bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-Rated Executive Function and Health-Related Quality of Life in Young Adults With Persistent Post-Concussion Symptoms: A Cross-Sectional Study
Authors: Thastum Mille Moeller , Schroeder Andreas , Evald Lars , Naess-Schmidt Erhard , Tuborgh Astrid , Jensen Jens Sondergaard , Svendsen Susanne Wulff , Nielsen Jørgen Feldbaek , Rask Charlotte Ulrikka 
Published: October 2021

Abstract

Objective
To assess self-reported executive dysfunction in young adult patients with persistent post-concussion symptoms (PCS) 2–6 months post-injury, and the association with self-reported Health-Related Quality of Life (HRQoL).

Method
This cross-sectional study carried out in a hospital setting was a secondary analysis of data from a separate randomized trial testing the effect of a novel intervention, “Get going After concussIoN ” (GAIN), for persistent PCS. Patients (18–30 years) were recruited from a clinical cohort of patients with a hospital diagnosis of concussion or referred by primary care physicians. Main measures were The Behaviour Rating Inventory of Executive Function—Adult Version providing two index scores, that is, the Metacognitive Index (MI) and the Behavioural Regulation Index (BRI), and the Quality of Life after Brain Injury—Overall Scale.

Results
Compared with normative data, patients had elevated scores (i.e., worse functioning) on both the MI and the BRI. In linear regression analysis, the MI score, but not the BRI score, was negatively associated with self-reported HRQoL (MI: slope = −.27, 95% confidence interval, CI [−.53, −.02], p = .03; BRI: slope = −.19, 95% CI [−.49, .13], p = .24), suggesting a positive association of subjective executive dysfunction and lower HRQoL. However, the association was attenuated after adjustment for self-reported psychological distress (MI: slope = −.09, 95% CI [−.34, .17], p = .51).

Conclusion
Self-reported executive dysfunction is common in young adult patients with persistent PCS, but not strongly associated with decreased HRQoL after adjusting for concurrent psychological distress.
Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper
Authors: McFarland Alexander G , Kennedy Nolan W , Mills Carolyn E , Tullman-Ercek Danielle , Huttenhower Curtis , Hartmann Erica M 
Published: October 2021

Abstract

Motivation
Identifying variant forms of gene clusters of interest in phylogenetically proximate and distant taxa can help to infer their evolutionary histories and functions. Conserved gene clusters may differ by only a few genes, but these small differences can in turn induce substantial phenotypes, such as by the formation of pseudogenes or insertions interrupting regulation. Particularly as microbial genomes and metagenomic assemblies become increasingly abundant, unsupervised grouping of similar, but not necessarily identical, gene clusters into consistent bins can provide a population-level understanding of their gene content variation and functional homology.

Results
We developed GeneGrouper, a command-line tool that uses a density-based clustering method to group gene clusters into bins. GeneGrouper demonstrated high recall and precision in benchmarks for the detection of the 23-gene Salmonella enterica LT2 Pdu gene cluster and four-gene Pseudomonas aeruginosa PAO1 Mex gene cluster among 435 genomes spanning mixed taxa. In a subsequent application investigating the diversity and impact of gene-complete and -incomplete LT2 Pdu gene clusters in 1130 S.enterica genomes, GeneGrouper identified a novel, frequently occurring pduN pseudogene. When investigated in vivo, introduction of the pduN pseudogene negatively impacted microcompartment formation. We next demonstrated the versatility of GeneGrouper by clustering distant homologous gene clusters and variable gene clusters found in integrative and conjugative elements.

Availability and implementation
GeneGrouper software and code are publicly available at https://pypi.org/project/GeneGrouper/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mapping flows on weighted and directed networks with incomplete observations
Authors: Smiljanić Jelena , Blöcker Christopher , Edler Daniel , Rosvall Martin 
Published: October 2021

AbstractDetecting significant community structure in networks with incomplete observations is challenging because the evidence for specific solutions fades away with missing data. For example, recent research shows that flow-based community detection methods can highlight spurious communities in sparse undirected and unweighted networks with missing links. Current Bayesian approaches developed to overcome this problem do not work for incomplete observations in weighted and directed networks that describe network flows. To overcome this gap, we extend the idea behind the Bayesian estimate of the map equation for unweighted and undirected networks to enable more robust community detection in weighted and directed networks. We derive an empirical Bayes estimate of the transitions rates that can incorporate metadata information and show how an efficient implementation in the community-detection method Infomap provides more reliable communities even with a significant fraction of data missing.
Hemolytic Anemia in Inflammatory Bowel Disease: Our “Gut” Tells Us to Blame the Drug
Authors: Berger Matthew , Abdalla Maisa , DeCross Arthur 
Published: October 2021

Abstract

Background
Several studies determined that autoimmune hemolytic anemia (AIHA) is a rare extraintestinal IBD manifestation, related to the underlying disease activity. However, evidence linking biologic therapy to AIHA is sparse.

Methods
This article reviews the evidence on the association of these clinical phenomena.

Results
There are two retrospective studies and a few case reports linking biologic therapies to AIHA.

Conclusions
While some autoimmune phenomenon triggered by our biologic therapies have been well recognized, we do not find the evidence associating these therapies to AIHA sufficiently compelling.
Dual antithrombotic treatment in chronic coronary syndrome: European Society of Cardiology criteria vs. CHADS-P2A2RC score
Authors: Würtz Morten , Olesen Kevin Kris Warnakula , Mortensen Martin Bødtker , Eikelboom John W , Mohammad Moman Aladdin , Erlinge David , Kristensen Steen Dalby , Maeng Michael 
Published: October 2021

Abstract

Aims
According to the 2019 European Society of Cardiology (ESC) guidelines on chronic coronary syndromes (CCS), adding a P2Y12 inhibitor or rivaroxaban to aspirin should be considered in high-risk patients. We estimated the proportion of patients eligible for treatment with the ESC criteria and examined if a recently validated risk score (CHADS-P2A2RC) could improve risk prediction.

Methods and results
We included 61 338 CCS patients undergoing first-time coronary angiography in Western Denmark (2003–16) and classified them according to the ESC criteria and the CHADS-P2A2RC score. The ESC criteria identified 33.9% as high risk, 53.3% as moderate risk, and 12.8% as low risk. The CHADS-P2A2RC score identified 24.9% as high risk (≥4 points), 48.1% as moderate risk (2–3 points), and 27.0% as low risk (≤1 points). Major adverse cardiovascular events per 100 person-years were 4.8 [95% confidence interval (CI) 4.6–5.0] in patients considered high risk with both schemes, 2.1 (95% CI 2.0–2.2) in patients considered high risk with the ESC but low-to-moderate risk with the CHADS-P2A2RC criteria, 3.8 (95% CI 3.6–4.1) in patients considered low-to-moderate risk with the ESC but high risk with the CHADS-P2A2RC criteria, and 1.5 (95% CI 1.5–1.6) in patients considered low-to-moderate risk with both schemes. The CHADS-P2A2RC score enabled correct downward risk reclassification of 5161 patients (8%) without events, yielding an improved specificity of 9.7%, a loss of sensitivity of 4.4%, and an overall net reclassification index of 0.053.

Conclusion
Based on the 2019 ESC guidelines, dual antithrombotic treatment should be considered in one-third of CCS patients. The CHADS-P2A2RC score improved risk classification and may particularly identify low-risk patients with limited benefit from treatment.
Continuing regular physical activity and maintaining body weight have a synergistic interaction in improving survival: a population-based cohort study including 6.5 million people
Authors: Lee Chang-Hoon , Han Kyung-Do , Kim Da Hye , Kwak Min-Sun 
Published: October 2021

Abstract

Aims
Continuing physical activity (PA) and maintaining body weight are tightly intertwined; however, no study investigated whether these two factors have interactions in terms of the mortality. The aim of this study is to elucidate whether continuing regular PA and maintaining body weight have interactions in terms of all-cause mortality risk.

Methods and results
Participants with health screening from both 2009 and 2011 without underlying cancer or cardiovascular disease were included. Physical activity change was grouped as remained active, inactive-to-active, active-to-inactive, or remained inactive. Body weight change was categorized as stable (weight change &lt; 5%), weight gain, or loss. Outcome included all-cause mortality. Of 6 572 984 total participants, 91 347 deaths occurred during a median 7.4-year follow-up. Compared with the remained active and stable weight group, most other groups had a higher mortality risk. The weight loss and remained inactive group [adjusted hazard ratio (aHR), 2.30; 95% confidence interval (CI), 2.22–2.38] and the weight gain and remained inactive group (aHR, 2.17; 95% CI, 2.09–2.25) showed the highest mortality risks. Among stable weight participants, the ranking of the groups from highest to lowest in terms of mortality risk was as follows: remained inactive (aHR, 1.46; 95% CI, 1.41–1.50), active-to-inactive (aHR, 1.24; 95% CI, 1.19–1.29), inactive-to-active (aHR, 1.15; 95% CI, 1.11–1.20), and remained active (reference). Remaining active and maintaining a stable body weight had a synergistic interaction on decreasing all-cause mortality risk (multiplicative P for interaction &lt; 0.001; relative excess risk due to interaction, 0.38; 95% CI, 0.31–0.46; attributable proportion, 0.18; 95% CI, 0.15–0.22).

Conclusions
Continuing regular PA as recommended and maintaining body weight have multiplicative and additive interactions on reducing all-cause mortality. Healthcare providers should emphasize the importance of both regular PA and body weight maintenance for the general public.
Between Interactions and Aggregates: The PolyQ Balance
Authors: Mier Pablo , Andrade-Navarro Miguel A 
Published: October 2021

Abstract
Polyglutamine regions (polyQ) are highly abundant consecutive runs of glutamine residues. They have been generally studied in relation to the so-called polyQ-associated diseases, characterized by protein aggregation caused by the expansion of the polyglutamine tract via a CAG-slippage mechanism. However, more than 4800 human proteins contain a polyQ, and only 9 of these regions are known to be associated with disease. Computational sequence studies and experimental structure determinations are completing a more interesting picture in which polyQ emerge as a motif for modulation of protein-protein interactions. But long polyQ regions may lead to an excess of interactions, and produce aggregates. Within this mechanistic perspective of polyQ function and malfunction, we discuss polyQ definition and properties such as variable codon usage, sequence and context structure imposition, functional relevance, evolutionary patterns in species-centered analyses, and open resources.
Identification of antibiotic collateral sensitivity and resistance interactions in population surveillance data
Authors: Zwep Laura B , Haakman Yob , Duisters Kevin L W , Meulman Jacqueline J , Liakopoulos Apostolos , van Hasselt J G Coen 
Published: October 2021

Abstract

Background
Collateral effects of antibiotic resistance occur when resistance to one antibiotic agent leads to increased resistance or increased sensitivity to a second agent, known respectively as collateral resistance (CR) and collateral sensitivity (CS). Collateral effects are relevant to limit impact of antibiotic resistance in design of antibiotic treatments. However, methods to detect antibiotic collateral effects in clinical population surveillance data of antibiotic resistance are lacking.

Objectives
To develop a methodology to quantify collateral effect directionality and effect size from large-scale antimicrobial resistance population surveillance data.

Methods
We propose a methodology to quantify and test collateral effects in clinical surveillance data based on a conditional t-test. Our methodology was evaluated using MIC data for 419 Escherichia coli strains, containing MIC data for 20 antibiotics, which were obtained from the Pathosystems Resource Integration Center (PATRIC) database.

Results
We demonstrate that the proposed approach identifies several antibiotic combinations that show symmetrical or non-symmetrical CR and CS. For several of these combinations, collateral effects were previously confirmed in experimental studies. We furthermore provide insight into the power of our method for multiple collateral effect sizes and MIC distributions.

Conclusions
Our proposed approach is of relevance as a tool for analysis of large-scale population surveillance studies to provide broad systematic identification of collateral effects related to antibiotic resistance, and is made available to the community as an R package. This method can help mapping CS and CR, which could guide combination therapy and prescribing in the future.
The ties that bind and transform: knowledge remittances, relatedness and the direction of technical change
Authors: Di Iasio Valentina , Miguelez Ernest 
Published: October 2021

AbstractThis study investigates whether high-skilled migration in a sample of OECD countries fosters technological diversification in the migrants’ countries of origin. We focus on migrant inventors and study their role as vectors of knowledge remittances. Further, we particularly analyze whether migrants spark related or unrelated diversification back home. To account for the uneven distribution of knowledge and migrants within the host countries, we break down the analysis at the metropolitan area level. Our results suggest that migrant inventors have a positive effect on the home countries’ technological diversification, particularly for developing countries and technologies with less related activities around—thus fostering unrelated diversification.
Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids
Authors: Lee Jeeyun , Willett Christopher S 
Published: October 2021

AbstractMitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.
Hanumān in Newar (Buddhist) Vihāras of the Kathmandu Valley
Authors: Bühnemann Gudrun 
Published: October 2021

Abstract
In his work Medieval Nepal (part 2: 864), the Nepalese scholar D.R. Regmi asserted that a (typical) Newar Buddhist monastery (vihāra) has Mahākāla, Hāritī, Gaṇeśa and Hanumān installed in wall niches as protectors. Earlier, Brian Hodgson’s informant Pandit Amṛtānanda (1774–1834) had made similar statements when describing the Buddhist vihāras in the city of Patan. In this article, I will present the results of a preliminary survey of iconic and aniconic representations of Hanumān in Newar Buddhist vihāras in the Kathmandu Valley. The latter include triangular openings which are either identified with Hanumān or, more specifically, designated as passages through which the divinity travels. The article also addresses Hanumān’s role in Newar Buddhism and legends about his conversion to Buddhism, illustrating the adaptability of this complex religious figure to various sectarian contexts.
The diverse nature and formation paths of slow rotator galaxies in the eagle simulations
Authors: Lagos Claudia del P , Emsellem Eric , van de Sande Jesse , Harborne Katherine E , Cortese Luca , Davison Thomas , Foster Caroline , Wright Ruby J 
Published: October 2021

ABSTRACT
We use a sample of z = 0 galaxies visually classified as slow rotators (SRs) in the eagle hydrodynamical simulations to explore the effect of galaxy mergers on their formation, characterize their intrinsic galaxy properties, and study the connection between quenching and kinematic transformation. SRs that have had major or minor mergers (mass ratios ≥0.3 and 0.1−0.3, respectively) tend to have a higher triaxiality parameter and ex-situ stellar fractions than those that had exclusively very minor mergers or formed in the absence of mergers (‘no-merger’ SRs). No-merger SRs are more compact, have lower black hole-to-stellar mass ratios and quenched later than other SRs, leaving imprints on their z = 0 chemical composition. For the vast majority of SRs we find that quenching, driven by active galactic nuclei feedback, precedes kinematic transformation, except for satellite SRs, in which these processes happen in tandem. However, in ≈50 per cent of these satellites, satellite–satellite mergers are responsible for their SR fate, while environment (i.e. tidal field and interactions with the central) can account for the transformation in the rest. By splitting SRs into kinematic sub-classes, we find that flat SRs prefer major mergers; round SRs prefer minor or very minor mergers; prolate SRs prefer gas-poor mergers. Flat and prolate SRs are more common among satellites hosted by massive haloes ($\gt 10^{13.6}\, \rm M_{\odot }$) and centrals of high masses ($M_{\star } \gt 10^{10.5}\, \rm M_{\odot }$). Although eagle galaxies display kinematic properties that broadly agree with observations, there are areas of disagreement, such as inverted stellar age and velocity dispersion profiles. We discuss these and how upcoming simulations can solve them.
ASAS-SN search for optical counterparts of gravitational-wave events from the third observing run of Advanced LIGO/Virgo
Authors: de Jaeger T , Shappee B J , Kochanek C S , Stanek K Z , Beacom J F , Holoien T W-S , Thompson Todd A , Franckowiak A , Holmbo S 
Published: October 2021

ABSTRACT
We report on the search for electromagnetic counterparts to the nine gravitational-wave events with a &gt;60 per cent probability of containing a neutron star during the third observing run (O3) of the Laser Interferometer Gravitational-Wave Observatory (LIGO)–Virgo Collaboration (LVC) with the All-Sky Automated Survey for SuperNovae (ASAS-SN). No optical counterparts associated with a gravitational-wave event were found. However, thanks to its network of telescopes, the average area visible to at least one ASAS-SN site during the first 10 h after the trigger contained ∼30 per cent of the integrated source location probability. Through a combination of normal operations and target-of-opportunity observations, ASAS-SN observations of the highest probability fields began within 1 h of the trigger for four of the events. After 24 h, ASAS-SN observed &gt;60 per cent of total probability for three events and &gt;40 per cent for all but one of the events. This is the largest area coverage to a depth of g = 18.5 mag from any survey with published coverage statistics for seven of the nine events. With its observing strategy, five sites around the world, and a large field of view, ASAS-SN will be one of the leading surveys to optically search for nearby neutron star mergers during LVC fourth observation run (O4).
Limits on the mass and initial entropy of 51 Eri b from Gaia EDR3 astrometry
Authors: Dupuy Trent J , Brandt G Mirek , Brandt Timothy D 
Published: October 2021

ABSTRACT
51 Eri b is one of the only young planets consistent with a wide range of possible initial entropy states, including the cold-start scenario associated with some models of planet formation by core accretion. The most direct way to constrain the initial entropy of a planet is by measuring its luminosity and mass at a sufficiently young age that the initial conditions still matter. We present the tightest upper limit on 51 Eri b’s mass yet (M &lt; 11 MJup at 2σ) using a cross-calibration of Hipparcos and Gaia EDR3 astrometry and the orbit-fitting code orvara. We also reassess its luminosity using a direct, photometric approach, finding $\log (\rm{L_{\rm bol}}/\rm{\mathrm{L}_{\odot }}) = -5.5\pm 0.2$ dex. Combining this luminosity with the 24 ± 3 Myr age of the β Pic moving group, of which 51 Eri is a member, we derive mass distributions from a grid of evolutionary models that spans a wide range of initial entropies. We find that 51 Eri b is inconsistent with the coldest-start scenarios, requiring an initial entropy of &gt;8 kB baryon−1 at 97 per cent confidence. This result represents the first observational constraint on the initial entropy of a potentially cold-start planet, and it continues the trend of dynamical masses for directly imaged planets pointing to warm- or hot-start formation scenarios.