title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=310 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: De novo assembly and characterization of the transcriptome of Morchella esculenta growth with selenium supplementation link: https://peerj.com/articles/17426 last-modified: 2024-05-31 description: Although Morchella esculenta (L.) Pers. is an edible and nutritious mushroom with significant selenium (Se)-enriched potential, its biological response to selenium stimuli remains unclear. This study explored the effect of selenium on mushroom growth and the global gene expression profiles of M. esculenta. While 5 µg mL−1selenite treatment slightly promoted mycelia growth and mushroom yield, 10 µg mL−1significantly inhibited growth. Based on comparative transcriptome analysis, samples treated with 5 µg mL−1 and 10 µg mL−1 of Se contained 16,061 (452 upregulated and 15,609 downregulated) and 14,155 differentially expressed genes (DEGs; 800 upregulated and 13,355 downregulated), respectively. Moreover, DEGs were mainly enriched in the cell cycle, meiosis, aminoacyl-tRNA biosynthesis, spliceosome, protein processing in endoplasmic reticulum pathway, and mRNA surveillance pathway in both selenium-treated groups. Among these, MFS substrate transporter and aspartate aminotransferase genes potentially involved in Se metabolism and those linked to redox homeostasis were significantly upregulated, while genes involved in isoflavone biosynthesis and flavonoid metabolism were significantly downregulated. Gene expression levels increased alongside selenite treatment concentration, suggesting that high Se concentrations promoted M. esculenta detoxification. These results can be used to thoroughly explain the potential detoxification and Se enrichment processes in M. esculenta and edible fungi. creator: Mengxiang Du creator: Shengwei Huang creator: Zihan Huang creator: Lijuan Qian creator: Yang Gui creator: Jing Hu creator: Yujun Sun uri: https://doi.org/10.7717/peerj.17426 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Du et al. title: A geometric morphometric protocol to correct postmortem body arching in fossil fishes link: https://peerj.com/articles/17436 last-modified: 2024-05-31 description: Postmortem body curvature introduces error in fish morphometric data. Compared to living fish, the causes of such body curvature in fossils may be due to additive taphonomic processes that have been widely studied. However, a protocol that helps to correct its effect upon morphometric data remains unexplored. Here, we test two different mathematical approaches (multivariate regression and the so-called ‘unbending functions’) available to tackle fish geometric morphometric data in two exceptionally preserved gonorynchiformes fossil fishes, Rubiesichthys gregalis and Gordichthys conquensis, from the Las Hoyas deposits (Early Cretaceous, Spain). Although both methods successfully correct body curvature (i.e., removing misleading geometric variation), our results show that traditional approaches applied in living fishes might not be appropriate to fossil ones, because of the additional anatomical alterations. Namely, the best result for 2D fossil fishes is achieved by correcting the arching of the specimens (mathematically “unbending” them). Ultimately, the effect of body curvature on morphometric data is largely taxon independent and morphological diversity mitigates its effect, but size is an important factor to take into account (because larger individuals tend to be less curved). creator: Carla San Román creator: Hugo Martín-Abad creator: Jesús Marugán-Lobón uri: https://doi.org/10.7717/peerj.17436 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 San Román et al. title: EvatCrop: a novel hybrid quasi-fuzzy artificial neural network (ANN) model for estimation of reference evapotranspiration link: https://peerj.com/articles/17437 last-modified: 2024-05-31 description: Reference evapotranspiration (ET0 ) is a significant parameter for efficient irrigation scheduling and groundwater conservation. Different machine learning models have been designed for ET0 estimation for specific combinations of available meteorological parameters. However, no single model has been suggested so far that can handle diverse combinations of available meteorological parameters for the estimation of ET0. This article suggests a novel architecture of an improved hybrid quasi-fuzzy artificial neural network (ANN) model (EvatCrop) for this purpose. EvatCrop yielded superior results when compared with the other three popular models, decision trees, artificial neural networks, and adaptive neuro-fuzzy inference systems, irrespective of study locations and the combinations of input parameters. For real-field case studies, it was applied in the groundwater-stressed area of the Terai agro-climatic region of North Bengal, India, and trained and tested with the daily meteorological data available from the National Centres for Environmental Prediction from 2000 to 2014. The precision of the model was compared with the standard Penman-Monteith model (FAO56PM). Empirical results depicted that the model performances remarkably varied under different data-limited situations. When the complete set of input parameters was available, EvatCrop resulted in the best values of coefficient of determination (R2 = 0.988), degree of agreement (d = 0.997), root mean square error (RMSE = 0.183), and root mean square relative error (RMSRE = 0.034). creator: Gouravmoy Banerjee creator: Uditendu Sarkar creator: Sanway Sarkar creator: Indrajit Ghosh uri: https://doi.org/10.7717/peerj.17437 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Banerjee et al. title: Effect of GnRH agonist down-regulation combined with hormone replacement treatment on reproductive outcomes of frozen blastocyst transfer cycles in women of different ages link: https://peerj.com/articles/17447 last-modified: 2024-05-31 description: ObjectiveTo investigate the effect of GnRH agonist (GnRH-a) down-regulation prior to hormone replacement treatment (HRT) to prepare the endometrium in frozen embryo transfer (FET) cycles in women of different ages.MethodsThis was a retrospective study, and after excluding patients with adenomyosis, endometriosis, severe endometrial adhesions, polycystic ovary syndrome (PCOS), and repeated embryo implantation failures, a total of 4,091 HRT cycles were collected. Patients were divided into group A (<35 years old) and group B (≥35 years old), and each group was further divided into HRT and GnRHa-HRT groups. The clinical outcomes were compared between groups.ResultsThere was no statistically significant difference in clinical outcomes between the HRT and GnRHa-HRT groups among women aged <35 years. In women of advanced age, higher rates of clinical pregnancy and live birth were seen in the GnRHa-HRT group. Logistic regression analysis showed that female age and number of embryos transferred influenced the live birth rate in FET cycles, and in women aged ≥ 35 years, the use of GnRH-a down-regulation prior to HRT improved pregnancy outcomes.ConclusionsIn elderly woman without adenomyosis, endometriosis, PCOS, severe uterine adhesions, and RIF, hormone replacement treatment with GnRH agonist for pituitary suppression can improve the live birth rate of FET cycles. creator: Jianghuan Xie creator: Jieqiang Lu creator: Huina Zhang uri: https://doi.org/10.7717/peerj.17447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Xie et al. title: Public transit mobility as a leading indicator of COVID-19 transmission in 40 cities during the first wave of the pandemic link: https://peerj.com/articles/17455 last-modified: 2024-05-31 description: BackgroundThe rapid global emergence of the COVID-19 pandemic in early 2020 created urgent demand for leading indicators to track the spread of the virus and assess the consequences of public health measures designed to limit transmission. Public transit mobility, which has been shown to be responsive to previous societal disruptions such as disease outbreaks and terrorist attacks, emerged as an early candidate.MethodsWe conducted a longitudinal ecological study of the association between public transit mobility reductions and COVID-19 transmission using publicly available data from a public transit app in 40 global cities from March 16 to April 12, 2020. Multilevel linear regression models were used to estimate the association between COVID-19 transmission and the value of the mobility index 2 weeks prior using two different outcome measures: weekly case ratio and effective reproduction number.ResultsOver the course of March 2020, median public transit mobility, measured by the volume of trips planned in the app, dropped from 100% (first quartile (Q1)–third quartile (Q3) = 94–108%) of typical usage to 10% (Q1–Q3 = 6–15%). Mobility was strongly associated with COVID-19 transmission 2 weeks later: a 10% decline in mobility was associated with a 12.3% decrease in the weekly case ratio (exp(β) = 0.877; 95% confidence interval (CI): [0.859–0.896]) and a decrease in the effective reproduction number (β = −0.058; 95% CI: [−0.068 to −0.048]). The mobility-only models explained nearly 60% of variance in the data for both outcomes. The adjustment for epidemic timing attenuated the associations between mobility and subsequent COVID-19 transmission but only slightly increased the variance explained by the models.DiscussionOur analysis demonstrated the value of public transit mobility as a leading indicator of COVID-19 transmission during the first wave of the pandemic in 40 global cities, at a time when few such indicators were available. Factors such as persistently depressed demand for public transit since the onset of the pandemic limit the ongoing utility of a mobility index based on public transit usage. This study illustrates an innovative use of “big data” from industry to inform the response to a global pandemic, providing support for future collaborations aimed at important public health challenges. creator: Jean-Paul R. Soucy creator: Shelby L. Sturrock creator: Isha Berry creator: Duncan J. Westwood creator: Nick Daneman creator: David Fisman creator: Derek R. MacFadden creator: Kevin A. Brown uri: https://doi.org/10.7717/peerj.17455 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Soucy et al. title: A genomic hotspot of diversifying selection and structural change in the hoary bat (Lasiurus cinereus) link: https://peerj.com/articles/17482 last-modified: 2024-05-31 description: BackgroundPrevious work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups.MethodsA chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison.ResultsTwelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa.DiscussionThis study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions. creator: Robert S. Cornman uri: https://doi.org/10.7717/peerj.17482 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy link: https://peerj.com/articles/17486 last-modified: 2024-05-31 description: Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in the pig industry but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. The present study aims to identify obese-specific biomarkers and key pathways correlated with ASFD in pigs. The ASF-related mRNA expression dataset GSE136754 was retrieved from the Gene Expression Omnibus (GEO) database and systematically analyzed using a comprehensive bioinformatics method. A total of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in the p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network, consisting of 540 nodes and 1,065 edges, was constructed, and the top ten genes with the highest degree scores—ABL1, HDAC1, CDC42, HDAC2, MRPS5, MRPS10, MDM2, JUP, RPL7L1 and UQCRFS1—were identified as hub genes in the whole PPI network. Especially HDAC1, MDM2, MRPS10 and RPL7L1 were identified as potential robust obese-specific biomarkers due to their significant differences in single gene expression levels and high ROC area; this was further verified by quantitative real-time PCR (qRT-PCR) on abdominal subcutaneous fat samples from obese-type (Saba) and lean-type (Large White) pigs. Additionally, a mRNA-miRNA-lncRNA ceRNA network consisting of four potential biomarkers, 15 miRNAs and 51 lncRNAs was established, and two targeted lncRNAs with more connections, XIST and NEAT1, were identified as potentially important regulatory factors. The findings of this study may provide novel insights into the molecular mechanism involved in ASFD. creator: Yongli Yang creator: Xiaoyi Wang creator: Mingli Li creator: Shuyan Wang creator: Huiyu Wang creator: Qiang Chen creator: Shaoxiong Lu uri: https://doi.org/10.7717/peerj.17486 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Anti-BIRC5 autoantibody serves as a valuable biomarker for diagnosing AFP-negative hepatocellular carcinoma link: https://peerj.com/articles/17494 last-modified: 2024-05-31 description: BackgroundAutoantibodies targeting tumor-associated antigens (TAAbs) have emerged as promising biomarkers for early cancer detection. This research aimed to assess the diagnostic capacity of anti-BIRC5 autoantibody in detecting AFP-negative hepatocellular carcinoma (ANHCC).MethodsThis research was carried out in three stages (discovery phase, validation phase, and evaluation phase) and included a total of 744 participants. Firstly, the anti-BIRC5 autoantibody was discovered using protein microarray, exhibiting a higher positive rate in ANHCC samples (ANHCCs) compared to normal control samples (NCs). Secondly, the anti-BIRC5 autoantibody was validated through enzyme-linked immunosorbent assay (ELISA) in 85 ANHCCs and 85 NCs from two clinical centers (Zhengzhou and Nanchang). Lastly, the diagnostic usefulness of the anti-BIRC5 autoantibody for hepatocellular carcinoma (HCC) was evaluated by ELISA in a cohort consisting of an additional 149 AFP-positive hepatocellular carcinoma samples (APHCCs), 95 ANHCCs and 244 NCs. The association of elevated autoantibody to high expression of BIRC5 in HCC was further explored by the database from prognosis, immune infiltration, DNA methylation, and gene mutation level.ResultsIn the validation phase, the area under the ROC curve (AUC) of anti-BIRC5 autoantibody to distinguish ANHCCs from NCs in Zhengzhou and Nanchang centers was 0.733 and 0.745, respectively. In the evaluation phase, the AUCs of anti-BIRC5 autoantibody for identifying ANHCCs and HCCs from NCs were 0.738 and 0.726, respectively. Furthermore, when combined with AFP, the AUC for identifying HCCs from NCs increased to 0.914 with a sensitivity of 77.5% and specificity of 91.8%. High expression of BIRC5 gene is not only correlated with poor prognosis of HCCs, but also significantly associated with infiltration of immune cells, DNA methylation, and gene mutation.ConclusionThe findings suggest that the anti-BIRC5 autoantibody could serve as a potential biomarker for ANHCC, in addition to its supplementary role alongside AFP in the diagnosis of HCC. Next, we can carry out specific verification and explore the function of anti-BIRC5 autoantibody in the occurrence and development of HCC. creator: Qing Li creator: Haiyan Liu creator: Han Wang creator: Wenzhuo Xiong creator: Liping Dai creator: Xiuzhi Zhang creator: Peng Wang creator: Hua Ye creator: Jianxiang Shi creator: Zhihao Fang creator: Keyan Wang uri: https://doi.org/10.7717/peerj.17494 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Identifying risk zones and landscape features that affect common leopard depredation link: https://peerj.com/articles/17497 last-modified: 2024-05-31 description: Human-wildlife conflict (HWC) is a pressing issue worldwide but varies by species over time and place. One of the most prevalent forms of HWC in the mid-hills of Nepal is human-common-leopard conflict (HLC). Leopard attacks, especially in forested areas, can severely impact villagers and their livestock. Information on HLC in the Gorkha district was scarce, thus making it an ideal location to identify high-risk zones and landscape variables associated with such events. Registered cases were collected and reviewed from the Division Forest Office (DFO) during 2019-2021. Claims from DFO records were confirmed with herders and villagers via eight focus group discussions. To enhance modeling success, researchers identified a total of 163 leopard attack locations on livestock, ensuring a minimum distance of at least 100 meters between locations. Using maximum entropy (MaxEnt) and considering 13 environmental variables, we mapped common leopard attack risk zones. True Skill Statistics (TSS) and area under receiver-operator curve (AUC) were used to evaluate and validate the Output. Furthermore, 10 replications, 1,000 maximum iterations, and 1000 background points were employed during modeling. The average AUC value for the model, which was 0.726 ± 0.021, revealed good accuracy. The model performed well, as indicated by a TSS value of 0.61 ± 0.03. Of the total research area (27.92 km2), about 74% was designated as a low-risk area, 19% as a medium-risk area, and 7% as a high-risk area. Of the 13 environmental variables, distance to water (25.2%) was the most significant predictor of risk, followed by distance to road (16.2%) and elevation (10.7%). According to response curves, the risk of common leopard is highest in the areas between 1.5 to 2 km distances from the water sources, followed by the closest distance from a road and an elevation of 700 to 800 m. Results suggest that managers and local governments should employ intervention strategies immediately to safeguard rural livelihoods in high-risk areas. Improvements include better design of livestock corrals, insurance, and total compensation of livestock losses. Settlements near roads and water sources should improve the design and construction of pens and cages to prevent livestock loss. More studies on the characteristics of victims are suggested to enhance understanding of common leopard attacks, in addition to landscape variables. Such information can be helpful in formulating the best management practices. creator: Thakur Silwal creator: Bijaya Neupane creator: Nirjala Raut creator: Bijaya Dhami creator: Binaya Adhikari creator: Amit Adhikari creator: Aakash Paudel creator: Shalik Ram Kandel creator: Mahamad Sayab Miya uri: https://doi.org/10.7717/peerj.17497 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Silwal et al. title: Effectiveness of in-group versus individually administered pain neuroscience education on clinical and psychosocial outcomes in patients with chronic low back pain: randomized controlled study protocol link: https://peerj.com/articles/17507 last-modified: 2024-05-31 description: Objective(1) This trial will compare the clinical and psychosocial effectiveness of in-group and individually pain neuroscience education (PNE) in patients with chronic low back pain (CLBP). In addition, (2) the influence of social determinants of health on post-treatment results will be analyzed.MethodsA three-arm randomized controlled trial will be conducted. Sixty-nine participants with CLBP will be recruited in a 1:1:1 ratio. Participants, assessor, and statistician will be blinded to group assignment. The PNE intervention will be adapted to the context of the participants. An experimental group (n = 33) will receive PNE in an in-group modality, the other experimental group (n = 33) will receive PNE in an individually modality and the control group (n = 33) will continue with usual care. Additionally, participants will be encouraged to stay active by walking for 20–30 min 3–5 times per week and will be taught an exercise to improve transversus abdominis activation (bracing or abdominal following). The outcome measures will be fear avoidance and beliefs, pressure pain threshold, pain self-efficacy, catastrophizing, pain intensity, and treatment expectation. Outcome measures will be collected at one-week before intervention, immediately post-intervention, and four-weeks post-intervention.ConclusionThe innovative approach of PNE oriented to fear beliefs proposed in this study could broaden the application strategies of this educational therapeutic modality. Impact. Contextualized PNE delivered by physical therapist could be essential to achieve a good cost-effectiveness ratio of this intervention to improve the clinical condition of people with CLBP. creator: Joaquín Salazar-Méndez creator: Iván Cuyul-Vásquez creator: Felipe Ponce-Fuentes creator: Rodrigo Núñez-Cortés creator: Guillermo Mendez-Rebolledo creator: Jorge Fuentes uri: https://doi.org/10.7717/peerj.17507 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Salazar-Méndez et al.