bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions between SARS-CoV-2 and influenza, and the impact of coinfection on disease severity: a test-negative design
Authors: Stowe Julia , Tessier Elise , Zhao H , Guy Rebecca , Muller-Pebody Berit , Zambon Maria , Andrews Nick , Ramsay Mary , Lopez Bernal Jamie 
Published: April 2021

Abstract

Background
The impact of SARS-CoV-2 alongside influenza is a major concern in the northern hemisphere as winter approaches.

Methods
Test data for influenza and SARS-CoV-2 from national surveillance systems between 20 January 2020 and 25 April 2020 were used to estimate influenza infection on the risk of SARS-CoV-2 infection. A test-negative design was used to assess the odds of SARS-CoV-2 in those who tested positive for influenza compared with those who tested negative. The severity of SARS-CoV-2 was also assessed using univariable and multivariable analyses.

Results
The risk of testing positive for SARS-CoV-2 was 58% lower among influenza-positive cases and patients with a coinfection had a risk of death of 5.92 (95% confidence interval: 3.21–10.91) times greater than among those with neither influenza nor SARS-CoV-2. The odds of ventilator use or death and intensive care unit admission or death were greatest among coinfected patients.

Conclusions
Coinfection of these viruses could have a significant impact on morbidity, mortality and health-service demand.
Validation of the VIRSeek SARS-CoV-2 Mplex Assay for Detection of SARS-CoV-2 on Stainless-Steel Surfaces: AOAC Performance Tested MethodSM 122006
Authors: Bleichner Laura , Bleicher Vera , Göhring Nadine , Kleiboeker Steven B 
Published: April 2021

Abstract

Background
The Eurofins GeneScan Technologies’ VIRSeek SARS-CoV-2 Mplex kit is a RT (reverse transcription) real-time polymerase chain reaction (RT-qPCR) assay for the detection of two targets on the N-gene (nucleocapsid) of SARS-CoV-2. An extraction control, that allows monitoring of the extraction procedure and PCR inhibition, is included.

Objective
In silico analysis and wet testing showed inclusivity and exclusivity of the assay. The complete workflow starting from surface swabbing (VIRSeek PATHOSwab kit), RNA extraction (VIRSeek RNAExtractor), RT-PCR (VIRSeek SARS-CoV-2 Mplex), and evaluation with FastFinder was validated in comparison to the CDC method for detection of SARS-CoV-2 on stainless steel.

Method
In silico analysis was performed by using the MFOLD online program. The matrix study was performed for stainless steel inoculated with SARS-CoV-2 isolated from the first documented US case of a traveler from Wuhan, China.

Results
For inclusivity, 15 764 sequences were analyzed and all mismatches (0.37% of the sequences had single mismatches) were considered non-critical. Cross reactivity for closely related viruses and background organisms was performed, resulting in correct exclusion of all. No significant differences were observed for the probability of detection (POD) study when comparing to the CDC method.

Conclusions
Results of the inclusivity and exclusivity study show that the assay is specific for detection of SARS-CoV-2. The POD study showed no statistically significant difference compared to the CDC reference method, results were identical for the uninoculated and the high level. For the fractional recovery level, the candidate method detected 9/17 samples leading to a POD of 0.47, the reference method detected 11/20 samples leading to a POD of 0.55.

Highlight
The complete workflow starting from swabbing of the surface (VIRSeek PATHOSwab kit), RNA extraction (VIRSeek RNAExtractor), RT-PCR (VIRSeek SARS CoV-2 Mplex) and evaluation with FastFinder was validated in comparison to the US Centers for Disease Control and Prevention method for detection of SARS-CoV-2 on Stainless Steel.
Squaring Things Up with R2: What It Is and What It Can (and Cannot) Tell You
Authors: Camirand Lemyre Félix , Chalifoux Kevin , Desharnais Brigitte , Mireault Pascal 
Published: April 2021

Abstract
The coefficient of correlation (r) and the coefficient of determination (R2 or r2) have long been used in analytical chemistry, bioanalysis and forensic toxicology as figures demonstrating linearity of the calibration data in method validation. We clarify here what these two figures are and why they should not be used for this purpose in the context of model fitting for prediction. R2 evaluates whether the data are better explained by the regression model used than by no model at all (i.e., a flat line of slope = 0 and intercept $\bar y$), and to what degree. Hopefully, in the context of calibration curves, the fact that a linear regression better explains the data than no model at all should not be a point of contention. Upon closer examination, a series of restrictions appear in the interpretation of these coefficients. They cannot indicate whether the dataset at hand is linear or not, because they assume that the regression model used is an adequate model for the data. For the same reason, they cannot disprove the existence of another functional relationship in the data. By definition, they are influenced by the variability of the data. The slope of the calibration curve will also change their value. Finally, when heteroscedastic data are analyzed, the coefficients will be influenced by calibration levels spacing within the dynamic range, unless a weighted version of the equations is used. With these considerations in mind, we suggest to stop using r and R2 as figures of merit to demonstrate linearity of calibration curves in method validations. Of course, this does not preclude their use in other contexts. Alternative paths for evaluation of linearity and calibration model validity are summarily presented.
A36 IMPACT OF DIGITAL HEALTH MONITORING IN THE MANAGEMENT OF INFLAMMATORY BOWEL DISEASE
Authors: Zhen J , Marshall J , Nguyen G C , Atreja A , Narula N 
Published: April 2021

Abstract

Background
Inflammatory bowel disease (IBD) affects over 270,000 Canadians and costs the healthcare system $1.28 billion dollars annually. With advancements in technology, a shift from the traditional ‘reactive’ approach to IBD management to a ‘proactive’ approach that integrates self-management strategies using digital health monitoring platforms could greatly benefit patient care.

Aims
The purpose of this study was to investigate the effect of implementing the IBD health monitoring platform, HealthPROMISE, in clinical practice and to evaluate whether its use leads to better quality of care, improved health outcomes, and reduce resource consumption in patients with IBD.

Methods
IBD patients were recruited in gastroenterology clinics and asked to install the HealthPROMISE application onto their smartphones. Patient satisfaction, quality of care, quality of life, patient symptoms, and resource utilization metrics were collected throughout the study and sent directly to their healthcare teams. Patients with abnormal symptom/short inflammatory bowel disease questionnaire (SIBDQ) scores were flagged for their physicians to follow up with. After one-year, patient outcome metrics were compared to baseline values.

Results
Overall, out of 59 patients enrolled in the study, 32 patients (54%) logged into the application at least once during the study period. The number of IBD-related ER visits/hospitalizations in the year of use compared to the prior year demonstrated a significant decrease from 25% of patients (8/32) to 3% (1/32) (p=0.03). Patients also reported an increase in their understanding of the nature/causes of their condition after using the application (p=0.026). No significant changes were observed in the number of quality indicators met (p = 0.67) or in SIBDQ scores (p=0.48).

Conclusions
Given the significant burden of IBD, there is a need to develop effective management strategies. This study demonstrated that digital health monitoring platforms may aid in reducing the number of ER visits and hospitalizations in IBD patients. Future studies evaluating acceptability and costs with a larger sample size would help determine the feasibility and generalizability of widely implementing mobile health applications in the management of IBD.

Funding Agencies
CCC
Physical Activity, Weight, and Outcomes in Patients Receiving Chemotherapy for Metastatic Breast Cancer (C40502/Alliance)
Authors: Ligibel Jennifer A , Huebner Luke , Rugo Hope S , Burstein Harold J , Toppmeyer Debra L , Anders Carey K , Ma Cynthia , Barry William T , Suman Vera , Carey Lisa A , Partridge Ann H , Hudis Clifford A , Winer Eric P 
Published: April 2021

Abstract

Background
Obesity and inactivity are associated with increased risk of cancer-related and overall mortality in breast cancer, but there are few data in metastatic disease.

Methods
Cancer and Leukemia Group B 40502 was a randomized trial of first-line taxane-based chemotherapy for patients with metastatic breast cancer. Height and weight were collected at enrollment. After 299 patients enrolled, the study was amended to assess recreational physical activity (PA) at enrollment using the Nurses’ Health Study Exercise Questionnaire. Associations with progression-free survival (PFS) and overall survival (OS) were evaluated using stratified Cox modeling (strata included hormone receptor status, prior taxane, bevacizumab use, and treatment arm). All statistical tests were 2-sided.

Results
A total of 799 patients were enrolled, and at the time of data lock, median follow-up was 60 months. At enrollment, median age was 56.7 years, 73.1% of participants had hormone receptor–positive cancers, 42.6% had obesity, and 47.6% engaged in less than 3 metabolic equivalents of task (MET) hours of PA per week (&lt;1 hour of moderate PA). Neither baseline body mass index nor PA was statistically significantly associated with PFS or OS, although there was a marginally statistically significant increase in PFS (hazard ratio = 0.83, 95% confidence interval = 0.79 to 1.02; P = .08) and OS (hazard ratio = 0.81, 95% confidence interval = 0.65 to 1.02; P = .07) in patients who reported PA greater than 9 MET hours per week vs 0-9 MET hours per week.

Conclusions
In a trial of first-line chemotherapy for metastatic breast cancer, rates of obesity and inactivity were high. There was no statistically significant relationship between body mass index and outcomes. More information is needed regarding the relationship between PA and outcomes.
Magnification bias in galaxy surveys with complex sample selection functions
Authors: von Wietersheim-Kramsta Maximilian , Joachimi Benjamin , van den Busch Jan Luca , Heymans Catherine , Hildebrandt Hendrik , Asgari Marika , Tr’oster Tilman , Unruh Sandra , Wright Angus H 
Published: April 2021

ABSTRACT
Gravitational lensing magnification modifies the observed spatial distribution of galaxies and can severely bias cosmological probes of large-scale structure if not accurately modelled. Standard approaches to modelling this magnification bias may not be applicable in practice as many galaxy samples have complex, often implicit, selection functions. We propose and test a procedure to quantify the magnification bias induced in clustering and galaxy–galaxy lensing (GGL) signals in galaxy samples subject to a selection function beyond a simple flux limit. The method employs realistic mock data to calibrate an effective luminosity function slope, αobs, from observed galaxy counts that can then be used with the standard formalism. We demonstrate this method for two galaxy samples derived from the Baryon Oscillation Spectroscopic Survey (BOSS) in the redshift ranges 0.2 &lt; z ≤ 0.5 and 0.5 &lt; z ≤ 0.75, complemented by mock data built from the MICE2 simulation. We obtain αobs = 1.93 ± 0.05 and αobs = 2.62 ± 0.28 for the two BOSS samples. For BOSS-like lenses, we forecast a contribution of the magnification bias to the GGL signal between the multipole moments, ℓ, of 100 and 4600 with a cumulative signal-to-noise ratio between 0.1 and 1.1 for sources from the Kilo-Degree Survey (KiDS), between 0.4 and 2.0 for sources from the Hyper Suprime-Cam survey (HSC), and between 0.3 and 2.8 for ESA Euclid-like source samples. These contributions are significant enough to require explicit modelling in future analyses of these and similar surveys. Our code is publicly available within the MagBEt module (https://github.com/mwiet/MAGBET).
Fountains and storms: the effects of AGN feedback and mergers on the evolution of the intracluster medium in the romulusc simulation
Authors: Chadayammuri Urmila , Tremmel Michael , Nagai Daisuke , Babul Arif , Quinn Thomas 
Published: April 2021

ABSTRACT
The intracluster medium (ICM) is a multiphase environment, dynamically regulated by active galactic nuclei (AGN), the motions of cluster galaxies, and mergers with other clusters or groups. AGN provide a central heating source capable of preventing runaway cooling flows and quenching star formation, but how they achieve this is still poorly understood. We investigate the effects of AGN feedback and mergers on the ICM using the high-resolution romulusc cosmological simulation of a 1014 M⊙ galaxy cluster. We demonstrate that AGN feedback regulates and quenches star formation in the brightest cluster galaxy gently, without any explosive episodes, and co-exists with a low entropy core with sub-Gyr cooling times. In contrast, the merger disrupts the ICM structure, heating the core and cutting off the supply of low-entropy, infalling gas that until then fuelled the AGN. We find that this removal of the low-entropy phase correlates with the ratio tcool / tff increasing above 30 in the core, matching observations that cooling gas is only found in clusters where this ratio is 5–30. Importantly, we find that evolution in the inner entropy profile and the ratio of cooling to free-fall time-scale are directly connected to the quenching of star formation in the BCG. This is in line with previous results from idealized simulations and confirmed here within a fully cosmological simulation for the first time.
IPC 2.0: prediction of isoelectric point and pKa dissociation constants
Authors: Kozlowski Lukasz Pawel 
Published: April 2021

AbstractThe isoelectric point is the pH at which a particular molecule is electrically neutral due to the equilibrium of positive and negative charges. In proteins and peptides, this depends on the dissociation constant (pKa) of charged groups of seven amino acids and NH+ and COO− groups at polypeptide termini. Information regarding isoelectric point and pKa is extensively used in two-dimensional gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), crystallisation, and mass spectrometry. Therefore, there is a strong need for the in silico prediction of isoelectric point and pKa values. In this paper, I present Isoelectric Point Calculator 2.0 (IPC 2.0), a web server for the prediction of isoelectric points and pKa values using a mixture of deep learning and support vector regression models. The prediction accuracy (RMSD) of IPC 2.0 for proteins and peptides outperforms previous algorithms: 0.848 versus 0.868 and 0.222 versus 0.405, respectively. Moreover, the IPC 2.0 prediction of pKa using sequence information alone was better than the prediction from structure-based methods (0.576 versus 0.826) and a few folds faster. The IPC 2.0 webserver is freely available at www.ipc2-isoelectric-point.org
The Relationship Between Trauma Exposure and Adult Tobacco Use: Analysis of the National Epidemiologic Survey on Alcohol and Related Conditions (III)
Authors: Budenz Alexandra , Klein Amanda , Prutzman Yvonne 
Published: April 2021

Abstract

Introduction
Previous research has examined cigarette smoking in trauma exposed populations. However, the relationships between trauma exposure and use of other tobacco products (eg, cigars, e-cigarettes) and specific trauma exposure characteristics that may be associated with tobacco use are understudied.

Aims and Methods
Using the 2012–2013 National Epidemiologic Survey on Alcohol and Related Conditions-III (N = 36 151 adults), we conducted weighted bivariate analyses of tobacco use among participants with no trauma exposure, trauma exposure, and trauma exposure with post-traumatic stress disorder (trauma + PTSD), stratified by tobacco product use. We also performed weighted logistic regressions testing relationships between trauma exposure and tobacco use, controlling for behavioral health (BH) conditions (mood, anxiety, substance use, personality disorders) and sociodemographics.

Results
Approximately 44% of participants had experienced trauma; 6% experienced trauma + PTSD. Trauma exposed participants had a higher prevalence of tobacco use (30%––46% vs. 22%) and poly-tobacco use (34%––35% vs. 28%) than unexposed participants. Cigarettes were the most used tobacco product; trauma + PTSD (19%), and trauma (15%) participants had a higher prevalence of e-cigarette use than unexposed participants (11%). Trauma exposure was associated with current tobacco use (AOR = 1.36 trauma + PTSD; 1.23 trauma) (but not former use), particularly among participants exposed to violence/abuse (AOR = 1.23). Personality and substance use disorders were strongly associated with current and former tobacco use.

Conclusions
Trauma exposure, PTSD, and experiences of violence/abuse are associated with current tobacco use. BH conditions may also play a role in current and former tobacco use. Recognizing and addressing trauma exposure and BH conditions among tobacco users may improve cessation rates in these populations.

Implications
This study contributes to research on tobacco use disparities in behavioral health populations by providing a comprehensive examination of tobacco use in trauma exposed individuals. Prior research has examined cigarette smoking, but not other tobacco product use in these populations. This study presents findings on multiple tobacco use behaviors (tobacco product, poly-tobacco use, cessation attempts) in trauma exposed populations and characteristics of trauma exposure (severity, type of traumatic event) associated with tobacco use. These findings underscore the importance of further examining the implications of trauma exposure for tobacco use and of screening and addressing trauma in cessation treatment.
Barn Owls select uncultivated habitats for hunting in a winegrape growing region of California
Authors: Castañeda Xerónimo A , Huysman Allison E , Johnson Matthew D 
Published: April 2021

Abstract
Large-scale conversion of uncultivated land to agriculture threatens wildlife and can diminish ecosystem services provided by nature. Understanding how wildlife provision ecosystem services may incentivize wildlife conservation in agricultural landscapes. Attracting Barn Owls (Tyto furcata) to nest on farms for pest management has been implemented worldwide but has not been evaluated in vineyard agroecosystems. Napa Valley, California, is a renowned winegrape growing region, and viticulturists encourage Barn Owl occupancy to help minimize damage from Botta’s pocket gophers (Thomomys bottae) and voles (Microtus spp.). This study modeled the use of habitats in space and time by hunting Barn Owls, providing information about their potential to provide the critical ecosystem service of pest consumption. We used global positioning system tags to track hunting owls and used a resource selection function to compare used and available habitats. We constructed the intensity of use and home range-movement maps using a time local convex hull analysis from location data. We found that Barn Owls selected uncultivated habitats when hunting, some of which were relatively rare on the landscape. Approximately, one-third of Barn Owl hunting locations occurred in vineyards, but this use was out of proportion to the availability of vineyards, which comprised 50% of the area around nest boxes. The owls’ use of vineyards increased with decreasing amount of selected uncultivated habitat in the landscape. However, as reported by a previous study, the occupancy of nest boxes in vineyards increases with uncultivated habitats nearby. Future research should model landscape composition to determine the amount of preferred habitat necessary to support occupancy as well as hunting in vineyards. A true test of pest management by Barn Owls awaits experimentation coupled with monitoring rodent populations.
Sensitivity of multiple vital rates for Ruffed Grouse in the Upper Great Lakes Region
Authors: Pollentier Christopher D , Hull Scott D , MacFarland David M 
Published: April 2021

AbstractEffective management of wildlife requires a full understanding of population dynamics and knowledge of potential drivers that influence population growth. The Ruffed Grouse (Bonasa umbellus) is a popular upland game bird widely distributed across the northern United States and Canada that has experienced population declines within portions of its range in response to forest maturation and habitat loss. Although the species has been extensively studied, few efforts have been made to synthesize demographic data into a sensitivity analysis to guide management actions. We reviewed the literature and compiled Ruffed Grouse vital rates from 14 field studies conducted across four decades (1982−2018) within the Upper Great Lakes region of Michigan, Minnesota, and Wisconsin, USA. We parameterized a deterministic matrix model to evaluate population dynamics and conducted sensitivity analyses to identify vital rates projected to have the greatest influence on the finite rate of population change (λ). Our modeling effort projected a stable but highly variable annual rate of population change (λ = 1.01; 95% CI = 0.88–1.14) for Ruffed Grouse in the Upper Great Lakes region. Stochastic rates of population change derived from spring drumming surveys (λ = 1.01; 95% CI = 0.61–1.45) and Christmas Bird Count surveys (λ = 0.99; 95% CI = 0.62–1.76) of the corresponding regional population provided validation of stable trends over the same time period as our demographic model. Prospective elasticities and variance-scaled sensitivities suggested λ would be greatly influenced by components of reproductive performance: nesting success, chick survival, and post-fledging juvenile survival. Retrospective analysis indicated that much of the overall variability in λ and annual productivity was also attributed to annual variation in nesting success. Management of this species has often focused on fall and overwinter survival, but population projection models provided little evidence that survival was the predominant factor affecting population growth of Ruffed Grouse in this region. A suite of confounding factors and demographic processes that drive population trends can differ significantly across a species’ range. In the Upper Great Lakes region, management efforts aimed at maximizing reproductive success would likely have the greatest potential influence on Ruffed Grouse population growth. Other types of systematic, regional survey data can also be useful for validating population trends derived from demographic modeling studies.