bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylotranscriptomics of liverworts: revisiting the backbone phylogeny and ancestral gene duplications
Authors: Dong Shanshan , Yu Jin , Zhang Li , Goffinet Bernard , Liu Yang 
Published: September 2022

Abstract

Background and Aims
With some 7300 extant species, liverworts (Marchantiophyta) represent one of the major land plant lineages. The backbone relationships, such as the phylogenetic position of Ptilidiales, and the occurrence and timing of whole-genome duplications, are still contentious.

Methods
Based on analyses of the newly generated transcriptome data for 38 liverworts and complemented with those publicly available, we reconstructed the evolutionary history of liverworts and inferred gene duplication events along the 55 taxon liverwort species tree.

Key Results
Our phylogenomic study provided an ordinal-level liverwort nuclear phylogeny and identified extensive gene tree conflicts and cyto-nuclear incongruences. Gene duplication analyses based on integrated phylogenomics and Ks distributions indicated no evidence of whole-genome duplication events along the backbone phylogeny of liverworts.

Conclusions
With a broadened sampling of liverwort transcriptomes, we re-evaluated the backbone phylogeny of liverworts, and provided evidence for ancient hybridizations followed by incomplete lineage sorting that shaped the deep evolutionary history of liverworts. The lack of whole-genome duplication during the deep evolution of liverworts indicates that liverworts might represent one of the few major embryophyte lineages whose evolution was not driven by whole-genome duplications.
VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization
Authors: Liu Shun , Zhou Jianchao , Feng Ziyan , Zhang Jiawen , Li Shuang , Jin Zilong , Zhang Chenfei , Li Shiliang , He Gaoqi , Li Honglin 
Published: September 2022

Abstract

Summary
Current pharmacophore-based virtual screening (VS) software has limited interactive capabilities and less intuitive screening processes. In this study, a novel tool named VRPharmer is proposed to perform the entire VS workflow in VR environments. VRPharmer enables users to interactively perceive computation processes and immersively observe molecular structures. Besides a typical screening mode (OPT mode), VRPharmer provides a unique interactive screening mode (SCORE mode) for freely exploring the optimal binding poses. Pharmacophore models are editable to study the impact of each feature and further refine the screening results. Moreover, molecular rendering algorithms are improved for precise representations.

Availability and implementation
VRPharmer is open-source software under the MIT license. The released version is available at https://github.com/VRPharmer/VRPharmer.

Supplementary information
Supplementary data are available at Bioinformatics online.
A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data
Authors: Li Ziyi , Wang Yizhuo , Ganan-Gomez Irene , Colla Simona , Do Kim-Anh 
Published: September 2022

AbstractMotivationSingle-cell RNA sequencing (scRNA-seq) has been widely used to decompose complex tissues into functionally distinct cell types. The first and usually the most important step of scRNA-seq data analysis is to accurately annotate the cell labels. In recent years, many supervised annotation methods have been developed and shown to be more convenient and accurate than unsupervised cell clustering. One challenge faced by all the supervised annotation methods is the identification of the novel cell type, which is defined as the cell type that is not present in the training data, only exists in the testing data. Existing methods usually label the cells simply based on the correlation coefficients or confidence scores, which sometimes results in an excessive number of unlabeled cells.ResultsWe developed a straightforward yet effective method combining autoencoder with iterative feature selection to automatically identify novel cells from scRNA-seq data. Our method trains an autoencoder with the labeled training data and applies the autoencoder to the testing data to obtain reconstruction errors. By iteratively selecting features that demonstrate a bi-modal pattern and reclustering the cells using the selected feature, our method can accurately identify novel cells that are not present in the training data. We further combined this approach with a support vector machine to provide a complete solution for annotating the full range of cell types. Extensive numerical experiments using five real scRNA-seq datasets demonstrated favorable performance of the proposed method over existing methods serving similar purposes.Availability and implementationOur R software package CAMLU is publicly available through the Zenodo repository (https://doi.org/10.5281/zenodo.7054422) or GitHub repository (https://github.com/ziyili20/CAMLU).Supplementary informationSupplementary data are available at Bioinformatics online.
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants
Authors: Aref Layla , Bastarache Lisa , Hughey Jacob J 
Published: September 2022

Abstract

Summary
Electronic health record (EHR) data linked to DNA biobanks are a valuable resource for understanding the phenotypic effects of human genetic variation. We previously developed the phenotype risk score (PheRS) as an approach to quantify the extent to which a patient’s clinical features resemble a given Mendelian disease. Using PheRS, we have uncovered novel associations between Mendelian disease-like phenotypes and rare genetic variants, and identified patients who may have undiagnosed Mendelian disease. Although the PheRS approach is conceptually simple, it involves multiple mapping steps and was previously only available as custom scripts, limiting the approach’s usability. Thus, we developed the phers R package, a complete and user-friendly set of functions and maps for performing a PheRS-based analysis on linked clinical and genetic data. The package includes up-to-date maps between EHR-based phenotypes (i.e. ICD codes and phecodes), human phenotype ontology terms and Mendelian diseases. Starting with occurrences of ICD codes, the package enables the user to calculate PheRSs, validate the scores using case-control analyses, and perform genetic association analyses. By increasing PheRS’s transparency and usability, the phers R package will help improve our understanding of the relationships between rare genetic variants and clinically meaningful human phenotypes.

Availability and implementation
The phers R package is free and open-source and available on CRAN and at https://phers.hugheylab.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Determination of the extent of dissection in early gastric cancer based on lymph node station power index
Authors: Jeon Chul-Hyo , Park Ki Bum , Kim Sojung , Seo Ho Seok , Kim In-Ho , Song Kyo Young , Lee Han Hong 
Published: September 2022

Abstract

Background
The relative prognostic value of each lymph node (LN) station remains undefined in the treatment of gastric cancer. This study aimed to develop a new method to evaluate LN station ranking and define the optimal extent of lymphadenectomy for early gastric cancer.

Methods
Clinical and histopathological information from patients who underwent curative gastrectomy with lymphadenectomy between 1989 and 2018 was reviewed. The LN station power index (LNPI) of each station was estimated using a LN retrieval frequency and the 5-year overall survival of patients with absence of LN at each station. External validation was conducted to evaluate the relevance of the LNPI.

Results
A training set was developed from examination of 7009 patient records. For most nodal stations, the absence of LN was significantly associated with a poor prognosis. For the perigastric stations, the prognostic value assessed using the LNPI was in the following order: LN 4 (LNPI = 19.68), LN 3 (LNPI = 17.58), LN 6 (LNPI = 15.16), LN 1 (LNPI = 6.71), LN 2 (LNPI = 4.64) and LN 5 (LNPI = 2.86). The value rank of the extra-gastric stations was in the following order: LN 8a (LNPI = 12.93), LN 7 (LNPI = 10.51) and LN 9 (LNPI = 9.70), but the index of LN 12a (LNPI = 4.79) was higher than that of LN 11 (LNPI = 4.78). These trends in the LNPI were similar in the validation patient cohort.

Conclusions
The LNPI is a simple tool to rank the priority of each LN station dissection. The optimal extent of D1 + lymphadenectomy using LNPI was determined to be D1 with LNs 7, 8a and 9.
Resource allocation strategies for survival and reproduction by an invasive pest in response to intermittent fasting
Authors: Ristyadi Dwi , He Xiong Z , Wang Qiao 
Published: September 2022

Abstract
Intermittent fasting (IF) is a type of dietary restriction that involves fasting periods in intervals, which has been used as a strategy to improve health and extend longevity. Regular fasting is common during the process of biological invasions in nature. Yet, it is not clear how invasive animals adjust their resource allocations to survival and reproduction when periodical starvation occurs. Here, we used Tetranychus ludeni, a haplodiploid spider mite and an important invasive pest of horticultural crops around the world, to investigate the effects of IF on its life history strategies. We show that IF increased the longevity in females but not in males probably because of differences in resource storage, metabolic rate, and mating cost between sexes. In response to IF, females traded off fecundity and egg size but not the number of daughters for longevity gain, suggesting that T. ludeni females can adjust their life history strategies for population survival and growth during invasion process. Eggs produced by fasted females realized the same hatch rate and resultant young had the same survival rate as those by unfasted ones. In addition, IF had transgenerational maternal effects which prolonged offspring development period. We suggest that the longer immature developmental period can increase the body size of resulting adults, compensating egg size loss for offspring fitness. Our findings provide insight into resource allocations as responses to fasting, knowledge of which can be used for evaluation of pest invasions and for management of animal survival and reproduction by dietary regulations.
Metabarcoding of fecal DNA reveals the broad and flexible diet of a globally endangered bird
Authors: Tang Keyi , Wang Yufeng , Wu Mengling , Wang Shufang , Fu Changkun , Zhang Zhengwang , Fu Yiqiang 
Published: September 2022

Abstract
Knowing the diet of endangered wild animals is a prerequisite for species-specific conservation and habitat management. The Sichuan partridge Arborophila rufipectus is a globally endangered Galliformes species endemic to the mountains of southwest China. Existing information on the diet of this species is biased and fragmented owing to traditional observation methods. Little is known about their dietary composition or how they respond to temporal variations in food resources throughout the year. In this study, a dietary analysis was performed on 60 fecal samples using DNA Metabarcoding of invertebrates and plants to determine the primary animal and plant components of the diet across 3 critical periods of adult life history (breeding, postbreeding wandering, and overwintering). Preys from the dipteran order, followed by the lepidopteran and araneaen spp., were the predominant, animal-derived foods. Symplocos, Rubus, Celastrus, Holboellia, and Actinidia spp. supply a large abundance of fruits and seeds for this omnivorous bird. Substantial temporal dietary changes among the 3 periods and a general shift toward lower dietary diversity during the breeding season were observed, suggesting that the Sichuan partridge can adjust their diet according to the availability of food resources and their own needs. Characterizing the composition and seasonal changes in Sichuan partridge diets informs the habitat management of native flora (the plant taxa that can generate berries and seeds, such as Symplocos, Rubus, Celastrus, and Holboellia, which are likely of conservation interest) to achieve full life-cycle conservation.
What are the contributions of maternal and paternal traits to fecundity and offspring development? A case study in an amphibian species, the spined toadBufo spinosus
Authors: Renoirt Matthias , Angelier Frédéric , Cheron Marion , Brischoux François 
Published: September 2022

AbstractAssessing the determinants of reproductive success is critical but often complicated because of complex interactions between parental traits and environmental conditions occurring during several stages of a reproductive event. Here, we used a simplified ecological situation—an amphibian species lacking post-oviposition parental care—and a laboratory approach to investigate the relationships between parental (both maternal and paternal) phenotypes (body size and condition) and reproductive success (fecundity, egg size, embryonic and larval duration, larval and metamorphic morphology). We found significant effects of maternal phenotype on fecundity, hatching success, and tadpole size, as well as on the duration of larval development. Interestingly, and more surprisingly, we also found a potential contribution of the paternal phenotype occurring during early (embryonic development duration) offspring development. Although our study focused on life-history traits such as body size and development duration, additional mechanisms involving physiological costs of development may well mediate the relationships between parental phenotypes and offspring development. Future studies are required to decipher the mechanisms underlying our findings in order to clarify the mechanistic basis of the links between parental phenotypes and offspring development.
Omission of intraoperative pyloric procedures in minimally invasive esophagectomy: assessing the impact on patients
Authors: Bolger Jarlath C , Lau Harry , Yeung Jonathan C , Darling Gail E 
Published: September 2022

SummaryPyloroplasty or pyloromyotomy is often undertaken during esophagectomy to aid gastric emptying postoperatively. Minimally invasive esophagectomy (MIE) frequently omits a pyloric procedure. The impact on perioperative outcomes and the need for subsequent interventions is unclear. This study assesses the requirements for endoscopic balloon dilation of the pylorus (EPD) following MIE. Patients undergoing MIE from 2016 to 2020 were reviewed. Patients undergoing open resection, or an intraoperative pyloric procedure were excluded. Demographic, clinical and pathological data were reviewed. Univariable and multivariable analysis were performed as appropriate. In total, 171 patients underwent MIE. There were no differences in age (median 65 vs. 65 years, P = 0.6), pathological stage (P = 0.10) or ASA status (P = 0.52) between those requiring and not requiring endoscopic pyloric dilation (EPD). Forty-three patients (25%) required EPD, with a total of 71 procedures. Twenty-seven patients (16%) had EPD on their index admission. Seventy-five patients (43%) had a postoperative complication. Higher ASA status was associated with increased requirement for EPD (odds ratio 10.8, P = 0.03). On multivariable analysis, there was no association between the need for a pyloric procedure and overall survival (P = 0.14). Eight patients (5%) required insertion of a feeding jejunostomy in the postoperative period, with no difference between those with or without EPD (P = 0.11). Two patients required subsequent surgical pyloromyotomy for delayed gastric emptying. Although pyloroplasty or pyloromyotomy can safely be excluded during MIE, a quarter of patients will require postoperative EPD procedures. The impact of excluding pyloric procedures on gastric emptying requires further study.
Trajectories of Depressive Symptoms Among Older Adults and in Adults With Hip Fracture: Analysis From the English Longitudinal Study of Ageing
Authors: Milton-Cole Rhian , Ayis Salma , O’Connell Matthew D L , Smith Toby , Sheehan Katie Jane 
Published: September 2022

Abstract

Background
This study aimed to determine trajectories of depressive symptoms among older adults in England, overall and for those with hip fracture. The study aimed to explore the differential characteristics of each trajectory identified.

Methods
Analysis of adults aged 60 years or more (n = 7 050), including a hip fracture subgroup (n = 384), from the English Longitudinal Study of Ageing. Latent class growth mixture modeling was completed. Depressive symptom prevalence was estimated at baseline. Chi-square tests were completed to compare baseline characteristics across trajectories.

Results
Three trajectories of depressive symptoms (no, mild, and moderate-severe) were identified overall and for those with hip fracture. The moderate-severe trajectory comprised 13.7% and 7% of participants for overall and hip fracture populations, respectively. The proportion of participants with depressive symptoms in the moderate-severe trajectory was 65.4% and 85.2% for overall and hip fracture populations, respectively. Depressive symptoms were stable over time, with a weak trend toward increasing severity for the moderate-severe symptom trajectory. Participants in the moderate-severe symptom trajectory were older, more likely to be female, live alone, and had worse health measures than other trajectories (p &lt; .001).

Conclusions
Older adults, and those with hip fracture, follow one of the 3 trajectories of depressive symptoms that are broadly stable over time. Depressive symptoms’ prevalence was higher for those with hip fracture and, when present, the symptoms were more severe than the overall population. Results suggest a role of factors including age, gender, and marital status in depressive symptom trajectories.
Changes in Body Mass Index on the Risk of Back Pain: Estimating the Impacts of Weight Gain and Loss
Authors: Ikeda Takaaki , Cooray Upul , Suzuki Yuta , Kinugawa Anna , Murakami Masayasu , Osaka Ken 
Published: September 2022

Abstract

Background
The relationship between obesity and back pain in older populations is poorly understood. This study aimed to examine (a) the impacts of changes in obesity status on back pain risk and (b) the heterogeneity in the influence of changes in obesity status according to muscle strength.

Methods
We analyzed 6 868 participants in waves 4 (2008–2009), 6 (2012–2013), and 7 (2014–2015) of the English Longitudinal Study of Ageing. The exposure comprised continuous body mass index (BMI) values, whereas the outcome comprised self-reported moderate or severe back pain. The targeted minimum loss-based estimator was used to estimate the impacts of hypothetical changes in BMI in each wave under 10 scenarios encompassing a 5%−25% hypothetical reduction/increase in BMI. We also performed stratified analysis using handgrip strength at the baseline.

Results
For the hypothetical reduction scenarios, a 10% (relative risk [RR]; 95% confidence interval [CI] = 0.82 [0.73–0.92], p = .001) reduction in BMI estimated a significantly lower back pain risk compared to the observed data. For the hypothetical increase scenarios, a 5% (RR [95% CI] = 1.11 [1.04–1.19], p = .002) increase in BMI estimated a significantly higher back pain risk. Increased BMI had a higher risk of back pain among those with weak strength when stratified by handgrip strength but not among those with strong strength.

Conclusion
Our study confirmed that weight gain leads to a greater risk of back pain as well as heterogeneity in the influence of changes in obesity status according to the handgrip strength.
Sheep fecal transplantation affects growth performance in mouse models by altering gut microbiota
Authors: Cheng Jiangbo , Zhang Xiaoxue , Zhang Deyin , Zhang Yukun , Li Xiaolong , Zhao Yuan , Xu Dan , Zhao Liming , Li Wenxin , Wang Jianghui , Zhou Bubo , Lin Changchun , Yang Xiaobin , Zhai Rui , Cui Panpan , Zeng Xiwen , Huang Yongliang , Ma Zongwu , Liu Jia , Wang Weimin 
Published: September 2022

Abstract
Animal growth traits are important and complex traits that determine the productivity of animal husbandry. There are many factors that affect growth traits, among which diet digestion is the key factor. In the process of animal digestion and absorption, the role of gastrointestinal microbes is essential. In this study, we transplanted two groups of sheep intestinal microorganisms with different body weights into the intestines of mice of the same age to observe the effect of fecal bacteria transplantation on the growth characteristics of the mouse model. The results showed that receiving fecal microbiota transplantation (FMT) had an effect on the growth traits of recipient mice (P &lt; 0.05). Interestingly, only mice receiving high-weight donor microorganisms showed differences. Use 16S rDNA sequencing technology to analyze the stool microorganisms of sheep and mice. The microbial analysis of mouse feces showed that receiving FMT could improve the diversity and richness of microorganisms (P &lt; 0.05), and the microbial composition of mouse feces receiving low-weight donor microorganisms was similar to that of the control group, which was consistent with the change trend of growth traits. The feces of high-weight sheep may have higher colonization ability. The same five biomarkers were identified in the donor and recipient, all belonging to Firmicutes, and were positively correlated with the body weight of mice at each stage. These results suggest that FMT affects the growth traits of receptors by remodeling their gut microflora.
Ethicolegal considerations of screening for brain injury in women who have experienced intimate partner violence
Authors: Boyle Quinn , Illes Judy , Simonetto Deana , van Donkelaar Paul 
Published: September 2022

Abstract
The vast majority of women who experience physical intimate partner violence (IPV) will likely suffer a brain injury (BI) as a result of the abuse. Accurate screening of IPV–BI can ensure survivors have access to appropriate health care and other supports, but screening results may also impact them receiving fair and equitable treatment in the legal system, and the justice they deserve. We used semi-structured interviews, combined with a contrastive vignette that described a realistic but hypothetical scenario involving IPV with or without BI, to explore the impact of BI on parenting disputes. Participants were lawyers (n = 12) whose focus is family law. Results highlight the potential adverse consequences of a positive BI screen that are influenced by the legal responsibility of counsel, the legal aid status of the woman, ongoing family dynamics, and the expectations of society while the focus on the best interests of the child is retained. Taken together, the findings reflect the legal vulnerability of women in decision-making about their capacity to parent after a BI. We conclude with recommendations for the future of IPV–BI screening aimed at mitigating risk and equipping women to navigate a legal system that has disadvantaged them, both historically and in the current context.
Multiseptate gallbladder presenting with biliary colic
Authors: Hopmann Peter , Tan Ellen , Lo David 
Published: September 2022

Abstract
Common diagnoses associated with right upper quadrant and epigastric pain include cholecystitis, peptic ulcer disease (PUD), biliary colic, gastroesophageal reflux disease (GERD) and irritable bowel syndrome (IBS). Multiseptate gallbladder is a rare congenital anomaly that can cause symptoms of biliary colic, however it may present with atypical symptoms, which can prolong definitive diagnosis and treatment. We present a case of multiseptate gallbladder in a 21-year-old female who initially presented with GERD and IBS. After multiple failed treatment regimens for IBS, she ultimately was found to have multiseptate gallbladder and was successfully treated with cholecystectomy.