bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anomalous gas in ESO 149-G003: a MeerKAT-16 view
Authors: Józsa Gyula I G , Thorat Kshitij , Kamphuis Peter , Sebokolodi Lerato , Maina Eric K , Wang Jing , Pieterse Daniëlle L A , Groot Paul , Ramaila Athanaseus J T , Serra Paolo , Andati Lexy A L , de Blok W J G , Hugo Benjamin V , Kleiner Dane , Maccagni Filippo M , Makhathini Sphesihle , Molnár Dániel Cs , Ramatsoku Mpati , Smirnov Oleg M , Bloemen Steven , Paterson Kerry , Vreeswijk Paul , McBride Vanessa , Klein-Wolt Marc , Woudt Patrick , Körding Elmar , Le Poole Rudolf , Goedhart Sharmila , Passmoor Sean S , Serylak Maciej , Dettmar Ralf-Jürgen 
Published: December 2020

ABSTRACT
ESO 149-G003 is a close-by, isolated dwarf irregular galaxy. Previous observations with the ATCA indicated the presence of anomalous neutral hydrogen ($\rm{H{\small I}}$) deviating from the kinematics of a regularly rotating disc. We conducted follow-up observations with the MeerKAT radio telescope during the 16-dish Early Science programme as well as with the MeerLICHT optical telescope. Our more sensitive radio observations confirm the presence of anomalous gas in ESO 149-G003, and further confirm the formerly tentative detection of an extraplanar $\rm{H{\small I}}$ component in the galaxy. Employing a simple tilted-ring model, in which the kinematics is determined with only four parameters but including morphological asymmetries, we reproduce the galaxy’s morphology, which shows a high degree of asymmetry. By comparing our model with the observed $\rm{H{\small I}}$, we find that in our model, we cannot account for a significant (but not dominant) fraction of the gas. From the differences between our model and the observed data cube, we estimate that at least 7–8 per cent of the $\rm{H{\small I}}$ in the galaxy exhibits anomalous kinematics, while we estimate a minimum mass fraction of less than 1 per cent for the morphologically confirmed extraplanar component. We investigate a number of global scaling relations and find that, besides being gas-dominated with a neutral gas-to-stellar mass ratio of 1.7, the galaxy does not show any obvious global peculiarities. Given its isolation, as confirmed by optical observations, we conclude that the galaxy is likely currently acquiring neutral gas. It is either re-accreting gas expelled from the galaxy or accreting pristine intergalactic material.
Shape, colour, and distance in weak gravitational flexion
Authors: Fabritius II Joseph M , Arena Evan J , Goldberg David M 
Published: December 2020

ABSTRACT
Canonically, elliptical galaxies might be expected to have a perfect rotational symmetry, making them ideal targets for flexion studies – however, this assumption has not been tested. We have undertaken an analysis of low- and high-redshift galaxy catalogues of known morphological type with a new gravitational lensing code, Lenser. Using colour measurements in the u − r bands and fit Sérsic index values, objects with characteristics consistent with early-type galaxies are found to have a lower intrinsic scatter in flexion signal than late-type galaxies. We find this measured flexion noise can be reduced by more than a factor of two at both low and high redshift.
Rampant False Detection of Adaptive Phenotypic Optimization by ParTI-Based Pareto Front Inference
Authors: Sun Mengyi , Zhang Jianzhi 
Published: December 2020

Abstract
Organisms face tradeoffs in performing multiple tasks. Identifying the optimal phenotypes maximizing the organismal fitness (or Pareto front) and inferring the relevant tasks allow testing phenotypic adaptations and help delineate evolutionary constraints, tradeoffs, and critical fitness components, so are of broad interest. It has been proposed that Pareto fronts can be identified from high-dimensional phenotypic data, including molecular phenotypes such as gene expression levels, by fitting polytopes (lines, triangles, tetrahedrons, and so on), and a program named ParTI was recently introduced for this purpose. ParTI has identified Pareto fronts and inferred phenotypes best for individual tasks (or archetypes) from numerous data sets such as the beak morphologies of Darwin’s finches and mRNA concentrations in human tumors, implying evolutionary optimizations of the involved traits. Nevertheless, the reliabilities of these findings are unknown. Using real and simulated data that lack evolutionary optimization, we here report extremely high false-positive rates of ParTI. The errors arise from phylogenetic relationships or population structures of the organisms analyzed and the flexibility of data analysis in ParTI that is equivalent to p-hacking. Because these problems are virtually universal, our findings cast doubt on almost all ParTI-based results and suggest that reliably identifying Pareto fronts and archetypes from high-dimensional phenotypic data are currently generally difficult.
Endoplasmic reticulum stress: a key regulator of the follicular microenvironment in the ovary
Authors: Harada Miyuki , Takahashi Nozomi , Azhary Jerilee Mk , Kunitomi Chisato , Fujii Tomoyuki , Osuga Yutaka 
Published: December 2020

ABSTRACT
Intra-ovarian local factors regulate the follicular microenvironment in coordination with gonadotrophins, thus playing a crucial role in ovarian physiology as well as pathological states such as polycystic ovary syndrome (PCOS). One recently recognized local factor is endoplasmic reticulum (ER) stress, which involves the accumulation of unfolded or misfolded proteins in the ER related to various physiological and pathological conditions that increase the demand for protein folding or attenuate the protein-folding capacity of the organelle. ER stress results in activation of several signal transduction cascades, collectively termed the unfolded protein response (UPR), which affect a wide variety of cellular functions. Recent studies have revealed diverse roles of ER stress in physiological and pathological conditions in the ovary. In this review, we summarize the most current knowledge of the regulatory roles of ER stress in the ovary, in the context of reproduction. The physiological roles of ER stress and the UPR in the ovary remain largely undetermined. On the contrary, activation of ER stress is known to impair follicular and oocyte health in various pathological conditions; moreover, ER stress also contributes to the pathogenesis of several ovarian diseases, including PCOS. Finally, we discuss the potential of ER stress as a novel therapeutic target. Inhibition of ER stress or UPR activation, by treatment with existing chemical chaperones, lifestyle intervention, or the development of small molecules that target the UPR, represents a promising therapeutic strategy.
Shrinkage improves estimation of microbial associations under different normalization methods
Authors: Badri Michelle , Kurtz Zachary D , Bonneau Richard , Müller Christian L 
Published: December 2020

Abstract
Estimation of statistical associations in microbial genomic survey count data is fundamental to microbiome research. Experimental limitations, including count compositionality, low sample sizes and technical variability, obstruct standard application of association measures and require data normalization prior to statistical estimation. Here, we investigate the interplay between data normalization, microbial association estimation and available sample size by leveraging the large-scale American Gut Project (AGP) survey data. We analyze the statistical properties of two prominent linear association estimators, correlation and proportionality, under different sample scenarios and data normalization schemes, including RNA-seq analysis workflows and log-ratio transformations. We show that shrinkage estimation, a standard statistical regularization technique, can universally improve the quality of taxon–taxon association estimates for microbiome data. We find that large-scale association patterns in the AGP data can be grouped into five normalization-dependent classes. Using microbial association network construction and clustering as downstream data analysis examples, we show that variance-stabilizing and log-ratio approaches enable the most taxonomically and structurally coherent estimates. Taken together, the findings from our reproducible analysis workflow have important implications for microbiome studies in multiple stages of analysis, particularly when only small sample sizes are available.
Risk Factors, Screening, and Treatment Challenges in Staphylococcus aureus Native Septic Arthritis
Authors: Gobao Valerie C , Alfishawy Mostafa , Smith Clair , Byers Karin E , Yassin Mohamed , Urish Kenneth L , Shah Neel B 
Published: December 2020

Abstract

Background
Staphylococcus aureus is the most common cause of native septic arthritis. Few studies have characterized this disease during the US opioid epidemic. The role of methicillin-resistant Staphylococcus aureus (MRSA) nasal screening in this disease has not been elucidated. We sought to identify risk factors and outcomes for S. aureus native septic arthritis and to evaluate MRSA screening in this disease.

Methods
A retrospective cohort study of native septic arthritis patients (2012–2016) was performed. Demographics, risk factors, and outcomes were compared between Staphylococcus aureus and other native septic arthritis infections. Sensitivity, specificity, and predictive values of MRSA screening were assessed.

Results
Two hundred fifteen cases of native septic arthritis were included. S. aureus was cultured in 64% (138/215). MRSA was cultured in 23% (50/215). S. aureus was associated with injection drug use (odds ratio [OR], 4.33; 95% CI, 1.74–10.81; P = .002) and switching antibiotics (OR, 3.92; 95% CI, 1.01–21.38; P = .032). For every 10-year increase in age, the odds of S. aureus decreased (OR, 0.72; 95% CI, 0.60–0.87; P = .001). For 1-unit increases in Charlson comorbidity index score, the odds of S. aureus decreased (OR, 0.82; 95% CI, 0.73–0.91; P = .0004). MRSA screening during admission demonstrated a sensitivity of 0.59, specificity of 0.96, positive predictive value of 0.85, and negative predictive value of 0.84 for MRSA native septic arthritis.

Conclusions
The opioid epidemic may be contributing to a demographic shift in native septic arthritis to younger, healthier individuals. S. aureus native septic arthritis has unique risks, including injection drug use. MRSA screening may be useful to rule in MRSA native septic arthritis.
Candida Infective Endocarditis: A Retrospective Study of Patient Characteristics and Risk Factors for Death in 703 United States Cases, 2015–2019
Authors: Huggins Jonathan P , Hohmann Samuel , David Michael Z 
Published: December 2020

Abstract

Background
Candida endocarditis is a rare, sometimes fatal complication of candidemia. Past investigations of this condition are limited by small sample sizes. We used the Vizient clinical database to report on characteristics of patients with Candida endocarditis and to examine risk factors for in-hospital mortality.

Methods
This was a multicenter, retrospective cohort study of 703 inpatients admitted to 179 US hospitals between October 2015 and April 2019. We reviewed demographic, diagnostic, medication administration, and procedural data from each patient’s initial encounter. Univariate and multivariate logistic regression analyses were used to identify predictors of in-hospital mortality.

Results
Of 703 patients, 114 (16.2%) died during the index encounter. One hundred fifty-eight (22.5%) underwent an intervention on a cardiac valve. On multivariate analysis, acute and subacute liver failure was the strongest predictor of death (odds ratio [OR], 9.2; 95% confidence interval [CI], 4.8 –17.7). Female sex (OR, 1.9; 95% CI, 1.2–3.0), transfer from an outside medical facility (OR, 1.8; 95% CI, 1.1–2.8), aortic valve pathology (OR, 2.7; 95% CI, 1.5–4.9), hemodialysis (OR, 2.1; 95% CI, 1.1–4.0), cerebrovascular disease (OR, 2.2; 95% CI, 1.2–3.8), neutropenia (OR, 2.5; 95% CI, 1.3–4.8), and alcohol abuse (OR, 2.9; 95% CI, 1.3–6.7) were also associated with death on adjusted analysis, whereas opiate abuse was associated with a lower odds of death (OR, 0.5; 95% CI, 0.2–0.9).

Conclusions
We found that the inpatient mortality rate was 16.2% among patients with Candida endocarditis. Acute and subacute liver failure was associated with a high risk of death, whereas opiate abuse was associated with a lower risk of death.
Pneumocystis and Severe Acute Respiratory Syndrome Coronavirus 2 Coinfection: A Case Report and Review of an Emerging Diagnostic Dilemma
Authors: Rubiano Carlos , Tompkins Kathleen , Sellers Subhashini A , Bramson Brian , Eron Joseph , Parr Jonathan B , Schranz Asher J 
Published: December 2020

Abstract
We present a case of a critically ill patient with coronavirus disease 2019 (COVID-19) found to have acquired immune deficiency syndrome and Pneumocystis jirovecii pneumonia (PCP). Coronavirus disease 2019 and PCP co-occurrence is increasingly reported and may complicate diagnostic and therapeutic strategies. Patients with severe COVID-19 should be screened for underlying immunocompromise and coinfections should be considered.
A Pilot Study of a Chronic Pain Self-Management Program Delivered by Community Health Workers to Underserved African American Older Adults
Authors: Janevic Mary , Robinson-Lane Sheria G , Murphy Susan L , Courser Rebecca , Piette John D 
Published: December 2020

Abstract

Objective
African American older adults living in disadvantaged communities are disproportionately burdened by disabling pain. To address their needs, we tested the feasibility and potential effects of a cognitive-behavioral chronic pain self-management program delivered by community health workers.

Design
A single-group, pre-post evaluation of the STEPS-2 (Seniors using Technology to Engage in Pain Self-management) intervention, in which participants learned pain-management skills through web-based videos. They were also given wearable activity trackers to facilitate incremental increases in walking. In weekly telephone calls, community health workers helped participants apply skills and set goals.

Subjects/setting
Thirty-one adults in Detroit, Michigan (97% African American, 97% female, mean 68.7 years), with chronic musculoskeletal pain.

Methods
Participants completed telephone surveys at baseline and eight weeks. We measured changes in PROMIS pain interference and pain intensity, as well as Patient Global Impression of Change in pain and functioning. Feasibility indicators included participant engagement and satisfaction, and fidelity to session protocols by community health workers.

Results
Participants on average completed 6.6/7 sessions, and 100% agreed or strongly agreed that they improved their understanding of pain management. Average community health worker fidelity score was 1.79 (0 to 2 scale). Pain interference decreased from baseline to post-program (T-score 61.6 to 57.3, P=.000), as did pain intensity (0 to 10 scale, 6.3 to 5.1, P=.004). Approximately 90% of participants reported that pain and function were at least “a little better” since baseline.

Conclusions
An intervention combining mobile health tools with support from community health workers holds promise for improving pain outcomes among underserved older adults.
Impact of Implementing an Academic Detailing Program on Opioid-Benzodiazepine Co-Prescribing Trends at the U.S. Department of Veterans Affairs
Authors: Bounthavong Mark , Lau Marcos K , Kay Chad L , Wells Daina L , Popish Sarah J , Harvey Michael A , Himstreet Julianne E , Grana Andrea , Freeman Blake A , Morillo Christina M , Christopher Melissa L D 
Published: December 2020

Abstract

Objectives
To assess the process and outcomes of academic detailing to enhance the Opioid Safety Initiative and the Psychotropic Drug Safety Initiative to reduce co-prescribing of opioid-benzodiazepine combinations in veterans.

Methods
A retrospective cohort design was conducted to evaluate the impact of implementing an academic detailing program on opioid-benzodiazepine co-prescribing between October 2014 through March 2019 at the U.S. Department of Veterans Affairs (VA). The primary outcome was the monthly prevalence of veterans (number per 1,000 population) who were co-prescribed opioid-benzodiazepine combination. Process measure was evaluated using implementation reach (proportion of providers who received academic detailing). Station-level analysis was performed using a linear fixed effects regression model to evaluate the rate of change in the prevalence of veterans co-prescribed opioid-benzodiazepine.

Results
Altogether 130 VA stations was included for analysis; 119 stations implemented opioid-related or benzodiazepine-related academic detailing, and 11 stations did not. Stations that had implemented academic detailing had a 33% greater monthly reduction on the opioid-benzodiazepine co-prescribing prevalence compared to stations that did not implement academic detailing (P = .036). In the linear fixed effects regression model, stations that were expected to have 100% of providers exposed to academic detailing were statistically associated with a greater decrease in the monthly prevalence of Veterans co-prescribed opioid-benzodiazepine by 4.9 veterans per 1,000 population (P &lt; .001) compared to stations with 0% of providers exposed to academic detailing.

Conclusions
Stations that implemented academic detailing and had a higher proportion of providers who were exposed to opioid- or benzodiazepine-related academic detailing had a significant decrease in the monthly prevalence of Veterans co-prescribed opioid-benzodiazepine combinations.
Association between E-cigarette use and chronic obstructive pulmonary disease in non-asthmatic adults in the USA
Authors: Antwi Godfred O , Rhodes Darson L 
Published: December 2020

Abstract

Background
Concern about the health impacts of e-cigarette use is growing; however, limited research exists regarding potential long-term health effects of this behavior. This study explored the relationship between e-cigarette use and COPD in a sample of US adults.

Methods
A secondary data analysis using data from the 2018 Behavioral Risk Factor Surveillance Survey in the USA was computed to examine associations between e-cigarette use and COPD controlling for conventional cigarette smoking status, past month leisure physical activity and demographic characteristics including age, sex, education, race, marital status and body mass index.

Results
Significant associations between e-cigarette use and COPD among former combustible cigarette smokers and those who reported never using combustible cigarettes were found. Compared with never e-cigarette users, the odds of having COPD were significantly greater for daily e-cigarette users (OR = 1.53; 95% CI: 1.11–2.03), occasional users (OR = 1.43, 95% CI: 1.13–1.80) and former users (OR = 1.46 95% CI: 1.28–1.67).

Conclusions
Findings from this study indicate a potential link between e-cigarette use and COPD. Further research to explore the potential effects of e-cigarette on COPD is recommended.
Vertical Education-Occupation Mismatch and Wage Inequality by Race/Ethnicity and Nativity among Highly Educated US Workers
Authors: Lu Yao , Li Xiaoguang 
Published: December 2020

AbstractDespite remarkable educational gains of minorities, ethnoracial wage inequality persists and has even expanded among highly educated workers. Conventional explanations for this inequality are primarily derived from comparing workers across different educational levels and are less salient for understanding inequalities within the highly educated workforce. This study examines a previously overlooked source of ethnoracial inequality among highly educated workers: vertical mismatch between workers’ educational level and the education requirements for their occupation. Using a longitudinal sample of college graduates from the Survey of Income and Program Participation, we find that vertical mismatch accounts for a large part of racial/ethnic and nativity wage inequality. Specifically, highly educated minorities (especially blacks and Hispanics) and immigrants (especially those holding a foreign degree) are disproportionately channeled into mismatched jobs and subsequently consigned to such positions. Also, highly educated Hispanics and Asians, as well as foreign-educated immigrants, face greater wage penalties of vertical mismatch. The findings offer new insights into a key source of ethnoracial and nativity stratification.
The Comparative Method is Not Macroevolution: Across-Species Evidence for Within-Species Process
Authors: Olson Mark E 
Published: December 2020

AbstractIt is common for studies that employ the comparative method for the study of adaptation, that is, documentation of potentially adaptive across-species patterns of trait–environment or trait–trait correlation, to be designated as “macroevolutionary.” Authors are justified in using “macroevolution” in this way by appeal to definitions such as “evolution above the species level.” I argue that regarding the comparative method as “macroevolutionary” is harmful because it hides in serious ways the true causal content of hypotheses tested with the comparative method. The comparative method is a means of testing hypotheses of adaptation and their alternatives. Adaptation is a population-level phenomenon, involving heritable interindividual variation that is associated with fitness differences. For example, given heritable intrapopulational variation, more streamlined individuals in populations of fast-moving aquatic animals have higher locomotory efficiency and thus better survivorship and more resources directed to reproduction than less streamlined ones. Direct evidence consistent with this population-level scenario includes the observation that many unrelated species of fast-moving aquatic animals have similar streamlined shapes, an example of the comparative method. Crucial to note in this example is that although the data are observed across species, the comparative method for studying adaptation tests hypotheses regarding standard population-level natural selection with no content that can be construed as “macro.” Even less “macro,” individual-level developmental dynamics can limit or bias the range of variants available for selection. Calling any of these studies “macroevolutionary” implies that some additional process is at work, shrouding the need to test adaptation hypotheses and study the range of variants that can be produced in development. [Adaptation; comparative method; constraint; macroevolution; optimality models; population biology.]