bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanotherapy Reprograms Aged Muscle Stromal Cells to Remodel the Extracellular Matrix during Recovery from Disuse
Authors: Hettinger Zachary R , Wen Yuan , Peck Bailey D , Hamagata Kyoko , Confides Amy L , Van Pelt Douglas W , Harrison Douglas A , Miller Benjamin F , Butterfield Timothy A , Dupont-Versteegden Esther E 
Published: March 2022

AbstractAging is accompanied by reduced remodeling of skeletal muscle extracellular matrix (ECM), which is exacerbated during recovery following periods of disuse atrophy. Mechanotherapy has been shown to promote ECM remodeling through immunomodulation in adult muscle recovery, but not during the aged recovery from disuse. In order to determine if mechanotherapy promotes ECM remodeling in aged muscle, we performed single cell RNA sequencing (scRNA-seq) of all mononucleated cells in adult and aged rat gastrocnemius muscle recovering from disuse, with (REM) and without mechanotherapy (RE). We show that fibroadipogenic progenitor cells (FAPs) in aged RE muscle are highly enriched in chemotaxis genes (Csf1), but absent in ECM remodeling genes compared to adult RE muscle (Col1a1). Receptor-ligand (RL) network analysis of all mononucleated cell populations in aged RE muscle identified chemotaxis-enriched gene expression in numerous stromal cell populations (FAPs, endothelial cells, pericytes), despite reduced enrichment of genes related to phagocytic activity in myeloid cell populations (macrophages, monocytes, antigen presenting cells). Following mechanotherapy, aged REM mononuclear cell gene expression resembled adult RE muscle as evidenced by RL network analyses and KEGG pathway activity scoring. To validate our transcriptional findings, ECM turnover was measured in an independent cohort of animals using in vivo isotope tracing of intramuscular collagen and histological scoring of the ECM, which confirmed mechanotherapy-mediated ECM remodeling in aged RE muscle. Our results highlight age-related cellular mechanisms underpinning the impairment to complete recovery from disuse, and also promote mechanotherapy as an intervention to enhance ECM turnover in aged muscle recovering from disuse.
Correcting Bias in Allele Frequency Estimates Due to an Observation Threshold: A Markov Chain Analysis
Authors: Gossmann Toni I. , Waxman David 
Published: March 2022

Abstract
There are many problems in biology and related disciplines involving stochasticity, where a signal can only be detected when it lies above a threshold level, while signals lying below threshold are simply not detected. A consequence is that the detected signal is conditioned to lie above threshold, and is not representative of the actual signal. In this work, we present some general results for the conditioning that occurs due to the existence of such an observational threshold. We show that this conditioning is relevant, for example, to gene-frequency trajectories, where many loci in the genome are simultaneously measured in a given generation. Such a threshold can lead to severe biases of allele frequency estimates under purifying selection. In the analysis presented, within the context of Markov chains such as the Wright–Fisher model, we address two key questions: (1) “What is a natural measure of the strength of the conditioning associated with an observation threshold?” (2) “What is a principled way to correct for the effects of the conditioning?”. We answer the first question in terms of a proportion. Starting with a large number of trajectories, the relevant quantity is the proportion of these trajectories that are above threshold at a later time and hence are detected. The smaller the value of this proportion, the stronger the effects of conditioning. We provide an approximate analytical answer to the second question, that corrects the bias produced by an observation threshold, and performs to reasonable accuracy in the Wright–Fisher model for biologically plausible parameter values.
A Chromosome-Scale Hybrid Genome Assembly of the Extinct Tasmanian Tiger (Thylacinus cynocephalus)
Authors: Feigin Charles , Frankenberg Stephen , Pask Andrew 
Published: March 2022

Abstract
The extinct Tasmanian tiger or thylacine (Thylacinus cynocephalus) was a large marsupial carnivore native to Australia. Once ranging across parts of the mainland, the species remained only on the island of Tasmania by the time of European colonization. It was driven to extinction in the early 20th century and is an emblem of native species loss in Australia. The thylacine was a striking example of convergent evolution with placental canids, with which it shared a similar skull morphology. Consequently, it has been the subject of extensive study. While the original thylacine assemblies published in 2018 enabled the first exploration of the species’ genome biology, further progress is hindered by the lack of high-quality genomic resources. Here, we present a new chromosome-scale hybrid genome assembly for the thylacine, which compares favorably with many recent de novo marsupial genomes. In addition, we provide homology-based gene annotations, characterize the repeat content of the thylacine genome, and show that consistent with demographic decline, the species possessed a low rate of heterozygosity even compared to extant, threatened marsupials.
Evaluation of methods for estimating coalescence times using ancestral recombination graphs
Authors: Y. C. Brandt Débora , Wei Xinzhu , Deng Yun , Vaughn Andrew H , Nielsen Rasmus 
Published: March 2022

AbstractThe ancestral recombination graph is a structure that describes the joint genealogies of sampled DNA sequences along the genome. Recent computational methods have made impressive progress toward scalably estimating whole-genome genealogies. In addition to inferring the ancestral recombination graph, some of these methods can also provide ancestral recombination graphs sampled from a defined posterior distribution. Obtaining good samples of ancestral recombination graphs is crucial for quantifying statistical uncertainty and for estimating population genetic parameters such as effective population size, mutation rate, and allele age. Here, we use standard neutral coalescent simulations to benchmark the estimates of pairwise coalescence times from 3 popular ancestral recombination graph inference programs: ARGweaver, Relate, and tsinfer+tsdate. We compare (1) the true coalescence times to the inferred times at each locus; (2) the distribution of coalescence times across all loci to the expected exponential distribution; (3) whether the sampled coalescence times have the properties expected of a valid posterior distribution. We find that inferred coalescence times at each locus are most accurate in ARGweaver, and often more accurate in Relate than in tsinfer+tsdate. However, all 3 methods tend to overestimate small coalescence times and underestimate large ones. Lastly, the posterior distribution of ARGweaver is closer to the expected posterior distribution than Relate’s, but this higher accuracy comes at a substantial trade-off in scalability. The best choice of method will depend on the number and length of input sequences and on the goal of downstream analyses, and we provide guidelines for the best practices.
Power across the global health landscape: a network analysis of development assistance 1990–2015
Authors: Fergus Cristin Alexis 
Published: March 2022

AbstractPower distribution across the global health landscape has undergone a fundamental shift over the past three decades. What was once a system comprised largely of bilateral and multilateral institutional arrangements between nation-states evolved into a varied landscape where these traditional actors were joined by a vast assemblage of private firms, philanthropies, non-governmental organizations and public–private partnerships. Financial resources are an explicit power source within global health that direct how, where and to whom health interventions are delivered, which health issues are (de)prioritized, how and by whom evidence to support policies and interventions is developed and how we account for progress. Financial resource allocations are not isolated decisions but rather outputs of negotiation processes and dynamics between actors who derive power from a multiplicity of sources. The aims of this paper are to examine the changes in the global health actor landscape and the shifts in power using data on disbursements of development assistance for health (DAH). A typology of actors was developed from previous literature and refined through an empirical analysis of DAH. The emergent network structure of DAH flows between global health actors and positionality of actors within the network were analysed between 1990 and 2015. The results reflect the dramatic shift in the numbers of actors, relationships between actors, and funding dispersal over this time period. Through a combination of the massive influx of new funding sources and a decrease in public spending, the majority control of financial resources in the DAH network receded from public entities to a vast array of civil society organizations and public–private partnerships. The most prominent of these was the Bill and Melinda Gates Foundation and the Global Fund for AIDS, TB and malaria, which rose to the third and fourth most central positions within the DAH network by 2015.
Mechanoscopy: A Novel Device and Procedure for in vivo Detection of Chronic Colitis in Mice
Authors: He Shijie , Azar Dara A , Esfahani Farid Nasr , Azar Golara A , Shazly Tarek , Saeidi Nima 
Published: March 2022

Abstract

Background
Gut stiffening caused by fibrosis plays a critical role in the progression of inflammatory bowel disease (IBD) and colon cancer. Previous studies have characterized the biomechanical response of healthy and pathological gut, with most measurements obtained ex vivo.

Methods
Here, we developed a device and accompanying procedure for in vivo quantification of gut stiffness, termed mechanoscopy. Mechanoscopy includes a flexible balloon catheter, pressure sensor, syringe pump, and control system. The control system activates the balloon catheter and performs automated measurements of the gut stress-strain biomechanical response.

Results
A gut stiffness index (GSI) is identified based on the slope of the obtained stress-strain response. Using a colitis mouse model, we demonstrated that GSI positively correlates with the extent of gut fibrosis, the severity of mucosal damage, and the infiltration of immune cells. Furthermore, a critical strain value is suggested, and GSI efficiently detects pathological gut fibrotic stiffening when the strain exceeds this value.

Conclusions
Based on these results, we envision that mechanoscopy and GSI will facilitate the clinical diagnosis of IBD.
National Prevalence of Psychological Distress and Use of Mental Health Care in Inflammatory Bowel Disease
Authors: Greywoode Ruby , Ullman Thomas , Keefer Laurie 
Published: March 2022

Abstract

Background
Individuals with inflammatory bowel disease (IBD) have elevated symptoms of anxiety and depression. The burden of such symptoms, accompanied by functional impairment in IBD, is not well documented, nor is utilization of mental health care in this population.

Methods
Adults ≥18 years were identified in the cross-sectional 2015–2016 National Health Interview Survey. Responses from the Kessler Index were used to estimate the national prevalence of psychological distress with impairment and mental health-care use in IBD. Factors associated with psychological distress with impairment in IBD were analyzed using logistic regression.

Results
The prevalence of psychological distress with impairment was significantly higher in IBD than non-IBD adults (7.69% vs. 3.50%, respectively; P &lt; .01). Among those with IBD and psychological distress with impairment, only a third (36.29%) had seen or talked to a mental health provider in the preceding 12 months. About half of these found the cost of mental health care unaffordable. On multivariable analysis, factors associated with psychological distress in IBD included increasing emergency room visits and trouble finding a health provider.

Conclusions
A significant number of adults with IBD in the United States have psychological distress accompanied by functional impairment. However, mental health care is underutilized in this population. Many of these individuals find the cost of mental health care unaffordable, struggle to find a health provider, and experience repeated emergency room visits. Ongoing efforts to improve mental health care in IBD should address issues of access and cost. Additionally, these efforts should seek to understand other barriers to mental health-care use.
Association Between the Clinical, Biochemical, and Endoscopic Activity of Inflammatory Bowel Diseases and Severity and Long-term Outcomes of Coronavirus Disease 2019—A Population-based Study
Authors: Attauabi Mohamed , Dahlerup Jens Frederik , Poulsen Anja , Hansen Malte Rosager , Vester-Andersen Marianne Kajbæk , Prahm August Pilegaard , Pedersen Natalia , Larsen Lone , Jess Tine , Neumann Anders , Haderslev Kent V , Molazahi Akbar , Lødrup Anders Berg , Glerup Henning , Oppfeldt Asser Mathiassen , Jensen Michael Dam , Theede Klaus , Kiszka-Kanowitz Marianne , Seidelin Jakob Benedict , Burisch Johan 
Published: March 2022

Lay Summary
This brief report investigated the impact of clinical, biochemical, and endoscopic activity of IBD on the severity and long-term outcomes of COVID-19 in a prospective population-based cohort. The study did not identify any association between IBD activity and COVID-19 outcomes.
Is the Medium the Message? Functional Diversity Across Abiotic Gradients in Freshwater Electric Fishes
Authors: Ford Kassandra L , Albert James S 
Published: March 2022

SynopsisEvolutionary transitions across abiotic gradients can occur among habitats at multiple spatial scales, and among taxa and biotas through a range of ecological and evolutionary time frames. Two diverse groups of electric fishes, Neotropical Gymnotiformes, and Afrotropical Mormyroidea, offer interesting examples of potentially convergent evolution in aspects of morphological, physiological, and life history traits. We examined biogeographical, morphological, and functional patterns across these two groups to assess the degree of convergence in association with abiotic environmental variables. While there are superficial similarities across the groups and continents, we found substantially more differences in terms of habitat occupancy, electric signal diversity, and morphological disparity. These differences likely correlate to differences in biogeographical histories across the Neotropics and Afrotropics, biotic factors associated with aquatic life and electric signals, and sampling issues plaguing both groups. Additional research and sampling are required to make further inferences about how electric fishes transition throughout diverse freshwater habitats across both microevolutionary and macroevolutionary scales.
Subsidies for innovative start-ups and firm entry
Authors: Accetturo Antonio 
Published: March 2022

Abstract
We provide a counterfactual evaluation of a policy implemented by two Italian regional governments (the autonomous provinces of Trento and Bolzano) to subsidize the entry of new and technologically advanced companies. Using a regression discontinuity design, we show that the subsidies were effective in stimulating the entry of new firms. The policy was able to increase the probability to create a new company by 30–40% points; the probability to create a firm for non-treated applicants averaged around 50%. We also analyze the economic impact of the program. Our estimates show that the policy did not raise (in the first 4 years) the innovation potential of treated firms (as measured by patenting activity); the value added generated by the policy in the first 3 years is equal to 3 million euros (the total amount of subsidies is 8 million).
Australian community pharmacists’ ability to identify the indications for dental prescriptions—a case vignette study
Authors: Park Joon Soo , Page Amy T , Wang Kate N , Tennant Marc , Kruger Estie 
Published: March 2022

Abstract

Objectives
Pharmacists are known as medicine experts. Dentists can independently prescribe and administer medications related to dental conditions such as antimicrobials, anti-inflammatories and analgesics. However, little is known about pharmacists’ knowledge and perceptions of medicines prescribed for dentistry. Therefore, this study aimed to assess community pharmacists’ ability to identify the indications for dental prescriptions using hypothetical vignettes.

Methods
Australian community pharmacists were invited through email and social media to undertake a web-based questionnaire consisting of nine case vignettes of dental prescriptions and their indicated uses in dental settings and two perception-based questions. The results were provided as a percentage of the correct answers to the case vignettes. In addition, Pearson chi-square tests were performed to examine associations between categorical variables.

Key findings
Of the 202 pharmacists who completed the questionnaire, the mean number of correct responses was 5 ± 2 (out of 9). More than three-quarters (78.5%) of pharmacists believed that thorough knowledge of prescriptions for dental ailments was necessary for safe and effective community pharmacy practice. In addition, nearly two-thirds (64.1%) felt confident that they could dispense medicines indicated for dental conditions safely and effectively.

Conclusions
The knowledge demonstrated by participants through correct identification of the indications for dental prescription was less than optimal. Professional development courses for pharmacists in dental ailments could prove beneficial.
Interpolation Polynomials, Bar Monomials, and Their Positivity
Authors: Naqvi Yusra , Sahi Siddhartha , Sergel Emily 
Published: March 2022

AbstractWe prove a conjecture of Knop–Sahi on the positivity of interpolation polynomials, which is an inhomogeneous generalization of Macdonald’s conjecture for Jack polynomials. We also formulate and prove the nonsymmetric version of this conjecture, and in fact, we deduce everything from an even stronger positivity result. This last result concerns certain inhomogeneous analogues of ordinary monomials that we call bar monomials. Their positivity involves in an essential way a new partial order on compositions that we call the bar order, and a new operation that we call a glissade.
Growth performance, bone mineralization, nutrient digestibility, and fecal microbial composition of multi-enzyme-supplemented low-nutrient diets for growing-finishing pigs
Authors: Hong Jinsu , Jlali Maamer , Cozannet Pierre , Preynat Aurelie , Adams Seidu , Scaria Joy , Woyengo Tofuko A 
Published: March 2022

Abstract
A study evaluated the effects of adding multi-enzyme mixture to diets deficient in net energy (NE), standardized ileal digestible (SID) amino acids (AA), standardized total tract digestible (STTD) P, and Ca on growth performance, bone mineralization, nutrient digestibility, and fecal microbial composition of grow-finish pigs. A total of 300 pigs (initial body weight [BW] = 29.2 kg) were housed by sex and BW in 45 pens of 7 or 6 pigs and fed 5 diets in a randomized complete block design. Diets were positive control (PC), and negative control 1 (NC1) or negative control 2 (NC2) without or with multi-enzyme mixture. The multi-enzyme mixture supplied at least 1,800, 1,244, 6,600, and 1,000 units of xylanase, β -glucanase, arabinofuranosidase, and phytase per kilogram of diet, respectively. The PC was adequate in all nutrients. The NC1 diet had lower content NE, SID AA, STTD P, and Ca than PC diet by about 7%, 7%, 32%, and 13%, respectively. The NC2 diet had lower NE, SID AA, STTD P, and Ca than PC diet by 7%, 7%, 50%, and 22%, respectively. The diets were fed in four phases based on BW: Phase 1: 29–45 kg, Phase 2: 45–70 kg, Phase 3: 70–90 kg, and Phase 4: 90–120 kg. Nutrient digestibility, bone mineralization, and fecal microbial composition were determined at the end of Phase 1. Pigs fed PC diet had greater (P &lt; 0.05) overall G:F than those fed NC1 diet or NC2 diet. Multi-enzyme mixture increased (P &lt; 0.05) overall G:F, but the G:F of the multi-enzyme mixture-supplemented diets did not reach (P &lt; 0.05) that of PC diet. Multi-enzyme mixture tended to increase (P = 0.08) femur breaking strength. Multi-enzyme mixture increased (P &lt; 0.05) the ATTD of GE for the NC2 diet, but unaffected the ATTD of GE for the NC1 diet. Multi-enzyme mixture decreased (P &lt; 0.05) the relative abundance of the Cyanobacteria and increased (P &lt; 0.05) relative abundance of Butyricicoccus in feces. Thus, the NE, SID AA, STTD P, and Ca could be lowered by about 7%, 7%, 49%, and 22%, respectively, in multi-enzyme mixture-supplemented diets without negative effects on bone mineralization of grow-finish pigs. However, multi-enzyme mixture supplementation may not fully restore G:F of the grow-finish pigs fed diets that have lower NE and SID AA contents than recommended by 7%. Since an increase in content of Butyricicoccus in intestine is associated with improved gut health, addition of the multi-enzyme mixture in diets for pigs can additionally improve their gut health.
1 The Battle of the Titans: Comparing Resuscitation Between 5 Centers Using the Burn Navigator
Authors: Rizzo Julie A , Coates Elsa , Salinas Jose , Serio-Melvin Maria , Pham Tam N , Foster Kevin N , Abdelfattah Kareem R , Liu Nehemiah T 
Published: March 2022

Abstract

Introduction
The goal of burn resuscitation is to provide the least amount of fluid necessary to maintain end-organ perfusion and prevent burn shock. The objective of this analysis was to examine how the Burn Navigator (BN), a clinical decision support tool in burn resuscitation, was utilized across 5 major burn centers in the United States.

Methods
A non-interventional, observational trial of 300 adult patients with embedded prospective and retrospective components was undertaken to examine the effectiveness of the BN in burn resuscitation. 5 ABA-verified burn centers enrolled patients. Data examining patient demographics, burn characteristics, fluid volumes, and resuscitation-related complications were examined. Statistical analysis compared the 5 sites in terms of these variables.

Results
A total of 285 patients were eligible for analysis. There was no difference among the centers in terms of average age (45.5 + 16.8 years), BMI (29.2 + 6.9), ISS (21.2 + 12.8), or median TBSA (34 [25.8, 47]). Primary crystalloid infusion volumes at 24 hours differed significantly when measured in ml/kg/TBSA (median 3.7 [2.9, 8.8], range 1.3 to 12.3). Similarly, total fluids, which includes colloid adjuncts, drip medications and enteral fluids, differed between groups when measured in both ml/kg (median 149.8 [106.5, 224.1], range 38.4 to 536.2) and ml/kg/TBSA (4.2 [3.3, 5.5], 1.7 to 15.3) at 24 hours. Post-hoc adjustment for pairwise comparisons resulted in a loss of significance between most of the sites. There was a total of 156 resuscitation-related complications reported across the 5 sites with an average incidence of 44.4 % incidence.

Conclusions
The Burn Navigator appeared to standardize fluid resuscitations across 5 major US burn centers. With primary fluid volumes near the Parkland formula, the device can be utilized effectively in burn centers, and further study should exam the utility of this device in facilities that do not commonly treat burn injuries, as well as the battlefield.