bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specific growth rates and growth stoichiometries of Saccharomycotina yeasts on ethanol as sole carbon and energy substrate
Authors: Warmerdam Marieke , Vieira-Lara Marcel A , Mans Robert , Daran Jean Marc , Pronk Jack T 
Published: December 2024

Abstract
Emerging low-emission production technologies make ethanol an interesting substrate for yeast biotechnology, but information on growth rates and biomass yields of yeasts on ethanol is scarce. Strains of 52 Saccharomycotina yeasts were screened for growth on ethanol. The 21 fastest strains, among which representatives of the Phaffomycetales order were overrepresented, showed specific growth rates in ethanol-grown shake-flask cultures between 0.12 and 0.46 h−1. Seven strains were studied in aerobic, ethanol-limited chemostats (dilution rate 0.10 h−1). Saccharomyces cerevisiae and Kluyveromyces lactis, whose genomes do not encode Complex-I-type NADH dehydrogenases, showed biomass yields of 0.59 and 0.56 gbiomass gethanol−1, respectively. Different biomass yields were observed among species whose genomes do harbour Complex-I-encoding genes: Phaffomyces thermotolerans (0.58 g g−1), Pichia ethanolica (0.59 g g−1), Saturnispora dispora (0.66 g g−1), Ogataea parapolymorpha (0.67 g g−1), and Cyberlindnera jadinii (0.73 g g−1). Cyberlindnera jadinii biomass showed the highest protein content (59 ± 2%) of these yeasts. Its biomass yield corresponded to 88% of the theoretical maximum that is reached when growth is limited by assimilation rather than by energy availability. This study suggests that energy coupling of mitochondrial respiration and its regulation will become key factors for selecting and improving yeast strains for ethanol-based processes.
Fast analysis of biobank-size data and meta-analysis using the BGLR R-package
Authors: Pérez-Rodríguez Paulino , de los Campos Gustavo , Wu Hao , Vazquez Ana I , Jones Kyle 
Published: December 2024

Abstract
Analyzing human genomic data from biobanks and large-scale genetic evaluations often requires fitting models with a sample size exceeding the number of DNA markers used (n&gt;p). For instance, developing polygenic scores for humans and genomic prediction for genetic evaluations of agricultural species may require fitting models involving a few thousand SNPs using data with hundreds of thousands of samples. In such cases, computations based on sufficient statistics are more efficient than those based on individual genotype–phenotype data. Additionally, software that admits sufficient statistics as inputs can be used to analyze data from multiple sources jointly without the need to share individual genotype–phenotype data. Therefore, we developed functionality within the BGLR R-package that generates posterior samples for Bayesian shrinkage and variable selection models from sufficient statistics. In this article, we present an overview of the new methods incorporated in the BGLR R-package, demonstrate the use of the new software through simple examples, provide several computational benchmarks, and present a real-data example using data from the UK-Biobank, All of Us, and the Hispanic Community Health Study/Study of Latinos cohort demonstrating how a joint analysis from multiple cohorts can be implemented without sharing individual genotype–phenotype data, and how a combined analysis can improve the prediction accuracy of polygenic scores for Hispanics—a group severely under-represented in genome-wide association studies data.
Biased social chromosome transmission in males of the fire ant Solenopsis invicta
Authors: Hettesheimer Daniel R , Zeng Haolin , Hunt Brendan G , Ross Kenneth G 
Published: December 2024

Abstract
Selfish genetic elements subvert the normal rules of inheritance to unfairly propagate themselves, often at the expense of other genomic elements and the fitness of individuals carrying them. Social life provides diverse avenues for the propagation of such elements. In the fire ant Solenopsis invicta, polymorphic social organization is controlled by a social chromosome, one variant of which (Sb) enhances its own transmission in polygyne colonies through effects on caste development and queen acceptance by workers. Whether the selfish effects of Sb extend to haploid (reproductive) males in this system is less clear. Here, we demonstrate a strong overrepresentation of the Sb social chromosome haplotype in reproductive males, relative to Mendelian expectations, in both the pupal and adult stages. We tested for the presence of selective execution of adult SB males by workers but did not detect such behavior. Combined with the presence of a strong imbalance in the haplotype frequencies already early in the pupal stage, these results indicate that the Sb supergene may distort male haplotype frequencies during larval or embryonic development. These findings are significant because they demonstrate yet another mode by which the selfish tendencies of the Sb supergene are manifested, illuminate complex interactions between Sb and the fire ant breeding system, inform the development of models of the population dynamics of Sb, and illustrate how a selfish supergene can increase in frequency in a population despite harboring deleterious mutations.
Complex Genomic Landscape of Inversion Polymorphism in Europe's Most Destructive Forest Pest
Authors: Mykhailenko Anastasiia , Zieliński Piotr , Bednarz Aleksandra , Schlyter Fredrik , Andersson Martin N , Antunes Bernardo , Borowski Zbigniew , Krokene Paal , Melin Markus , Morales-García Julia , Müller Jörg , Nowak Zuzanna , Schebeck Martin , Stauffer Christian , Viiri Heli , Zaborowska Julia , Babik Wiesław , Nadachowska-Brzyska Krystyna 
Published: December 2024

Abstract
In many species, polymorphic genomic inversions underlie complex phenotypic polymorphisms and facilitate local adaptation in the face of gene flow. Multiple polymorphic inversions can co-occur in a genome, but the prevalence, evolutionary significance, and limits to complexity of genomic inversion landscapes remain poorly understood. Here, we examine genome-wide genetic variation in one of Europe's most destructive forest pests, the spruce bark beetle Ips typographus, scan for polymorphic inversions, and test whether inversions are associated with key traits in this species. We analyzed 240 individuals from 18 populations across the species' European range and, using a whole-genome resequencing approach, identified 27 polymorphic inversions covering ∼28% of the genome. The inversions vary in size and in levels of intra-inversion recombination, are highly polymorphic across the species range, and often overlap, forming a complex genomic architecture. We found no support for mechanisms such as directional selection, overdominance, and associative overdominance that are often invoked to explain the presence of large inversion polymorphisms in the genome. This suggests that inversions are either neutral or maintained by the combined action of multiple evolutionary forces. We also found that inversions are enriched in odorant receptor genes encoding elements of recognition pathways for host plants, mates, and symbiotic fungi. Our results indicate that the genome of this major forest pest of growing social, political, and economic importance harbors one of the most complex inversion landscapes described to date and raise questions about the limits of intraspecific genomic architecture complexity.
Neo-Sex Chromosome Evolution in Treehoppers Despite Long-Term X Chromosome Conservation
Authors: Palmer Droguett Daniela H , Fletcher Micah , Alston Ben T , Kocher Sarah , Cabral-de-Mello Diogo C , Wright Alison E 
Published: December 2024

Abstract
Sex chromosomes follow distinct evolutionary trajectories compared to the rest of the genome. In many cases, sex chromosomes (X and Y or Z and W) significantly differentiate from one another resulting in heteromorphic sex chromosome systems. Such heteromorphic systems are thought to act as an evolutionary trap that prevents subsequent turnover of the sex chromosome system. For old, degenerated sex chromosome systems, chromosomal fusion with an autosome may be one way that sex chromosomes can “refresh” their sequence content. We investigated these dynamics using treehoppers (hemipteran insects of the family Membracidae), which ancestrally have XX/X0 sex chromosomes. We assembled the most complete reference assembly for treehoppers to date for Umbonia crassicornis and employed comparative genomic analyses of 12 additional treehopper species to analyze X chromosome variation across different evolutionary timescales. We find that the X chromosome is largely conserved, with one exception being an X-autosome fusion in Calloconophora caliginosa. We also compare the ancestral treehopper X with other X chromosomes in Auchenorrhyncha (the clade containing treehoppers, leafhoppers, spittlebugs, cicadas, and planthoppers), revealing X conservation across more than 300 million years. These findings shed light on chromosomal evolution dynamics in treehoppers and the role of chromosomal rearrangements in sex chromosome evolution.
SpudDB: a database for accessing potato genomic data
Authors: Hamilton John P , Brose Julia , Buell C Robin 
Published: December 2024

Abstract
Potato is a key food crop with a complex, polyploid genome. Advancements in sequencing technologies coupled with improvements in genome assembly algorithms have enabled generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato. The SpudDB database houses potato genome sequence and annotation, with the doubled monoploid DM 1–3 516 R44 (hereafter DM) genome serving as the reference genome and haplotype. Diverse annotation data types for DM genes are provided through a suite of Gene Report Pages including gene expression profiles across 438 potato samples. To further annotate potato genes based on expression, 65 gene co-expression modules were constructed that permit the identification of tightly co-regulated genes within DM across development and responses to wounding, abiotic stress, and biotic stress. Genome browser views of DM and 28 other potato genomes are provided along with a download page for genome sequence and annotation. To link syntenic genes within and between haplotypes, syntelogs were identified across 25 cultivated potato genomes. Through access to potato genome sequences and associated annotations, SpudDB can enable potato biologists, geneticists, and breeders to continue to improve this key food crop.
Objectively Measured Physical Activity Using Wrist-Worn Accelerometers as a Predictor of Incident Alzheimer’s Disease in the UK Biobank
Authors: Zhao Angela , Cui Erjia , Leroux Andrew , Zhou Xinkai , Muschelli John , Lindquist Martin A , Crainiceanu Ciprian M 
Published: December 2024

Abstract

Background
Alzheimer’s disease (AD) affects over 6 million people and is the seventh-leading cause of death in the United States. This study compares wrist-worn accelerometry-derived PA measures against traditional risk factors for incident AD in the UK Biobank.

Methods
Of 42 157 UK Biobank participants 65 years and older who had accelerometry data and no prior AD diagnosis, 157 developed AD by April 1, 2021 (264 988 person-years or on average 6.2 years of follow-up). Twelve traditional predictors and 8 accelerometer-based physical activity (PA) measures were used in single- and multivariate Cox models. Their predictive performances for future AD diagnosis were compared across models using the repeated cross-validated concordance (rcvC). To account for potential reverse causality, sensitivity analyses were conducted by removing dropouts and cases within the first 6 months, 1 year, and 2 years.

Results
The best-performing individual predictors of incident AD were age (p &lt; .0001, rcvC = 0.658) and moderate-to-vigorous PA (MVPA, p = .0001, rcvC = 0.622). Forward selection produced a model that included age, diabetes, and MVPA (rcvC = 0.681). Adding MVPA to the model containing age and diabetes improved its rcvC from 0.665 to 0.681 (p = .0030), more than all other potential risk factors considered.

Conclusions
Objective PA summaries are the best single predictors among modifiable risk factors with a predictive performance close to that of age. Adding PA summaries to traditional risk factors for AD substantially increases the predictive performance of these models. Increasing MVPA by 14.5 minutes per day reduces the hazard substantially, equivalent to 2 years younger.
Intentional Strategic Changes in the National Institute on Aging’s RCMAR Program: Broadening its Scope and Reach to Strengthen its Impact
Authors: Gerald Melissa S , Major Laura 
Published: December 2024

Abstract
Since 1997, the Resource Centers for Minority Aging Research (RCMAR) program, supported by the Division of Behavioral and Social Research (BSR) at the National Institute on Aging, has served as BSR’s flagship mentoring program for early-career scientists from diverse backgrounds. Over the years, it has undergone significant changes to address evolving institutional priorities and societal needs. This article highlights the motivations behind programmatic shifts in the fifth funding cycle (2018–2023) and the guiding principles for RCMAR VI (2023–present). Key developments in RCMAR V included the launch of RCMARs focused on Alzheimer’s disease (AD) and Alzheimer’s disease-related dementias (ADRD), a refined emphasis on behavioral and social research, and the decoupling of workforce diversity from health disparities research. Building on lessons learned from the prior funding cycle—amid challenges posed by the coronavirus disease 2019 pandemic and leadership transitions—RCMAR VI offers enriched research, training, and mentorship opportunities while introducing equitable governance structures and clearer, broader expectations for success. The new RCMAR National Coordinating Center plays a crucial role in fostering collaboration, standardizing evaluation, and leading activities to broaden the program’s impact. With a renewed focus on high-priority behavioral and social research on aging, AD/ADRD, and health disparities, RCMAR VI is poised to diversify the scientific workforce and advance discoveries.
GPU-accelerated Kendall distance computation for large or sparse data
Authors: Akhtyamov Pavel , Nabi Ausaaf , Gafurov Vladislav , Sizykh Alexey , Favorov Alexander , Medvedeva Yulia , Stupnikov Alexey 
Published: December 2024

Abstract

Background
Current experimental practices typically produce large multidimensional datasets. Distance matrix calculation between elements (e.g., samples) for such data, although being often necessary in preprocessing for statistical inference or visualization, can be computationally demanding. Data sparsity, which is often observed in various experimental data modalities, such as single-cell sequencing in bioinformatics or collaborative filtering in recommendation systems, may pose additional algorithmic challenges.

Results
We present GPU-Assisted Distance Estimation Software (GADES), a graphical processing unit (GPU)–enhanced package that allows for massively paralleled Kendall-$\tau$ distance matrices computation. The package’s architecture involves specific memory management, which lifts the limits for the data size imposed by GPU memory capacity. Additional algorithmic solutions provide a means to address the data sparsity problem and reinforce the acceleration effect for sparse datasets. Benchmarking against available central processing unit–based packages on simulated and real experimental single-cell RNA sequencing or single-cell ATAC sequencing datasets demonstrated significantly higher speed for GADES compared to other methods for both sparse and dense data processing, with additional performance boost for the sparse data.

Conclusions
This work significantly contributes to the development of computational strategies for high-performance Kendall distance matrices computation and allows for the efficient processing of Big Data with the power of GPU. GADES is freely available at https://github.com/lab-medvedeva/GADES-main.
A novel prenatal alcohol use risk perception model: feedback from a Delphi process
Authors: Erng May Na , Reid Natasha , Moritz Karen M , van Driel Mieke 
Published: December 2024

Abstract
Understanding prenatal alcohol exposure (PAE) risk perception is important for the communication and prevention of alcohol use during pregnancy. A previous systematic review has explored the dimensions and influencing factors of women’s PAE risk perceptions, leading to the construction of Pregnancy Alcohol Use Risk Perception (PARP) conceptual model. This study aims to refine the PARP model using a Delphi process. A total of 37 international experts participated, 17 completed all three online surveys between May 2022 and December 2022. The online survey consisted of Likert-scale and free-text responses on the usefulness and clarity of the components and the design of the PARP model. Likert-scale responses were analysed using descriptive statistics. Free-text responses were analysed using a reflexive thematic analysis approach. The model was amended following participants’ responses. Four characteristics underpinned the revised model—relevance-to-self and the negotiations of risks, inter-relatedness of affect with the cognitive processing of risk, contextual influences of individual, sociocultural and institutional/political/organizational rendering a socioecological perspective to PAE risks perception and the dynamic characteristics of PAE risk perception. The acknowledgement of PAE risk perceptions and the contextual influences can support development of targeted and tailored messages and health education materials.
A novel insight into the antidepressant effect of cannabidiol: possible involvement of the 5-HT1A, CB1, GPR55, and PPARγ receptors
Authors: Miao Yang , Zhao Fei , Guan Wei 
Published: December 2024

Abstract

Background
Depression is a prevalent and disabling disorder that poses serious problems in mental health care, and rapid antidepressants are novel treatments for this disorder. Cannabidiol (CBD), a non-intoxicating phytocannabinoid, is thought to have therapeutic potential due to its important neurological and anti-inflammatory properties. Despite major advances in pharmacotherapy in experimental animals, the exact mechanism of antidepressant-like effects remains to be elucidated.

Methods
In this paper, we review the current state of knowledge on the antidepressant properties of CBD in numerous experimental and clinical studies.

Results
Accumulating evidence suggests that CBD has antidepressant properties in humans and animals with few side effects, suggesting that CBD may be a potential antidepressant. Furthermore, we discuss CBD may therefore provide a potential treatment to exert antidepressant-like effects through various molecular targets, reducing inflammation, and enhancing neurogenesis.

Conclusions
Taken together with the growing popularity of CBD as a medicine, these findings extend the limited knowledge on the antidepressant effects of CBD. This potentially opens up new therapeutic means for the patients with depression.
Impact of Pandemic-Induced Service Disruptions and Behavioral Changes on Hepatitis C Virus and HIV Transmission Amongst People Who Inject Drugs: A Modeling Study
Authors: Wang Jasmine , Genberg Becky L , Feder Kenneth A , Kirk Gregory D , Mehta Shruti H , Grantz Kyra , Wesolowski Amy 
Published: December 2024

Abstract

Background
The coronavirus disease 2019 (COVID-19) pandemic may have disproportionally impacted vulnerable groups such as people who inject drugs (PWID) through reduced health care services as well as social changes from pandemic mitigation measures. Understanding how the COVID-19 pandemic and associated mitigation strategies subsequently changed the trajectory of hepatitis C virus (HCV) and human immunodeficiency virus (HIV) transmission is critical to estimating disease burdens, identifying outbreak risk, and developing informed intervention strategies.

Methods
Using behavioral data from the AIDS Linked to the IntraVenous Experience (ALIVE) study, an ongoing community-based cohort of PWID in Baltimore, United States, and an individual-based network model, we explored the impacts of service disruptions combined with changes in social networks and injecting behaviors of PWID on HCV and HIV transmission.

Results
Analyses of ALIVE data showed that during the pandemic, there was an acceleration in injection cessation trajectories overall, but those who continued injecting increased the frequency of injection; at the same time, individual drug-use networks became smaller and the probability of injecting with others decreased. Simulation results demonstrated that HCV and HIV prevalence increased from service disruptions alone, but these effects were mitigated when including observed behavior changes in addition.

Conclusions
Model results combined with rich individual behavioral data indicated that pandemic-induced behavioral changes of PWID that lasted longer than service disruptions could have offset the increasing disease burden caused by disrupted service access during the pandemic.
The Neisseria meningitidis Urethritis Clade (NmUC) Acts as a “Chimeric Pathogen” During Infection of Primary, Human Male, Urethral Epithelial Cells
Authors: Tzeng Yih-Ling , Esposito Danillo L A , Nederveld Andrew G , Hardison Rachael L , Carter Alexandria M , Stephens David S , Norris Turner Abigail , Bazan Jose A , Edwards Jennifer L 
Published: December 2024

Abstract

Background
Male urethritis cases, caused by a novel clade of nongroupable Neisseria meningitidis (NmUC, “the clade”), have been reported globally.

Methods
To test whether genetic features unique to NmUC confer a colonization and survival advantage to NmUC during urethral infection, NmUC, gonococcal, and nonclade meningococcal strains were comparatively evaluated in primary, human male, urethral epithelial cell (UEC) infection studies.

Results
NmUC strains were more invasive in UECs than the gonococcal strains tested, which could not be attributed to loss of capsule expression alone. Whereas gonococci and NmUC strains survived and proliferated within UECs, negligible survival was observed for nonclade meningococcal strains. NmUC infection of UECs was impaired when host receptors known to mediate gonococcal or meningococcal interactions with epithelial cells were blocked. We found that fHbp contributes to clade survival independent of its ability to bind extracellular factor H, and that the gonococcal denitrification pathway, particularly NorB, plays an important role in promoting clade intracellular survival.

Conclusions
Whereas mechanisms used by NmUC to infect UECs are shared with other neisserial strains, hybrid mechanisms unique to the clade also mediate infection and allow adaptation to the male urethra. Thus, NmUC is a “chimeric pathogen,” displaying facets of gonococcal and meningococcal pathogenesis.