bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Cross-Sectional Decision-Making Approach to Inform Neuropsychological Battery Development in Professional Hockey
Authors: Bruce Jared M , Meeuwisse Willem , Thelen Joan , Hutchison Michael G , Comper Paul , Echemendia Ruben J 
Published: November 2021

AbstractObjectiveNeuropsychologists commonly use a large battery of tests to inform clinical decisions. Decision analysis can be used to determine which individual tests play a role in the decision-making process. The objective of this project was to conduct quantitative and qualitative decision analysis of decisions by team neuropsychologists with professional hockey players being evaluated as part of the National Hockey League (NHL)/NHL Players Association Concussion Protocol.MethodWe extracted neuropsychological data from an NHL clinical program database. Team neuropsychologists evaluated concussed players using a hybrid neuropsychological test battery. The neuropsychologists then determined whether players were experiencing concussion-related cognitive difficulties. Logistic regression was used to examine which tests accounted for unique variance in the decision-making process. We also conducted a survey of NHL neuropsychologists, asking them to rate the usefulness of each test in the battery.ResultsFive of the fifteen measures accounted for unique variance in team neuropsychologists’ decisions, including the ImPACT Verbal Memory Composite, Visual Motor Composite, Reaction Time Composite, Symptom Score, and Brief Visuospatial Memory Test—Revised Delayed Recall. Notable discrepancies were uncovered between quantitative indications of usefulness and self-reported qualitative perceptions of test usefulness when making decisions. Qualitatively, clinicians reported that the Hopkins Verbal Learning Test—Revised, Symbol Digit Modalities Test, ImPACT Reaction Time, and Color Trails 2 were the most useful tests when making decisions.ConclusionsAlong with validation studies, decision analysis can be used as part of a comprehensive evaluation process to inform the development of best-practice batteries for use among athletes with sports concussion.
Computational modeling of mRNA degradation dynamics using deep neural networks
Authors: Yaish Ofir , Orenstein Yaron 
Published: November 2021

Abstract

Motivation
messenger RNA (mRNA) degradation plays critical roles in post-transcriptional gene regulation. A major component of mRNA degradation is determined by 3′-UTR elements. Hence, researchers are interested in studying mRNA dynamics as a function of 3′-UTR elements. A recent study measured the mRNA degradation dynamics of tens of thousands of 3′-UTR sequences using a massively parallel reporter assay. However, the computational approach used to model mRNA degradation was based on a simplifying assumption of a linear degradation rate. Consequently, the underlying mechanism of 3′-UTR elements is still not fully understood.

Results
Here, we developed deep neural networks to predict mRNA degradation dynamics and interpreted the networks to identify regulatory elements in the 3′-UTR and their positional effect. Given an input of a 110 nt-long 3′-UTR sequence and an initial mRNA level, the model predicts mRNA levels of eight consecutive time points. Our deep neural networks significantly improved prediction performance of mRNA degradation dynamics compared with extant methods for the task. Moreover, we demonstrated that models predicting the dynamics of two identical 3′-UTR sequences, differing by their poly(A) tail, performed better than single-task models. On the interpretability front, by using Integrated Gradients, our convolutional neural networks (CNNs) models identified known and novel cis-regulatory sequence elements of mRNA degradation. By applying a novel systematic evaluation of model interpretability, we demonstrated that the recurrent neural network models are inferior to the CNN models in terms of interpretability and that random initialization ensemble improves both prediction and interoperability performance. Moreover, using a mutagenesis analysis, we newly discovered the positional effect of various 3′-UTR elements.

Availability and implementation
All the code developed through this study is available at github.com/OrensteinLab/DeepUTR/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Effects of Flower Patch Density on Pollinator Visitation
Authors: Barley Tristan A , Martinez Algarin Michael G , Bauer Jonathan T 
Published: November 2021

AbstractThere is conflicting research regarding how conspecific plant density can affect pollinator visitation, with some studies indicating dense flower patches will receive more visitors and other studies demonstrating the opposite. This study investigated the effects of conspecific density on pollinator visitation in a restored prairie. Three plant species, Penstemon digitalis (Nutt. ex Sims) (Lamiales: Plantaginaceae), Monarda fistulosa (L.) (Lamiales: Lamiaceae), and Eryngium yuccifolium (Michx.) (Apiales: Apiaceae), were observed, with visiting pollinators recorded. Conspecific density did not have an effect on total pollinator visitation rates for any of the focal plant species. However, different groups of pollinators varied in their responses to flower density, notably with larger Bombus spp. tending to visit dense flowering patches more than did other groups of bees. This suggests that plant density may impact certain pollinators differently than others. These results also indicate a possible mechanism through which multiple pollinator species can coexist while only one flowering resource is available, with the foraging behavior of smaller bees potentially allowing them to avoid competition with larger, social bees. Furthermore, a comparison of seed weight demonstrated that E. yuccifolium plants tended to have larger seed sets in isolated individuals, suggesting that flowers in large patches may be pollinated less effectively and are competing for, rather than facilitating, pollinator visits.
Patient partnership in cardiovascular clinical trials
Authors: Zannad Faiez , Chauhan Cynthia , Gee Patrick O , Hartshorne-Evans Nick , Hernandez Adrian F , Mann Marilyn K , Martinez Robin , Mehran Roxana 
Published: November 2021

Abstract
Patients are ultimately the end-users of medical therapies and need to be actively integrated as contributors and decision-makers in the process of product development throughout product lifecycles. This is increasingly being recognized by patients, investigators, regulators, payers, sponsors, and medical journals. However, cardiovascular research remains behind other fields in terms of the extent of patient involvement and awareness of clinical trials in cardiovascular research. True patient partnerships in cardiovascular therapeutic development may permit more rapid recognition of unmet needs, ensure alignment of product development priorities with patient priorities, improve efficiency of trials (e.g. recruitment), and ensure outcomes of value to patients are being measured in trials (e.g. quality of life). This paper reviews ongoing initiatives and remaining opportunities to accomplish contributive patient involvement in cardiovascular clinical research.
Genome-wide association study of mitochondrial copy number
Authors: Gentiluomo Manuel , Giaccherini Matteo , Gào Xīn , Guo Feng , Stocker Hannah , Schöttker Ben , Brenner Hermann , Canzian Federico , Campa Daniele 
Published: November 2021

Abstract
Mitochondrial DNA copy number (mtDNAcn) variation has been associated with increased risk of several human diseases in epidemiological studies. The quantification of mtDNAcn performed with real-time PCR is currently considered the de facto standard among several techniques. However, the heterogeneity of the laboratory methods (DNA extraction, storage, processing) used could give rise to results that are difficult to compare and reproduce across different studies. Several lines of evidence suggest that mtDNAcn is influenced by nuclear and mitochondrial genetic variability, however this relation is largely unexplored. The aim of this work was to elucidate the genetic basis of mtDNAcn variation. We performed a genome-wide association study (GWAS) of mtDNAcn in 6836 subjects from the ESTHER prospective cohort, and included, as replication set, the summary statistics of a GWAS that used 295 150 participants from the UK Biobank. We observed two novel associations with mtDNAcn variation on chromosome 19 (rs117176661), and 12 (rs7136238) that reached statistical significance at the genome-wide level. A polygenic score that we called mitoscore including all known single nucleotide polymorphisms explained 1.11% of the variation of mtDNAcn (p = 5.93 × 10−7). In conclusion, we performed a GWAS on mtDNAcn, adding to the evidence of the genetic background of this trait.
A Systematic Literature Review of Relational Autonomy in Dialysis Decision Making
Authors: Sledge Renata , Meyer Dixie , Zubatsky Max , Heiden-Rootes Katie , Philipneri Marie , Browne Teri 
Published: November 2021

Abstract
Nephrology interdisciplinary guidelines, professional codes of ethics, principle-based ethical standards, and literature promote patient autonomy and self-determination through shared decision making as ethical practice. Healthcare professionals are accountable for practice that is mindful of the impact of cultural diversity and community on the values and beliefs of the patient, an important part of shared decision making (SDM). Despite previous research regarding dialysis decision making, relational autonomy in chronic kidney disease (CKD) and end-stage kidney disease SDM conversations is not well understood. This systematic literature review used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework for identifying peer-reviewed literature on SDM for CKD. The findings were summarized into four broad themes: (1) promoting autonomy is a foundation of medical caring; (2) providers have a responsibility to respond to their asymmetrical social power; (3) autonomy is situated within the context of the patient; and (4) dialogue is a tool that negotiates clinical recommendations and patient goals. The caring practices of promoting autonomy with a dialogical resolution of a conflict acknowledging the interdependence of the parties and the patient’s social–relational situatedness support a perspective of relational autonomy in dialysis decision-making practice and research.
Barriers and facilitators for the inclusion of fertility care in reproductive health policies in Africa: a qualitative evidence synthesis
Authors: Afferri Anna , Allen Haddijatou , Booth Andrew , Dierickx Susan , Pacey Allan , Balen Julie 
Published: November 2021

Abstract

BACKGROUND
Infertility affects over 50 million couples worldwide and impacts people’s social and emotional wellbeing. In low- and middle-income countries, particularly across Africa, the inclusion of fertility care into reproductive health (RH) policies remains fragmented or non-existent.

OBJECTIVE AND RATIONALE
This review aims to provide a framework for understanding the inclusion (or lack thereof) of fertility care in RH policies in African settings. It synthesizes the barriers and facilitators to such inclusion, with a view to uncovering the positioning of fertility care in broader health systems and on the agendas of key stakeholders such as health policymakers and practitioners.

SEARCH METHODS
A qualitative evidence synthesis was performed, systematically searching papers and grey literature. Searches were conducted in MEDLINE, EMBASE, CINAHL, Web of Science and Scopus between February and April 2020. No date restrictions were applied. Language was limited to publications written in English and French. Two reviewers independently screened titles and abstracts, and extracted data, applying thematic coding. The quality of the included papers was evaluated using The Joanna Briggs Institute Checklist for Text and Opinion Papers.

OUTCOMES
The search identified 744 papers, of which 20 were included. Findings were organized under four cross-cutting categories, namely: perceived importance of infertility; influence of policy context; resource availability and access; and perceived quality of care. Across these categories, key barriers to the inclusion of fertility care in RH policies were limited political commitment, under-recognition of the burden of infertility and high costs associated with ART. Conversely, facilitators comprised specialized training on infertility for healthcare providers, standard procedures for ART safety and guidelines and North–South/South–South collaborations.

WIDER IMPLICATIONS
The inclusion of fertility care in African RH policies depends upon factors that include the recognition of infertility as a disease, strong political engagement and proactivity and affordability of ART through opportunities for partnership with the private sector, which ease costs on the public health system. Further qualitative and quantitative research, including context-specific analysis and in-depth comparative approaches across diverse African countries, will help to delineate differential impacts of local and global factors on fertility care to address this neglected RH issue.
Ascending aortic extension to increase aortopulmonary space after comprehensive stage II palliation
Authors: Brancaccio Gianluca , Trezzi Matteo , Secinaro Aurelio , Iacobelli Roberta , Perri Gianluigi , Filippelli Sergio , Bordonaro Veronica , Galletti Lorenzo 
Published: November 2021

Abstract
Aortic reconstruction at the time of the comprehensive stage II (CSII) procedure can be complicated by compression within the aortopulmonary space resulting in airway or pulmonary artery narrowing. We describe our experience with 2 patients with hypoplastic left heart syndrome and pulmonary artery stenosis after the CSII procedure. Both patients underwent an aortic extension with a Hemashield interposition graft to open up the aortopulmonary space. The patients were discharged from the hospital. In all cases the aortopulmonary space was enlarged, and the pulmonary arteries and airway were free from compression. Aortic extension is an option to be considered in children with pulmonary artery compression who previously had a CSII procedure.
Candida auris susceptibility on surfaces coated with the antifungal drug caspofungin
Authors: Lamont-Friedrich Stephanie J , Kidd Sarah E , Giles Carla , Griesser Hans J , Coad Bryan R 
Published: November 2021

Abstract

Candida auris is known to survive for weeks on solid material surfaces. Its longevity contributes to medical device contamination and spread through healthcare facilities. We fabricated antifungal surface coatings by coating plastic and glass surfaces with a thin polymer layer to which the antifungal drug caspofungin was covalently conjugated. Caspofungin-susceptible and -resistant C. auris strains were inhibited on these surfaces by 98.7 and 81.1%, respectively. Cell viability studies showed that this inhibition was fungicidal. Our findings indicate that C. auris strains can be killed on contact when exposed to caspofungin that is reformulated as a covalently-bound surface layer.

Lay summary
Candida auris is pathogenic, multidrug resistant yeast with the ability to survive on surfaces and remain transmissible for long periods of time in healthcare settings. In this study, we have prepared an antifungal surface coating and demonstrated its ability to kill adhering C. auris cells on contact.
The GALAH Survey: dependence of elemental abundances on age and metallicity for stars in the Galactic disc
Authors: Sharma Sanjib , Hayden Michael R , Bland-Hawthorn Joss , Stello Dennis , Buder Sven , Zinn Joel C , Spina Lorenzo , Kallinger Thomas , Asplund Martin , De Silva Gayandhi M , D’Orazi Valentina , Freeman Ken C , Kos Janez , Lewis Geraint F , Lin Jane , Lind Karin , Martell Sarah L , Schlesinger Katharine J , Simpson Jeffrey D , Zucker Daniel B , Zwitter Tomaž , Chen Boquan , Cotar Klemen , Kafle Prajwal R , Khanna Shourya , Tepper-Garcia Thor , Wang Purmortal , Wittenmyer Rob A 
Published: November 2021

ABSTRACT
Using data from the GALAH survey, we explore the dependence of elemental abundances on stellar age and metallicity among Galactic disc stars. We find that the abundance of most elements can be predicted from age and [Fe/H] with an intrinsic scatter of about 0.03 dex. We discuss the possible causes for the existence of the abundance–age–metallicity relations. Using a stochastic chemical enrichment scheme that takes the volume of supernovae remnants into account, we show the intrinsic scatter is expected to be small, about 0.05 dex or even smaller if there is additional mixing in the ISM. Elemental abundances show trends with both age and metallicity and the relationship is well described by a simple model in which the dependence of abundance ([X/Fe]) on age and [Fe/H] are additively separable. Elements can be grouped based on the direction of their abundance gradient in the (age,[Fe/H]) plane and different groups can be roughly associated with three distinct nucleosynthetic production sites, the exploding massive stars, the exploding white dwarfs, and the AGB stars. However, the abundances of some elements, like Co, La, and Li, show large scatter for a given age and metallicity, suggesting processes other than simple Galactic chemical evolution are at play. We also compare the abundance trends of main-sequence turn-off (MSTO) stars against that of giants, whose ages were estimated using asteroseismic information from the K2 mission. For most elements, the trends of MSTO stars are similar to that of giants. The existence of abundance relations implies that we can estimate the age and birth radius of disc stars, which is important for studying the dynamic and chemical evolution of the Galaxy.
MASCOT: an ESO–ARO legacy survey of molecular gas in nearby SDSS-MaNGA galaxies – I. First data release, and global and resolved relations between H2 and stellar content
Authors: Wylezalek D , Cicone C , Belfiore F , Bertemes C , Cazzoli S , Wagg J , Wang (王无忌) W , Aravena M , Maiolino R , Martin S , Bothwell M S , Brownstein J R , Bundy K , De Breuck C 
Published: November 2021

ABSTRACT
We present the first data release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA)–Arizona Radio Observatory (ARO) Survey of CO Targets (MASCOT), a European Southern Observatory public spectroscopic survey conducted at the ARO. We measure the CO(1–0) line emission in a sample of 187 nearby galaxies selected from the MaNGA survey that has obtained integral field unit (IFU) spectroscopy for a sample of ∼10 000 galaxies at low redshift. The main goal of MASCOT is to probe the molecular gas content of star-forming galaxies with stellar masses &gt;109.5 M⊙ and with associated MaNGA IFU observations and well-constrained quantities like stellar masses, star formation rates, and metallicities. In this paper, we present the first results of the MASCOT survey, providing integrated CO(1–0) measurements that cover several effective radii of the galaxy and present CO luminosities, CO kinematics, and estimated H2 gas masses. We observe that the decline of the galaxy star formation rate with respect to the star formation main sequence increases with the decrease of molecular gas and with a reduced star formation efficiency, in agreement with results of other integrated studies. Relating the molecular gas mass fractions with the slope of the stellar age gradients inferred from the MaNGA observations, we find that galaxies with lower molecular gas mass fractions tend to show older stellar populations close to the galactic centre, while the opposite is true for galaxies with higher molecular gas mass fractions, providing tentative evidence for inside-out quenching.
Cosmological constraints from gas mass fractions of massive, relaxed galaxy clusters
Authors: Mantz Adam B , Morris R Glenn , Allen Steven W , Canning Rebecca E A , Baumont Lucie , Benson Bradford , Bleem Lindsey E , Ehlert Steven R , Floyd Benjamin , Herbonnet Ricardo , Kelly Patrick L , Liang Shuang , von der Linden Anja , McDonald Michael , Rapetti David A , Schmidt Robert W , Werner Norbert , Wright Adam 
Published: November 2021

ABSTRACT
We present updated cosmological constraints from measurements of the gas mass fractions (fgas) of massive, dynamically relaxed galaxy clusters. Our new data set has greater leverage on models of dark energy, thanks to the addition of the Perseus cluster at low redshifts, two new clusters at redshifts z ≳ 1, and significantly longer observations of four clusters at 0.6 &lt; z &lt; 0.9. Our low-redshift (z &lt; 0.16) fgas data, combined with the cosmic baryon fraction measured from the cosmic microwave background (CMB), imply a Hubble constant of h = 0.722 ± 0.067. Combining the full fgas data set with priors on the cosmic baryon density and the Hubble constant, we constrain the dark energy density to be ΩΛ = 0.865 ± 0.119 in non-flat Lambda cold dark matter (cosmological constant) models, and its equation of state to be $w=-1.13_{-0.20}^{+0.17}$ in flat, constant-w models, respectively 41 per cent and 29 per cent tighter than our previous work, and comparable to the best constraints available from other probes. Combining fgas, CMB, supernova, and baryon acoustic oscillation data, we also constrain models with global curvature and evolving dark energy. For the massive, relaxed clusters employed here, we find the scaling of fgas with mass to be consistent with a constant, with an intrinsic scatter that corresponds to just ∼3 per cent in distance.
The emergence of dark matter-deficient ultra-diffuse galaxies driven by scatter in the stellar mass–halo mass relation and feedback from globular clusters
Authors: Trujillo-Gomez Sebastian , Kruijssen J M Diederik , Reina-Campos Marta 
Published: November 2021

ABSTRACT
In addition to their low stellar densities, ultra-diffuse galaxies (UDGs) have a broad variety of dynamical mass-to-light ratios, ranging from dark matter (DM) dominated systems to objects nearly devoid of DM. To investigate the origin of this diversity, we develop a simple, semi-empirical model that predicts the structural evolution of galaxies, driven by feedback from massive star clusters, as a function of their departure from the mean SMHM relation. The model predicts that a galaxy located ≳ 0.5 dex above the mean relation at Mhalo = 1010 M⊙ will host a factor of ∼10–100 larger globular cluster (GC) populations, and that feedback from these GCs drives a significant expansion of the stellar component and loss of DM compared to galaxies on the SMHM relation. This effect is stronger in haloes that collapse earlier and have enhanced star formation rates at $z\gtrsim 2$, which leads to increased gas pressures, stellar clustering, and mean cluster masses, and significantly enhances the energy loading of galactic winds and its impact on the DM and stellar orbits. The impact on galaxy size and DM content can be large enough to explain observed galaxies that contain nearly the universal baryon fraction, as well as NGC 1052-DF2 and DF4 and other isolated UDGs that contain almost no DM. The trend of increasing galaxy size with GC specific frequency observed in galaxy clusters also emerges naturally in the model. Our predictions can be tested with large and deep surveys of the stellar and GC populations in dwarfs and UDGs. Because stellar clustering drives the efficiency of galactic winds, it may be a dominant factor in the structural evolution of galaxies and should be included as an essential ingredient in galaxy formation models.