bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient Elastography Measures of Hepatic Steatosis and Fibrosis Are Associated With Body Composition Among US Adolescents
Authors: Unalp-Arida Aynur , Ruhl Constance E. 
Published: June 2022

Objectives:
Obesity-related fatty liver disease impacts long-term adolescent liver health. We examined transient elastography assessed hepatic steatosis and fibrosis distributions and relationships with body composition and lifestyle factors in a United States national adolescent population sample.

Methods:
Liver stiffness and controlled attenuation parameter (CAP) were assessed on 1080 non-Hispanic white, non-Hispanic black, non-Hispanic Asian, and Hispanic boys and girls aged 12–19 years in the National Health and Nutrition Examination Survey (NHANES) 2017–2018. Participants underwent anthropometry and dual-energy x-ray absorptiometry (DXA).

Results:
Compared with girls, boys had higher mean CAP (223.7 dB/m vs 215.3 dB/m) and liver stiffness (5.1 kPa vs 4.9 kPa). CAP and liver stiffness increased markedly with body mass index (BMI). In multivariable-adjusted analysis, CAP in the upper quartile was associated with Hispanic and non-Hispanic Asian ethnicity and increased BMI, waist-to-hip ratio, systolic blood pressure, and sedentary time, and decreased physical activity and Healthy Eating Index-2015 score. In multivariable-adjusted analysis, liver stiffness in the upper quartile was associated with male sex, non-Hispanic black ethnicity, and increased BMI, alanine aminotransferase, CAP, and serum cotinine. DXA total percent fat and trunk fat percent were positively related to CAP (P < 0.001 for each), but not to liver stiffness with multivariable adjustment. Results were similar with CAP and liver stiffness as continuous characteristics.

Conclusions:
In US adolescents, increased anthropometric and DXA body composition measures and lifestyle factors were associated with higher CAP and liver stiffness. Transient elastography and similar noninvasive markers may be utilized for early detection of liver disease in high-risk pediatric populations.
Guidelines for botulinum neurotoxin injection for facial contouring
Authors: Yi Kyu-Ho , Lee Hyung-Jin , Hur Hye-Won , Seo Kyle K , Kim Hee-Jin 
Published: June 2022

Summary:The hypertrophied temporalis and masseter muscles give a muscular shaped and bulky contour to the face. Botulinum neurotoxin injection methods are commonly used for facial contouring; however, adverse effects have been reported owing to a lack of delicate anatomical information. The anatomical considerations when injecting botulinum neurotoxin into the temporalis and masseter muscles have been reviewed in the present study. Current knowledge on the localization of the botulinum neurotoxin injection point with more recent anatomical dissection and modified Sihler’s staining procedures was assessed. We found that for the muscles, the injection point can be more precisely demarcated. Optimal injection sites are presented for the temporalis and masseter muscles, and the injection technique has been suggested. We propose the optimal injection sites in relation to external anatomical landmarks for the frequently injected muscles of the face to facilitate the efficiency of botulinum neurotoxin injections. In addition, these guidelines would aid in more precise practice without the adverse effects of botulinum neurotoxin.
Voided Volume for Assessment of Bladder Emptying After Female Pelvic Floor Surgery: A Randomized Controlled Trial
Authors: Popiel Patrick , Getaneh Feven , Yeh Judy , Rickey Leslie , Bercik Richard , Harmanli Oz 
Published: June 2022

Importance
To study alternative voiding trial (VT) methods after urogynecologic surgery that may potentially decrease catheterization.

Objective
The aim of the study is to compare voiding assessment based on a minimum spontaneous voided volume of 150 mL with the standard retrograde fill (RF) approach in women after urogynecologic procedures.

Study Design
Women undergoing urogynecologic surgery were randomized to RF or spontaneous void (SV) groups. Women in the RF group had their bladders backfilled with 300 mL of saline before catheter removal, those in the SV group did not. To pass the VT, patients in the RF group were required to void 150 mL at one time within 60 minutes, and patients in the SV group had to do the same within 6 hours. The primary outcome was the VT failure rate. We also compared the false pass rate, urinary tract infections, satisfaction, and preference of VT method.

Results
One hundred nine women were enrolled in the study, 54 had SV and 55 underwent RF. Baseline characteristics were not significantly different other than history of prior hysterectomy. There was no significant difference in procedures between the groups. There was no difference in VT failure rate between the groups—SV (7.4%) and RF (12.7%, P = 0.39). The false pass rate was 0 in each group. Urinary tract infection rates were similar between SV (14.8%) and RF (14.5%) groups (P = 0.34). Patient satisfaction for VT method was not significantly different.

Conclusions
Spontaneous VT was not superior to retrograde void trial. Therefore, we cannot recommend one method of VT after urogynecologic surgery.
Condensation
Voiding assessment based on minimum SV of 150 mL is comparable with VT with RF after surgeries for prolapse and urinary incontinence.
Multi-ancestry GWAS for venous thromboembolism identifies novel loci followed by experimental validation in zebrafish
Authors: Wolford Brooke N. , Zhao Yakun , Surakka Ida , Wu Kuan-Han H. , Yu Xinge , Richter Catherine E. , Bhatta Laxmi , Brumpton Ben , Desch Karl , Thibord Florian , Klarin Derek , Johnson Andrew D. , Trégouët David-Alexandre , Damrauer Scott M. , Smith Nicholas L. ,   INVENT,   MVP, Lo Faro Valeria , Tsuo Kristin ,   Global Biobank Meta-analysis Initiative (GBMI), Daly Mark , Neale Ben , Zhou Wei , Shavit Jordan A. , Willer Cristen. J. 
Published: June 2022

SUMMARYGenome wide association study (GWAS) results for Venous Thromboembolism (VTE) across 9 international cohorts of the Global Biobank Meta-analysis Initiative (GBMI), with representation across six ancestry groups (cases=27,987, controls=1,035,290), were combined using inverse-variance weighted meta-analysis. This multi-ancestry GWAS resulted in 38 genome-wide significant loci, 9 of which are potentially novel. For each autosomal locus we performed gene prioritization using seven independent, yet converging, lines of evidence. Through prioritization we identified genes known for VTE (e.g., F5, F11, VWF), genes known to modify blood coagulation (e.g., STAB2), and genes without known coagulation mechanisms from functional studies (e.g., PLCG2, TC2N). We evaluated the function of six prioritized genes, including F7 as a positive control, using laser mediated endothelial injury to induce thrombosis in zebrafish. We used CRISPR/Cas9 to knock down these potentially causal genes and measured time to occlusion after laser injury. From this assay we have supportive evidence for a role of RASIP1 and TC2N in the modification of human VTE, and suggestive evidence for STAB2 and TSPAN15. This study expands the currently identified genomic architecture of VTE through biobank-based multi-ancestry GWAS, in silico candidate gene predictions, and in vivo functional follow-up of novel candidate genes.
Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes
Authors: Jaakkola Maria K. , Kukkonen-Macchi Anu , Suomi Tomi , Elo Laura L. 
Published: June 2022

SummaryWe introduce a new method for Pathway Analysis of Longitudinal data (PAL), which is suitable for complex study designs, such as longitudinal data. The main advantages of PAL are the use of pathway structures and the suitability of the approach for study settings beyond currently available tools. We demonstrate the performance of PAL with three longitudinal datasets related to the early development of type 1 diabetes, involving different study designs and only subtle biological signals. Transcriptomic and proteomic data are represented among the test data. An R package implementing PAL is publicly available athttps://github.com/elolab/PAL.MotivationPathway analysis is a frequent step in studies involving gene or protein expression data, but most of the available pathway methods are designed for simple case versus control studies of two sample groups without further complexity. The few available methods allowing the pathway analysis of more complex study designs cannot use pathway structures or handle the situation where the variable of interest is not defined for all samples. Such scenarios are common in longitudinal studies with so long follow up time that healthy controls are required to identify the effect of normal aging apart from the effect of disease development, which is not defined for controls. PAL is the first available pathway method to analyse such high-investment datasets.
Understanding the mechanism ofTrikatuin type 2 diabetes mellitus and lipid-related metabolic disorders: A network pharmacology approach
Authors: Chhabra Varun , Wadhawan Mohit , Katiyar Amit , Khuntia Bharat Krushna , Sharma Vandna , Rathore Shubhangi , kaur Punit , Sharma Gautam 
Published: June 2022

AbstractObjectiveTrikatu is an Indian polyherbal formulation comprising three herbs, i.e., Zingiber officinale, Piper longum, and Piper nigrum. It is traditionally used to treat metabolic disorders such as type 2 diabetes mellitus (T2DM), dyslipidemia, and obesity. However, its mechanism of action remains unknown. This study aims to explore the underlying therapeutic mechanism of Trikatu in T2DM and lipid metabolic disorders using network pharmacology (NP).MethodsTrikatu phytochemicals were retrieved from various databases and screened on the basis of druglikeness and oral bioavailability (>30%) score. Putative targets of the bioactive phytochemicals were identified using TargetNet, Similarity Ensemble Approach, and Swiss Target Prediction databases. Protein-protein interaction (PPI) network of overlapping targets of phytochemicals and metabolic disorders was constructed using NetworkAnalyst 3.0. The Bioactive Phytochemical-Target-Pathway (BP-T-P) network was constructed using cytoscape v3.8.2, and the key targets of Trikatu were analyzed by Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment.ResultsTwenty bioactive phytochemicals and 102 targets of Trikatu were identified. PPI network and enrichment analysis showed that 51 targets of Trikatu phytochemicals such as RXRA, STAT3 and ESR1, GSK3B, TNF, NOS2/3 regulate pathways like insulin resistance, steroid hormone biosynthesis, regulation of lipolysis in adipocytes, adipocytokine & cGMP-PKG signalling pathways, arachidonic acid metabolism and bile secretion. The results were validated by molecular docking which showed that RXRA, STAT3 and ESR1 strongly interact with their ligands alpha gurjunene, beta-sitosterol, piperlongumine, genistein and E-beta carotene, respectively.ConclusionHence, the multiple target and multiple pathway approach of Trikatu can be further explored in pharmacokinetics / Pharmacodynamics studies.
Partial reuse of circadian clock genes along parallel clines of diapause in two moth species
Authors: Yu Yue , Huang Li-Li , Xue Fang-Sen , Dopman Erik B. 
Published: June 2022

ABSTRACTUnderstanding the molecular basis of repeated evolution is essential for improving our ability to predict evolution. Genes repeatedly used in independent cases of adaptation to similar environments are strong candidates for predicting adaptation across phylogeny. The Asian corn borer (Ostrinia furnacalis; ACB) and the European corn borer (Ostrinia nubilalis; ECB) are two closely related moths that display remarkable adaptability to a wide range of climate on two separate continents, largely manifesting as changes in the timing of diapause (dormancy), but the genetic basis of parallel clinal responses remains to be characterized. We extensively sampled the ACB cline in China in a genome-wide association study (GWAS) using pooled sequencing data (Pool-seq). We characterized the genetic basis of clinal diapause response in ACB and showed that genes involved in circadian rhythm were over-represented among the candidate genes under spatially varying selection. Comparing with previous results from ECB, we found that the circadian clock gene period (per), but not pigment-dispersing factor receptor (Pdfr), was repeatedly used, but the alleles were not shared between the species. The corn borers’ shared adaptability is likely based inperbut seemingly through independent mutational paths.
Tracing the origin of fish immunoglobulins
Authors: Mirete-Bachiller Serafin , Gambón-Deza Francisco 
Published: June 2022

AbstractWe have studied the origin of immunoglobulin genes in fish. There are two evolutionary lines of bony fish, Actinopterygii and Sarcopterygii. The former gave rise to most of the current fish and the latter to the animals that went to land. Non-teleost actinopterygians are significant evolutionary, sharing a common ancestor with sarcopterygians. There are three different immunoglobulin isotypes in ray-finned fish: IgM, IgD and IgT. We deduce that translocon formation in immunoglobulins genes occurred already in non-teleost Actinopterygii. We establish a relationship between no teleosts and teleostean fish at the domain level of different immunoglobulins. We found two evolutionary lines of immunoglobulin. A line that starts from Immunoglobulin M and another from an ancestral Immunoglobulin W. The M line is stable, and the W line gives rise to the IgD of the fish. Immunoglobulin T emerges by recombination between both lines.
The effect of breaking up sedentary time with calisthenics on neuromuscular function: a preliminary study
Authors: Mear Emily , Gladwell Valerie , Pethick Jamie 
Published: June 2022

AbstractProlonged sedentary behaviour has a detrimental effect on neuromuscular function and is associated with decreased muscle strength and force control, and a decreased ability to maintain balance. Breaking up sedentary time with regular bouts of physical activity has numerous health benefits, though the effects on neuromuscular function are unknown. This study aimed to investigate the effect of breaking up sedentary time with calisthenic exercise on neuromuscular function. To that end, 17 healthy adults, who spent ≥6 hours a day sitting, were randomly assigned to a four-week calisthenics intervention (n = 8) or a control group (n = 9). The calisthenics intervention involved performing up to eight sets of exercises during the working day (09:00-17:00); with one set consisting of eight repetitions of five different exercises (including squats and lunges). Before and immediately after the intervention, measures of knee extensor maximal voluntary contraction (MVC; right leg only) and submaximal force control (measures of the magnitude and complexity of force fluctuations; right leg only), and dynamic balance (Y balance test; both legs) were taken. The calisthenics intervention resulted in a significant increase in knee extensor MVC (P= 0.036), significant decreases in the standard deviation (P0.031) and coefficient of variation (P= 0.016) of knee extensor force fluctuations during contractions at 40% MVC, and a significant increase in Y balance test posterolateral reach with left leg stance (P= 0.046). These results suggest that breaking up sedentary time with calisthenics may be effective at increasing muscle strength, force steadiness and dynamic balance.New findingsWhat is the central question of this study?This study sought to determine whether breaking up sedentary time with a (4-week) calisthenics exercise intervention could improve neuromuscular function.What is the main finding and its importance?A 4-week calisthenic exercise intervention increased knee extensor maximal strength, knee extensor force steadiness during submaximal contractions, and aspects of dynamic balance. These results indicate the regularly breaking up sedentary time with calisthenics can mitigate against the negative effects of prolonged sedentary time.
MaD: Macromolecular Descriptors for Integrative Dynamic Modeling Supported by Cryo-EM Data
Authors: Träger Sylvain , Peraro Matteo Dal 
Published: June 2022

AbstractThe determination of atomic structures of large flexible systems remains a challenging task despite the recent advances in cryo-electron microscopy (cryo-EM) and de novo protein structure prediction. Few hybrid methods truly consider dynamics because deriving appropriate conformational ensembles and scoring functions robust to conformational differences is not trivial. We present here Macromolecular Descriptors (MaD) which, inspired by traditional computer vision concepts, remedies some of these limitations. MaD identifies feature points and encodes local structural information around them into resolution- and conformation-invariant descriptors. Efficient matching of descriptors from cryo-EM densities at low and medium resolution with those of high-resolution component structures yields a robust and accurate assembly prediction that does not require other experimental or computational input. Fast, scalable and easy to use, this method is able to incorporate native dynamic features as extracted from molecular simulations and identify the models that best match the target electron density. Therefore, MaD addresses some of the unanswered needs of the community in terms of the integrative modeling of large and flexible macromolecular complexes.
Scene-selective brain regions respond to embedded objects of a scene
Authors: Aminoff Elissa M. , Durham Tess 
Published: June 2022

AbstractObjects are fundamental to scene understanding. Scenes are defined by embedded objects and how we interact with them. Paradoxically, scene processing in the brain is typically discussed in contrast to object processing. Using the BOLD5000 dataset (Chang et al., 2019), we examined whether objects within a scene predicted the neural representation of scenes, as measured by fMRI in humans. Stimuli included 1,179 unique scenes across 18 semantic categories. Object composition of scenes were compared across scene exemplars in different semantic categories, and separately, in exemplars of the same category. Neural representations in scene- and object-preferring brain regions were significantly related to which objects were in a scene, with the effect at times stronger in the scene-preferring regions. The object model accounted for more variance when comparing scenes within the same semantic category to scenes from different categories. Thus, the functional role of scene-preferring regions should include the processing of objects. This suggests visual processing regions may be better characterized with respect to which processes are engaged when interacting with the stimulus category, such as processing groups of objects in scenes, or processing a single object in our foreground, rather than the stimulus category itself.
Adaptation of a quantitative trait to a changing environment: new analytical insights on the asexual and infinitesimal sexual models
Authors: Garnier J. , Cotto O. , Bouin E. , Bourgeron T. , Lepoutre T. , Ronce O. , Calvez V. 
Published: June 2022

AbstractPredicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits subject to stabilizing selection around an optimal phenotype, whose value is shifted continuously through time. In this context, the population fate results from the equilibrium distribution of the trait, relative to the moving optimum. Such a distribution may vary with the shape of selection, the system of reproduction, the number of loci, the mutation kernel or their interactions. Here, we develop a methodology that provides quantitative measures of population maladaptation and potential of survival directly from the entire profile of the phenotypic distribution, without any a priori on its shape. We investigate two different systems of reproduction (asexual and infinitesimal sexual models of inheritance), with various forms of selection. In particular, we recover that fitness functions such that selection weakens away from the optimum lead to evolutionary tipping points, with an abrupt collapse of the population when the speed of environmental change is too high. Our unified framework allows deciphering the mechanisms that lead to this phenomenon. More generally, it allows discussing similarities and discrepancies between the two systems of reproduction, which are ultimately explained by different constraints on the evolution of the phenotypic variance. We demonstrate that the mean fitness in the population crucially depends on the shape of the selection function in the infinitesimal sexual model, in contrast with the asexual model. In the asexual model, we also investigate the effect of the mutation kernel and we show that kernels with higher kurtosis tend to reduce maladaptation and improve fitness, especially in fast changing environments.HighlightsAdaptation to a changing environment may generate non Normal phenotypic distribution.The phenotypic variance at equilibrium truly depends on reproduction model;Selection shapes mean fitness only in sexual infinitesimal model;Weak selection away from the optimum leads to evolutionary tipping points with fast changes;Frequent mutations with large effects reduce maladaptation and improve fitness.
Meta-analysis of diurnal transcriptomics reveals strong patterns of concordance and discordance in mouse liver
Authors: Brooks Thomas G. , Manjrekar Aditi , Grant Gregory R. 
Published: June 2022

AbstractThe accumulation of public transcriptomic timeseries data enables robust meta-analyses that were not possible until recently. To assess the consistency of biological rhythms across studies, 43 public mouse liver tissue timeseries totaling 805 RNA-seq samples were obtained and analyzed. Only the control groups of each study were included, in order to create comparable data. Technical factors in RNA-seq library preparation were the largest contributors to transcriptome-level differences, beyond biological or experiment-specific factors such as lighting conditions. Core clock genes were remarkably consistent in phase across all studies, while phase distributions of other periodic genes were generally less consistent. Overlap of genes identified as rhythmic across studies was generally low, up to around 50% between some of the highest sample count studies. Distributions of phases of significant genes were remarkably inconsistent across studies, but genes consistently identified as rhythmic clustered near ZT0 and ZT12 in acrophase. Data was integrated across studies in a JIVE analysis, which showed that the top two components of joint within-study variation are determined by time of day. A shape-invariant model with random effects was fit to the genes to identify the underlying shape of the rhythms, consistent across all studies. This revealed the extent of asymmetric and multimodal genes.