bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage
Authors: Rasmussen Malthe Sebro , Garcia-Erill Genís , Korneliussen Thorfinn Sand , Wiuf Carsten , Albrechtsen Anders 
Published: September 2022

Abstract
The site frequency spectrum is an important summary statistic in population genetics used for inference on demographic history and selection. However, estimation of the site frequency spectrum from called genotypes introduces bias when working with low-coverage sequencing data. Methods exist for addressing this issue but sometimes suffer from 2 problems. First, they can have very high computational demands, to the point that it may not be possible to run estimation for genome-scale data. Second, existing methods are prone to overfitting, especially for multidimensional site frequency spectrum estimation. In this article, we present a stochastic expectation–maximization algorithm for inferring the site frequency spectrum from NGS data that address these challenges. We show that this algorithm greatly reduces runtime and enables estimation with constant, trivial RAM usage. Furthermore, the algorithm reduces overfitting and thereby improves downstream inference. An implementation is available at github.com/malthesr/winsfs.
Five-Factor Model Personality Traits and the Trajectory of Episodic Memory: Individual-Participant Meta-Analysis of 471,821 Memory Assessments from 120,640 Participants
Authors: Sutin Angelina R , Brown Justin , Luchetti Martina , Aschwanden Damaris , Stephan Yannick , Terracciano Antonio 
Published: September 2022

AbstractObjectivesFive-factor model (FFM) personality traits are associated with concurrent memory function and risk of incident dementia but are less consistently associated with the change in episodic memory. The present research analyzes multiple large-scale studies with a consistent analytic approach to evaluate the association between personality and change in episodic memory over time.MethodAcross nine public longitudinal data sets, 120,640 participants provided 471,821 memory assessments over up to 26 years (age range 18–108). FFM traits were tested as predictors of the average level (intercept) and change over time (slope) of episodic memory. Results from the individual samples were meta-analyzed to summarize the associations.ResultsConsistent with expectations for the intercept, higher neuroticism was associated with worse memory performance, whereas higher openness and conscientiousness were associated with better performance; extraversion and agreeableness were also associated with better performance. Higher neuroticism and lower conscientiousness were related to declines in memory only in samples with more than two assessments of memory. The other three traits were unrelated to memory slope. The pattern was similar when participants with dementia were excluded from the analysis, and the association with the slope was not moderated by age.DiscussionFFM traits have a robust association with average memory performance. Higher neuroticism and lower conscientiousness were associated with declines in memory performance only among samples with more than two memory assessments. The heterogeneity across studies suggests that multiple memory assessments are needed to reliably detect change over time, which may be one reason for past inconsistencies across studies.
Complexity awareness among university students in Switzerland during the Covid-19 pandemic
Authors: Nigg Carina , Benkert Richard , Tadesse Lidya , Abel Thomas 
Published: September 2022

SummaryPublic health challenges relating to Covid-19 are highly complex and reasons behind preventive measures can be difficult to understand. Complexity awareness, an important part of healthy literacy, may help young people to understand the situation and act accordingly. However, we could not find any tools to assess complexity awareness during a pandemic in the literature. The purpose of this study was to develop pandemic-specific items to assess complexity awareness and explore relationships with sociodemographic characteristics in university students. Based on critical health literacy concepts and expert knowledge from public health, we developed four survey items, which were answered by 3616 Swiss university students online as part of the COVID-19 International Student Well-Being Study. Relationships between awareness and sociodemographic characteristics were explored using logistic regression and odds ratio (OR). Results showed that 49.6% of the students demonstrated limited and 50.4% demonstrated high complexity awareness. Being female (OR = 1.26; 95% CI 1.07–1.47), having highly educated parents (OR = 1.29; 95% CI 1.06–1.57), and being at a practically oriented university (OR = 0.79; 95% CI 0.64–0.97) was associated with high awareness. Covid-19-related complexity awareness varied significantly among university students, indicating that they have difficulties in dealing with complex information and processes in this pandemic. The results call for action to support students in understanding the complexity of this pandemic and to investigate complexity awareness in the general population.
Integration of transcriptome-wide association study with neuronal dysfunction assays provides functional genomics evidence for Parkinson’s disease genes
Authors: Li Jiayang , Amoh Bismark Kojo , McCormick Emma , Tarkunde Akash , Zhu Katy Fan , Perez Alma , Mair Megan , Moore Justin , Shulman Joshua M , Al-Ramahi Ismael , Botas Juan 
Published: September 2022

Abstract
Genome-wide association studies (GWAS) have markedly advanced our understanding of the genetics of Parkinson’s disease (PD), but they currently do not account for the full heritability of PD. In many cases it is difficult to unambiguously identify a specific gene within each locus because GWAS does not provide functional information on the identified candidate loci. Here we present an integrative approach that combines transcriptome-wide association study (TWAS) with high-throughput neuronal dysfunction analyses in Drosophila to discover and validate candidate PD genes. We identified 160 candidate genes whose misexpression is associated with PD risk via TWAS. Candidates were validated using orthogonal in silico methods and found to be functionally related to PD-associated pathways (i.e. endolysosome). We then mimicked these TWAS-predicted transcriptomic alterations in a Drosophila PD model and discovered that 50 candidates can modulate α-Synuclein(α-Syn)-induced neurodegeneration, allowing us to nominate new genes in previously known PD loci. We also uncovered additional novel PD candidate genes within GWAS suggestive loci (e.g. TTC19, ADORA2B, LZTS3, NRBP1, HN1L), which are also supported by clinical and functional evidence. These findings deepen our understanding of PD, and support applying our integrative approach to other complex trait disorders.
Risk of adverse neonatal outcomes among pregnant women with disabilities
Authors: Gleason Jessica L , Grewal Jagteshwar , Chen Zhen , Cernich Alison N , Grantz Katherine L 
Published: September 2022

Abstract

Background
To compare risk of neonatal morbidities between women with and without documented disability and to evaluate mediation of these associations by pre-term birth and caesarean delivery.

Methods
Using data from the Consortium on Safe Labor (2002–2008; n = 223 385), we evaluated risk of 22 neonatal outcomes among singleton deliveries using ICD-9 codes to define physical (n = 1733), sensory (n = 250) and intellectual disability (n = 91). Adjusted relative risk (aRR) was estimated for each outcome among each category of disability, and among women with any disability using Poisson regression models with robust variance. Causal mediation methods evaluated pre-term birth and caesarean delivery as mediators.

Results
Compared with no disability, neonates of women with any disability had higher risk of nearly all neonatal outcomes, including pre-term birth (aRR = 1.77; 95% CI 1.62–1.94), small for gestational age (SGA) (aRR = 1.25; CI 1.11–1.41), neonatal intensive care unit (NICU) admission (aRR = 1.70; CI 1.54–1.87), seizures (aRR = 2.81; CI 1.54–5.14), cardiomyopathy (aRR = 4.92; CI 1.15–20.95), respiratory morbidities (aRR ranged from 1.33–2.08) and death (aRR = 2.31; CI 1.38–3.87). Women with disabilities were more likely to have a maternal indication for pre-term delivery, including pre-pregnancy diabetes (aRR = 3.80; CI 2.84–5.08), chronic hypertension (aRR = 1.46; CI 0.95–2.25) and severe pre-eclampsia/eclampsia (aRR = 1.47; CI 1.19–1.81). Increased risk varied but was generally consistent across all disability categories. Most outcomes were partially mediated by pre-term birth, except SGA, and heightened risk remained for NICU admissions, respiratory distress syndrome, anaemia and a composite of any adverse outcome (aRR = 1.21; CI 1.10–1.32).

Conclusion
Neonates of women with disabilities were at higher risk of a broad range of adverse neonatal outcomes, including death. Risks were not fully explained by pre-term birth.
Investigation of Neurofunctional Changes Over the Course of Electroconvulsive Therapy
Authors: Gruzman Rebecca , Hartling Corinna , Domke Ann-Kathrin , Stippl Anna , Carstens Luisa , Bajbouj Malek , Gärtner Matti , Grimm Simone 
Published: September 2022

Abstract

Background
Electroconvulsive therapy (ECT) is an effective treatment for patients suffering from depression. Yet the exact neurobiological mechanisms underlying the efficacy of ECT and indicators of who might respond best to it remain to be elucidated. Identifying neural markers that can inform about an individual’s response to ECT would enable more optimal treatment strategies and increase clinical efficacy.

Methods
Twenty-one acutely depressed inpatients completed an emotional working memory task during functional magnetic resonance imaging before and after receiving treatment with ECT. Neural activity was assessed in 5 key regions associated with the pathophysiology of depression: bilateral dorsolateral prefrontal cortex and pregenual, subgenual, and dorsal anterior cingulate cortex. Associations between brain activation and clinical improvement, as reflected by Montgomery-Åsberg Depression Rating Scale scores, were computed using linear regression models, t tests, and Pearson correlational analyses.

Results
Significant neurobiological prognostic markers or changes in neural activity from pre- to post ECT did not emerge.

Conclusions
We could not confirm normalization effects and did not find significant neural markers related to treatment response. These results demonstrate that the search for reliable and clinically useful biomarkers for ECT treatment remains in its initial stages and still faces challenges.
Reference Interval for Serum L-Homoarginine Determined with Enzyme-Linked Immunosorbent Assay in the Population-Based Study of Health in Pomerania
Authors: Schwedhelm Edzard , Cordts Kathrin , Moritz Eileen , Wesemann Reinhard , Choe Chi-un , Böger Rainer , Ittermann Till , Dörr Marcus , Friedrich Nele , Bahls Martin 
Published: September 2022

Abstract

Background
Low levels of the endogenous amino acid L-homoarginine are a risk factor for cardiovascular morbidity and mortality. For individual risk prediction, commercially available test systems are mandatory. This study aims at formulating sex- and age-specific reference intervals of serum L-homoarginine determined with an ELISA.

Methods
We determined reference intervals for serum L-homoarginine stratified by age and sex in a sample of 1285 healthy participants of the Study of Health in Pomerania (SHIP)-TREND cohort after exclusion of participants with cardiovascular diseases, diabetes mellitus, hypertension, metabolic syndrome, elevated liver enzymes, chronic kidney disease stages III or IV, or body mass index &gt;25 kg/m2. Serum L-homoarginine was determined applying a commercially available ELISA.

Results
The reference cohort included 836 women (median age 41, 25th and 75th percentiles are 32 and 50 years) and 449 men (median age 38, 25th, and 75th percentiles are 30 and 49 years). The median serum concentration of L-homoarginine was 1.93 (25th 1.49; 75th 2.60) µmol/L in women and 2.02 (25th 1.63; 75th 2.61) µmol/L in men (P = 0.04). The reference intervals (2.5th to 97.5th percentile) were 0.89–5.29 µmol/L for women and 1.09–3.76 µmol/L for men. The L-homoarginine serum concentration declined over age decades in both sexes and a notable interaction with sex hormone intake in women was observed.

Conclusions
The novelty of our study is that we determined reference intervals specific for the L-isomer being lower than those previously reported for homoarginine in SHIP and thus might be helpful in identifying individuals suitable for oral L-homoarginine supplementation.
An interactive fitness-for-use data completeness tool to assess activity tracker data
Authors: Cho Sylvia , Ensari Ipek , Elhadad Noémie , Weng Chunhua , Radin Jennifer M , Bent Brinnae , Desai Pooja , Natarajan Karthik 
Published: September 2022

Abstract

Objective
To design and evaluate an interactive data quality (DQ) characterization tool focused on fitness-for-use completeness measures to support researchers’ assessment of a dataset.

Materials and Methods
Design requirements were identified through a conceptual framework on DQ, literature review, and interviews. The prototype of the tool was developed based on the requirements gathered and was further refined by domain experts. The Fitness-for-Use Tool was evaluated through a within-subjects controlled experiment comparing it with a baseline tool that provides information on missing data based on intrinsic DQ measures. The tools were evaluated on task performance and perceived usability.

Results
The Fitness-for-Use Tool allows users to define data completeness by customizing the measures and its thresholds to fit their research task and provides a data summary based on the customized definition. Using the Fitness-for-Use Tool, study participants were able to accurately complete fitness-for-use assessment in less time than when using the Intrinsic DQ Tool. The study participants perceived that the Fitness-for-Use Tool was more useful in determining the fitness-for-use of a dataset than the Intrinsic DQ Tool.

Discussion
Incorporating fitness-for-use measures in a DQ characterization tool could provide data summary that meets researchers needs. The design features identified in this study has potential to be applied to other biomedical data types.

Conclusion
A tool that summarizes a dataset in terms of fitness-for-use dimensions and measures specific to a research question supports dataset assessment better than a tool that only presents information on intrinsic DQ measures.
Bare collapse, formation of neutron star binaries and fast optical transients
Authors: Mor Ron , Livne Eli , Piran Tsvi 
Published: September 2022

ABSTRACT
‘Bare collapse’, the collapse of a bare stellar core into a neutron star with a very small mass ejection links two seemingly unrelated phenomena: the formation of binary neutron star (BNS) systems and the observations of fast and luminous optical transients. We carried out calculations of the collapse due to electron-capture of both evolutionary and synthetic isentropic bare stellar cores. We find that the collapse results in the formation of a light ∼1.3M⊙ neutron star and an ejection of ∼0.1M⊙ at ∼0.1c. The outer shell of the ejecta is composed of 56Ni that can power an ultra-stripped supernova. The models we explored can explain most of the observed fast optical flares but not the brightest ones. Collapse of cores surrounded by somewhat more massive envelopes can produce larger amounts of 56Ni and explain brighter flares. Alternatively, those events can arise due to interaction of the very energetic ejecta with winds that were ejected from the progenitor a few days before the collapse.There are no data bases used.
Spiral instabilities: mode saturation and decay
Authors: Sellwood J A , Carlberg R G 
Published: September 2022

ABSTRACT
This paper continues a series reporting different aspects of the behaviour of disc galaxy simulations that support spiral instabilities. The focus in this paper is to demonstrate how linear spiral instabilities saturate and decay, and how the properties of the disc affect the limiting amplitude of the spirals. Once again, we employ idealized models that each possess a single instability that we follow until it has run its course. Remarkably, we find a tight correlation between the growth rate of the mode and its limiting amplitude, albeit from only six simulations. We show that non-linear orbit deflections near corotation cause the mode to saturate, and that the more time available in a slowly growing mode creates the critical deflections at lower amplitude. We also find that scattering at the inner Lindblad resonance is insignificant until after the mode has saturated. Our objective in this series of papers, which we believe we have now achieved, has been to develop a convincing and well-documented account of the physical behaviour of the spiral patterns that have been observed in simulations by others, and by ourselves, for many decades. Understanding the simulations is an important step towards the greater objective, which is to find observational evidence from galaxies that could confront the identified mechanism.
Influenza Vaccine Effectiveness: Analysis of the Impact of Repeated Vaccinations in Military Health System Beneficiaries
Authors: Richard Stephanie A , Fairchok Mary , Coles Christian , Burgess Timothy H , Colombo Rhonda E 
Published: September 2022

Abstract

Background
Influenza has long burdened the Military Health System (MHS). This study assesses the impact of repeated annual vaccination on influenza vaccine effectiveness (VE).

Methods
This retrospective, case control study using the test-negative design utilized data extracted from the MHS Data Repository (MDR). Cases had a positive influenza test and controls sought care for an influenza-like illness within 2 weeks of a case, had no positive influenza tests, and were matched by sex, race, age, and location. Vaccine effectiveness was assessed using conditional logistic regression separately for those who received inactivated and live attenuated influenza vaccines (LAIV).

Results
A total of 6860 cases and controls were identified in the MDR, among whom 53% were vaccinated in all 3 seasons. Among those who received inactivated influenza vaccine during the current season, VE ranged from 26% to 37% (2012/13 [A(H3N2)]: VE 26%, 95% confidence interval [CI] = 1%–45%; 2013/14 [A(H1N1)pdm09]: VE 37%, 95% CI = 18%–52%; 2014/15 [A(H3N2)]: VE 31%, 95% CI = 17%–42%). The VE ranged from 25% to 49% for those only vaccinated this season (2012/13 [A(H3N2)]: VE 38%, 95% CI = −3% to 63%; 2013/14 [A(H1N1)pdm09]: VE 49%, 95% CI = 11%–71%; 2014/15 [A(H3N2)]: VE 25%, 95% CI = −7% to 48%). The VE was more variable in those who received LAIV in the current season. No statistically significant differences in VE were observed between those frequently vaccinated and those vaccinated only during the current season.

Conclusions
These results underscore the value of annual influenza vaccinations for preventing infection while highlighting the need for continued improvements in influenza vaccine effectiveness.
Demographic declines over time and variable responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada
Authors: Saracco James F , Pyle Peter , Kaschube Danielle R , Kohler Monica , Godwin Christine M , Foster Kenneth R 
Published: September 2022

Abstract
Habitat loss and disturbance from industrial resource development may be contributing to declines in boreal bird populations. We applied hierarchical multi-species models to data from 31 bird species at 38 Monitoring Avian Productivity and Survivorship (MAPS) stations to assess 10-year (2011–2020) demographic trends and responses to energy sector disturbance (human footprint proportion) in the Athabasca oil sands region of Alberta, Canada. Adult captures, productivity, and residency probability all declined over the study period, and adult apparent survival probability also tended to decline. Consistent with the hypothesis that habitat loss may be driving declines, trends in adult captures, productivity, and survival were all more negative at stations with larger increases in disturbance over the study period. Species associated with early seral stages were more commonly captured at more disturbed stations, while species typical of mature forests were more commonly captured at less disturbed stations. Productivity was positively correlated with disturbance within 5-km of stations after controlling for disturbance within 1-km of stations, suggesting the importance of earlier successional habitat for post-fledging birds in the larger landscape. Adult apparent survival showed relatively little response to disturbance; stresses experienced beyond the breeding grounds likely play a larger role in influencing survival. Residency probability was negatively related to disturbance within 1-km scale of stations and could reflect processes affecting the ability of birds to establish or maintain territories in disturbed landscapes. We conclude that successional habitats that result from natural regeneration or restoration in disturbed areas, as well as decreased future footprint through recovery of mature forests and limiting of new disturbances, will both be important components of efforts to reverse population declines and maintain bird populations in the region.
W. E. B. Du Bois as Anticolonialist Activist and Theoretician
Authors: Danns George K. , Henry Paget 
Published: September 2022

Abstract
This chapter identifies seven tenets of social thought that characterize W. E. B. Du Bois as an anticolonial activist and theoretician. Race is a preeminent and determinant factor in explaining the human condition. Africa and Africans, though pivotal and legitimate entities in human civilization, have been written out of prevailing historical narratives and must be restored. White racism and White supremacy are not ageless and enduring features of human history but emerged and crystallized during the nineteenth and twentieth centuries as ideological and epistemic derivatives of western global capitalism. Racial capitalism—not just class-based capitalism—is the driver of the social order, both in America and across the globe. Inhumane conflicts and violence are hallmarks of the emergence, development, and sustenance of capitalism. Religion has provided moral justification for both the enslavement and colonization of Africans and people of color. The color line is an entrenched identifier of systemic global White supremacy.
Studies of Gender and Popular Music in Africa
Authors: Clark Msia Kibona , Nikoi Nii Kotei 
Published: September 2022

Abstract
This chapter examines post-2000 scholarship on gendered representations in African popular music from scholars based both in Africa and in the West. The authors explore the historical and geographical development of contemporary scholarship on the topic, and the voices and scholarly spaces that have often been centered. Numerous studies approach gender and popular music from interdisciplinary fields, such as African studies, women’s studies, and cultural studies. Methods often employed in these studies include textual analysis of song lyrics, and, predominantly, ethnographies to understand performers, performance spaces, and audiences. The authors also discuss the power dynamics of researchers and their interactions with the local African communities they work with. In addition, the authors focus on questions of access and inclusion of African based scholars and institutes.