bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence of Colon Cancer Among Medicaid Beneficiaries With or Without Human Immunodeficiency Virus Under Comparable Colorectal Cancer Screening Patterns
Authors: Rudolph Jacqueline E , Calkins Keri L , Zhang Xueer , Zhou Yiyi , Pirsl Filip , Xu Xiaoqiang , Wentz Eryka , Lau Bryan , Joshu Corinne E 
Published: April 2024

AbstractBackgroundPeople with human immunodeficiency virus (HIV; PWH) in the United States have a lower incidence of colon cancer than the general population. The lower incidence may be explained by differences in receipt of screening. Thus, we sought to estimate colon cancer incidence under scenarios in which Medicaid beneficiaries, with or without HIV, followed the same screening protocols.MethodsWe used data from 1.5 million Medicaid beneficiaries who were enrolled in 14 US states in 2001–2015 and aged 50–64 years; 72 747 beneficiaries had HIV. We estimated risks of colon cancer and death by age, censoring beneficiaries when they deviated from 3 screening protocols, which were based on Medicaid's coverage policy for endoscopies during the time period, with endoscopy once every 2, 4, or 10 years. We used inverse probability weights to control for baseline and time-varying confounding and informative loss to follow-up. Analyses were performed overall, by sex, and by race/ethnicity.ResultsPWH had a lower incidence of colon cancer than beneficiaries without HIV. Compared with beneficiaries without HIV, the risk difference at age 65 years was −1.6% lower (95% confidence interval, −2.3% to −.7%) among PWH with the 2-year protocol and −0.8% lower (−1.3% to −.3%) with the 10-year protocol. Results were consistent across subgroup and sensitivity analyses.ConclusionsOur findings suggest that the lower risk of colon cancer that has been observed among PWH aged 50–64 years compared with those without HIV is not due to differences in receipt of lower endoscopy. Keywords: colon cancer, colorectal cancer screening, endoscopy, Medicaid, human immunodeficiency virus
Relating ciliary propulsion morphology and flow to particle acquisition in marine planktonic ciliates II: the oligotrich ciliate Strombidium capitatum
Authors: Jiang Houshuo , Buskey Edward J 
Published: April 2024

Abstract
The marine oligotrich ciliate Strombidium capitatum is a cruise-feeder, relying on ciliary motion and propulsion flow to individually detect and capture particles. High-speed, high-magnification digital imaging revealed that the cell swims forward by sweeping its anterior adoral membranelles (AAMs) backward, achieving a mean path-averaged speed of U = 1.7 mm s−1 (31 cell-lengths per second). Particle detection occurs through either hydrodynamic signal perception or ciliary contact perception, with a mean reaction distance of R = 20.4 μm. While executing a ciliary reversal of AAMs to handle and capture a perceived particle, the cell coordinates the ciliary motion of ventral adoral membranelles (VAMs, the “lapel”) with the ciliary reversal of AAMs (the “collar”), causing a sudden halt of cell motion, thereby functioning as a motion “brake” that is crucial for effective particle capture. The encounter rate with small prey particles is calculated using πR2U (~8.0 μL h−1, equivalent to ~ 3.5 × 106 cell volumes per day). Based on hydrodynamic modeling results, it is hypothesized that spatial structures of the flow velocity vector and acceleration fields in front of the swimming cell are essential for pushing an embedded particle forward, creating a strong enough slip velocity and hydrodynamic signal for prey perception, even for a neutrally buoyant small particle.
Performance-related pain and disability among music students versus professional musicians: a multicenter study using a validated tool
Authors: Zão Ana , Altenmüller Eckart , Azevedo Luís 
Published: April 2024

Abstract

Objective
To evaluate prevalence of performance-related pain among musicians and compare pain characteristics, associated disability and approach to pain management, between music students and professional musicians.

Methods
A multicenter cross-sectional study was performed in a multi-stage stratified cluster random sample of 585 musicians, stratified by music students (294, among which 234 were at pre-university level and 60 at university level) and professional musicians (291). The main outcome was performance-related pain, measured by Performance-related Pain among Musicians Questionnaire (PPAM). Secondary outcomes were: pain management approach, physical activity levels, fatigue, distress, and health-related quality of life.

Results
The lifetime prevalence of performance-related pain was 55.0% (n = 322), being significantly higher among professionals (57.5% vs 42.5%, P &lt; .001). Pain intensity scores were significantly higher in professional musicians (P &lt; .05), but pain interference in performance was higher among music students, who also reported significantly higher levels of fatigue (P = .008) and distress (P &lt; .001), and lower quality of life (P &lt; .001). Regardless of the high levels of pain intensity and interference, fatigue, anxiety and depression, and low levels of quality of life, 33% musicians who developed pain had never looked for healthcare (this proportion is significantly higher for music students, 57%, P &lt; .001).

Conclusions
We present the first multicenter study on performance-related pain among musicians with different backgrounds, using a validated tool, and distinguishing music students from professional musicians. Performance-related pain is a highly prevalent and disabling condition among musicians, however, its proper evaluation and management are still often underappreciated, contributing to significant impairments and reduced quality of life.
Drug-induced impairment of mitochondrial fatty acid oxidation and steatosis: assessment of causal relationship with 45 pharmaceuticals
Authors: Buron Nelly , Porceddu Mathieu , Loyant Roxane , Martel Cécile , Allard Julien A , Fromenty Bernard , Borgne-Sanchez Annie 
Published: April 2024

Abstract
Drug-induced liver injury (DILI) represents a major issue for pharmaceutical companies, being a potential cause of black-box warnings on marketed pharmaceuticals, or drug withdrawal from the market. Lipid accumulation in the liver also referred to as steatosis, may be secondary to impaired mitochondrial fatty acid oxidation (mtFAO). However, an overall causal relationship between drug-induced mtFAO inhibition and the occurrence of steatosis in patients has not yet been established with a high number of pharmaceuticals. Hence, 32 steatogenic and 13 nonsteatogenic drugs were tested for their ability to inhibit mtFAO in isolated mouse liver mitochondria. To this end, mitochondrial respiration was measured with palmitoyl-l-carnitine, palmitoyl-CoA + l-carnitine, or octanoyl- l-carnitine. This mtFAO tri-parametric assay was able to predict the occurrence of steatosis in patients with a sensitivity and positive predictive value above 88%. To get further information regarding the mechanism of drug-induced mtFAO impairment, mitochondrial respiration was also measured with malate/glutamate or succinate. Drugs such as diclofenac, methotrexate, and troglitazone could inhibit mtFAO secondary to an impairment of the mitochondrial respiratory chain, whereas dexamethasone, olanzapine, and zidovudine appeared to impair mtFAO directly. Mitochondrial swelling, transmembrane potential, and production of reactive oxygen species were also assessed for all compounds. Only the steatogenic drugs amiodarone, ketoconazole, lovastatin, and toremifene altered all these 3 mitochondrial parameters. In conclusion, our tri-parametric mtFAO assay could be useful in predicting the occurrence of steatosis in patients. The combination of this assay with other mitochondrial parameters could also help to better understand the mechanism of drug-induced mtFAO inhibition.
Leaf morpho-anatomical adjustments in a Quercus pubescens forest after 10 years of partial rain exclusion in the field
Authors: Laoué Justine , Gea-Izquierdo Guillermo , Dupouyet Sylvie , Conde María , Fernandez Catherine , Ormeño Elena 
Published: April 2024

Abstract
In the Mediterranean region, a reduction of annual precipitation and a longer and drier summer season are expected with climate change by the end of the century, eventually endangering forest survival. To cope with such rapid changes, trees may modulate their morpho-anatomical and physiological traits. In the present study, we focused on the variation in leaf gas exchange and different leaf morpho-anatomical functional traits of Quercus pubescens Willd. in summer using a long-term drought experiment in natura consisting of a dynamic rainfall exclusion system where trees have been submitted to amplified drought (AD) (~−30% of annual precipitation) since April 2012 and compared them with trees under natural drought (ND) in a Mediterranean forest. During the study, we analyzed net CO2 assimilation (An), stomatal conductance (gs), transpiration (E), water-use efficiency (WUE), stomatal size and density, density of glandular trichomes and non-glandular trichomes, thickness of the different leaf tissues, specific leaf area and leaf surface. Under AD, tree functioning was slightly impacted, since only An exhibited a 49% drop, while gs, E and WUE remained stable. The decrease in An under AD was regulated by concomitant lower stomatal density and reduced leaf thickness. Trees under AD also featured leaves with a higher non-glandular trichome density and a lower glandular trichome density compared with ND, which simultaneously limits transpiration and production costs. This study points out that Q. pubescens exhibits adjustments of leaf morpho-anatomical traits which can help trees to acclimate to AD scenarios as those expected in the future in the Mediterranean region.
Discovery of optimal cell type classification marker genes from single cell RNA sequencing data
Authors: Liu Angela , Peng Beverly , Pankajam Ajith V. , Duong Thu Elizabeth , Pryhuber Gloria , Scheuermann Richard H. , Zhang Yun 
Published: April 2024

AbstractThe use of single cell/nucleus RNA sequencing (scRNA-seq) technologies that quantitively describe cell transcriptional phenotypes is revolutionizing our understanding of cell biology, leading to new insights in cell type identification, disease mechanisms, and drug development. The tremendous growth in scRNA-seq data has posed new challenges in efficiently characterizing data-driven cell types and identifying quantifiable marker genes for cell type classification. The use of machine learning and explainable artificial intelligence has emerged as an effective approach to study large-scale scRNA-seq data. NS-Forest is a random forest machine learning-based algorithm that aims to provide a scalable data-driven solution to identify minimum combinations of necessary and sufficient marker genes that capture cell type identity with maximum classification accuracy. Here, we describe the latest version, NS-Forest version 4.0 and its companion Python package (https://github.com/JCVenterInstitute/NSForest), with several enhancements to select marker gene combinations that exhibit highly selective expression patterns among closely related cell types and more efficiently perform marker gene selection for large-scale scRNA-seq data atlases with millions of cells. By modularizing the final decision tree step, NS-Forest v4.0 can be used to compare the performance of user-defined marker genes with the NS-Forest computationally-derived marker genes based on the decision tree classifiers. To quantify how well the identified markers exhibit the desired pattern of being exclusively expressed at high levels within their target cell types, we introduce the On-Target Fraction metric that ranges from 0 to 1, with a metric of 1 assigned to markers that are only expressed within their target cell types and not in cells of any other cell types. NS-Forest v4.0 outperforms previous versions on its ability to identify markers with higher On-Target Fraction values for closely related cell types and outperforms other marker gene selection approaches at classification with significantly higher F-beta scores when applied to datasets from three human organs - brain, kidney, and lung.
Short-Term Disruption of TGFβ Signaling in Adult Mice Renders the Aorta Vulnerable to Hypertension-Induced Dissection
Authors: Jiang Bo , Ren Pengwei , He Changshun , Wang Mo , Murtada Sae-Il , Chen Yu , Ramachandra Abhay B. , Li Guangxin , Qin Lingfeng , Assi Roland , Schwartz Martin A. , Humphrey Jay D. , Tellides George 
Published: April 2024

AbstractHypertension and transient increases in blood pressure from extreme exertion are risk factors for aortic dissection in patients with age-related vascular degeneration or inherited connective tissue disorders. Yet, the common experimental model of angiotensin II-induced aortopathy in mice appears independent of high blood pressure as lesions do not occur in response to an alternative vasoconstrictor, norepinephrine, and are not prevented by co-treatment with a vasodilator, hydralazine. We investigated vasoconstrictor administration to adult mice 1 week after disruption of TGFβ signaling in smooth muscle cells. Norepinephrine increased blood pressure and induced aortic dissection by 7 days and even within 30 minutes that was rescued by hydralazine; results were similar with angiotensin II. Changes in regulatory contractile molecule expression were not of pathological significance. Rather, reduced synthesis of extracellular matrix yielded a vulnerable aortic phenotype by decreasing medial collagen, most dynamically type XVIII, and impairing cell-matrix adhesion. We conclude that transient and sustained increases in blood pressure cause dissection in aortas rendered vulnerable by inhibition of TGFβ-driven extracellular matrix production by smooth muscle cells. A corollary is that medial fibrosis, a frequent feature of medial degeneration, may afford some protection against aortic dissection.
Phylogeography of bar-tailed godwits: pre-LGM structure in Beringia and westward colonization of post-glacial Europe
Authors: Conklin Jesse R. , Verkuil Yvonne I. , Lefebvre Margaux J.M. , Battley Phil F. , Bom Roeland A. , Gill Robert E. , Hassell Chris J. , ten Horn Job , Ruthrauff Daniel R. , Tibbitts T. Lee , Tomkovich Pavel S. , Warnock Nils , Piersma Theunis , Fontaine Michaël C. 
Published: April 2024

ABSTRACTIn migratory birds, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased geographic structure, and limited flexibility to respond to change. We used nextRAD sequencing of 14,318 single-nucleotide polymorphisms to explore the population genetics and phylogeographic history of the bar-tailed godwit,Limosa lapponica, a migratory shorebird with six recognized subspecies and known for making the longest non-stop flights of any landbird. Using scenario-testing in an Approximate Bayesian Computation framework, we infer that bar-tailed godwits existed in three main lineages at the Last Glacial Maximum (LGM), when much of their present-day Arctic and sub-Arctic breeding range persisted in a large, unglaciated Siberian-Beringian refugium. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspeciesL. l. baueri; in the west, one lineage diversified into three extant subspeciesL. l. lapponica,taymyrensis, andyamalensis, the former two of which migrate through previously glaciated western Europe. We also detected unrecognized population structure among bar-tailed godwits wintering in Europe, wherein a significant proportion of purportedlapponicaindividuals were in facttaymyrensis, necessitating a re-assessment of the migrations, ecology, and population estimates for these subspecies. In the global range of this long-distance migrant, we found evidence of both (1) fidelity to rigid behavioral routines promoting fine-scale geographic population structure (in the east), and (2) flexibility to colonize recently available migratory flyways and non-breeding areas (in the west).
Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy
Authors: Bianco Eliana , Bonassera Martina , Uliana Federico , Tilma Janny , Winkler Martin , Zencir Sevil , Albert Benjamin , Oborská-Oplová Michaela , Dechant Reinhard , Hugener Jannik , Panse Vikram Govind , Pilhofer Martin , Kimmig Philipp , Peter Matthias 
Published: April 2024

AbstractRibosome abundance in changing environments is governed by biogenesis and degradation, but the underlying mechanisms regulating these opposing processes remain unknown. Here we show that Suppressor of Tom1 (Stm1), a dormancy factor protecting cytosolic ribosomes during starvation, has an unexpected function to promote ribosome biogenesis during exponential growth conditions. Indeed, Stm1 transiently localizes to the nucleolus and engages with pre-ribosomal particles. Stm1 upregulates transcription of ribosomal protein genes by directly binding the activation domain (AD) of the transcription factor Ifh1. These novel Stm1 functions confer rapamycin-sensitivity and are mediated by its C-terminal intrinsically disordered region (IDR), which is dispensable for ribosome hibernation. We conclude that Stm1 regulates ribosome homeostasis linking ribosome biogenesis and ribosome dormancy.
Quantifying competition between two demersal fish species from spatiotemporal stomach content data
Authors: Lindmark Max , Maioli Federico , Anderson Sean C. , Gogina Mayya , Bartolino Valerio , Sköld Mattias , Ohlsson Mikael , Eklöf Anna , Casini Michele 
Published: April 2024

AbstractCompetition is challenging to quantify in nature and inference is often made on indirect patterns of potential competition (e.g., trends in population trajectories and overlap in spatiotemporal distribution and resource use). However, these indicators are not direct measures of fitness, nor do they say if the contested resource is limited in supply, which are key features of competition. We combine stomach content and biomass density data from scientific bottom trawl surveys to evaluate if food competition is occurring between two dominant demersal fish species in the southern Baltic Sea: Atlantic cod (Gadus morhua) and flounder (Platichthysspp.). We use multivariate generalized linear latent variable models (GLLVMs) to quantify diet similarities across the domain, diet overlap indices to test if predator density drives diet overlap at intermediate spatial scales, and spatiotemporal generalized linear mixed models (GLMMs) fit to individual-level prey weights to evaluate effects of local-scale covariates. We find clear dietary clusters by species and size. The latter is especially pronounced in cod, which shift from benthic to pelagic prey at around 30 cm. The dietary overlap is low and does not decline with predator density. However, signs of resource partitioning to reduce interspecific food competition are evident in the local-scale analysis. As flounder densities increase, small and large cod tend to feed less on the isopodSaduria entomon— an important prey species. However, the benthic prey weight in small cod, and benthic and total prey weight in large cod, are not affected by flounder densities, suggesting that interspecific food competition is not limiting cod feeding but affects their diet composition. We find some support for intraspecific food competition in large cod and flounder. Our study illustrates the importance of local-scale processes when inferring food competition from stomach content data, and such results are important for quantifying ecological interactions.
Uncovering the bequeathing potential of Apoptotic Mesenchymal Stem Cells via small Extracellular Vesicles for its enhanced immunomodulatory ability
Authors: Mendiratta Meenakshi , Mendiratta Mohini , Sharma Yashvi , Sahoo Ranjit K. , Malhotra Neena , Mohanty Sujata 
Published: April 2024

AbstractSmall Extracellular Vesicles (sEVs) derived from Mesenchymal Stem Cells (MSCs) have emerged as a promising avenue for cell-free therapeutics in regenerative medicine. These vesicles, endowed with regenerative cargo inherited from their parent cells, have attracted attention for their role in immunomodulation and ROS alleviation. Notably, the deliberate induction of apoptosis in MSCs prior to Extracellular Vesicles (EVs) isolation has been identified as a strategy to augment the regenerative capabilities of MSCs-EVs, as certain reports have suggested that MSCs undergo apoptosis to exert their therapeutic effect post-transplantation. Moreover, selecting an optimal tissue source for deriving MSC-sEVs is equally crucial to ensure consistent and improved clinical outcomes.Multiple attributes of MSCs like their antioxidant, Immunomodulatory & regenerative properties make them particularly appealing for clinical studies, wherein mechanisms such as paracrine secretions and efferocytosis play pivotal roles. This investigation meticulously explores the comparative immunomodulatory & antioxidant capabilities of Apoptotic sEVs (Apo-sEVs) with Viable sEVs (V-sEVs) obtained from both Bone Marrow (BM) and Wharton’s Jelly (WJ)-derived MSCs, using anin vitroliver injury model. The findings from the present study contribute valuable insights into the comparative efficacy of Apo-sEVs and V-sEVs. This will aid in addressing a critical gap in understanding the role of apoptosis in enhancing the reparative capability of MSCs-sEVs. It also aims to shed light on the optimal source of MSCs for generating Apo-sEVs in translational applications.GRAPHICAL ABSTARCT
Sample multiplexing for retinal single-cell RNA-sequencing
Authors: Ma Justin , Chu Ting Kuan , Polo Prieto Maria , Park Yong , Li Yumei , Chen Rui , Mardon Graeme , Frankfort Benjamin J , Tran Nicholas M 
Published: April 2024

SummaryRare cell populations can be challenging to characterize using microfluidic single-cell RNA sequencing (scRNA-seq) platforms. Typically, the population of interest must be enriched and pooled from multiple biological specimens for efficient collection. However, these practices preclude the resolution of sample origin together with phenotypic data and are problematic in experiments in which biological or technical variation is expected to be high (e.g., disease models, genetic perturbation screens, or human samples). One solution is sample multiplexing whereby each sample is tagged with a unique sequence barcode that is resolved bioinformatically. We have established a scRNA-seq sample multiplexing pipeline for mouse retinal ganglion cells using cholesterol-modified-oligos and utilized the enhanced precision to investigate cell type distribution and transcriptomic variance across retinal samples. As single cell transcriptomics are becoming more widely used to research development and disease, sample multiplexing represents a useful method to enhance the precision of scRNA-seq analysis.