Dongmei Li creator: Yuanming Pan uri: https://doi.org/10.7717/peerj.13233 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wu et al. title: Genetic diversity and population structure of muscovy duck (Cairina moschata) from Nigeria link: https://peerj.com/articles/13236 last-modified: 2022-04-15 description: The domestic Muscovy duck (Cairina moschata) provide unique genetic resources patterned by both tropical environmental conditions and human activities, the evaluation of their genetic diversity and population structure will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the variation in mtDNA cytochrome b and nuclear DNA CYP2U1 sequences of 378 Nigerian Muscovy ducks (comprising of 287 de novo and 91 downloaded) plus 80 published sequences of Muscovy ducks from India. The results showed high haplotype diversity (0.800 ± 0.023) among Nigerian Muscovy duck populations with 91 distinct haplotypes for the nuclear DNA CYP2U1 gene but low (0.266 ± 0.033) for cytochrome b with 31 haplotypes. The median-joining networks of both markers grouped Nigerian Muscovy ducks into two; the first group consisting of only Nigerian Muscovy duck populations, and the second group Nigerian with Indian populations. Neutrality test results indicated that Nigerian populations experienced recent population expansion and/or genetic hitchhiking. A geographic signal was absent in line with previously studied poultry species in Nigeria. The most prominent haplotype dominated across all regions in Nigeria, which may be due to extensive genetic intermixing except for the Indian population (FST = 0.02550, P = 0.01075). This indicated low genetic differentiation between and within Nigerian Muscovy duck as revealed by the suitability of the nuclear DNA CYP2U1 gene. creator: Adeniyi C. Adeola creator: Foluke E. Sola-Ojo creator: Yusuf A. Opeyemi creator: Abel O. Oguntunji creator: Lotanna Micah Nneji creator: Muslim K. Ewuola creator: Semiu F. Bello creator: Wasiu A. Olaniyi creator: Adeosun T. Adesoji creator: Alex P. Karuno creator: Oscar J. Sanke creator: Ebiakpo Lucky Daniel uri: https://doi.org/10.7717/peerj.13236 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Adeola et al. title: Long forgotten: Eunice woodwardi Baird, 1869 (Annelida, Eunicidae) revisited, with an insight on internal anatomy link: https://peerj.com/articles/13126 last-modified: 2022-04-14 description: Eunice woodwardiBaird, 1869, originally described from the Ría de A Coruña (NW Iberian Peninsula), has been overlooked and never reported from the Atlantic coast of Spain after original description and the subsequent redescription of the holotype. In the present study, we revised comparatively the holotype, newly collected specimens of this species and specimens identified as Eunice vittata (Delle Chiaje, 1829) from western Mediterranean Sea. The validity of E. woodwardi is supported and previous descriptions are complemented after a throughout study of the external morphology by means of light compound microscopy and scanning electron microscopy, and that of the internal anatomy by histological sectioning and micro-computed tomography. The presence of eyes, nuchal organs, dorsal and ventral ciliary organs on parapodial cirri and paired nephridia in most segments is confirmed in E. woodwardi; the digestive tract is clearly regionalized and divided into pharynx, oesophagus, stomach, fore, mid- and hind intestine. The presence of E. woodwardi in the Ría de Ferrol is also reported, and we suggest that previous records of E. vittata in NW Iberian Peninsula should be reviewed. Eunice woodwardi is distinguished by a set of characters such as having non-articulated and non-constricted cephalic appendages, the maxillary formula, the range of branchial distribution, maximum number of branchial filaments, number of limbate and compound falciger chaetae per parapodium, the presence of an apical mucro in the guard of falciger chaetae blades and the number of teeth in pectinate chaetae. Epibiont Ciliophora on branchiae are also reported. creator: María Barroso creator: Juan Moreira creator: Julio Parapar uri: https://doi.org/10.7717/peerj.13126 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Barroso et al. title: Using a mechanistic framework to model the density of an aquatic parasite Ceratonova shasta link: https://peerj.com/articles/13183 last-modified: 2022-04-14 description: Ceratonova shasta is a myxozoan parasite endemic to the Pacific Northwest of North America that is linked to low survival rates of juvenile salmonids in some watersheds such as the Klamath River basin. The density of C. shasta actinospores in the water column is typically highest in the spring (March–June), and directly influences infection rates for outmigrating juvenile salmonids. Current management approaches require quantities of C. shasta density to assess disease risk and estimate survival of juvenile salmonids. Therefore, we developed a model to simulate the density of waterborne C. shasta actinospores using a mechanistic framework based on abiotic drivers and informed by empirical data. The model quantified factors that describe the key features of parasite abundance during the period of juvenile salmon outmigration, including the week of initial detection (onset), seasonal pattern of spore density, and peak density of C. shasta. Spore onset was simulated by a bio-physical degree-day model using the timing of adult salmon spawning and accumulation of thermal units for parasite development. Normalized spore density was simulated by a quadratic regression model based on a parabolic thermal response with river water temperature. Peak spore density was simulated based on retained explanatory variables in a generalized linear model that included the prevalence of infection in hatchery-origin Chinook juveniles the previous year and the occurrence of flushing flows (≥171 m3/s). The final model performed well, closely matched the initial detections (onset) of spores, and explained inter-annual variations for most water years. Our C. shasta model has direct applications as a management tool to assess the impact of proposed flow regimes on the parasite, and it can be used for projecting the effects of alternative water management scenarios on disease-induced mortality of juvenile salmonids such as with an altered water temperature regime or with dam removal. creator: H. Eve Robinson creator: Julie D. Alexander creator: Jerri L. Bartholomew creator: Sascha L. Hallett creator: Nicholas J. Hetrick creator: Russell W. Perry creator: Nicholas A. Som uri: https://doi.org/10.7717/peerj.13183 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Robinson et al. title: The potency of minerals to reduce oriental fruit fly infestation in chili fruits link: https://peerj.com/articles/13198 last-modified: 2022-04-14 description: IntroductionsIn many areas, particularly in Asia, the oriental fruit fly Bactrocera dorsalis (Hendel) causes considerable fruit damage on various plants. The fruit fly causes significant economic losses every year due to reduced fruit quantity and quality as well as export restrictions. This study aimed to examine the potency of minerals in controlling the oriental fruit fly infestation in chili fruits.MethodsExperiments were conducted under laboratory and semi-field conditions using randomized block design. Ten minerals (i.e. kaolin, talc, zinc oxide, bentonite, sulfur, dolomite, calcium oxide, calcium hydroxide, calcium carbonate, and zeolite) and an untreated control were tested under laboratory conditions. Twenty chili fruits at a green stage were soaked in each mineral suspension (2%, w/v), air-dried, and placed in a trial cage (23-L plastic container) containing 20 female oriental fruit flies. In a semi-field bioassay using a screen cage (100 cm × 70 cm × 120 cm), 20 female oriental fruit flies were exposed to a fruit-bearing chili plant sprayed with mineral suspension.ResultsTalc and calcium oxide significantly reduced the numbers of visiting fruit flies, oviposition holes, and eggs laid, as well as the percentage of infested chili fruits in a laboratory bioassay. Calcium hydroxide was substantially better than talc in controlling fruit fly infestation in a semi-field bioassay, although it was not significantly different from calcium oxide and calcium carbonate.ConclusionOverall, calcium oxide is a viable option for the long-term control of the oriental fruit fly on chili fruits. Calcium oxide could be utilized as the push component of a push-pull strategy to manage oriental fruit fly infestation in chili fruits because of its potential to inhibit the number of visiting fruit flies and oviposition. creator: Josua Crystovel Pangihutan creator: Danar Dono creator: Yusup Hidayat uri: https://doi.org/10.7717/peerj.13198 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pangihutan et al. title: ELOVL2-AS1 inhibits migration of triple negative breast cancer link: https://peerj.com/articles/13264 last-modified: 2022-04-14 description: In this study, we identified a key enhancer RNA (eRNA) region in breast cancer (BRCA) by applying an integrated analysis method. Reported eRNA region and genes affected by them were selected as presumed target pairs. Kaplan–Meier (KM) survival and correlation analyses were performed to screen valuable eRNA region. Based on the KM value and its correlation with the paired target genes, we carefully selected ELOVL2-AS1 as a potential key eRNA region in BRCA. Subsequently, we analyzed the expression of ELOVL2-AS1 and ELOVL2 in four BRCA subtypes and in different BRCA cell lines. The expression of ELOVL2-AS1 and ELOVL2 in triple negative breast cancer (TNBC) was significantly lower than those in Luminal A. After that, we analyzed the function of genes that are positively correlated with ELOVL2-AS1. We found that the co-expression gene mainly related to cilia and cilia characteristics of TNBC is significantly weaker than that of Luminal A. Considering the stronger invasion and metastasis of TNBC (compared with Luminal A) and the close relationship between decreased cilia and metastasis, we overexpressed ELOVL2-AS1 in TNBC and observed its effect on cell migration. The results show that it can inhibit the migration of TNBC. Finally, we analyzed the assay for transposase-accessible chromatin sequencing data, chromatin interaction analysis with paired-end tag sequencing data, and chromatin immunoprecipitation sequencing data and identified the chromatin interaction between ELOVL2-AS1 and ELOVL2, suggesting a direct regulatory interaction. creator: Mingda Zhu creator: Jingyang Zhang creator: Guangyu Li creator: Zhenzhen Liu uri: https://doi.org/10.7717/peerj.13264 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhu et al. title: Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy link: https://peerj.com/articles/13265 last-modified: 2022-04-14 description: Cardiomyopathy (CMP) constitutes a diverse group of myocardium diseases affecting the pumping ability of the heart. Genetic predisposition is among the major factors affecting the development of CMP. Globally, there are over 100 genes in autosomal and mitochondrial DNA (mtDNA) that have been reported to be associated with the pathogenesis of CMP. However, most of the genetic studies have been conducted in Western countries, with limited data being available for the Asian population. Therefore, this study aims to investigate the mutation spectrum in the mitochondrial genome of 145 CMP patients in Malaysia. Long-range PCR was employed to amplify the entire mtDNA, and whole mitochondrial genome sequencing was conducted on the MiSeq platform. Raw data was quality checked, mapped, and aligned to the revised Cambridge Reference Sequence (rCRS). Variants were named, annotated, and filtered. The sequencing revealed 1,077 variants, including 18 novel and 17 CMP and/or mitochondrial disease-associated variants after filtering. In-silico predictions suggested that three of the novel variants (m.8573G>C, m.11916T>A and m.11918T>G) in this study are potentially pathogenic. Two confirmed pathogenic variants (m.1555A>G and m.11778G>A) were also found in the CMP patients. The findings of this study shed light on the distribution of mitochondrial mutations in Malaysian CMP patients. Further functional studies are required to elucidate the role of these variants in the development of CMP. creator: Sheh Wen Kuan creator: Kek Heng Chua creator: E-Wei Tan creator: Lay Koon Tan creator: Alexander Loch creator: Boon Pin Kee uri: https://doi.org/10.7717/peerj.13265 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kuan et al. title: Pre-competition mental energy and performance relationships among physically disabled table tennis players link: https://peerj.com/articles/13294 last-modified: 2022-04-14 description: Energy is essential to human daily functioning and performance. However, the association of mental energy with athletes’ performance has rarely been examined. We attempted to examine the pre-competition mental energy–performance relationships by two studies. Study 1 administered Athletic Mental Energy Scale (AMES, Lu et al., 2018) to nine elite physically-disabled table tennis players one day before competition in 5 international tournaments. Then, we collected their subjective performance after each competition. In Study 2, we sampled 77 National-level physically-disabled table tennis players and examined the pre-competition mental energy-performance relationship as the procedure in Study 1. Results from Study 1 provided initial findings of how pre-competition mental energy is associated with performance and portrayed in elite physically-disabled table tennis players. Results from Study 2 further confirmed the pre-competition mental energy- performance relationships. We suggested future studies to examine the mental energy–performance relationships in physically-disabled and abled athletes and different sports. creator: Wen-Chuan Chuang creator: Frank J.H. Lu creator: Diane L. Gill creator: Bin-Bin Fang uri: https://doi.org/10.7717/peerj.13294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chuang et al. title: First DNA barcode library for the ichthyofauna of the Jos Plateau (Nigeria) with comments on potential undescribed fish species link: https://peerj.com/articles/13049 last-modified: 2022-04-13 description: Located in the central region of northern Nigeria, the Jos Plateau covers approximately 9,400 km² with an average altitude of 1,280 m and constitutes a unique terrestrial ecoregion known as the Jos Plateau forest-grassland mosaic. The biota of the Jos Plateau include endemic elements, but very limited information is available on its ichthyofauna. This is despite the fact that the ancient plateau contributes to several large rivers spanning multiple major drainage systems including the Niger and Benue Rivers, and Lake Chad. This study provides the first species list for the fishes of the Jos Plateau based mainly on 175 DNA barcoded museum voucher specimens representing 20 species, and another three species without a DNA barcode. In total, 23 species from eight families and 17 genera were collected from the Jos Plateau including five putatively new species, four in the family Cyprinidae and one in the Clariidae. With ten species, the Cyprinidae is the most diverse fish family on the Jos Plateau, followed by Clariidae and Cichlidae, each with three species. The study also provides data on species distribution and habitat parameters including information on water chemistry that strongly suggests that selected water bodies are heavily impacted by anthropogenic activities. Urgent management steps are required to preserve the unique and diverse fish communities of the Jos Plateau and their habitats. creator: Michael Olaoluwa Popoola creator: Frédéric Dieter Benedikt Schedel creator: Paul DN Hebert creator: Ulrich Kurt Schliewen uri: https://doi.org/10.7717/peerj.13049 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Popoola et al. title: Determination of exercise intensity domains during upright versus supine cycling: a methodological study link: https://peerj.com/articles/13199 last-modified: 2022-04-13 description: BackgroundThere is a growing interest among the research community and clinical practitioners to investigate cardiopulmonary exercise test (CPET) procedures and protocols utilized in supine cycling.Materials and MethodsThe current study investigated the effects of posture on indicators of exercise intensity including gas exchange threshold (GET), respiratory compensation point (RCP), and the rate of peak oxygen uptake (V̇O2 peak), as well as the role of V̇O2 mean response time (MRT) in determining exercise intensity domains in nineteen healthy men (age: 22 ± 3 years). Two moderate-intensity step-transitions from 20 to 100 Watt (W) were completed, followed by a maximal CPET. After completing the ramp test, participants performed a constant-load at 90% of their attained peak power output (PPO).ResultsNo differences were observed in the V̇O2 MRT between the two positions, although the phase II-time constant (τV̇O2p) was 7 s slower in supine position compared to upright (p = 0.001). The rate of O2 uptake in the supine position at GET and RCP were lower compared to the upright position (208 ± 200 mL·min−1 (p = 0.007) and 265 ± 235 mL·min−1 (p = 0.012) respectively). Besides, V̇O2 peak was significantly decreased (by 6%, p = 0.002) during supine position. These findings were confirmed by the wide limits of agreement between the measures of V̇O2 in different postures (V̇O2 peak: −341 to 859; constant-load test: −528 to 783; GET: −375 to 789; RCP: −520 to 1021 all in mL·min−1).ConclusionSince an accurate identification of an appropriate power output (PO) from a single-visit CPET remains a matter of debate, especially for supine cycling, we propose that moderate-intensity step-transitions preceding a ramp CPET could be a viable addition to ensure appropriate exercise-intensity domain determination, in particular upon GET-based prescription. creator: Damir Zubac creator: Vladimir Ivančev creator: Vincent Martin creator: Antonio Dello Iacono creator: Cécil J.W. Meulenberg creator: Adam C. McDonnell uri: https://doi.org/10.7717/peerj.13199 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zubac et al. title: Effects of nitrogen and phosphorus addition on growth and leaf nitrogen metabolism of alfalfa in alkaline soil in Yinchuan Plain of Hetao Basin link: https://peerj.com/articles/13261 last-modified: 2022-04-13 description: Alkaline soil is widely distributed in China. Its rational utilization is an effective measure to solve land shortage and improve the environment. Alfalfa is characterized by strong salt and alkali tolerance and high yield and protein content. Nitrogen (N) and phosphorus (P) are the main nutrients for plant growth, and N metabolism is one of the primary forms of plant metabolism, which plays a vital role in quality and yield formation. The exploration of the effect of N and P on N metabolism and alfalfa growth will provide a theoretical basis for scientific fertilization for alfalfa in the alkaline soil of the Yinchuan Plain of the Hetao Basin. Therefore, a 2-year experiment of N and P addition was conducted. Six treatments were set up with a randomized block design, including without N (WN), medium N (MN), high N (HN), without P (WP), medium P (MP), and high P (HP). It was found that the MN and MP treatments increased plant height, stem diameter, stem/leaf, dry/fresh, and dry matter of alfalfa. The HN and HP treatments inhibited alfalfa biomass formation. The MN and MP treatments increased key products and enzymes of leaf N metabolism of alfalfa and promoted activities of leaf nitrate reductase (NR), glutamine synthase (GS), glutamate synthase (GOGAT), glutamic-oxalacetic transaminase (GOT), and glutamic-pyruvate transaminase (GPT), and inhibited activities of leaf protease of alfalfa. The MN and MP treatments increased contents of leaf N, P, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3−-N), total chlorophyll, and protein and reduced leaf chlorophyll a/b and amino acid, results after HN and HP treatments were opposite. The correlation among leaf P, N, NO3−-N, amino acid, and protein reached significant levels (P < 0.01). It is suggested that MN and MP treatments can improve the yield and quality of alfalfa by increasing key products and enzymes of N metabolism and can be adopted to promote alfalfa production in the alkaline soil of the Yinchuan Plain of the Hetao Basin. creator: Gu Xudong creator: Zhang Fengju creator: Wang Teng creator: Xie Xiaowei creator: Jia Xiaohui creator: Xu Xing uri: https://doi.org/10.7717/peerj.13261 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xudong et al. title: Identifying and characterizing Stagonosporopsis cucurbitacearum causing spot blight on Pinellia ternata in China link: https://peerj.com/articles/13278 last-modified: 2022-04-13 description: BackgroundPinellia ternata (Thunb.), a perennial herbal plant in the Araceae family, has great medicinal value and market demand. In August 2020, an outbreak of severe leaf spot blight disease resulted in a huge yield loss of P. ternata. It is necessary to isolate and identify the pathogens that cause spot blight on P. ternata.MethodsIn this study, we isolated and identified the pathogens by fulfilling Koch’s postulates. Disease samples with typical spot blight symptoms were collected and pathogens were isolated from the diseased tissues. The pathogen was identified based on its biological characteristics and molecular analysis of internal transcribed (rDNA-ITS) and large subunit (LSU) sequences. Phylogenetic tree were constructed using MEGA7 software and pathogenicity tests were performed using in vivo inoculation. Finally, the pathogen was recovered and identified from the inoculated plants.ResultsBased on Koch’s postulates, we identified the pathogen causing spot blight on P. ternata as Stagonosporopsis cucurbitacearum. To our knowledge, this is the first study to explore spot blight on P. ternata caused by S. cucurbitacearum in China. creator: Jia Zhou creator: Jiawei Xu creator: Rong Xu creator: Qiaohuan Chen creator: Yunhan Wang creator: Bisheng Huang creator: Dahui Liu creator: Yuhuan Miao uri: https://doi.org/10.7717/peerj.13278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhou et al. title: PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification link: https://peerj.com/articles/13300 last-modified: 2022-04-13 description: MotivationSince the identification of the novel coronavirus (SARS-CoV-2), the scientific community has made a huge effort to understand the virus biology and to develop vaccines. Next-generation sequencing strategies have been successful in understanding the evolution of infectious diseases as well as facilitating the development of molecular diagnostics and treatments. Thousands of genomes are being generated weekly to understand the genetic characteristics of this virus. Efficient pipelines are needed to analyze the vast amount of data generated. Here we present a new pipeline designed for genomic analysis and variant identification of the SARS-CoV-2 virus.ResultsPipeCoV shows better performance when compared to well-established SARS-CoV-2 pipelines, with a lower content of Ns and higher genome coverage when compared to the Wuhan reference. It also provides a variant report not offered by other tested pipelines.Availabilityhttps://github.com/alvesrco/pipecov. creator: Renato R. M. Oliveira creator: Tatianne Costa Negri creator: Gisele Nunes creator: Inácio Medeiros creator: Guilherme Araújo creator: Fabricio de Oliveira Silva creator: Jorge Estefano Santana de Souza creator: Ronnie Alves creator: Guilherme Oliveira uri: https://doi.org/10.7717/peerj.13300 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Oliveira et al. title: Sleep health of Australian community tennis players during the COVID-19 lockdown link: https://peerj.com/articles/13045 last-modified: 2022-04-12 description: BackgroundPoorer sleep health outcomes have been documented in the general population during the COVID-19 outbreak. However, the impact of the COVID-19 outbreak on sleep health outcomes in specific population groups, including the sporting community, has not been extensively investigated. This study evaluated sleep health outcomes and their relationship with lifestyle behaviours during the initial COVID-19 lockdown period in Australian community tennis players.MethodsThis cross-sectional study evaluated sleep health outcomes and lifestyle behaviours using an online survey. The survey was disseminated online between the 24th of April and the 6th of June 2020 and comprised the Sleep Health Index, Sleep Satisfaction Tool and questions regarding weekly hours of tennis play, general physical activity, training location and alcohol consumption. Two-hundred and eighty-five individuals completed the survey.ResultsCompared to normative data, respondents displayed positive sleep health values during the initial COVID-19 lockdown period, with median values (IQR) of 85.3 (73.4, 91.7) and 64.8 (54.4, 73.4) for the Sleep Health Index and Sleep Satisfaction Tool, respectively. Sleep health outcomes were not significantly correlated (p > 0.05) with tennis play (Tb = 0.054–0.077), physical activity (Tb = −0.008 to 0.036), training location (Tb = −0.012 to −0.005) or alcohol consumption (Tb = −0.079 to −0.018).ConclusionPositive sleep health values were observed in Australian community-level tennis players during the initial COVID-19 pandemic. Sleep health values were not associated with lifestyle behaviours. Other unexplored factors may have influenced sleep health outcomes, including personal finances and socialisation, however these factors need to be investigated in future studies. creator: Philipp Beranek creator: Travis Cruickshank creator: Olivier Girard creator: Kazunori Nosaka creator: Danielle Bartlett creator: Mitchell Turner uri: https://doi.org/10.7717/peerj.13045 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Beranek et al. title: Maternal self-efficacy and emotional well-being in Chilean adolescent mothers: the relationship with their children’s social-emotional development link: https://peerj.com/articles/13162 last-modified: 2022-04-12 description: BackgroundLow maternal self-efficacy and high levels of anxiety, depression, and stress can be triggered in adolescent mothers due to an incomplete development process that makes them physically or psychologically unprepared for the responsibilities of motherhood and parenting. These factors may be linked to difficulties with their children’s social-emotional development. The present study aims to: (a) analyze the relationship between maternal self-efficacy and stress, depression, and anxiety levels in low-income adolescent mothers; (b) examine the relationship between maternal self-efficacy and well-being with children’s social-emotional development; and (c) describe the effects of maternal self-efficacy on children’s social-emotional development, mediated by maternal well-being.MethodsA sample of 79 dyads comprising low-income Chilean adolescent mothers aged from 15 to 21 years old (M = 19.1, SD = 1.66) and their children aged 10 to 24 months (M = 15.5, SD = 4.2) participated in this research. A set of psychometric scales was used to measure maternal self-efficacy (Parental Evaluation Scale, EEP), the mothers’ anxiety and depression (Hospital Anxiety and Depression Scale, HADS), maternal stress (Parental Stress Scale, PSS), and the children’s social-emotional development (Ages and Stages Questionnaire Socio-emotional, ASQ-SE). Bivariate analyses and mediation models were employed to estimate and test the relevant relationships.ResultsA bivariate analysis showed that maternal self-efficacy was negatively related to the mother’s anxiety, depression, and stress. Moreover, there was a significant relationship between maternal self-efficacy and maternal stress, and children’s self-regulation and social-emotional development. Maternal self-efficacy, mediated by maternal anxiety, depression, and stress scores, had a significant effect on the development of children’s self-regulation.ConclusionsThe results confirm the importance of adolescent mothers’ emotional well-being and maternal self- efficacy with respect to their children’s social-emotional development. This makes it necessary to have detailed information about how emotional and self-perception status influences a mother’s role in the development of her children. creator: Laura Léniz-Maturana creator: Rosa Vilaseca creator: David Leiva uri: https://doi.org/10.7717/peerj.13162 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Léniz-Maturana et al. title: Diurnal pattern of salivary alpha-amylase and cortisol under citric acid stimulation in young adults link: https://peerj.com/articles/13178 last-modified: 2022-04-12 description: BackgroundSaliva composition has diurnal variations. Citric acid stimulation plays a major role in the change of salivary flow rate and salivary composition. However, diurnal variations and sex differences in salivary alpha-amylase (sAA), pH, salivary flow rate (SFR), and salivary cortisol before and after citric acid stimulation remain unclear.MethodsWe recruited 30 healthy volunteers, including 15 women (24.7 ± 1.0 years old) and 15 men (25.3 ± 1.3 years old). At four time points (T1, 7:00; T2, 10:00; T3, 16:00; and T4, 20:00), saliva was collected from healthy volunteers before and after citric acid stimulation; and sAA, pH, SFR and salivary cortisol were measured and compared between men and women.ResultsThere were circadian fluctuations in sAA activity, SFR, pH, and cortisol level both before and after citric acid stimulation, and the diurnal fluctuations of these indexes were not affected by citric acid stimulation. There were significant differences in salivary cortisol between men and women before and after acid stimulation in T1. Neither SFR nor pH showed sex-related differences before or after acid stimulation. The variation trend of sAA activity was contrary to that of cortisol, with a significant negative correlation.ConclusionsOur data suggest that sAA and cortisol showed diurnal fluctuation, and the variation characteristics of male and female under resting state and acid stimulation were basically the same. The variation trend of salivary alpha-amylase activity was opposite to that of cortisol, with significant negative correlation. Our findings may enable the selection of the correct sampling time for research and the selection of appropriate sampling strategies in studies investigating chronic psychosocial conditions. creator: Haimei Xie creator: Xiaomei Zheng creator: Ye Huang creator: Weihao Li creator: Wenkai Wang creator: Qiao Li creator: Jiangtao Hou creator: Lulu Luo creator: Xiuying Kuang creator: Chuan-quan Lin uri: https://doi.org/10.7717/peerj.13178 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xie et al. title: Identification of the original plants of cultivated Bupleuri Radix based on DNA barcoding and chloroplast genome analysis link: https://peerj.com/articles/13208 last-modified: 2022-04-12 description: Bupleuri Radix is the dry root of certain species of the genus Bupleurum and is commonly used in traditional Chinese medicine. The increasing global demand for Bupleuri Radix cannot be fulfilled with wild populations only. Therefore, cultivated Bupleurum is now the main commercial source of this medicinal product. Different species of Bupleurum show different medicinal properties and clinical effects, making reliable authentication and assignment of correct botanical origin for medicinal species critical. However, accurate identification of the cultivated Bupleurum species is difficult due to dramatic morphological variations resulting from cultivation. In this study, we sampled 56 cultivated Bupleurum populations of six different morphotypes (Types A-F) from the main production areas of China, and 10 wild populations of four species were used as reference materials. Conventional DNA barcoding was conducted to identify cultivated Bupleurum species. Additionally, verification based on complete chloroplast genomes was performed and new chloroplast markers were developed and evaluated. The combination of these methods resulted in the successful identification of all cultivated Bupleurum individuals. Three chloroplast regions are recommended as additional barcodes for the genus: ycf4_cemA, psaJ_rpl33, and ndhE_ndhG. This is a reliable and promising strategy that can be applied to the authentication of natural products and the identification of other medicinal plant species with similar taxonomic problems. creator: Gaixia Zhang creator: Hui Wang creator: Linchun Shi creator: Yang Liu creator: Ruyu Yao creator: Chun Sui creator: Chengmin Yang creator: Hongliang Ji creator: Qiuling Wang creator: Jianhe Wei uri: https://doi.org/10.7717/peerj.13208 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Effect of extracts from eggs of Helix aspersa maxima and Helix aspersa aspersa snails on Caco-2 colon cancer cells link: https://peerj.com/articles/13217 last-modified: 2022-04-12 description: BackgroundColorectal cancer is the third most commonly diagnosed cancer. Natural compounds, administered together with conventional chemotherapeutic agent(s) and/or radiotherapy, may be a novel element in the combination therapy of this cancer. Considering the anticancer properties of compounds derived from different tissues of various snail species confirmed earlier, the purpose of the present research was to evaluate the effect of extracts from eggs of Helix aspera maxima and Helix aspersa aspersa snails, and fractions of extracts containing particles of different molecular weights on Caco-2 human epithelial colorectal adenocarcinoma cells.MethodsThe extracts and fractions were analyzed for antioxidant activity, phenols and total carbohydrates using colorimetric methods. Lipid peroxidation products and glutathione in eggs were also examined using these methods. Crude protein and fat in eggs were determined. Molecular weights of egg proteins and glycoproteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Astaxanthin, selected vitamins and amino acids in eggs were measured using liquid chromatography methods, and minerals by emission spectroscopy, mass spectrometry or X-ray fluorescence. The action of extracts on the cell viability was determined by the MTT (methylthiazolyldiphenyl-tetrazolium bromide) test, based on the mitochondrial oxidative activity, after 24 and 72 h of treatment. The influence of fractions on the cell viability was assayed after 24 h. The effect of extracts on the percentage of live and dead cells was evaluated by the trypan blue assay, in which live cells exclude trypan blue, while dead cells take up this dye, after 12, 24, 48 and 72 h of treatment. Their influence on the integrity of cell membranes was determined based on the activity of LDH (lactate dehydrogenase), released from damaged cells, after 24 and 72 h of treatment. Then, the effect of extracts on the content of lipid peroxidation products in cells was examined using colorimetric method, after 24 h of treatment. Their influence on types of cell death was determined by flow cytometry, after this time.ResultsThe extracts and their fractions containing molecules <3 kDa decreased the cell viability, after 24 h of treatment. The extracts reduced the percentage of live cells (also after 48 h), increased the degree of cell membrane damage and the amount of lipid peroxidation products, induced apoptosis and reduced necrosis.ConclusionsAntioxidants, phenols, lipid peroxidation products, anticancer peptides, restriction of methionine, appropriate ratio of essential amino acids to non-essential amino acids, vitamin D3, Ca, Mg, S, Cu, Mn, Zn, Se and other bioactive compounds comprised in the extracts and their additive and synergistic effects may have influenced Caco-2 cells. Natural extracts or the chemical compounds contained in them might be used in the combination therapy of colorectal cancer, which requires further research. creator: Magdalena Matusiewicz creator: Karolina Marczak creator: Barbara Kwiecińska creator: Julia Kupis creator: Klara Zglińska creator: Tomasz Niemiec creator: Iwona Kosieradzka uri: https://doi.org/10.7717/peerj.13217 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Matusiewicz et al. title: New insights into the cranial osteology of the Early Cretaceous paracryptodiran turtle Lakotemys australodakotensis link: https://peerj.com/articles/13230 last-modified: 2022-04-12 description: Lakotemys australodakotensis is an Early Cretaceous paracryptodire known from two shells and a skull from the Lakota Formation of South Dakota, USA. Along with the Early Cretaceous Arundelemys dardeni and the poorly known Trinitichelys hiatti, Lakotemys australodakotensis is generally retrieved as an early branching baenid, but more insights into the cranial anatomy of these taxa is needed to obtain a better understanding of paracryptodiran diversity and evolution. Here, we describe the skull of Lakotemys australodakotensis using micro-computed tomography to provide the anatomical basis for future phylogenetic analyses that will be needed to investigate more precisely the intrarelationships of Paracryptodira. Preliminary comparisons reveal that the cranial anatomy of Lakotemys australodakotensis is very similar to that of the Aptian-Albian basal baenid Arundelemys dardeni, that both taxa exhibit a remarkable combination of derived characters found in baenodds and characters found in non-baenid paracryptodires, particularly Pleurosternidae, and that Lakotemys australodakotensis is the only known baenid to date to possess a canal for the palatine artery. creator: Yann Rollot creator: Serjoscha W. Evers creator: Richard L. Cifelli creator: Walter G. Joyce uri: https://doi.org/10.7717/peerj.13230 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Rollot et al. title: Physical activity questionnaire for older children (PAQ-C): Arabic translation, cross-cultural adaptation, and psychometric validation in school-aged children in Saudi Arabia link: https://peerj.com/articles/13237 last-modified: 2022-04-12 description: The validity of the Physical Activity Questionnaire for Older Children (PAQ-C) has been mostly studied in North America and Europe. We investigated the psychometric validation of the Arabic version of the PAQ-C in students in Saudi Arabia. The students (n = 327, age = 8–14 years) of six primary schools in the Majmaah region participated in the study. Participants completed the PAQ-C, and their demographics were recorded. The PAQ-C scores satisfied the following factor analysis assumptions: diagonal elements of the anti-image correlation matrix (>0.5), Bartlett’s test of sphericity (p < 0.001), determinant (>0.00001), Kaiser–Meyer–Olkin test of sampling adequacy (>0.8), and communality (all values > 0.2). Exploratory factor analysis results were inconclusive, with two measures favoring a 2-factor solution (Kaiser’s criteria (Eigenvalue ≥ 1), and cumulative variance rule (>40%)); whereas, the scree test and the Monte Carlo parallel analysis favored a 1-factor structure. The confirmatory factor analysis favored a 1-factor solution: highest CFI, lowest RMSEA, non-significant χ2 statistics, and lowest χ2/df. The values of item-total correlation, corrected item-total correlation, and Cronbach’s alpha if an item was deleted, ranged from 0.20–0.57, 0.42–0.64, and 0.70–0.75, respectively. The PAQ-C showed a Cronbach’s alpha of 0.74. A 1-factor structure of the Arabic version of the PAQ-C had adequate psychometric validity in schoolchildren in Saudi Arabia. creator: Mohamed Sherif Sirajudeen creator: Mohamed Waly creator: Md. Dilshad Manzar creator: Mazen Alqahtani creator: Msaad Alzhrani creator: Ahmad Alanazi creator: Radhakrishnan Unnikrishnan creator: Hariraja Muthusamy creator: Rashmi Saibannavar creator: Wafa Alrubaia uri: https://doi.org/10.7717/peerj.13237 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sirajudeen et al. title: Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1 link: https://peerj.com/articles/13241 last-modified: 2022-04-12 description: Candidate phylum KSB1 is composed of uncultured bacteria and has been reported across various environments. However, the phylogeny and metabolic potential of KSB1 have not been studied comprehensively. In this study, phylogenomic analysis of KSB1 genomes from public databases and eleven metagenome-assembled genomes (MAGs) from marine and hydrothermal sediments revealed that those genomes were clustered into four clades. Isolation source and relative abundance of KSB1 genomes showed that clade I was particularly abundant in bioreactor sludge. Genes related to dissimilatory reduction of nitrate to ammonia (DNRA), the last step of denitrification converting nitrous oxide to nitrogen and assimilatory sulfur reduction were observed in the expanded genomes of clade I, which may due to horizontal gene transfer that frequently occurred in bioreactor. Annotation and metabolic reconstruction of clades II and IV showed flagellum assembly and chemotaxis genes in the genomes, which may indicate that exploration and sensing for nutrients and chemical gradients are critical for the two clades in deep-sea and hydrothermal sediment. Metabolic potentials of fatty acids and short-chain hydrocarbons utilization were predicted in clades I and IV of KSB1. Collectively, phylogenomic and metabolic analyses of KSB1 clades provide insight into their anaerobic heterotrophic lifestyle and differentiation in potential ecological roles. creator: Qingmei Li creator: Yingli Zhou creator: Rui Lu creator: Pengfei Zheng creator: Yong Wang uri: https://doi.org/10.7717/peerj.13241 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Factors related to overweight and obese populations maintaining metabolic health link: https://peerj.com/articles/13242 last-modified: 2022-04-12 description: BackgroundFor people who are overweight or obese, maintaining a metabolically healthy status can decrease the risks of developing cardiovascular diseases and Type 2 diabetes. Despite this, only a limited amount of research has discussed the metabolically healthy overweight and obesity (MHOO) population in Asia and the factors associated with them maintaining their metabolic health.MethodsThis study enrolled 195 MHOO participants from communities in northern Taiwan during 2009–2010 (baseline). Of the 195 participants, 89 completed the follow-up assessment after a median follow-up time of nine years. Body type was determined by body mass index (BMI, kg/m2). We defined overweight as a BMI ≥ 24 kg/m2 and <27 kg/m2 and defined obese as a BMI ≥ 27 kg/m2. Metabolic health was defined as the absence of cardiometabolic diseases and the presence of ≤1 of the cardiometabolic risk factors, namely hypertension, hyperglycemia, hypertriglyceridemia, and low serum high-density lipoprotein cholesterol. Metabolic health, BMI, and other covariates were evaluated at both baseline and follow-up. Generalized estimating equations (GEE) models were used to analyze the factors associated with maintenance of metabolic health during the follow-up period.ResultsAt baseline, the mean age of the study participants was 47.4 (SD 5.3) years and 46 (51.7%) of the participants were women. There were 51 (57.3%) individuals who maintained their metabolic health status at the time of the nine-year follow-up. The detrimental factors pertaining to metabolic health included older age, longer duration until follow-up, BMI ≥ 27 kg/m2, and increase in waist circumference. No significant relationships were observed between sociodemographic factors and lifestyle factors, such as sex, level of education, cigarette smoking, alcohol consumption, and physical activity, and sustained metabolic health among MHOO individuals.ConclusionsTo maintain metabolic health and prevent negative changes in health status, control of bodyweight and waist circumference should remain a priority for MHOO individuals even when there are no metabolic disorders present. creator: Yi-Hsuan Lin creator: Hsiao-Ting Chang creator: Yen-Han Tseng creator: Harn-Shen Chen creator: Shu-Chiung Chiang creator: Tzeng-Ji Chen creator: Shinn-Jang Hwang uri: https://doi.org/10.7717/peerj.13242 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lin et al. title: Icaritin attenuates 6-OHDA-induced MN9D cell damage by inhibiting oxidative stress link: https://peerj.com/articles/13256 last-modified: 2022-04-12 description: BackgroundWe assessed whether ICT can alleviate 6-OHDA-induced cell damage via inhibition of oxidative stress by evaluating the protective effect of icaritin (ICT) against 6-hydroxydopamine (6-OHDA)-induced MN9D cell damage and further determined the mechanism by which ICT reduces oxidative stress.MethodsMN9D cells were treated with 6-OHDA, to study the mechanism underlying the neuroprotective effect of ICT. MN9D cell damage was assessed by the CCK-8 assay, flow cytometry was performed to measure the content of reactive oxygen species (ROS) in cells, a superoxide dismutase (SOD) kit was used to evaluate SOD activity, and Western blotting was used to measure the expression of α-synuclein (α-Syn), Tyrosine hydroxylase (TH), nuclear factor erythroid-2 related factor 2 (Nrf2), and heme oxygenase-1 (HO-1).ResultsICT reduced damage to MN9D cells induced by 6-OHDA. ICT increased SOD activity and TH expression and reduced ROS production and α-Syn expression. ICT promoted the translocation of Nrf2 from the cytoplasm to the nucleus and further increased the protein expression of HO-1.ConclusionsICT protects against 6-OHDA-induced dopaminergic neuronal cell injury by attenuating oxidative stress, and the mechanism is related to modulate the activities of Nrf2, HO-1 protein, and SOD. creator: Xinyu Zhou creator: Nanqu Huang creator: Xiaoyi Hou creator: Li Zhu creator: Yiman Xie creator: Zhisheng Ba creator: Yong Luo uri: https://doi.org/10.7717/peerj.13256 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhou et al. title: Expression and promoter analysis of MEP pathway enzyme-encoding genes in Pinus massoniana Lamb link: https://peerj.com/articles/13266 last-modified: 2022-04-12 description: The methylerythritol phosphate (MEP) pathway provides the universal basic blocks for the biosynthesis of terpenoids and plays a critical role in the growth and development of higher plants. Pinus massoniana is the most valuable oleoresin producer tree with an extensive terrestrial range. It has the potential to produce more oleoresin with commercial value, while being resistant to pine wood nematode (PWN) disease. For this study, eleven MEP pathway associated enzyme-encoding genes and ten promoters were isolated from P. massoniana. Three PmDXS and two PmHDR existed as multi-copy genes, whereas the other six genes existed as single copies. All eleven of these MEP enzymes exhibited chloroplast localization with transient expression. Most of the MEP genes showed higher expression in the needles, while PmDXS2, PmDXS3, and PmHDR1 had high expression in the roots. The expressions of a few MEP genes could be induced under exogenous elicitor conditions. The functional complementation in a dxs-mutant Escherichia coli strain showed the DXS enzymatic activities of the three PmDXSs. High throughput TAIL PCR was employed to obtain the upstream sequences of the genes encoding for enzymes in the MEP pathway, whereby abundant light responsive cis-elements and transcription factor (TF) binding sites were identified within the ten promoters. This study provides a theoretical basis for research on the functionality and transcriptional regulation of MEP enzymes, as well as a potential strategy for high-resin generation and improved genetic resistance in P. massoniana. creator: Peihuang Zhu creator: Yu Chen creator: Fan Wu creator: Miaojing Meng creator: Kongshu Ji uri: https://doi.org/10.7717/peerj.13266 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhu et al. title: Ecomorphospace occupation of large herbivorous dinosaurs from Late Jurassic through to Late Cretaceous time in North America link: https://peerj.com/articles/13174 last-modified: 2022-04-11 description: Following the Late Jurassic, megaherbivore communities in North America undergo a dramatic turnover in faunal composition: sauropods decline to the point of becoming relatively minor components of ecosystems, stegosaurs become extinct, and hadrosaurids, ceratopsids and ankylosaurs rise in diversity and abundance. Although a variety of causes have been proposed to account for the dramatic decrease in sauropod diversity following the Late Jurassic and could have also been applicable to the disappearance of stegosaurs, the potential for competitive replacement of sauropods by hadrosauroids as an explanation has been previously dismissed due to morphological differences without further investigation. Using twelve ecomorphological correlates of the skull, this study provides a preliminary investigation into ecomorphospace occupation of major megaherbivore clades from the Late Jurassic through to the Late Cretaceous of North America and assess if morphological differences were enough to have potentially facilitated dietary niche partitioning between sauropods and iguanodontians and stegosaurs and ankylosaurs. Overlap in reconstructed ecomorphospace was observed between sauropods (particularly non-diplodocid sauropods) and iguanodontians, as would be expected if morphological differences were not enough to facilitate niche partitioning, contrary to original claims used to dismiss the competitive replacement hypothesis. Overlap was also observed between stegosaurs and ankylosaurs, particularly between Late Cretaceous ankylosaurs. Whether this overlap is reflective competitive replacement or opportunistic occupation of recently vacated niches will require further assessment as sampling of some clades prior to the Late Cretaceous is too poor to make a reliable assessment and several underlying assumptions necessary for competition to occur (e.g., resource limitation) still need investigation. Teasing out the cause(s) of the ‘sauropod decline’ and extinction of stegosaurs in North America following the Late Jurassic will require future research not only into the competitive exclusion hypothesis, but other hypotheses as well with better sampling from Early Cretaceous and Late Jurassic intervals. creator: Taia Wyenberg-Henzler uri: https://doi.org/10.7717/peerj.13174 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wyenberg-Henzler title: Effects of exergaming on executive function of older adults: a systematic review and meta-analysis link: https://peerj.com/articles/13194 last-modified: 2022-04-11 description: BackgroundExecutive function (EF) involves a series of high-level processes, such as inhibition, switching, and updating. Aging-related cognitive decline has been shown to be strongly associated with EF worsening. The aims of this study were to perform a meta-analysis to evaluate the effects of exergaming, an emerging intervention, on EF performance in older adults and to conduct a moderator analysis of exergaming effects on EF.MethodsRandomized controlled trials examining exergaming influences on EF in older adults were collated by searching the Web of Science, Elsevier Science, PubMed, and Google Scholar databases. Statistical data were quantified in Comprehensive Meta-analysis software. Overall EF and EF domains (inhibition, switching, and updating) were analyzed separately.ResultsA total of 15 studies were included. The meta-analysis results indicated that exergaming had a significant influence on overall EF in the older adult (standardized mean difference (SMD) = 0.349, 95% confidence interval (CI) [0.191–0.506], p < 0.001). The same effects were also found in EF domains of inhibition (SMD = 0.415, 95% CI [0.102–0.729], p = 0.009), switching (SMD = 0.243, 95% CI [0.071–0.415], p = 0.005), and updating (SMD = 0.366, 95% CI [0.140–0.592], p = 0.002). The effects of exergaming on overall EF were found to be moderated by the frequency of the intervention (Q(1) = 3.537, p = 0.06).ConclusionExergaming was confirmed to improve overall EF, as well as in older adults, and the effect of exergaming on EF was shown to be moderated by intervention frequency. creator: Jiahui Jiang creator: Wei Guo creator: Biye Wang uri: https://doi.org/10.7717/peerj.13194 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Jiang et al. title: A model of multiple tumor marker for lymph node metastasis assessment in colorectal cancer: a retrospective study link: https://peerj.com/articles/13196 last-modified: 2022-04-11 description: BackgroundAssessment of colorectal cancer (CRC) lymph node metastasis (LNM) is critical to the decision of surgery, prognosis, and therapy strategy. In this study, we aimed to develop and validate a multiple tumor marker nomogram for predicting LNM in CRC patients.MethodsA total of 674 patients who met the inclusion criteria were collected and randomly divided into primary cohort and internal test cohort at a ratio of 7:3. An external test cohort enrolled 178 CRC patients from the West China Hospital. Clinicopathologic variables were obtained from electronic medical records. The least absolute shrinkage and selection operator (LASSO) and interquartile range analysis were carried out for variable dimensionality reduction and feature selection. Multivariate logistic regression analysis was conducted to develop predictive models of LNM. The performance of the established models was evaluated by the receiver operating characteristic (ROC) curve, calibration belt, and clinical usefulness.ResultsBased on minimum criteria, 18 potential features were reduced to six predictors by LASSO and interquartile range in the primary cohort. The model demonstrated good discrimination and ROC curve (AUC = 0.721 in the internal test cohort, AUC = 0.758 in the external test cohort) in LNM assessment. Good calibration was shown for the probability of CRC LNM in the internal and external test cohorts. Decision curve analysis illustrated that multi-tumor markers nomogram was clinically useful.ConclusionsThe study proposed a reliable nomogram that could be efficiently and conveniently utilized to facilitate the assessment of individually-tailored LNM in patients with CRC, complementing imaging and biopsy tests. creator: Jiangping Fu creator: Mengjie Tu creator: Yin Zhang creator: Yan Zhang creator: Jiasi Wang creator: Zhaoping Zeng creator: Jie Li creator: Fanxin Zeng uri: https://doi.org/10.7717/peerj.13196 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fu et al. title: A long noncoding RNA GTF2IRD2P1 suppresses cell proliferation in bladder cancer by inhibiting the Wnt/β‑catenin signaling pathway link: https://peerj.com/articles/13220 last-modified: 2022-04-11 description: BackgroundThere is growing evidence that long non-coding RNAs (LncRNAs) are key in the development of a variety of human tumors. However, the role of lncRNA GTF2IRD2P1 has not been well studied in cancer. The impact of GTF2IRD2P1 on the biological function and clinical relevance in bladder cancer is largely unknown. This study aimed to investigate the biological role of GTF2IRD2P1 in bladder evolution and carcinogenesis.MethodsWe used bioinformatics to obtain the lncRNA GTF2IRD2P1 from bladder urothelial carcinoma (BLCA) in The Cancer Genome Atlas (TCGA) database. The expression of lncRNA GTF2IRD2P1 was detected by qRT-PCR. The CCK8 assay and flow cytometry were used to detect the lncRNA GTF2IRD2P1 function on the proliferation of bladder cancer cells. A western blot was used to calculate the protein level of cell cycle proteins and Wnt signaling pathway proteins. The effect of lncRNA GTF2IRD2P1 on tumorigenesis of bladder cancer was confirmed by a xenograft nude mouse model.ResultsGTF2IRD2P1 expression was found to be lower in both human bladder cancer tissues and cell lines (UM-UC-3, RT4, and 5637), and elevated in T24 compared to the corresponding normal controls. GTF2IRD2P1 expression was also enhanced after transfection of UM-UC-3 cells with the overexpression vector. Meanwhile, overexpression of GTF2IRD2P1 inhibited the proliferation of UM-UC-3 and prolonged the cell cycle. The silencing of GTF2IRD2P1 significantly increased the proliferation and shortened the cell cycle of T24 cells and induced Wnt signaling activity to promote the progression of bladder cancer. Similarly, the transplanted tumor nude mouse model demonstrated that silencing GTF2IRD2P1 strengthens the progression of bladder cancer by targeting the Wnt signaling pathway. creator: Zhuo Huang creator: Hongbin Gao creator: Liangliang Qing creator: Biao Wang creator: Chaoyong He creator: Ning Luo creator: Chuncheng Lu creator: Shipeng Fan creator: Peng Gu creator: Hui Zhao uri: https://doi.org/10.7717/peerj.13220 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Huang et al. title: The effect of the COVID-19 pandemic on health care workers’ anxiety levels: a meta-analysis link: https://peerj.com/articles/13225 last-modified: 2022-04-11 description: BackgroundThe COVID-19 pandemic has been declared a public health emergency of international concern, causing excessive anxiety among health care workers. Additionally, publication bias and low-quality publications have become widespread, which can result in the dissemination of unreliable information. A meta-analysis was performed for this study with the following two aims: (1) to examine the prevalence of anxiety among health care workers and determine whether it has increased owing to the COVID-19 pandemic and (2) to investigate whether there has been an increase in publication bias.MethodsAll relevant studies published between 2015 and 2020 were searched in electronic databases (namely Web of Science, PubMed, Embase, PsycInfo, PsyArXiv, and medRxiv). The heterogeneity of the studies was assessed using the I2 statistic. The effect size (prevalence rate of anxiety) and 95% CI for each study were also calculated. We used moderator analysis to test for the effect of the COVID-19 pandemic on health care workers’ anxiety levels and to detect publication bias in COVID-19 studies. We assessed publication bias using funnel plots and Egger’s regression.ResultsA total of 122 studies with 118,025 participants met the inclusion criteria. Eighty-eight articles (75,066 participants) were related to COVID-19, 13 articles (9,222 participants) were unrelated to COVID-19 (i.e., articles related to other outbreaks, which were excluded), and 21 preprints (33,737 participants) were related to COVID-19. The pooled meta-analysis prevalence was 33.6% (95% CI [30.5−36.8]; 95% PI [6.5−76.3]). Moderator analysis revealed no significant differences between articles related to COVID-19 and those unrelated to COVID-19 (p = 0.824). Moreover, no significant differences were found between articles and preprints related to COVID-19 (p = 0.843). Significant heterogeneity was observed in each subgroup. An Egger’s test revealed publication bias in both articles and preprints related to COVID-19 (p < 0.001).ConclusionsDetermining whether the anxiety state of health care workers is altered by the COVID-19 pandemic is currently difficult. However, there is evidence that their anxiety levels may always be high, which suggests that more attention should be paid to their mental health. Furthermore, we found a substantial publication bias; however, the quality of the studies was relatively stable and reliable. creator: Lunbo Zhang creator: Ming Yan creator: Kaito Takashima creator: Wenru Guo creator: Yuki Yamada uri: https://doi.org/10.7717/peerj.13225 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Diel gene expression improves software prediction of cyanobacterial operons link: https://peerj.com/articles/13259 last-modified: 2022-04-11 description: Cyanobacteria are important participants in global biogeochemical process, but their metabolic processes and genomic functions are incompletely understood. In particular, operon structure, which can provide valuable metabolic and genomic insight, is difficult to determine experimentally, and algorithmic operon predictions probably underestimate actual operon extent. A software method is presented for enhancing current operon predictions by incorporating information from whole-genome time-series expression studies, using a Machine Learning classifier. Results are presented for the marine cyanobacterium Crocosphaera watsonii. A total of 15 operon enhancements are proposed. The source code is publicly available. creator: Philip Heller uri: https://doi.org/10.7717/peerj.13259 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Heller title: Times and partners are a-changin’: relationships between declining food abundance, breeding success, and divorce in a monogamous seabird species link: https://peerj.com/articles/13073 last-modified: 2022-04-08 description: Seabirds exhibit considerable adjustment capacity to cope with environmental changes during the breeding season and to maximize lifetime reproductive output. For example, divorce has been proposed to be an adaptive behavioral strategy in social monogamous species, as a response to poor conditions and low breeding success. Here, we studied divorce at the population and individual levels in northern gannets (Morus bassanus, hereafter gannets) nesting on Bonaventure island (Quebec, Canada). At the population level, we used Granger’s method for detecting and quantifying temporal causality between time series (from 2009 to 2019) of divorce rate and breeding success of gannets (n = 809) and we evaluated the relationship between breeding success and biomass of their two principal prey (Atlantic mackerel, Scomber scombrus, and Atlantic herring, Clupea harengus). Our results indicated that breeding success is mainly influenced by the spawning-stock biomass of Atlantic mackerel, and a decrease in breeding success is followed by an increase in divorce rate with a 1-year lag. However, the effect of the interaction between breeding success and year on the proportion of individuals that divorced showed significant inter-annual variation. At the individual level, our results support the adaptive strategy hypothesis of divorce. Indeed, gannets that changed partners did so following a reproductive failure, and there was an increase in breeding success 1 year following the divorce. Being central place foragers, opportunities for dispersal and adaptation are often limited for breeding seabirds in a context of low food abundance. We suggest that behavioral flexibility expressed as divorce would be an efficient short-term strategy for maintaining reproductive performance. creator: David Pelletier creator: Magella Guillemette uri: https://doi.org/10.7717/peerj.13073 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pelletier and Guillemette title: The effect of delirium information training given to intensive care nurses on patient care: quasi-experimental study link: https://peerj.com/articles/13143 last-modified: 2022-04-08 description: BackgroundTraining programs aiming to improve delirium diagnosis and management skills increase nurses’ care efficiency and improve patients’ health outcomes. This study was conducted to examine the effect of delirium information training on patient care by intensive care nurses.MethodsIn the research, one group pretest-posttest quasi-experimental design was used. The study sample consisted of 30 nurses working in four intensive care units of a university hospital between November 05, 2018, and February 15, 2019. The Personal Information Form, the Checklist for the Care of the Patient in Delirium, and the Confusion Assessment Scale for the Intensive Care Unit were used to collect the data. Intensive care nurses were provided with information training supported by a training booklet in two sessions of 40 min each.ResultsIn the study, according to the Checklist for the Care of the Patient in Delirium, while the pre-test point average of the nurses was 6.17 ± 2.29, the post-test point average had increased to 11.17 ± 1.51 (p < 0.001). After the training, it was determined that there was a significant increase in the percentage of nurses who stated that they evaluated and detected whether their patients had pain, hallucinations, and delusions (p < 0.001). As a result, it has been determined that providing delirium information training to intensive care nurses positively affects the care of patients with delirium. In addition, it has been determined that with the Confusion Assessment Scale for Intensive Care Unit, nurses can provide the care they need to patients at risk in terms of delirium by identifying delirium. creator: Fulya Yıldırım creator: Serpil Türkleş creator: Hilal Altundal Duru uri: https://doi.org/10.7717/peerj.13143 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yıldırım et al. title: Quantitative trait loci mapping and candidate gene analysis of stoma-related traits in wheat (Triticum aestivum L.) glumes link: https://peerj.com/articles/13262 last-modified: 2022-04-08 description: The photosynthesis of wheat glumes makes important contributions to the yield. Stomata play a crucial role in regulating photosynthesis and transpiration in plants. However, the genetic base of wheat glume stomata is not fully understood. In this study, stomatal length (SL), stomatal width (SW), stomatal density (SD), potential conductance index (PCI) of stomata, stomatal area (SA), and stomatal relative area (SRA) were measured in different parts of wheat glumes from a doubled haploid (DH) population and their parents. Quantitative trait loci (QTLs) of these traits were anchored on a high-density genetic linkage map of the DH population. A total of 61 QTLs for stoma-related traits were mapped onto 16 chromosomes, and each one accounted for 3.63 to 19.02% of the phenotypic variations. Two QTL hotspots were detected in two marker intervals, AX-109400932∼AX-110985652 and AX-108972184∼AX-108752564, on chromosome 6A. Five possibly candidate genes (TraesCS6A02G105400, TraesCS6A02G106400, TraesCS6A02G115100, TraesCS6A02G115400, and TraesCS6A02G116200) for stoma-related traits of wheat glumes were screened out , according to their predicted expression levels in wheat glumes or spikes. The expression of these genes may be induced by a variety of abiotic stresses. These findings provide insights for cloning and functional characterization of stoma-related candidate genes in wheat glumes. creator: Ning Li creator: Fanfan Dong creator: Tongtong Liu creator: Jinwen Yang creator: Yugang Shi creator: Shuguang Wang creator: Daizhen Sun creator: Ruilian Jing uri: https://doi.org/10.7717/peerj.13262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: The association between Geographic Information System-based neighborhood built environmental factors and accelerometer-derived light-intensity physical activity across the lifespan: a cross-sectional study link: https://peerj.com/articles/13271 last-modified: 2022-04-08 description: BackgroundEvidence on associations between environmental factors and accelerometer-derived light-intensity physical activity (LPA) is scarce. The aim of this study was to examine associations between Geographic Information System (GIS)-based neighborhood built environmental factors and accelerometer-derived LPA, and to investigate the moderating effect of age group (adolescents, adults, older adults) on these associations.MethodsObjective data were used from three similar observational studies conducted in Ghent (Belgium) between 2007 and 2015. Accelerometer data were collected from 1,652 participants during seven consecutive days, and GIS-based neighborhood built environmental factors (residential density, intersection density, park density, public transport density, entropy index) were calculated using sausage buffers of 500 m and 1,000 m around the home addresses of all participants. Linear mixed models were performed to estimate the associations.ResultsA small but significant negative association was observed between residential density (500 m buffer) and LPA in the total sample (B = −0.002; SE = 0.0001; p = 0.04), demonstrating that every increase of 1,000 dwellings per surface buffer was associated with a two minute decrease in LPA. Intersection density, park density, public transport density and entropy index were not related to LPA, and moderating effects of age group were absent.ConclusionsThe small association, in combination with other non-significant associations suggests that the neighborhood built environment, as classically measured in moderate-to-vigorous intensity physical activity research, is of limited importance for LPA. More research is needed to unravel how accelerometer-derived LPA is accumulated, and to gain insight into its determinants. creator: Sofie Compernolle creator: Lieze Mertens creator: Jelle Van Cauwenberg creator: Iris Maes creator: Delfien Van Dyck uri: https://doi.org/10.7717/peerj.13271 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Compernolle et al. title: The regulation of hsacirc_004413 promotes proliferation and drug resistance of gastric cancer cells by acting as a competing endogenous RNA for miR-145-5p link: https://peerj.com/articles/12629 last-modified: 2022-04-07 description: BackgroundWhether circRAN, which acts as a microRNA sponge, plays a role in 5-fluorouracil (5-Fu) resistant gastric cancer has not been reported. In this study, a 5-Fu resistant cell line with an IC50 of 16.59 µM was constructed.MethodsUsing comparative analysis of circRNA in the transcriptomics of resistant and sensitive strains, 31 differentially expressed circRNAs were detected, and the microRNA interacting with them was predicted.ResultsHsacirc_004413 was selected for verification in drug resistant and sensitive cells. By interfering with hsacirc_004413 using antisense RNA, the sensitivity of drug resistant cells to 5-Fu was significantly promoted, and the apoptosis and necrosis of the cells were significantly increased. In sensitive cells, inhibition by inhibitors enhanced the resistance of cells to 5-Fu. We hypothesize that hsacirc_004413 makes gastric cancer cells resistant to 5-Fu mainly through adsorption of miR-145-5p. creator: Fusheng Zhou creator: Weiqun Ding creator: Qiqi Mao creator: Xiaoyun Jiang creator: Jiajie Chen creator: Xianguang Zhao creator: Weijia Xu creator: Jiaxin Huang creator: Liang Zhong creator: Xu Sun uri: https://doi.org/10.7717/peerj.12629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhou et al. title: The first fossil immature of Elmidae: an unusual riffle beetle larva preserved in Baltic amber link: https://peerj.com/articles/13025 last-modified: 2022-04-07 description: Elmidae, riffle beetles, have both adult and immature stages that show specializations for water environments. Fossils of adults of Elmidae are already known from amber, however a record of immatures was so far lacking. We report here the first fossil larva of Elmidae, preserved in Baltic amber. To be able to access details of the body hidden by inclusions and “Verlumung” we conducted, in addition to optical documentation methods, micro-CT and synchrotron documentation methods. The larva is characterised by prominent dorso-lateral and lateral processes and a plate-like ventral operculum at the end of the abdomen. The new fossil has similarities in the general body shape and the prominent characters with some modern larvae of Elmidae. The posterior protrusions on the trunk end possibly represent gills, which would imply that fossil larvae of Elmidae also led a water-related life style similar to modern representatives. creator: Ana Zippel creator: Viktor A. Baranov creator: Jörg U. Hammel creator: Marie K. Hörnig creator: Carolin Haug creator: Joachim T. Haug uri: https://doi.org/10.7717/peerj.13025 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zippel et al. title: Antagonistic co-contraction can minimize muscular effort in systems with uncertainty link: https://peerj.com/articles/13085 last-modified: 2022-04-07 description: Muscular co-contraction of antagonistic muscle pairs is often observed in human movement, but it is considered inefficient and it can currently not be predicted in simulations where muscular effort or metabolic energy are minimized. Here, we investigated the relationship between minimizing effort and muscular co-contraction in systems with random uncertainty to see if muscular co-contraction can minimize effort in such system. We also investigated the effect of time delay in the muscle, by varying the time delay in the neural control as well as the activation time constant. We solved optimal control problems for a one-degree-of-freedom pendulum actuated by two identical antagonistic muscles, using forward shooting, to find controller parameters that minimized muscular effort while the pendulum remained upright in the presence of noise added to the moment at the base of the pendulum. We compared a controller with and without feedforward control. Task precision was defined by bounding the root mean square deviation from the upright position, while different perturbation levels defined task difficulty. We found that effort was minimized when the feedforward control was nonzero, even when feedforward control was not necessary to perform the task, which indicates that co-contraction can minimize effort in systems with uncertainty. We also found that the optimal level of co-contraction increased with time delay, both when the activation time constant was increased and when neural time delay was added. Furthermore, we found that for controllers with a neural time delay, a different trajectory was optimal for a controller with feedforward control than for one without, which indicates that simulation trajectories are dependent on the controller architecture. Future movement predictions should therefore account for uncertainty in dynamics and control, and carefully choose the controller architecture. The ability of models to predict co-contraction from effort or energy minimization has important clinical and sports applications. If co-contraction is undesirable, one should aim to remove the cause of co-contraction rather than the co-contraction itself. creator: Anne D. Koelewijn creator: Antonie J. Van Den Bogert uri: https://doi.org/10.7717/peerj.13085 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Koelewijn and Van Den Bogert title: Alleviation of drought stress by root-applied thiourea is related to elevated photosynthetic pigments, osmoprotectants, antioxidant enzymes, and tubers yield and suppressed oxidative stress in potatoes cultivars link: https://peerj.com/articles/13121 last-modified: 2022-04-07 description: The growth and productivity of plants are enhanced by the use of thiourea (TU) under stressful conditions. When TU is applied as a rooting medium, it improves plant growth characteristics and other physiological parameters in stressed environment. A pot experiment was conducted in the botanical garden of the Government College University, Faisalabad 38000, Pakistan to examine the TU-mediated fluctuations in some crucial physio-biochemical parameters and the oxidative defense of potatoes under a restricted water supply. For this purpose, two potato cultivars (potato-SH-5 and potato-FD-73) were sown in pots containing 10 kg of soil. Water was regularly applied to the pots until germination. After 2 weeks of germination, drought stress with 65% field capacity was imposed, while the control was subjected to 100% field capacity. TU, as a rooting medium, was applied at the vegetative stage (0 (no application), 0.5, 0.75 mM). A substantial reduction in the total number of leaves, leaf area, tuber biomass (fresh and dry weight), photosynthetic pigments, membrane permeability, and leaf relative water content (RWC) was recorded in plants under drought stress conditions as compared to control plants. The damaging effects of water stress were more critical for cv. potato-FD-73 as compared to cv. potato-SH-5. In contrast, drought stress enhanced the malondialdehyde (MDA) and hydrogen peroxide (H2O2) content while also increased antioxidant enzyme activities (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)) and triggered the accumulation of soluble proteins, soluble sugars, proline, and phenolic and anthocyanin contents. However, TU applied as rooting medium at 0.5 and 0.75 mM was effective in reducing the detrimental effects of water stress in both cultivars. Furthermore, increasing levels of TU enhanced chlorophyll pigments, dissolved proteins, complete dissolved sugars, and enzymatic capabilities of POD, SOD, and CAT, while reducing the MDA and H2O2 in both cultivars under stress conditions. In conclusion, TU improved the yield and chlorophyll pigments of potato plants by mitigating the adverse effects of drought stress through reduced EL, MDA, and H2O2 contents and improved activities of enzymatic and non-enzymatic antioxidants and osmoprotectants. creator: Muhammad Hamzah Saleem creator: Xiukang Wang creator: Abida Parveen creator: Shagufta Perveen creator: Saqib Mehmood creator: Sajid Fiaz creator: Sajjad Ali creator: Sajjad Hussain creator: Muhammad Adnan creator: Naeem Iqbal creator: Aishah Alatawi creator: Shafaqat Ali uri: https://doi.org/10.7717/peerj.13121 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Saleem et al. title: The soft tissue and skeletal anatomy of two Late Jurassic ichthyosaur specimens from the Solnhofen archipelago link: https://peerj.com/articles/13173 last-modified: 2022-04-07 description: Ichthyosaurs from the Solnhofen Lagerstätte are among the only examples of soft tissue preservation in the major Middle Jurassic–middle Cretaceous family Ophthalmosauridae. However, few such specimens are currently described, and the taphonomical pathways for the preservation of soft tissue are not well understood. In order to answer this, two new ichthyosaur specimens, one nearly complete and one isolated tail, are described here. The nearly complete specimen is assigned to Aegirosaurus sp. It is accompanied by large amounts of incrustation pseudomorphs (epimorphs) of soft tissue preserved as apatite. It also preserves a nearly complete gastral basket, for the first time in ophthalmosaurids. Soft tissue samples were analyzed using X-ray diffraction (XRD) and scanning electron microscopy (SEM) coupled with energy dispersive spectroscopy (EDS) analysis. The analyses confirm the presence of apatite, with phosphate most likely derived from the body itself. creator: Lene L. Delsett creator: Henrik Friis creator: Martina Kölbl-Ebert creator: Jørn H. Hurum uri: https://doi.org/10.7717/peerj.13173 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Delsett et al. title: Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine link: https://peerj.com/articles/13207 last-modified: 2022-04-07 description: The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae. creator: Luiz Henrique M. Fonseca creator: Alison G. Nazareno creator: Verônica A. Thode creator: Alexandre R. Zuntini creator: Lúcia G. Lohmann uri: https://doi.org/10.7717/peerj.13207 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Fonseca et al. title: A new basal ichthyosauromorph from the Lower Triassic (Olenekian) of Zhebao, Guangxi Autonomous Region, South China link: https://peerj.com/articles/13209 last-modified: 2022-04-07 description: Here we describe a newly discovered basal ichthyosauromorph from the Lower Triassic of South China, Baisesaurus robustus gen. et sp. nov. The only known specimen of this new species was collected from the Lower Triassic (Olenekian) Luolou Formation in the Zhebao region of Baise City, on the northwest margin of the Nanpanjiang Basin, and comprises a partial skeleton including the ribs, the gastralia, a limb element, 12 centra, and seven neural arches. Comparisons to a wide variety of Early Triassic marine reptiles show Baisesaurus robustus to be a basal ichthyosauromorph based on the following features: neural arches lack transverse processes; dorsal ribs are slender, and not pachyostotic even proximally; and median gastral elements have long, sharp anterior processes. The limb element is long and robust, and is most likely to be a radius. Baisesaurus robustus is large (estimated length more than 3 m) relative to early ichthyosauromorphs previously discovered in China, and shares noteworthy morphological similarities with Utatsusaurus hataii, particularly with regard to body size and the morphology of the probable radius. Baisesaurus robustus also represents the first record of an Early Triassic ichthyosauromorph from Guangxi Autonomous Region, extending the known geographic distribution of ichthyosauromorphs in South China. creator: Jicheng Ren creator: Haishui Jiang creator: Kunpeng Xiang creator: Corwin Sullivan creator: Yongzhong He creator: Long Cheng creator: Fenglu Han uri: https://doi.org/10.7717/peerj.13209 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ren et al. title: Burden of COVID-19: a preliminary analysis in the population of Saudi Arabia link: https://peerj.com/articles/13219 last-modified: 2022-04-07 description: BackgroundCoronavirus infection (COVID-19) has resulted in an unprecedented number of human deaths and economic losses. Analyzing the role of disease in different groups of people is useful for determining the burden of disease. As a result, the purpose of this study was to investigate the influence of COVID-19 on the Saudi Arabian population’s quality of life, with a particular emphasis on the likely fall in their life expectancy.MethodsA cross-sectional and retrospective analysis of 2,988 patients’ databases was performed to assess COVID-19-induced mortality and complications in the community. The data was gathered from official websites that track the disease’s impact daily between July and October 2021. On the acquired data, disability-adjusted life years (DALYs) and relative risk analysis were performed. The data was statistically analyzed using SPSS IBM 25. The Pearson’s correlation test was used to examine the relationship between age and disease impact. The significance of the findings was determined by using a P value of less than 0.05.ResultsThe data from the study indicated that the positive test rate, infection rate, and mortality rate in the population were 1.84% [+0.11/-0.39 of 95% confidence interval (CI)], 1.54% (+0.38/-0.52 of CI), and 1.59% (+0.4/-0.7 of CI), respectively. Highest percentage of mortality was observed in Riyadh (17%), followed by Jeddah (8.7%) and Makkah (7.5%). The DALYs/100,000 inhabitants increased progressively as the age of the population increased, and the highest value was found for those over 70 years old (25.73 ± 2.09). Similarly, the risk outcome (55%) increased significantly (p = 0.037) from 40 years onwards, and the maximum was observed at above 70 years (184%, p = 0.006). The correlation analysis indicated a significant association (p = 0.032) between age and COVID-19 induced mortality from the 40-year-old population onwards.ConclusionThe current study found that the COVID-19 load in Saudi Arabia was comparable to that in nations that were said to have performed well during the pandemic. DALYs increased from 40 years to 60 years, although people over 60 years had a lower life expectancy and were more susceptible to infection. After 60 years, the occurrence of numerous co-morbid illnesses may have added to the population’s burden of COVID-19. Further research in this area may yield a more precise estimate of the COVID-19-induced burden on the entire population. creator: Syed Mohammed Basheeruddin Asdaq creator: Syed Imam Rabbani creator: Mohammed Kanan Alshammari creator: Reem Saud Alshammari creator: Mehnaz Kamal creator: Mohd Imran creator: Noufah Aqeel AlShammari creator: May Faiz Al Twallah creator: Abdulmjeed Hussain Alshahrani uri: https://doi.org/10.7717/peerj.13219 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Asdaq et al. title: Validating an inertial measurement unit for cricket fast bowling: a first step in assessing the feasibility of diagnosing back injury risk in cricket fast bowlers during a tele-sport-and-exercise medicine consultation link: https://peerj.com/articles/13228 last-modified: 2022-04-07 description: This study aimed to validate an array-based inertial measurement unit to measure cricket fast bowling kinematics as a first step in assessing feasibility for tele-sport-and-exercise medicine. We concurrently captured shoulder girdle relative to the pelvis, trunk lateral flexion, and knee flexion angles at front foot contact of eight cricket medium-fast bowlers using inertial measurement unit and optical motion capture. We used one sample t-tests and 95% limits of agreement (LOA) to determine the mean difference between the two systems and Smallest Worth-while Change statistic to determine whether any differences were meaningful. A statistically significant (p < 0.001) but small mean difference of −4.7° ± 8.6° (95% Confidence Interval (CI) [−3.1° to −6.4°], LOA [−22.2 to 12.7], SWC 3.9°) in shoulder girdle relative to the pelvis angle was found between the systems. There were no statistically significant differences between the two systems in trunk lateral flexion and knee flexion with the mean differences being 0.1° ± 10.8° (95% CI [−1.9° to 2.2°], LOA [−22.5 to 22.7], SWC 1.2°) and 1.6° ± 10.1° (95% CI [−0.2° to 3.3°], LOA [−19.2 to 22.3], SWC 1.9°) respectively. The inertial measurement unit-based system tested allows for accurate measurement of specific cricket fast bowling kinematics and could be used in determining injury risk in the context of tele-sport-and-exercise-medicine. creator: Keegan Harnett creator: Brenda Plint creator: Ka Yan Chan creator: Benjamin Clark creator: Kevin Netto creator: Paul Davey creator: Sean Müller creator: Simon Rosalie uri: https://doi.org/10.7717/peerj.13228 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Harnett et al. title: Historical significance and taxonomic status of Ischyrodon meriani (Pliosauridae) from the Middle Jurassic of Switzerland link: https://peerj.com/articles/13244 last-modified: 2022-04-07 description: Ischyrodon meriani is an obscure pliosaurid taxon established upon an exceptionally large tooth crown of a probable Callovian (Middle Jurassic) age that originates from Wölflinswil, Canton of Aargau, Switzerland. Despite being known for almost two centuries, the specimen remains poorly researched. Historically, I. meriani has been associated, or even considered conspecific, with Pliosaurus macromerus and Liopleurodon ferox. However, neither of the two hypotheses have been tested through detailed comparisons or using modern quantitative methods. Here, we redescribe the type of Ischyrodon meriani, illustrate it, and compare to teeth of thalassophonean pliosaurids, with special focus on Jurassic representatives of the clade. Multivariate analyses show close similarities to L. ferox but comparable structures to those of I. meriani, including a distinctive pattern of the apicobasal ridges, are also observable in some mid-Cretaceous brachauchenines from the ‘Polyptychodon’ assemblage of East and South East England. While it is likely that I. meriani represents a Liopleurodon-like taxon, or is indeed conspecific with L. ferox, which would make I. meriani the proper name for the species, any such taxonomic considerations are hindered by the fragmentary nature of the type specimens of both these taxa as well as limited knowledge of the dental variability within and between individual jaws of L. ferox. Currently, I. meriani is best treated as a nomen dubium. Finally, we discuss the potential implications of I. meriani being conspecific with L. ferox, and additionally provide a commentary on the taxonomic status of Liopleurodon. creator: Daniel Madzia creator: Sven Sachs creator: Christian Klug uri: https://doi.org/10.7717/peerj.13244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Madzia et al. title: Soil metabolomics and bacterial functional traits revealed the responses of rhizosphere soil bacterial community to long-term continuous cropping of Tibetan barley link: https://peerj.com/articles/13254 last-modified: 2022-04-07 description: Continuous cropping often leads to an unbalanced soil microbial community, which in turn negatively affects soil functions. However, systematic research of how these effects impact the bacterial composition, microbial functional traits, and soil metabolites is lacking. In the present study, the rhizosphere soil samples of Tibetan barley continuously monocropped for 2 (CCY02), 5 (CCY05), and 10 (CCY10) years were collected. By utilizing 16S high-throughput sequencing, untargeted metabolomes, and quantitative microbial element cycling smart chips, we examined the bacterial community structure, soil metabolites, and bacterial functional gene abundances, respectively. We found that bacterial richness (based on Chao1 and Phylogenetic Diversity [PD] indices) was significantly higher in CCY02 and CCY10 than in CCY05. As per principal component analysis (PCA), samples from the continuous monocropping year tended to share more similar species compositions and soil metabolites, and exhibited distinct patterns over time. The results of the Procrustes analysis indicated that alterations in the soil metabolic profiles and bacterial functional genes after long-term continuous cropping were mainly mediated by soil microbial communities (P < 0.05). Moreover, 14 genera mainly contributed to the sample dissimilarities. Of these, five genera were identified as the dominant shared taxa, including Blastococcus, Nocardioides, Sphingomonas, Bacillus, and Solirubrobacter. The continuous cropping of Tibetan barley significantly increased the abundances of genes related to C-degradation (F = 9.25, P = 0.01) and P-cycling (F = 5.35, P = 0.03). N-cycling significantly negatively correlated with bacterial diversity (r =  − 0.71, P = 0.01). The co-occurrence network analysis revealed that nine hub genera correlated with most of the functional genes and a hub taxon, Desulfuromonadales, mainly co-occurred with the metabolites via both negative and positive correlations. Collectively, our findings indicated that continuous cropping significantly altered the bacterial community structure, functioning of rhizosphere soils, and soil metabolites, thereby providing a comprehensive understanding of the effects of the long-term continuous cropping of Tibetan barley. creator: Yuan Zhao creator: Youhua Yao creator: Hongyan Xu creator: Zhanling Xie creator: Jing Guo creator: Zhifan Qi creator: Hongchen Jiang uri: https://doi.org/10.7717/peerj.13254 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhao et al. title: Physical and functional properties of fish gelatin-based film incorporated with mangrove extracts link: https://peerj.com/articles/13062 last-modified: 2022-04-06 description: BackgroundThe fishery processing industry produces a remarkable number of by-products daily. Fish skin accounts for one of the significant wastes produced. Fish skin, however, can be subjected to extraction to yield gelatine and used as the primary raw material for edible film production. To increase the functionality of edible films, bioactive compounds can be incorporated into packaging. Mangroves produce potential bioactive compounds that are suitable as additional agents for active packaging. This study aimed to create a fish gelatine-based edible film enriched with mangrove extracts and to observe its mechanical and biological properties.MethodsTwo mangrove species (Bruguiera gymnorhiza and Sonneratia alba) with four extract concentrations (control, 0.05%, 0.15%, 0.25%, and 0.35%) were used to enrich edible films. The elongation, water vapour transmission, thickness, tensile strength, moisture content, antioxidant and antibacterial properties of the resulting packaging were analysed.ResultsThe results showed that the mangrove species and extract concentration significantly affected (p < 0.05) the physical properties of the treated films such as elongation (16.89–19.38%), water vapour transmission (13.31–13.59 g/m2), and active packaging-antioxidant activities (12.36%–60.98%). The thickness, tensile strength, and water content were not significantly affected. Potent antioxidant activity and relatively weak antimicrobial activity of this active gelatine packaging were observed. creator: Rahmi Nurdiani creator: Rica D.A. Ma’rifah creator: Ihda K. Busyro creator: Abdul A. Jaziri creator: Asep A. Prihanto creator: Muhamad Firdaus creator: Rosnita A. Talib creator: Nurul Huda uri: https://doi.org/10.7717/peerj.13062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nurdiani et al. title: Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs link: https://peerj.com/articles/13133 last-modified: 2022-04-06 description: BackgroundSponge microbiomes are essential for the function and survival of their host and produce biologically active metabolites, therefore, they are ideal candidates for ecological, pharmacologic and clinical research. Next-generation sequencing (NGS) has revealed that many factors, including the environment and host, determine the composition and structure of these symbiotic communities but the controls of this variation are not well described. This study assessed the microbial communities associated with two marine sponges of the genera Aplysina (Nardo, 1834) and Ircinia (Nardo, 1833) in rocky reefs from Punta Arena de la Ventana (Gulf of California) and Pichilingue (La Paz Bay) in the coast of Baja California Sur, México to determine the relative importance of environment and host in structuring the microbiome of sponges.MethodsSpecimens of Aplysina sp were collected by scuba diving at 10 m and 2 m; Ircinia sp samples were collected at 2 m. DNA of sponge-associated prokaryotes was extracted from 1 cm3 of tissue, purified and sent for 16S amplicon sequencing. Primer trimmed pair-ended microbial 16S rDNA gene sequences were merged using Ribosomal Database Project (RDP) Paired-end Reads Assembler. Chao1, Shannon and Simpson (alpha) biodiversity indices were estimated, as well permutational analysis of variance (PERMANOVA), and Bray-Curtis distances.ResultsThe most abundant phyla differed between hosts. Those phyla were: Proteobacteria, Acidobacteria, Cyanobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes. In Ircinia sp the dominant phylum was Acidobacteria. Depth was the main factor influencing the microbial community, as analysis of similarities (ANOSIM) showed a significant difference between the microbial communities from different depths.ConclusionMicrobial diversity analysis showed that depth was more important than host in structuring the Aplysina sp and Ircinia sp microbiome. This observation contrast with previous reports that the sponge microbiome is highly host specific. creator: Bárbara González-Acosta creator: Aarón Barraza creator: César Guadarrama-Analco creator: Claudia J. Hernández-Guerrero creator: Sergio Francisco Martínez-Díaz creator: César Salvador Cardona-Félix creator: Ruth Noemí Aguila-Ramírez uri: https://doi.org/10.7717/peerj.13133 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 González-Acosta et al. title: Study on the mechanism of Danshen-Guizhi drug pair in the treatment of ovarian cancer based on network pharmacology and in vitro experiment link: https://peerj.com/articles/13148 last-modified: 2022-04-06 description: Our study aims to explore the active components and mechanisms of the Danshen-Guizhi drug pair in treating ovarian cancer by network pharmacology and in vitro experiment. The “component-target-pathway” diagram of the Danshen-Guizhi drug pair was established by network pharmacology, and the effective active components, important targets as well as potential mechanisms of the Danshen-Guizhi drug pair were analyzed. The predicted results were verified by molecular docking and in vitro experiments. The main active components of the Danshen-Guizhi drug pair in the treatment of ovarian cancer are salviolone, luteolin, β-sitosterol and tanshinone IIA. The main core target is PTGS2. The pathways involved mainly include the cancer pathway, PI3K-Akt signaling pathway, and IL-17 signaling pathway. The molecular docking results showed that salviolone and tanshinone IIA had good binding ability to the target. The expression of PTGS2 mRNA and PGE2 in ovarian cells were significantly inhibited by salviolone. The mechanism of the Danshen-Guizhi drug pair in the treatment of ovarian cancer may be regulating cell proliferation, apoptosis and tumor immunity. This provides a theoretical basis for the clinical development and application of the Danshen-Guizhi drug pair. creator: Chongzhen Qin creator: Menglin Wu creator: Xinru Wang creator: Wenda Zhang creator: Guangzhao Qi creator: Na-Yi Wu creator: Xiaoting Liu creator: Yaoyao Lu creator: Jingmin Zhang creator: Yuna Chai uri: https://doi.org/10.7717/peerj.13148 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Qin et al. title: Transcriptome profiling reveals stress-responsive gene networks in cattle muscles link: https://peerj.com/articles/13150 last-modified: 2022-04-06 description: In meat-producing animals, preslaughter operations (e.g., transportation, mixing unfamiliar animals, food and water deprivation) may be a source of stress with detrimental effects on meat quality. The objective of this work was to study the effect of emotional and physical stress by comparing the transcriptomes of two muscles (M. longissimus thoracis, LT and M. semitendinosus, ST) in Normand cows exposed to stress (n = 16) vs. cows handled with limited stress (n = 16). Using a microarray, we showed that exposure to stress resulted in differentially expressed genes (DEGs) in both muscles (62 DEGs in LT and 32 DEGs in ST, of which eight were common transcription factors (TFs)). Promoter analysis of the DEGs showed that 25 cis transcriptional modules were overrepresented, of which nine were detected in both muscles. Molecular interaction networks of the DEGs targeted by the most represented cis modules helped identify common regulators and common targets involved in the response to stress. They provided elements showing that the transcriptional response to stress is likely to (i) be controlled by regulators of energy metabolism, factors involved in the response to hypoxia, and inflammatory cytokines; and (ii) initiate metabolic processes, angiogenesis, corticosteroid response, immune system processes, and satellite cell activation/quiescence. The results of this study demonstrate that exposure to stress induced a core response to stress in both muscles, including changes in the expression of TFs. These factors could relay the physiological adaptive response of cattle muscles to cope with emotional and physical stress. The study provides information to further understand the consequences of these molecular processes on meat quality and find strategies to attenuate them. creator: Isabelle Cassar-Malek creator: Lise Pomiès creator: Anne de la Foye creator: Jérémy Tournayre creator: Céline Boby creator: Jean-François Hocquette uri: https://doi.org/10.7717/peerj.13150 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cassar-Malek et al. title: Life history and ossification patterns in Miguashaia bureaui reveal the early evolution of osteogenesis in coelacanths link: https://peerj.com/articles/13175 last-modified: 2022-04-06 description: The study of development is critical for revealing the evolution of major vertebrate lineages. Coelacanths have one of the longest evolutionary histories among osteichthyans, but despite access to extant representatives, the onset of their weakly ossified endoskeleton is still poorly understood. Here we present the first palaeohistological and skeletochronological study of Miguashaia bureaui from the Upper Devonian of Canada, pivotal for exploring the palaeobiology and early evolution of osteogenesis in coelacanths. Cross sections of the caudal fin bones show that the cortex is made of layers of primary bone separated by lines of arrested growth, indicative of a cyclical growth. The medullary cavity displays remnants of calcified cartilage associated with bony trabeculae, characteristic of endochondral ossification. A skeletochronological analysis indicates that rapid growth during a short juvenile period was followed by slower growth in adulthood. Our new analysis highlights the life history and palaeoecology of Miguashaia bureaui and reveals that, despite differences in size and habitat, the poor endoskeletal ossification known in the extant Latimeria chalumnae can be traced back at least 375 million years ago. creator: Jorge Mondéjar Fernández creator: François J. Meunier creator: Richard Cloutier creator: Gaël Clément creator: Michel Laurin uri: https://doi.org/10.7717/peerj.13175 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mondéjar Fernández et al. title: False memories when viewing overlapping scenes link: https://peerj.com/articles/13187 last-modified: 2022-04-06 description: Humans can memorize and later recognize many objects and complex scenes. In this study, we prepared large photographs and presented participants with only partial views to test the fidelity of their memories. The unpresented parts of the photographs were used as a source of distractors with similar semantic and perceptual information. Additionally, we presented overlapping views to determine whether the second presentation provided a memory advantage for later recognition tests. Experiment 1 (N = 28) showed that while people were good at recognizing presented content and identifying new foils, they showed a remarkable level of uncertainty about foils selected from the unseen parts of presented photographs (false alarm, 59%). The recognition accuracy was higher for the parts that were shown twice, irrespective of whether the same identical photograph was viewed twice or whether two photographs with overlapping content were observed. In Experiment 2 (N = 28), the memorability of the large image was estimated by a pre-trained deep neural network. Neither the recognition accuracy for an image part nor the tendency for false alarms correlated with the memorability. Finally, in Experiment 3 (N = 21), we repeated the experiment while measuring eye movements. Fixations were biased toward the center of the original large photograph in the first presentation, and this bias was repeated during the second presentation in both identical and overlapping views. Altogether, our experiments show that people recognize parts of remembered photographs, but they find it difficult to reject foils from unseen parts, suggesting that their memory representation is not sufficiently detailed to rule them out as distractors. creator: Filip Děchtěrenko creator: Jiří Lukavský uri: https://doi.org/10.7717/peerj.13187 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Děchtěrenko and Lukavský title: Early Pleistocene large mammals from Maka’amitalu, Hadar, lower Awash Valley, Ethiopia link: https://peerj.com/articles/13210 last-modified: 2022-04-06 description: The Early Pleistocene was a critical time period in the evolution of eastern African mammal faunas, but fossil assemblages sampling this interval are poorly known from Ethiopia’s Afar Depression. Field work by the Hadar Research Project in the Busidima Formation exposures (~2.7–0.8 Ma) of Hadar in the lower Awash Valley, resulted in the recovery of an early Homo maxilla (A.L. 666-1) with associated stone tools and fauna from the Maka’amitalu basin in the 1990s. These assemblages are dated to ~2.35 Ma by the Bouroukie Tuff 3 (BKT-3). Continued work by the Hadar Research Project over the last two decades has greatly expanded the faunal collection. Here, we provide a comprehensive account of the Maka’amitalu large mammals (Artiodactyla, Carnivora, Perissodactyla, Primates, and Proboscidea) and discuss their paleoecological and biochronological significance. The size of the Maka’amitalu assemblage is small compared to those from the Hadar Formation (3.45–2.95 Ma) and Ledi-Geraru (2.8–2.6 Ma) but includes at least 20 taxa. Bovids, suids, and Theropithecus are common in terms of both species richness and abundance, whereas carnivorans, equids, and megaherbivores are rare. While the taxonomic composition of the Maka’amitalu fauna indicates significant species turnover from the Hadar Formation and Ledi-Geraru deposits, turnover seems to have occurred at a constant rate through time as taxonomic dissimilarity between adjacent fossil assemblages is strongly predicted by their age difference. A similar pattern characterizes functional ecological turnover, with only subtle changes in dietary proportions, body size proportions, and bovid abundances across the composite lower Awash sequence. Biochronological comparisons with other sites in eastern Africa suggest that the taxa recovered from the Maka’amitalu are broadly consistent with the reported age of the BKT-3 tuff. Considering the age of BKT-3 and biochronology, a range of 2.4–1.9 Ma is most likely for the faunal assemblage. creator: John Rowan creator: Ignacio A. Lazagabaster creator: Christopher J. Campisano creator: Faysal Bibi creator: René Bobe creator: Jean-Renaud Boisserie creator: Stephen R. Frost creator: Tomas Getachew creator: Christopher C. Gilbert creator: Margaret E. Lewis creator: Sahleselasie Melaku creator: Eric Scott creator: Antoine Souron creator: Lars Werdelin creator: William H. Kimbel creator: Kaye E. Reed uri: https://doi.org/10.7717/peerj.13210 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rowan et al. title: A low-cost benthic incubation chamber for in-situ community metabolism measurements link: https://peerj.com/articles/13116 last-modified: 2022-04-05 description: Benthic incubation chambers facilitate in-situ metabolism studies in shallow water environments. They are used to isolate the water surrounding a study organism or community so that changes in water chemistry can be quantified to characterise physiological processes such as photosynthesis, respiration, and calcification. Such field measurements capture the biological processes taking place within the benthic community while incorporating the influence of environmental variables that are often difficult to recreate in ex-situ settings. Variations in benthic chamber designs have evolved for a range of applications. In this study, we built upon previous designs to create a novel chamber, which is (1) low-cost and assembled without specialised equipment, (2) easily reproducible, (3) minimally invasive, (4) adaptable to varied substrates, and (5) comparable with other available designs in performance. We tested the design in the laboratory and field and found that it achieved the outlined objectives. Using non-specialised materials, we were able to construct the chamber at a low cost (under $20 USD per unit), while maintaining similar performance and reproducibility with that of existing designs. Laboratory and field tests demonstrated minimal leakage (2.08 ± 0.78% water exchange over 4 h) and acceptable light transmission (86.9 ± 1.9%), results comparable to those reported for other chambers. In the field, chambers were deployed in a shallow coastal environment in Akumal, Mexico, to measure productivity of seagrass, and coral-, algae-, and sand-dominated reef patches. In both case studies, production rates aligned with those of comparable benthic chamber deployments in the literature and followed established trends with light, the primary driver of benthic metabolism, indicating robust performance under field conditions. We demonstrate that our low-cost benthic chamber design uses locally accessible and minimal resources, is adaptable for a variety of field settings, and can be used to collect reliable and repeatable benthic metabolism data. This chamber has the potential to broaden accessibility and applications of in-situ incubations for future studies. creator: Jennifer Mallon creator: Anastazia T. Banaszak creator: Lauren Donachie creator: Dan Exton creator: Tyler Cyronak creator: Thorsten Balke creator: Adrian M. Bass uri: https://doi.org/10.7717/peerj.13116 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mallon et al. title: RNA sequencing reveals novel LncRNA/mRNAs co-expression network associated with puerarin-mediated inhibition of cardiac hypertrophy in mice link: https://peerj.com/articles/13144 last-modified: 2022-04-05 description: BackgroundEvidence has demonstrated that puerarin is a potential medicine for the treatment of cardiac hypertrophy. However, the precise underlying molecular mechanisms of the protective effect of puerarin are still unclear. Here, we aimed to explore the regulatory mechanisms of lncRNAs/mRNAs co-expression network in a cardiac hypertrophy mouse model after puerarin treatment.MethodsA mouse model of cardiac hypertrophy was established by transverse aortic constriction (TAC). The echocardiography, tissue staining and western blot were used to examine the protective effect of puerarin. Then RNA sequencing (RNA-seq) was carried out to analyze systematically mRNAs and lncRNAs expression. The target lncRNA were confirmed using qRT-PCR. Moreover, a coding/non-coding gene co-expression network were established to find the interaction of lncRNA and mRNAs. The biological process, cellular component, molecular function and pathways of different expression mRNAs targeted by lncRNA were explored using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis.ResultsPuerarin exhibited an obvious inhibitory effect in cardiac hypertrophy in TAC model. RNA-seq analysis was performed to investigate the lncRNAs and mRNAs expression patterns of cardiomyocytes in sham and TAC groups treated with or without puerarin. RNA-seq identified that TAC downregulated four lncRNAs, which could be revised by puerarin treatment (|log2 Fold change| > 2 and FDR < 0.05). Among them, expression alterations of lncRNA Airn (antisense of Igf2r non-protein coding RNA) was confirmed by qRT-PCR. Pearson’s correlation coefficients of co-expression levels suggested that there was an interactive relationship between Airn and 2,387 mRNAs (r > 0.95 or r < −0.95). Those co-expressed mRNAs were enriched in some important biological processes such as translational initiation, cell proliferation, insulin-like growth factor binding and poly(A) RNA binding. KEGG analyses suggested that those Airn-interacted mRNAs were enriched in endocytosis, signaling pathways regulating pluripotency of stem cells and the Jak-STAT pathway.ConclusionPuerarin may exert beneficial effects on cardiac hypertrophy through regulating the lncRNAs/mRNAs co-expression network. creator: Shan Ye creator: Weiyan Chen creator: Caiwen Ou creator: Min-Sheng Chen uri: https://doi.org/10.7717/peerj.13144 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ye et al. title: Does size matter? An analysis of the niche width and vulnerability to climate change of fourteen species of the genus Crotalus from North America link: https://peerj.com/articles/13154 last-modified: 2022-04-05 description: The niche comprises the set of abiotic and biotic environmental conditions in which a species can live. Consequently, those species that present broader niches are expected to be more tolerant to changes in climatic variations than those species that present reduced niches. In this study, we estimate the amplitude of the climatic niche of fourteen species of rattlesnakes of the genus Crotalus to evaluate whether those species that present broader niches are less susceptible to the loss of climatically suitable zones due to the projected climate change for the time period 2021–2040. Our results suggest that for the species under study, the breadth of the niche is not a factor that determines their vulnerability to climatic variations. However, 71.4% of the species will experience increasingly inadequate habitat conditions, mainly due to the increase in temperature and the contribution that this variable has in the creation of climatically suitable zones for most of these species. creator: Jorge Luis Becerra-López creator: Raciel Cruz-Elizalde creator: Aurelio Ramírez-Bautista creator: Itzel Magno-Benítez creator: Claudia Ballesteros-Barrera creator: Javier Alvarado-Díaz creator: Robert W. Bryson Jr creator: Uriel Hernández-Salinas creator: César A. Díaz-Marín creator: Christian Berriozabal-Islas creator: Karen Fraire-Galindo creator: Juan Tello-Ruiz creator: Alexander Czaja creator: María Guadalupe Torres-Delgado uri: https://doi.org/10.7717/peerj.13154 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Becerra-López et al. title: Evaluating the reliability of media reports for gathering information about illegal wildlife trade seizures link: https://peerj.com/articles/13156 last-modified: 2022-04-05 description: Illegal wildlife trade (IWT) is threatening many species across the world. It is important to better understand the scale and characteristics of IWT to inform conservation priorities and actions. However, IWT usually takes place covertly, meaning that the data on species, trade routes and volumes is limited. This means that conservationists often have to rely on publicly available law enforcement reports of seizures as potential indicators of the magnitude and characteristics of IWT. Still, even these data may be difficult to access, leading conservationists to use media reports of seizures instead. This is the case in countries like Nepal, which have limited capacity in data keeping and reporting, and no centralized data management system. Yet reliance on media reports risks introducing further biases, which are rarely acknowledged or discussed. Here we characterize IWT in Nepal by comparing data from three sources of information on IWT between January 2005 and July 2017: seizure reports from three Nepali national daily newspapers, official seizure records for Kathmandu district, and data on additional enforcement efforts against IWT in Nepal. We found a strong positive correlation between the number of official and media-reported seizures over time, but media under-reported seizure numbers, with 78% of seizures going unreported. Seizures of charismatic, protected species were reported more often and seizure reports involving tigers were most likely to be reported (57%). Media reports appeared to be a good indicator of trends and the species being seized but not overall seizure number, with the media largely underestimating total seizure numbers. Therefore, media reports cannot be solely relied upon when it comes to informing conservation decision-making. We recommend that conservationists triangulate different data sources when using seizure data reported in the media to more rigorously characterise IWT. creator: Kumar Paudel creator: Amy Hinsley creator: Diogo Veríssimo creator: Ej Milner-Gulland uri: https://doi.org/10.7717/peerj.13156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Paudel et al. title: Identification and charactering of APX genes provide new insights in abiotic stresses response in Brassica napus link: https://peerj.com/articles/13166 last-modified: 2022-04-05 description: Ascorbate peroxidase (APX) plays an important role in scavenging H2O2 and balancing ROS content in plant cells, which is of great significance for the growth and development of life and resistance to external stress. However, up to now, APXs in Brassica napus (B. napus) have not been systematically characterized. In this study, a total of 26 BnaAPX genes were identified, which were distributed on 13 chromosomes and divided into five phylogenetic branches. Gene structure analysis showed that they had a wide varied number of exons while BnaAPXs proteins contained more similar motifs in the same phylogenetic branches. qRT-PCR analysis of 26 BnaAPX gene expression patterns showed that three putative cytosol BnaAPX genes BnaAPX1, BnaAPX2, BnaAPX9, two putatice microsomal genes BnaAPX18 and BnaAPX25 were up-regulated rapidly and robustly under high salt, water shortage and high temperature stresses. In addition, the above three abiotic stresses led to a significant increase in APX activity. The results provide basic and comprehensive information for further functional characterization of APX gene family in B. napus. creator: Jiao Pan creator: Lei Zhang creator: Min Chen creator: Yuxuan Ruan creator: Peifang Li creator: Zhihui Guo creator: Boyu Liu creator: Ying Ruan creator: Mu Xiao creator: Yong Huang uri: https://doi.org/10.7717/peerj.13166 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Pan et al. title: A new juvenile Yamaceratops (Dinosauria, Ceratopsia) from the Javkhlant Formation (Upper Cretaceous) of Mongolia link: https://peerj.com/articles/13176 last-modified: 2022-04-05 description: Here we report a new articulated skeleton of Yamaceratops dorngobiensis (MPC-D 100/553) from the Khugenetjavkhlant locality at the Shine Us Khudag (Javkhlant Formation, ?Santonian-Campanian) of the eastern Gobi Desert, Mongolia, which represents the first substantially complete skeleton and the first juvenile individual of this taxon. The specimen includes a nearly complete cranium and large portions of the vertebral column and appendicular skeleton. Its skull is about 2/3 the size of the holotype specimen, based on mandibular length. Its juvenile ontogenetic stage is confirmed by multiple indicators of skeletal and morphological immaturity known in ceratopsians, such as the long-grained surface texture on the long bones, the smooth external surface on the postorbital, open neurocentral sutures of all caudal vertebrae, a large orbit relative to the postorbital and jugal, the low angle of the lacrimal ventral ramus relative to the maxillary teeth row, narrow frontal, and straight ventral edge of the dentary. Osteohistological analysis of MPC-D 100/553 recovered three lines of arrested growth, implying around 3 years of age when it died, and verified this specimen’s immature ontogenetic stage. The specimen adds a new autapomorphy of Yamaceratops, the anteroventral margin of the fungiform dorsal end of the lacrimal being excluded from the antorbital fossa. Furthermore, it shows a unique combination of diagnostic features of some other basal neoceratopsians: the ventrally hooked rostral bone as in Aquilops americanus and very tall middle caudal neural spines about or more than four times as high as the centrum as in Koreaceratops hwaseongensis, Montanoceratops cerorhynchus, and Protoceratops andrewsi. The jugal with the subtemporal ramus deeper than the suborbital ramus as in the holotype specimen is also shared with A. americanus, Liaoceratops yanzigouensis, and juvenile P. andrewsi. Adding 38 new scorings into the recent comprehensive data matrix of basal Neoceratopsia and taking into account the ontogenetically variable characters recovered Y. dorngobiensis as the sister taxon to Euceratopsia (Leptoceratopsidae plus Coronosauria). A second phylogenetic analysis with another matrix for Ceratopsia also supported this position. The new phylogenetic position of Y. dorngobiensis is important in ceratopsian evolution, as this taxon represents one of the basalmost neoceratopsians with a broad, thin frill and hyper-elongated middle caudal neural spines while still being bipedal. creator: Minyoung Son creator: Yuong-Nam Lee creator: Badamkhatan Zorigt creator: Yoshitsugu Kobayashi creator: Jin-Young Park creator: Sungjin Lee creator: Su-Hwan Kim creator: Kang Young Lee uri: https://doi.org/10.7717/peerj.13176 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Son et al. title: Validation of a dual-task exercise program to improve balance and gait speed in older people (DualPro): a Delphi study link: https://peerj.com/articles/13204 last-modified: 2022-04-05 description: BackgroundMost physical exercise programs for older people work the physical component in isolation, excluding cognitive aspects. Previous studies reported that both components (physical and cognitive) are necessary for correct functioning of older people in the society.PurposeTo create and validate a dual-task exercise program (DualPro) to improve balance and gait speed in older people.MethodsExpert consensus or the Delphi Method was used for validation. A group of 17 experts in neurorehabilitation and geriatrics was recruited to assess the proposed exercise program. They were selected taking into account their experience in clinical practice as well as their knowledge of the subject through the use of the expert competence coefficient (K). Online questionnaires were sent with a total of 11 exercises, which had to be rated using a “Likert” scale from 1 to 7.ResultsTwo rounds were conducted to achieve 100% consensus in all exercises. The interquartile range of each exercise in both rounds was stable. During the second round, the relative interquartile range was less than 15% in all the questions, thus demonstrating consensus among the experts.ConclusionExperts in neurorehabilitation and geriatrics have concluded the validity of the progressive and systematized program of dual-task exercises focused on improving balance and gait speed for older people. This exercise program can help in the homogenization of the use of dual-task exercises in future studies and in professional practice. creator: Luz Adriana Varela-Vásquez creator: Montserrat Girabent-Farrés creator: Almudena Medina-Rincón creator: Sandra Rierola-Fochs creator: Javier Jerez-Roig creator: Eduard Minobes-Molina uri: https://doi.org/10.7717/peerj.13204 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Varela-Vásquez et al. title: Influence of biological maturation status on selected anthropometric and physical fitness variables in adolescent male volleyball players link: https://peerj.com/articles/13216 last-modified: 2022-04-05 description: BackgroundThe identification of sport talent among adolescent athletes is a topic that in recent years has been a major focus of interest for both the scientific community and sport managers. Both anthropometry and physical performance through fitness tests have demonstrated to be key elements. Biological maturation, due to its influence on anthropometric variables and physical fitness, has also been studied in relation to sport talent identification.ObjectiveTo analyse differences according to biological maturation status in anthropometric characteristics and performance in physical fitness tests, and to determine which variables predict better performance in physical fitness tests in adolescent volleyball players.MethodsA cross-sectional design was followed to collect the data. A total of 48 male sub-elite volleyball players (14.17 ± 0.73 years) completed a socio-demographic and sports ad hoc questionnaire. Anthropometric variables were measured following the guidelines of the International Society for the Advancement in Kinanthropometry (ISAK) including four basic measurements (body mass, height, sitting height and arm span); eight skinfolds (triceps, biceps, subscapular, iliac crest, supraspinale, abdominal, thigh and calf); four girths (arm relaxed, flexed and tensed arm, middle thigh and calf); five breadths (biacromial, biileocrestal, humerus, femur and bi-styloid); three lengths (acromiale-radiale, radiale-stylion and stylion-medio dactilion); and a height (ilioespinale). Physical fitness was assessed, including the sit-and-reach, back scratch, long jump, medicine ball throw, counter movement jump (CMJ), 20 meters sprint, and agility tests. Furthermore, maturity offset and age at peak height velocity (APHV) was calculated.ResultsSignificant differences were found in the body mass (Mean Difference, MD = 20.86–30.75), height (MD = 11.72–19.09), sitting height (MD = 4.27–10.27), arm span (MD = 12.91–20.78), body mass index (MD = 3.72–5.63), upper limb length (MD = 7.76), corrected muscle girths (MD = 2.06–9.31), ∑6 and 8 skinfolds (MD = 3.67–50.21) fat mass and percentage (MD = 0.30–11.58), muscle (MD = 4.13–10.64) and bone mass (MD = 1.61–3.54) (p < 0.001–0.030), showing higher values the early maturers. In the physical fitness tests, significant differences were observed in the medicine ball throw (MD = 1.26–2.80) and in CMJ power (MD = 156.71–379.85) (p < 0.001). Regression models identified fat mass percentage predicted worse physical test performance (p < 0.001), while age, maturation offset, muscle and bone variables were predictors of better physical performance (p < 0.001).ConclusionsSignificant differences based upon the stages of biological maturation were found in the anthropometric and physical condition variables in favor of the players whose maturation process was more advanced, with the variables related to fat and adipose, muscle and bone development conditioning their performance in the physical condition tests. creator: Mario Albaladejo-Saura creator: Raquel Vaquero-Cristóbal creator: Juan A. García-Roca creator: Francisco Esparza-Ros uri: https://doi.org/10.7717/peerj.13216 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Albaladejo-Saura et al. title: Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis link: https://peerj.com/articles/13222 last-modified: 2022-04-05 description: BackgroundDendrobium catenatum is a valuable traditional medicinal herb with high commercial value. D. catenatum stems contain abundant polysaccharides which are one of the main bioactive components. However, although some genes related to the synthesis of the polysaccharides have been reported, more key genes need to be further elucidated.ResultsIn this study, the contents of polysaccharides and mannose in D. catenatum stems at four developmental stages were compared, and the stems’ transcriptomes were analyzed to explore the synthesis mechanism of the polysaccharides. Many genes involved in starch and sucrose metabolisms were identified by KEGG pathway analysis. Further analysis found that sucrose synthase (SUS; EC 2.4.1.13) gene maybe participated in the polysaccharide synthesis. Hence, we further investigated the genomic characteristics and evolution relationships of the SUS family in plants. The result suggested that the SUS gene of D. catenatum (DcSUS) had undergone the expansion characterized by tandem duplication which might be related to the enrichment of the polysaccharides in D. catenatum stems. Moreover, expression analyses of the DcSUS displayed significant divergent patterns in different tissues and could be divided into two main groups in the stems with four developmental stages.ConclusionIn general, our results revealed that DcSUS is likely involved in the metabolic process of the stem polysaccharides, providing crucial clues for exploiting the key genes associated with the polysaccharide synthesis. creator: Min Jiang creator: Shangyun Li creator: Changling Zhao creator: Mingfu Zhao creator: Shaozhong Xu creator: Guosong Wen uri: https://doi.org/10.7717/peerj.13222 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Jiang et al. title: Geochemical characteristics of strontium isotopes in a coastal watershed: implications for anthropogenic influenced chemical weathering and export flux link: https://peerj.com/articles/13223 last-modified: 2022-04-05 description: Coastal watershed are essential in transporting dissolved loads from terrestrial biogeochemical process of surface environment to the adjacent oceans. The solute chemistry of coastal river water contains significant information about environmental processes under the impact of both natural lithology and anthropogenic pressure. In this study, strontium (Sr) isotopes and water chemistry data of the Jiulongjiang (JLJ) river water were analyzed in detail to trace the contribution of bedrock weathering, and quantify Sr flux to the East China Sea (ECS). The dissolved Sr contents ranged 0.07–0.90 μmol L−1 and greatly fluctuated where tributaries encountered, and 87Sr/86Sr values relatively fluctuated between 0.7140 and 0.7514. Silicate weathering was identified to be the predominant contribution of riverine dissolved loads. Strontium flux to the ocean in dry season was estimated to be 689.2 tons per year, implying an essential influence on oceanic strontium evolution. In accordance with forward model, the silicate weathering rate and CO2 consumption rate were 55.7 tons km−2 per year and 16.9 × 105 mol km−2 per year, respectively, slightly higher than world average. Considering anthropogenic impacts alongside the river, the integrated effect of lower runoff and longer retention time of river water in dry season may aggravate weathering processes. Although CO2 sink by silicate weathering in JLJ seems less than the sink in world’s central reservoirs, it should still be taken into consideration for coastal carbon budget. These findings highlight the use of geochemical characteristics of strontium and its isotopes in identifying weathering process and output flux to the ocean, which provides basic data for sustainable coastal water resource management. creator: Shitong Zhang creator: Guilin Han creator: Jie Zeng uri: https://doi.org/10.7717/peerj.13223 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds in alkaline grasslands link: https://peerj.com/articles/13226 last-modified: 2022-04-05 description: BackgroundSoil seed banks play a central role in vegetation dynamics and may be an important source of ecological restoration. However, the vast majority of seed bank studies examined only the uppermost soil layers (0–10 cm); hence, our knowledge on the depth distribution of seed bank and the ecological significance of deeply buried seeds is limited. The aim of our study was to examine the fine-scale vertical distribution of soil seed bank to a depth of 80 cm, which is one of the largest studied depth gradients so far. Our model systems were alkaline grasslands in East-Hungary, characterised by harsh environmental conditions, due to Solonetz soil reference group with Vertic horizon. We asked the following questions: (1) How do the seedling density and species richness of soil seed bank change along a vertical gradient and to what depth can germinable seeds be detected? (2) What is the relationship between the depth distribution of the germinable seeds and the species traits?MethodsIn each of the five study sites, four soil cores (4 cm diameter) of 80 cm depth were collected with an auger for soil seed bank analysis. Each sample was divided into sixteen 5-cm segments by depth (320 segments in total). Samples were concentrated by washing over sieves and then germinated in an unheated greenhouse. Soil penetration resistance was measured in situ next to each core location (0–80 cm depth, 1-cm resolution). We tested the number and species richness of seedlings observed in the soil segments (N = 320), using negative binomial generalized linear regression models, in which sampling layer and penetration resistance were the predictor variables. We ran the models for morphological groups (graminoids/forbs), ecological groups (grassland species/weeds) and life-form categories (short-lived/perennial). We also tested whether seed shape index, seed mass, water requirement or salt tolerance of the species influence the vertical distribution of their seed bank.ResultsGerminable seed density and species richness in the seed bank decreased with increasing soil depth and penetration resistance. However, we detected nine germinable seeds of six species even in the deepest soil layer. Forbs, grassland species and short-lived species occurred in large abundance in deep layers, from where graminoids, weeds and perennial species were missing. Round-shaped seeds were more abundant in deeper soil layers compared to elongated ones, but seed mass and ecological indicator values did not influence the vertical seed bank distribution. Our research draws attention to the potential ecological importance of the deeply buried seeds that may be a source of recovery after severe disturbance. As Vertisols cover 335 million hectares worldwide, these findings can be relevant for many regions and ecosystems globally. We highlight the need for similar studies in other soil and habitat types to test whether the presence of deep buried seeds is specific to soils with Vertic characteristics. creator: Ágnes Tóth creator: Balázs Deák creator: Katalin Tóth creator: Réka Kiss creator: Katalin Lukács creator: Zoltán Rádai creator: Laura Godó creator: Sándor Borza creator: András Kelemen creator: Tamás Miglécz creator: Zoltán Bátori creator: Tibor József Novák creator: Orsolya Valkó uri: https://doi.org/10.7717/peerj.13226 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tóth et al. title: Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept link: https://peerj.com/articles/13232 last-modified: 2022-04-05 description: The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krąpiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as “marshes” (marshland surface), “shrubs” (shrub surface), and “forests” (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequence of the effects of both internal factors and external ones, originating from the entire river’s catchment, which is in accord with the basic assumptions of the RCC. creator: Joanna Pakulnicka creator: Paweł Buczyński creator: Edyta Buczyńska creator: Edyta Stępień creator: Agnieszka Szlauer-Łukaszewska creator: Robert Stryjecki creator: Aleksandra Bańkowska creator: Vladimir Pešić creator: Ewa Filip creator: Andrzej Zawal uri: https://doi.org/10.7717/peerj.13232 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pakulnicka et al. title: Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata) link: https://peerj.com/articles/13245 last-modified: 2022-04-05 description: BackgroundGut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level.MethodsGut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3–V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing.ResultsThe gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail. creator: Zihao Zhou creator: Hongying Wu creator: Dinghong Li creator: Wenlong Zeng creator: Jinlong Huang creator: Zhengjun Wu uri: https://doi.org/10.7717/peerj.13245 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhou et al. title: Montreal Cognitive Assessment (MoCA) performance in Huntington’s disease patients correlates with cortical and caudate atrophy link: https://peerj.com/articles/12917 last-modified: 2022-04-04 description: Huntington’s Disease (HD) is an autosomal neurodegenerative disease characterized by motor, cognitive, and psychiatric symptoms. Cognitive impairment develops gradually in HD patients, progressing later into a severe cognitive dysfunction. The Montreal Cognitive Assessment (MoCA) is a brief screening test commonly employed to detect mild cognitive impairment, which has also been useful to assess cognitive decline in HD patients. However, the relationship between MoCA performance and brain structural integrity in HD patients remains unclear. Therefore, to explore this relationship we analyzed if cortical thinning and subcortical nuclei volume differences correlated with HD patients’ MoCA performance. Twenty-two HD patients and twenty-two healthy subjects participated in this study. T1-weighted images were acquired to analyze cortical thickness and subcortical nuclei volumes. Group comparison analysis showed a significantly lower score in the MoCA global performance of HD patients. Also, the MoCA total score correlated with cortical thinning of fronto-parietal and temporo-occipital cortices, as well as with bilateral caudate volume differences in HD patients. These results provide new insights into the effectiveness of using the MoCA test to detect cognitive impairment and the brain atrophy pattern associated with the cognitive status of prodromal/early HD patients. creator: Gabriel Ramirez-Garcia creator: Victor Galvez creator: Rosalinda Diaz creator: Aurelio Campos-Romo creator: Juan Fernandez-Ruiz uri: https://doi.org/10.7717/peerj.12917 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ramirez-Garcia et al. title: TMT labeled comparative proteomic analysis reveals spleen active immune responses during Clostridium perfringens type C infected piglet diarrhea link: https://peerj.com/articles/13006 last-modified: 2022-04-04 description: BackgroundClostridium perfringens (C. perfringens) type C is the principal pathogenic clostridia of swine, frequently causing hemorrhagic diarrhea, even necrotic enteritis in piglets, leading to severe economic loss for swine industr ies worldwide. However, there are no specific and effective prevention measures. Therefore, clarifying the molecular mechanisms of hosts against pathogenesis infection is very important to reduce the incidence of C. perfringens type C infected piglet diarrhea disease.MethodsWe performed an TMT labeling-based quantitative spleen proteomic analysis of the control group (SC), tolerance group (SR) and susceptible group (SS) to identify the differentially expressed proteins (DEPs), and screened potential molecular markers of piglet spleen tissues in response to C. perfringens type C infection.ResultsIn this study, a total of 115, 176 and 83 DEPs were identified in SR vs SC, SS vs SC, and SR vs SC, respectively, which may play the important regulatory roles in the process of piglet spleens in response toC. perfringens type C-infected diarrhea diseases. GO enrichment analysis revealed that the DEPs were mostly significantly enriched in acute inflammatory response, defense response, antimicrobial response, transporter activity, cellular metabolic process and so on, and KEGG pathway enrichment analysis showed that the significantly enriched immune related pathways of the PPAR signaling pathway, IL-17 signaling pathway, antigen processing and presentation, which hints at the immune defense process of piglet spleen against C. perfringens infection. This study helps to elucidate the protein expressional pattern of piglet spleen against C. perfringens type C-infected diarrhea disease, which can contribute to the prevention and control for pig diarrhea disease and the further development of diarrhea resistant pig breeding. creator: Xiaoli Wang creator: Xiaoyu Huang creator: Qiaoli Yang creator: Zunqiang Yan creator: Pengfei Wang creator: Xiaoli Gao creator: Ruirui Luo creator: Shuangbao Gun uri: https://doi.org/10.7717/peerj.13006 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al. title: Combining biomedical knowledge graphs and text to improve predictions for drug-target interactions and drug-indications link: https://peerj.com/articles/13061 last-modified: 2022-04-04 description: Biomedical knowledge is represented in structured databases and published in biomedical literature, and different computational approaches have been developed to exploit each type of information in predictive models. However, the information in structured databases and literature is often complementary. We developed a machine learning method that combines information from literature and databases to predict drug targets and indications. To effectively utilize information in published literature, we integrate knowledge graphs and published literature using named entity recognition and normalization before applying a machine learning model that utilizes the combination of graph and literature. We then use supervised machine learning to show the effects of combining features from biomedical knowledge and published literature on the prediction of drug targets and drug indications. We demonstrate that our approach using datasets for drug-target interactions and drug indications is scalable to large graphs and can be used to improve the ranking of targets and indications by exploiting features from either structure or unstructured information alone. creator: Mona Alshahrani creator: Abdullah Almansour creator: Asma Alkhaldi creator: Maha A. Thafar creator: Mahmut Uludag creator: Magbubah Essack creator: Robert Hoehndorf uri: https://doi.org/10.7717/peerj.13061 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Alshahrani et al. title: Diagnostics of tissue involved injury occurrence of top-level judokas during the competition: suggestion for prevention link: https://peerj.com/articles/13074 last-modified: 2022-04-04 description: BackgroundJudo, as a high-intensity contact sport, may lead to the occurrence of injuries, especially in competitions. This work aims to assess the likelihood of soft and hard tissue injuries in top-level judokas during competition with defining factors that determine the probability of injury occurrence.MethodsThe injuries that occurred in 123 official international competitions from 2005–2019 were recorded by the European Judo Union (EJU) Medical Commission as a survey that was a part of the EJU Injury Registration form with internal consistency shown by a Crombach Alpha of 0.69. This survey data identified factors such as: sex, anatomical localisation of injury, type of injury, tissue involved and mechanisms of the injury. A total of 650 tissue injuries were reported correctly in terms of tissue injury definition.ResultsThe most frequent soft tissue injury (STI) reported was a ligament STI (48.15%), closely followed by skin STI (12.15%) and muscles STI (11.38%). In turn, the most frequent hard tissue injury occurred in bones (8.56%). The highest rates of injuries occurred during the fight in the standing position (78%). Injuries in the standing position mainly occurred while executing a throw (25.85%) and followed by the attempt to throw, i.e., the action of reaching the throwing position (22.30%), grip fighting (15.07%), and during falls (14.77%). Opposite to this, fight in groundwork reached only 18.30% soft and hard tissue injuries combined. The ongoing registration of injuries during judo combat and training and the early diagnosis of risk factors for injuries are the basis for the development of effective strategies for injury prevention and further treatment. creator: Wieslaw Blach creator: Peter Smolders creator: Jozef Simenko creator: Krzysztof Mackala uri: https://doi.org/10.7717/peerj.13074 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Blach et al. title: Biochemical composition and function of subalpine shrubland and meadow soil microbiomes in the Qilian Mountains, Qinghai–Tibetan plateau, China link: https://peerj.com/articles/13188 last-modified: 2022-04-04 description: Microorganisms participate in the soil biogeochemical cycle. Therefore, investigating variations in microbial biomass, composition, and functions can provide a reference for improving soil ecological quality due to the sensitivity of microorganisms to vegetation coverage changes. However, the differences in soil microorganisms between shrubland and meadow have not been investigated in ecologically vulnerable subalpine areas. This study aimed to investigate the biochemical composition and functions of the soil microbial community under two shrublands and a meadow at high altitudes (3,400–3,550 m). Three sites under two shrublands, Rhododendron thymifolium (RHO) and Potentilla fruticosa (POT), and one meadow dominated by Kobresia myosuroides (MEA), were selected on the southern slope of the Qilian Mountains on the northeastern edge of the Qinghai–Tibetan Plateau, China. Soil physicochemical properties, the microbial community composition expressed by the phospholipid fatty acid (PLFA) biomarker, and enzyme activities were analyzed as well as their relationships. The results showed that water holding capacity and the soil carbon, nitrogen, and potassium content in RHO and POT were higher than those in the MEA. Moreover, the soil active carbon, dissolved organic carbon, total nitrogen, and dissolved total nitrogen content in RHO were higher than those in POT. The abundance of total PLFAs, bacteria, and fungi beneath the shrublands was considerably higher than that in the MEA. The PLFA abundance in RHO was significantly higher than that in POT. The fungal-to-bacterial ratio of RHO and POT was significantly higher than that in the MEA. The activities of β-glucosidase, cellobiohydrolase, and leucine aminopeptidase were the highest in RHO among the three vegetation types, followed by POT and MEA. The redundancy analysis indicated that the biochemical composition of the soil microorganisms and enzyme activities were driven by total nitrogen, dissolved organic carbon, water holding capacity, and soil organic carbon. Therefore, shrublands, which have higher biomass, can improve soil moisture status, increase soil carbon and nitrogen content (especially active carbon and active nitrogen), and further increase the abundance of total PLFAs, bacteria, and fungi. The increase of microbial biomass indirectly enhances the activity of relevant soil enzymes. The variations in PLFA abundance and enzyme activities can be attributed to shrub species, especially evergreen shrubs, which create more favorable conditions for soil microorganisms. This study provides a theoretical basis for investigating the soil biogeochemical cycle and a scientific basis for soil management and vegetation restoration in the subalpine regions. creator: Qiuyun Fan creator: Yuguo Yang creator: Yuqing Geng creator: Youlin Wu creator: Zhanen Niu uri: https://doi.org/10.7717/peerj.13188 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Fan et al. title: Comparison of changes in fecal microbiota of calves with and without dam link: https://peerj.com/articles/12826 last-modified: 2022-04-01 description: In pastoral areas and semi-agricultural and semi-pastoral areas of Sichuan, beef cattle breeding mode is mainly dependent on nature to raise livestock. On the one hand, owing to the shortage of forage grass in spring, cows suffer from malnutrition. On the other hand, competition for milk between human and livestock further deepens the malnutrition of newborn calves, and the mortality rate even exceeds 40%, resulting in serious waste of beef cattle source resources. The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome. Sixteen healthy calves (Yak ♂ × Pian cattle ♀, with similar birthday 0 ± 2 d and body weight 13.1 ± 1.13 kg), were selected and randomly divided into two groups. The control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the whole 95 days formal experimental period. Fecal samples were collected on 35, 65 and 95 days of age for high-throughput sequencing. The α-diversity was different between the two groups on day 35; however, the bacterial species richness and diversity was almost not different on day 95. Principal coordinates analysis revealed significant difference between the two groups on all the three time points, and the timepoints of day 65 and 95 were closer and separated from the timepoints of day 35 in calves with dam, whereas the timepoints of day 35 and 65 were closer and separated from day 95 in calves without dam. As time passed, the abundance of Firmicutes increased, while Proteobacteria and Actinobacteria decreased in calves with dam. But in calves without dam, the abundance of Bacteroidetes and Proteobacteria increased on day 65 and then decreased on day 95. In genus level, the relative abundance of Bacteroides decreased in calf with dam while its abundance increased first and then decreased in calf without dam but both resulted in the range of 3.5~4.5%. The relative abundance of Lactobacillus decreased, whereas Ruminococcaceae UCG-005 increased in both groups as the calf grew up. It was concluded that the richness and evenness of the microbial communities was higher in calves with dam than without dam, and a stable gut microbiome in calve with dam is established earlier than calf without dam. creator: Mengya Li creator: Zhisheng Wang creator: Lizhi Wang creator: Bai Xue creator: Rui Hu creator: Huawei Zou creator: Siqiang Liu creator: Ali Mujtaba Shah creator: Quanhui Peng uri: https://doi.org/10.7717/peerj.12826 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Comparison of surface wind speed and wind speed profiles in the Taklimakan Desert link: https://peerj.com/articles/13001 last-modified: 2022-04-01 description: Near-surface (10 m) wind speed (NWS) plays a crucial role in many areas, including the hydrological cycle, wind energy production, and the dispersion of air pollution. Based on wind speed data from Tazhong and the northern margins of the Taklimakan Desert in Xiaotang in spring, summer, autumn, and winter of 2014 and 2015, statistical methods were applied to determine the characteristics of the diurnal changes in wind speed near the ground and the differences in the wind speed profiles between the two sites. The average wind speed on a sunny day increased slowly with height during the day and rapidly at night. At heights below 4 m the wind speed during the day was higher than at night, whereas at 10 m the wind speed was lower during the day than at night. The semi-empirical theory and Monin–Obukhov (M–O) similarity theory were used to fit the NWS profile in the hinterland of the Tazhong Desert. A logarithmic law was applied to the neutral stratification wind speed profile, and an exponential fitting correlation was used for non-neutral stratification. The more unstable the stratification, the smaller the n. Using M–O similarity theory, the “linear to tens of” law was applied to the near-neutral stratification. According to the measured data, the distribution of φM with stability was obtained. The γm was obtained when the near-surface stratum was stable in the hinterland of Tazhong Desert and the βm was obtained when it was unstable. In summer, γm and βm were 5.84 and 15.1, respectively, while in winter, γm and βm were 1.9 and 27.1, respectively. creator: Xinchun Liu creator: Yongde Kang creator: Hongna Chen creator: Hui Lu uri: https://doi.org/10.7717/peerj.13001 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al.