bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increasing Pediatricians' Scholarly Productivity on and off the Tenure Track
Authors: Tumin Dmitry , Baumgarten Nathan , Buckman Cierra , Kuehn Devon , Higginson Jason D. 
Published: February 2022

Introduction:
Physician faculty have increasingly been appointed to nontenure track positions, which provide limited support for scholarly activity. We evaluated how a centralized departmental research group affected the scholarly productivity of faculty on and off the tenure track.

Methods:
A research team providing both mentorship and logistical study support was implemented in 2018. We identified a pre-intervention cohort of physician faculty employed in July 2016, and a postintervention cohort, employed in July 2018. A publication search was conducted for these cohorts in the period 2017 to 2018 and 2019 to 2020, respectively.

Results:
Seventy-five faculty were included in the analysis, with approximately two-thirds appointed on the clinical (nontenure) track. In the pre-intervention cohort (n = 59), 15 faculty (25%) had at least one publication in the period 2017 to 2018. In the postintervention cohort (n = 59), 33 faculty (56%) published at least one article in the period 2019 to 2020 (P = .001). Multivariable random-effects regression analysis confirmed that postintervention, odds of publishing in a given year increased for both clinical-track and tenure-track faculty.

Conclusion:
Both clinical and tenure-track faculty contribute to the academic mission at medical schools, yet scholarly activity is supported and rewarded for tenure-track faculty more often than for clinical-track faculty. Our centralized research team successfully fostered scholarly activity among both clinical-track and tenure-track faculty.
Graduate Medical Education Can Be an Impetus for Behavior Changes in Physicians in Practice: Point-Of-Care Ultrasound Faculty Development Intervention in Anesthesiology
Authors: Zisblatt Lara , Byrne Melissa , Chen Fei , Caldwell Matthew 
Published: February 2022

Introduction:
While there is growing evidence to suggest that point-of-care ultrasound (POCUS) may aid in clinical decision-making in the perioperative setting and there are new requirements that anesthesiology residents must be trained in POCUS, few practicing anesthesiologists use POCUS in their practice. The goal of this investigation is to determine whether a multifaceted faculty development program helps a group of faculty members incorporate POCUS into their practice.

Methods:
This intervention had five parts: (1) online prework, (2) 2-day workshop, (3) follow-up hands-on sessions, (4) regular communication, and (5) equipment acquisition. This is a pretest/posttest, single group, observational study where the main outcome measure is the number of POCUS examinations documented and the number of providers who performed at least one examination. In addition, presurveys and postsurveys were administered to determine whether there was a change in confidence and self-reported use of POCUS.

Results:
The number of examinations completed and the number of providers completing examinations by month both seemed to increase over time between May 2017 and October 2018. Between August 2017 and October 2018, the number of examinations completed per month increased by a rate of approximately one examination per month (starting with one examination in May 2017) and the number of providers completing examinations increased by a rate of approximately 0.61 providers per month (staring with one provider in May 2017).

Discussion:
This study shows that an intervention that targets interested faculty can increase the use of POCUS in practice and residents' perceptions of teaching.
Prevalence of Private and Public Health Insurance Among Transgender and Gender Diverse Adults
Authors: Downing Jae , Lawley Kendall A. , McDowell Alex 
Published: February 2022

Background:
Little is known about how health insurance payer types differ between transgender and gender diverse (TGD) people and cisgender people. Much of what is known about insurance coverage among TGD adults has been based on research from claims and electronic health record data, which excludes individuals who have not accessed gender-affirming care. Research designed to understand how TGD populations pay for health care to best inform care interventions and public insurance policies is lacking.

Objective:
The objective of this study was to examine differences in the prevalence of public and private health insurance between transgender and cisgender adults.

Methods:
Using data from the Behavioral Risk Factor Surveillance System, this study estimated prevalence of health insurance coverage among TGD and cisgender adults residing in 22 states that administered the Sexual Orientation and Gender Identity module and the Healthcare Access module from 2014 to 2019. This study estimated the odds of health insurance coverage (no insurance, private insurance, public insurance) among cisgender adults compared with TGD adults.

Results:
TGD people had greater odds of being uninsured compared with cisgender women. Among nondisabled, nonelderly respondents, TGD adults had lower odds of having private insurance and higher odds of public insurance compared with cisgender men. Among respondents who were likely Medicaid-eligible, TGD respondents had lower odds of having public insurance and higher odds of being uninsured compared with cisgender women.

Conclusion:
These findings provide foundational information about the payer mix among TGD people and provide insight into barriers to health insurance that TGD adults may face.
Testosterone Changes in Men With Obesity and Type 2 Diabetes 6 Months After Sleeve Gastrectomy With Transit Bipartition
Authors: Taskin Halit E. , Al Muzaffer 
Published: February 2022

Background:
Metabolic/bariatric surgery has been shown to increase testosterone in males with obesity. This study investigated the effect of the novel metabolic/bariatric surgery procedure, sleeve gastrectomy with transit bipartition (SG-TB), on serum total testosterone and metabolic variable changes in men with obesity and type 2 diabetes.

Methods:
In a prospective single-center cohort study, laboratory samples were analyzed preoperatively and at 6 months following SG-TB in patients with a body mass index (BMI) ≥30 kg/m2. Changes in metabolic parameters and testosterone were evaluated.

Results:
Between July 2018 and March 2019, 166 patients with a mean baseline BMI of 34.9±3.8 kg/m2 (mean age 51.5±9.3 y), glycosylated hemoglobin 9.5±1.3%, and testosterone 3.1±1.3 underwent SG-TB. At 6-month follow-up, mean excess BMI loss was 70.2±24.3%; glycosylated hemoglobin, 6.6±1.1% (P<0.001); and testosterone, 4.5±1.5 (P<0.001).

Conclusion:
In the early term following SG-TB, more than any other factor assessed, BMI loss was found to be a significant driver of improvement in testosterone levels. Regardless of preoperative obesity classification, patients with initially low testosterone attained significantly increased testosterone levels at 6-month follow-up.
CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure
Authors: Escobedo Nahuel , Cahui Ronaldo Romario Tunque , Caruso Gastón , Ríos Emilio García , Hirsh Layla , Monzon Alexander Miguel , Parisi Gustavo , Palopoli Nicolas 
Published: February 2022

AbstractSummaryA collection of conformers that exist in a dynamical equilibrium defines the native state of a protein. The structural differences between them describe their conformational diversity, a defining characteristic of the protein with an essential role in multiple cellular processes. Since most proteins carry out their functions by assembling into complexes, we have developed CoDNaS-Q, the first online resource to explore conformational diversity in homooligomeric proteins. It features a curated collection of redundant protein structures with known quaternary structure. CoDNaS-Q integrates relevant annotations that allow researchers to identify and explore the extent and possible reasons of conformational diversity in homooligomeric protein complexes.Availability and implementationCoDNaS-Q is freely accessible at http://ufq.unq.edu.ar/codnasq/. The data can be retrieved from the website. The source code of the database can be downloaded from https://github.com/SfrRonaldo/codnas-q.Contactnpalopoli@unq.edu.ar
Design of a Versatile Microfluidic Device for Imaging Precision-Cut-Tissue Slices
Authors: Rafiei Nafiseh , Au Aaron , Moghadam Mohammadamir G. , Regeenes Romario , Wang Yufeng , Yip Christopher M. , Gaisano Herbert , Rocheleau Jonathan V. 
Published: February 2022

AbstractPrecision-cut-tissues (PCT), which preserve many aspects of a tissue’s microenvironment, are typically imaged using conventional sample dishes and chambers. These can require large amounts of reagent and, when used for flow-through experiments, the shear forces applied on the tissues are often ill-defined. Their physical design also makes it difficult to image large volumes and repetitively image smaller regions of interest in the living slice. We report here on the design of a versatile microfluidic device capable of holding mouse or human pancreas PCTs for 3D fluorescence imaging using confocal and selective plane illumination microscopy (SPIM). Our design positions PCTs within a 5 × 5 mm × 140 µm deep chamber fitted with 150 µm tall channels to facilitate media exchange. Shear stress in the device is localized to small regions on the surface of the tissue and can be easily controlled. This design allows for media exchange at flow rates ~10-fold lower than those required for conventional chambers. Finally, this design allows for imaging the same immunofluorescently labelled PCT with high resolution on a confocal and with large field of view on a SPIM, without adversely affecting image quality.
Comparative evaluation of glomerular morphometric techniques reveals differential technical artefacts between FSGS and normal glomeruli
Authors: Basgen John M , Reghuvaran Anand C , Lin Qisheng , Banu Khadija , Shi Hongmei , Pell John , DiRito Jenna , Tietjen Gregory T , Perincheri Sudhir , Moledina Dennis G , Wilson Francis Perry , Menon Madhav C 
Published: February 2022

AbstractMorphometric estimates of mean glomerular volume (MGV) have clinical implications, over and above histologic data. However, MGV estimation is time-consuming, could waste tissue sections and requires expertise limiting its utility in retrospective clinical studies.MethodsWe evaluated MGV using both plastic and paraffin-embedded tissue from control and FSGS mice (n=10 each) using the gold-standard Disector/Cavalieri technique (Vglom-Cav) and other reported techniques [2- or 3-profile technique, Weibel-Gomez method (W-G)]. Within Vglom-Cav we examined the precision of MGV estimation while using MGVs obtained from 5- or 10-individual glomeruli measurements vs the true mean (20 glomeruli).ResultsIn both FSGS and controls, we identified an acceptable precision of 10-glomerular sampling vs true MGV within Vglom-Cav technique [88 (79-94) % of MGV obtained were within 10% of the true MGV]. The 5-glomerular sampling was less precise [70 (56, 81) % of MGV obtained were within 10% of true MGV]. In plastic based techniques, 2- or 3-profile MGVs showed greater concordance with Vglom-Cav, than W-G MGV. The new 3-profile technique offered incremental benefit to the existing 2-profile method (improved Lin’s concordance in control and FSGS animals). We observed a consistent reduction of Vglom values within control animals (52+/-0.06%) in paraffin-embedded tissue (vs corresponding methods in plastic) demonstrating a clear shrinkage artefact due to tissue processing. FSGS glomeruli showed significantly less and more variable shrinkage artefact likely due to glomerular fibrosis.ConclusionWe report the precision of 5- or 10-glomerular sampling for MGV estimation using controls and FSGS animals. We demonstrate and quantify the shrinkage bias in MGV during tissue processing for paraffin-embedding that also differentiated control animals and FSGS. Our findings have implications for experimental studies using glomerular morphometry.
Proteogenomics analysis to identify acquired resistance-specific alterations in melanoma PDXs on MAPKi therapy
Authors: Manna Kanishka , Dharanipragada Prashanthi , Alkam Duah , Avaritt Nathan L. , Washam Charity L. , Robeson Michael S. , Edmondson Ricky D. , Mackintosh Samuel G. , Yang Zhentao , Wang Yan , Lomeli Shirley H. , Moriceau Gatien , Byrum Stephanie D. , Lo Roger S. , Tackett Alan J. 
Published: February 2022

AbstractTherapeutic approaches to treat melanoma include small molecule drugs that target activating protein mutations in pro-growth signaling pathways like the MAPK pathway. While beneficial to the approximately 50% of patients with activating BRAFV600 mutation, mono- and combination therapy with MAPK inhibitors is ultimately associated with acquired resistance. To better characterize the mechanisms of MAPK inhibitor resistance in melanoma, we utilize patient-derived xenografts and apply proteogenomic approaches leveraging genomic, transcriptomic, and proteomic technologies that permit the identification of resistance-specific alterations and therapeutic vulnerabilities. A specific challenge for proteogenomic applications comes at the level of data curation to enable multi-omics data integration. Here, we present a proteogenomic approach that uses custom curated databases to identify unique resistance-specific alternations in melanoma PDX models of acquired MAPK inhibitor resistance. We demonstrate this approach with a NRASQ61L melanoma PDX model from which resistant tumors were developed following treatment with a MEK inhibitor. Our multi-omics strategy addresses current challenges in bioinformatics by leveraging development of custom curated proteogenomics databases derived from individual resistant melanoma that evolves following MEK inhibitor treatment and is scalable to comprehensively characterize acquired MAPK inhibitor resistance across patient-specific models and genomic subtypes of melanoma.
Demise of Marimermithida refines primary routes of transition to parasitism in roundworms
Authors: Tchesunov Alexei V. , Nikolaeva Olga V. , Rusin Leonid Yu. , Sanamyan Nadezda P. , Panina Elena G. , Miljutin Dmitry M. , Gorelysheva Daria I. , Pegova Anna N. , Khromova Maria R. , Mardashova Maria V. , Mikhailov Kirill V. , Yushin Vladimir V. , Petrov Nikolai B. , Lyubetsky Vassily A. , Nikitin Mikhail A. , Aleoshin Vladimir V. 
Published: February 2022

ABSTRACTNematodes (roundworms) are ubiquitous animals commonly dominating in ecological communities and networks, with many parasites and pathogen vectors of great economic and medical significance. Nematode parasites are remarkably diverse in life strategies and adaptations at a great range of hosts and dimension scales, from whales to protozoan cells. Their life history is intricate and requires understanding to study the genomic, structural and ecological bases of successful transitions to parasitism. Based on analyses of rDNA for a representative sampling of host-associated and free-living groups, we dismiss the last higher-rank nematode taxon uniting solely parasitic forms (Marimermithida) and show that primarily marine parasitism emerged independently and repeatedly within only few free-living lineages. We re-evaluate the significance of some traditionally important phenotypic characters and report the phenomenon of dramatic adaptation to parasitism on very short evolutionary timescales. A cross-phylum character interpretation vindicates that non-intestinal (in-tissue or cavitary) host capture was likely a primary route of transition to truly exploitive parasitism (vs. intestinal commensalism) in roundworms, and extant nematode parasitoids (larval parasites) infesting the host body cavity or internal organs realise this primary lifestyle. Parasitism may have evolved in nematodes as part of innate pre-adaptations to crossing environmental boarders, and such transitions have been accomplished multiple times successfully in the phylum history.
StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data
Authors: Hu Han , Tan Yuxiang , Li Chenhao , Chen Junyu , Kou Yan , Xu Zhenjiang Zech , Liu Yang-Yu , Tan Yan , Dai Lei 
Published: February 2022

AbstractBackgroundMicrobial strains of variable functional capacities co-exist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data.MethodsHere we present StrainPanDA (Strain-level Pangenome Decomposition Analysis), a novel method that uses the pangenome coverage profile of multiple metagenomic samples to simultaneously reconstruct the composition and gene content variation of co-existing strains in microbial communities.ResultsWe systematically validate the accuracy and robustness of StrainPanDA using synthetic datasets. To demonstrate the power of gene-centric strain profiling, we then apply StrainPanDA to analyze the gut microbiome samples of infants, as well as patients treated with fecal microbiota transplantation. We show that the linked reconstruction of strain composition and gene content profiles is critical for understanding the relationship between microbial adaptation and strain-specific functions (e.g., nutrient utilization, pathogenicity).ConclusionsStrainPanDA can be applied to metagenomic datasets to detect association between molecular functions and microbial/host phenotypes to formulate testable hypotheses and gain novel biological insights at the strain or subspecies level.
Genetic and epigenetic driven variation in regulatory regions activity contribute to adaptation and evolution under endocrine treatment
Authors: Slaven Neil , Lopes Rui , Canale Eleonora , Ivanoiu Diana , Pacini Claudia , Monteiro Barbosa Ines Amorim , Bleu Melusine , Bravaccini Sara , Ravaioli Sara , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio G. , Barozzi Iros , Magnani Luca 
Published: February 2022

AbstractComprehensive profiling of hormone-dependent breast cancer (HDBC) has identified hundreds of protein-coding alterations contributing to cancer initiation1, 2, but only a handful have been linked to endocrine therapy resistance, potentially contributing to 40% of relapses1, 3–9. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ integrative functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers10, gene promoters, and boundaries of topologically associating domains11. Massive parallel perturbation in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance12, 13 and endocrine therapy resistance9. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies non-coding changes involved in therapy resistance. Overall, our data uncover actionable transient transcriptional programs critical for dormant persister cells and unveil new regulatory nodes driving evolutionary trajectories towards disease progression.
Emergent regulation of ant foraging frequency through a computationally inexpensive forager movement rule
Authors: Baltiansky Lior , Frankel Guy , Feinerman Ofer 
Published: February 2022

1AbstractAnt colonies regulate foraging in response to their collective hunger, yet the mechanism behind this distributed regulation remains unclear. Previously, by imaging food flow within ant colonies we showed that the frequency of foraging events declines linearly with colony satiation ([1]). Our analysis implied that as a forager distributes food in the nest, two factors affect her decision to exit for another foraging trip: her current food load and its rate of change. Sensing these variables can be attributed to the forager’s individual cognitive ability. Here, new analyses of the foragers’ trajectories within the nest imply a different way to achieve the observed regulation. Instead of an explicit decision to exit, foragers merely tend toward the depth of the nest when their food load is high and toward the nest exit when it is low. Thus, the colony shapes the forager’s trajectory by controlling her unloading rate, while she senses only her current food load. Using an agent-based model and mathematical analysis, we show that this simple mechanism robustly yields emergent regulation of foraging frequency. These findings demonstrate how the embedding of individuals in physical space can reduce their cognitive demands without compromising their computational role in the group.
Uniformity of spheroid-on-chip by surface treatment of PDMS microfluidic platforms
Authors: Azizipour Neda , Avazpour Rahi , Sawan Mohamad , Rosenzweig Derek H. , Ajji Abdellah 
Published: February 2022

AbstractSpheroids have emerged as a more reliable model for drug screening when compared with 2D culture models. Microfluidic based biochips have many advantages over other 3D cell culture models for drug testing on spheroids, including precise control of the cellular microenvironment. The control of the cell adhesion to the surface is one of the most important challenges affecting the size and the geometry of the spheroids which could be controlled by appropriate surface engineering methods. We have studied the modification of the PDMS surface properties treated by applying different concentrations of the two anti-fouling coatings (BSA and Pluronic F-68). The desired treatment of PDMS surface effectively inhibits cell adhesion to the surface and promotes cells self-aggregations to form more uniform and healthy spheroids for a longer period of time. The microscopic observations with qualitative and quantitate data revealed that surface properties drastically affect the number of the spheroids formed on-chip and their geometry. We used human breast cancer cell line (MDA-MB-231-GFP) while the concentration of the chemical coatings and incubation time were adjusted. Proper repellent PDMS surfaces were provided with minimum cell attachment and facilitated spheroid formation when compared with non-treated PDMS. The results demonstrate fundamental and helpful patterns for microfluidic based cell culture applications to improve the quantity and quality of spheroid formation on-chip which are strongly manipulated by surface properties (i.e., morphology, roughness, wettability and etc.)