bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing
Authors: Suljič Alen , Zorec Tomaž Mark , Zakotnik Samo , Vlaj Doroteja , Kogoj Rok , Knap Nataša , Petrovec Miroslav , Poljak Mario , Avšič-Županc Tatjana , Korva Miša 
Published: June 2024

Abstract
The emergence and rapid spread of SARS-CoV-2 prompted the global community to identify innovative approaches to diagnose infection and sequence the viral genome because at several points in the pandemic positive case numbers exceeded the laboratory capacity to characterize sufficient samples to adequately respond to the spread of emerging variants. From week 10, 2020, to week 13, 2023, Slovenian routine complete genome sequencing (CGS) surveillance network yielded 41 537 complete genomes and revealed a typical molecular epidemiology with early lineages gradually being replaced by Alpha, Delta, and finally Omicron. We developed a targeted next-generation sequencing based variant surveillance strategy dubbed Spike Screen through sample pooling and selective SARS-CoV-2 spike gene amplification in conjunction with CGS of individual cases to increase throughput and cost-effectiveness. Spike Screen identifies variant of concern (VOC) and variant of interest (VOI) signature mutations, analyses their frequencies in sample pools, and calculates the number of VOCs/VOIs at the population level. The strategy was successfully applied for detection of specific VOC/VOI mutations prior to their confirmation by CGS. Spike Screen complemented CGS efforts with an additional 22 897 samples sequenced in two time periods: between week 42, 2020, and week 24, 2021, and between week 37, 2021, and week 2, 2022. The results showed that Spike Screen can be applied to monitor VOC/VOI mutations among large volumes of samples in settings with limited sequencing capacity through reliable and rapid detection of novel variants at the population level and can serve as a basis for public health policy planning.
NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach
Authors: Xue Zhengfa , Zhou Aifen , Zhu Xiaoyan , Li Linxuan , Zhu Huanhuan , Jin Xin , Wang Jiayin 
Published: June 2024

Abstract
Non-invasive prenatal testing (NIPT) is a quite popular approach for detecting fetal genomic aneuploidies. However, due to the limitations on sequencing read length and coverage, NIPT suffers a bottleneck on further improving performance and conducting earlier detection. The errors mainly come from reference biases and population polymorphism. To break this bottleneck, we proposed NIPT-PG, which enables the NIPT algorithm to learn from population data. A pan-genome model is introduced to incorporate variant and polymorphic loci information from tested population. Subsequently, we proposed a sequence-to-graph alignment method, which considers the read mis-match rates during the mapping process, and an indexing method using hash indexing and adjacency lists to accelerate the read alignment process. Finally, by integrating multi-source aligned read and polymorphic sites across the pan-genome, NIPT-PG obtains a more accurate z-score, thereby improving the accuracy of chromosomal aneuploidy detection. We tested NIPT-PG on two simulated datasets and 745 real-world cell-free DNA sequencing data sets from pregnant women. Results demonstrate that NIPT-PG outperforms the standard z-score test. Furthermore, combining experimental and theoretical analyses, we demonstrate the probably approximately correct learnability of NIPT-PG. In summary, NIPT-PG provides a new perspective for fetal chromosomal aneuploidies detection. NIPT-PG may have broad applications in clinical testing, and its detection results can serve as a reference for false positive samples approaching the critical threshold.
FOXL2 regulates RhoA expression to change actin cytoskeleton rearrangement in granulosa cells of chicken pre-ovulatory follicles
Authors: Li Xuelian , Du Hongting , Zhou Haobo , Huang Ying , Tang Shuixin , Yu Chengzhi , Guo Yan , Luo Wei , Gong Yanzhang 
Published: June 2024

Abstract
Forkhead box L2 (FOXL2) is an indispensable key regulator of female follicular development, and it plays important roles in the morphogenesis, proliferation, and differentiation of follicle granulosa cells, such as establishing normal estradiol signaling and regulating steroid hormone synthesis. Nevertheless, the effects of FOXL2 on granulosa cell morphology and the underlying mechanism remain unknown. Using FOXL2 ChIP-seq analysis, we found that FOXL2 target genes were significantly enriched in the actin cytoskeleton-related pathways. We confirmed that FOXL2 inhibited the expression of RhoA, a key gene for actin cytoskeleton rearrangement, by binding to TCATCCATCTCT in RhoA promoter region. In addition, FOXL2 overexpression in granulosa cells induced the depolymerization of F-actin and disordered the actin filaments, resulting in a slowdown in the expansion of granulosa cells, while FOXL2 silencing inhibited F-actin depolymerization and stabilized the actin filaments, thereby accelerating granulosa cell expansion. RhoA/ROCK pathway inhibitor Y-27632 exhibited similar effects to FOXL2 overexpression, even reversed the actin polymerization in FOXL2 silencing granulosa cells. This study revealed for the first time that FOXL2 regulated granulosa cell actin cytoskeleton by RhoA/ROCK pathway, thus affecting granulosa cell expansion. Our findings provide new insights for constructing the regulatory network of FOXL2 and propose a potential mechanism for facilitating rapid follicle expansion, thereby laying a foundation for further understanding follicular development.
PPARG is dispensable for bovine embryo development up to tubular stages
Authors: Pérez-Gómez Alba , González-Brusi Leopoldo , Flores-Borobia Inés , Martínez De Los Reyes Nuria , Toledano-Díaz Adolfo , López-Sebastián Antonio , Santiago Moreno Julián , Ramos-Ibeas Priscila , Bermejo-Álvarez Pablo 
Published: June 2024

Abstract
Following blastocyst hatching, ungulate embryos undergo a prolonged preimplantation period termed conceptus elongation. Conceptus elongation constitutes a highly susceptible period for embryonic loss, and the embryonic requirements during this process are largely unknown, but multiple lipid compounds have been identified in the fluid nourishing the elongating conceptuses. Peroxisome proliferator-activated receptors mediate the signaling actions of prostaglandins and other lipids, and, between them, PPARG has been pointed out to play a relevant role in conceptus elongation by a functional study that depleted PPARG in both uterus and conceptus. The objective of this study has been to determine if embryonic PPARG is required for bovine embryo development. To that aim, we have generated bovine PPARG knock-out embryos in vitro using two independent gene ablation strategies and assessed their developmental ability. In vitro development to Day 8 blastocyst was unaffected by PPARG ablation, as total, inner cell mass, and trophectoderm cell numbers were similar between wild-type and knock-out D8 embryos. In vitro post-hatching development to D12 was also comparable between different genotypes, as embryo diameter, epiblast cell number, embryonic disk formation, and hypoblast migration rates were unaffected by the ablation. The development of tubular stages equivalent to E14 was assessed in vivo, following a heterologous embryo transfer experiment, observing that the development of extra-embryonic membranes and of the embryonic disk was not altered by PPARG ablation. In conclusion, PPARG ablation did not impaired bovine embryo development up to tubular stages.
Enhancement of excimer formation ability by modulating the length of Side-chains in polyhedral oligomeric silsesquioxane (POSS) and application for fluorescence sensors for metal cations
Authors: Narikiyo Hayato , Gon Masayuki , Tanaka Kazuo , Chujo Yoshiki 
Published: June 2024

Abstract
Polyhedral oligomeric silsesquioxane (POSS) is a molecule with an inorganic cubic structure and organic side chains which has attracted great attention for its potential to modify luminophores with applications to luminescent materials. In this study, pyrenes-integrated POSSs with various lengths of side chains were synthesized and the effect of the length on luminescent properties was evaluated. In optical measurements, highly efficient excimer emission was observed under dilute solution conditions. Higher values of intensity ratios of excimer to monomer emissions were detected in the shortest side chains. It is likely that shorter side chains of POSS lead to more efficient intramolecular interaction. Interestingly, we also found that the luminescence changed in response to metal cations in the dilute solutions. From this mechanistic study, we found that metal cations such as Cu2+ can accelerate hydrolysis at the linker moiety. As a result, highly sensitive luminescent sensors were obtained. These data show that POSS can work as a reaction field where chemical reactions are accelerated through the accumulation of reactive species.
Increasing community prevalence of extended-spectrum beta-lactamase-producing Escherichia coli in urine is associated with increasing district-level antibiotic consumption
Authors: Nunes Larissa Hermann de Souza , Ribeiro Victoria Stadler Tasca , Salviato Rafael Buttini , de Andrade Ana Paula , Suss Paula Hansen , Vicenzi Fernando José , Hino Adriano Akira Ferreira , Telles João Paulo , Tuon Felipe Francisco 
Published: June 2024

Abstract
This study aimed to analyze ESBL-producing Escherichia coli prevalence in urine samples collected between 2011–2019 in Curitiba, a large city in Brazil, and relating it to antibiotic consumption and sanitary conditions. This is a longitudinal study correlating prevalence of ESBL-producing E. coli isolates from urine samples with district-level antibiotic consumption and sociodemographic data during 2011–2019. E. coli isolates were tested for antibiotic susceptibility and ESBL by an automated method. Statistical analysis applied linear regressions, pooled ordinary least squares, and fixed effects models for districts or years. The Chow and Hausman tests indicated that the fixed effects model for individual districts fitted best. Chi-square test was used for qualitative variables (statistical significance was set when P &lt; 0.05). Among the 886 535 urine sample cultures, 9.9% of isolates were ESBL-producing E. coli. Their prevalence increased from 4.7% in 2012 to 19.3% in 2019 (P &lt; 0.0001; R2 = 0.922). This progressive increase correlated with age (P = 0.007; R2 = 0.8725) and male gender (P &lt; 0.001) and increased antibiotic consumption (P = 0.0386; R2 = 0.47). The fixed effects model showed that district influences ESBL prevalence and that antibiotic consumption explains 20%–30% of this variation, with an increase of one defined daily dose accounting for an increase of 0.02084 percentage points of ESBL. The increasing prevalence of ESBL-producing E. coli can, to a considerable extent, be explained by increasing antibiotic consumption.
Association of Frailty With Risk of Incident Hospital-Treated Infections in Middle-Aged and Older Adults: A Large-Scale Prospective Cohort Study
Authors: Xu Minzhi , Gong Yanhong , Yin Xiaoxv 
Published: June 2024

Abstract

Background
Although frailty is associated with a range of adverse health outcomes, its association with the risk of hospital-treated infections is uncertain.

Methods
A total of 416 220 participants from the UK Biobank were included in this prospective cohort study. Fried phenotype was adopted to evaluate frailty, which included 5 aspects (gait speed, physical activity, grip strength, exhaustion, and weight). More than 800 infectious diseases were identified based on electronic health records. Cox proportional models were used to estimate the associations.

Results
During a median 12.3 years (interquartile range 11.4–13.2) of follow-up (4 747 345 person-years), there occurred 77 988 (18.7%) hospital-treated infections cases. In the fully adjusted model, compared with participants with nonfrail, the hazard ratios (HRs) (95% confidence intervals [CIs]) of those with prefrail and frail for overall hospital-treated infections were 1.22 (1.20, 1.24) and 1.78 (1.72–1.84), respectively. The attributable risk proportion of prefrail and frail were 18.03% and 43.82%. Similarly, compared to those without frailty, the HRs (95% CIs) of those with frailty for bacterial infections were 1.76 (1.70–1.83), for viral infections were 1.62 (1.44–1.82), and for fungal infections were 1.75 (1.47–2.08). No association was found between frailty and parasitic infections (HR: 1.17; 95% CI: 0.62–2.20).

Conclusions
Frailty was significantly associated with a higher risk of hospital-treated infections, except for parasitic infections. Studies evaluating the effectiveness of implementing frailty assessments are needed to confirm our results.
Racial–Ethnic Gaps in Pandemic-Related Economic Hardship: Age Differences Among Older Adults
Authors: Wiemers Emily E , Lin I-Fen , Wiersma Strauss Anna , Chin Janecca A , Hotz V Joseph , Seltzer Judith A 
Published: June 2024

Abstract

Objectives
Racial–ethnic disparities in experiences of economic hardship during the pandemic are well documented in the population overall and among older adults. Existing research shows that this economic hardship was much less common at older than younger ages. Little is known about the intersection of racial–ethnic and age disparities in pandemic-related hardship in later life. This research report investigated racial–ethnic gaps in economic hardship by age group among older adults.

Methods
Data were from the 2018 and 2020 U.S. Health and Retirement Study (HRS) including the 2020 coronavirus disease 2019 module. We estimated Heckman-corrected linear probability models to examine differences in experiences of pandemic-related economic hardship in the 2020 HRS by race–ethnicity (non-Hispanic White, non-Hispanic Black, U.S.-born Hispanic, foreign-born Hispanic) across age groups (55–64, 65–74, 75+). In the multivariable analysis, we controlled for sociodemographic characteristics, participation in social programs, pre-existing health conditions and behaviors, and economic resources from the 2018 HRS.

Results
Experiences of economic hardship declined with age within each racial–ethnic group. Racial–ethnic gaps in hardship remained at older ages without any controls. However, when all controls were added, racial–ethnic gaps in economic hardship were eliminated for those ages 75+. Individual characteristics prior to the pandemic explained racial–ethnic differences in hardship for the oldest adults (75+) but did not explain gaps for those ages 55–74.

Discussion
Results point to structural factors generating new racial–ethnic gaps in pandemic-related economic hardship among those approaching retirement (ages 55–74) that did not affect the oldest adults (ages 75+).
Digital Skills, STEM Occupation, and Job Automation Risks Among the Older Workers in the United States
Authors: Yamashita Takashi , Narine Donnette , Chidebe Runcie C W , Kramer Jenna W , Karam Rita , Cummins Phyllis A , Smith Thomas J 
Published: June 2024

Abstract

Background and Objectives
Advancing automation technologies are replacing certain occupations such as those involving simple food preparation more than occupations such as those in STEM fields (e.g., engineering and health care). Older workers generally face higher job automation risks in part due to their lower levels of digital skills. A better understanding of the associations between job automation risk, digital skills, and type of occupation (e.g., STEM vs non-STEM) can facilitate preparations for job automation and workforce population aging.

Research Design and Methods
We analyzed a nationally representative sample (N = 1,560) of middle-aged and older U.S. workers aged 50–74 years from the 2012/2014/2017 Program for International Assessment of Adult Competencies (PIAAC) restricted-use file. The estimated job automation risks (i.e., percentage of jobs to be automated in the next decades) were derived from the previous studies. PIAAC digital problem-solving skills proficiency (measured on a scale of 0–500 points) was assessed based on a series of practical digital tasks (e.g., finding a job research website that does not require registration).

Results
Linear regression analysis showed that greater digital skill proficiency (b = −0.04, p &lt; .05) and STEM occupations (b = −17.78, p &lt; .001) each were associated with lower job automation risks, even after adjusting for a series of demographic, socioeconomic, and civic engagement characteristics.

Discussion and Implications
Education and labor policy interventions to promote digital skills among older workers and non-STEM workers may better prepare an aging workforce for the dynamic labor market needs in the United States.
Clutch Size, but Not Egg Volume, Increases with Rainfall in an Arid-Dwelling Bird
Authors: Liebl Andrea L , Steen Andrew J , O'Neill Louis G , Savage James L , Russell Andrew F 
Published: June 2024

Synopsis
Understanding how animals maximize reproductive success in variable environments is important in determining how populations will respond to increasingly extreme weather events predicted in the face of changing climates. Although temperature is generally considered a key factor in reproductive decisions, rainfall is also an important predictor of prey availability in arid environments. Here, we test the impact of weather (i.e., rainfall and temperature) on female reproductive investment in an arid-dwelling bird (i.e., clutch size and egg volume) and tradeoffs between the two. We predicted that female chestnut-crowned babblers (Pomatostomus ruficeps), endemic to the arid region of Australia, would increase clutch size at the expense of egg volume in response to variation in rainfall and temperature. We found that over 14 breeding seasons, clutch size decreased with increasing temperature, but increased following more rain. Egg volume, on the other hand, became larger as temperatures increased and, although not related to the amount of rain, was related to the number of days since the last rainfall. Finally, egg size decreased as clutch size increased, indicating a tradeoff between the two reproductive parameters. Our results suggest that chestnut-crowned babblers breed reactively in response to variable environments. We expect that clutch size variation in response to rain may reflect the impact of rain on arthropod abundance, whereas the effect of temperature may represent an established decline in clutch size observed in other seasonal breeders. As the tradeoff between clutch size and egg volume was modest and clutch sizes were modified to a greater extent than egg volumes in response to rainfall, we suggest selection is more likely to increase offspring number than quality, at least in favorable years. Our results support the idea that reproductive investment is variable in fluctuating environments, which has implications for species living in habitats experiencing more extreme and less predictable weather as the global climate changes.
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression
Authors: Coolen Silvia , Rogowska-van der Molen Magda A , Kwakernaak Ineke , van Pelt Johan A , Postma Jelle L , van Alen Theo , Jansen Robert S , Welte Cornelia U 
Published: June 2024

Abstract
The Southern green shield bug, Nezara viridula, is an invasive piercing and sucking pest insect that feeds on crop plants and poses a threat to global food production. Given that insects are known to live in a close relationship with microorganisms, our study provides insights into the community composition and function of the N. viridula-associated microbiota and its effect on host–plant interactions. We discovered that N. viridula hosts both vertically and horizontally transmitted microbiota throughout different developmental stages and their salivary glands harbor a thriving microbial community that is transmitted to the plant while feeding. The N. viridula microbiota was shown to aid its host with the detoxification of a plant metabolite, namely 3-nitropropionic acid, and repression of host plant defenses. Our results demonstrate that the N. viridula-associated microbiota plays an important role in interactions between insects and plants and could therefore be considered a valuable target for the development of sustainable pest control strategies.
Rumen microbiome-driven insight into bile acid metabolism and host metabolic regulation
Authors: Zhang Boyan , Jiang Xianzhe , Yu Yue , Cui Yimeng , Wang Wei , Luo Hailing , Stergiadis Sokratis , Wang Bing 
Published: June 2024

Abstract
Gut microbes play a crucial role in transforming primary bile acids (BAs) into secondary forms, which influence systemic metabolic processes. The rumen, a distinctive and critical microbial habitat in ruminants, boasts a diverse array of microbial species with multifaceted metabolic capabilities. There remains a gap in our understanding of BA metabolism within this ecosystem. Herein, through the analysis of 9371 metagenome-assembled genomes and 329 cultured organisms from the rumen, we identified two enzymes integral to BA metabolism: 3-dehydro-bile acid delta4,6-reductase (baiN) and the bile acid:Na + symporter family (BASS). Both in vitro and in vivo experiments were employed by introducing exogenous BAs. We revealed a transformation of BAs in rumen and found an enzyme cluster, including L-ribulose-5-phosphate 3-epimerase and dihydroorotate dehydrogenase. This cluster, distinct from the previously known BA-inducible operon responsible for 7α-dehydroxylation, suggests a previously unrecognized pathway potentially converting primary BAs into secondary BAs. Moreover, our in vivo experiments indicated that microbial BA administration in the rumen can modulate amino acid and lipid metabolism, with systemic impacts underscored by core secondary BAs and their metabolites. Our study provides insights into the rumen microbiome’s role in BA metabolism, revealing a complex microbial pathway for BA biotransformation and its subsequent effect on host metabolic pathways, including those for glucose, amino acids, and lipids. This research not only advances our understanding of microbial BA metabolism but also underscores its wider implications for metabolic regulation, offering opportunities for improving animal and potentially human health.
Non-Western Agency in Refugee Humanitarianism: Turkey and ‘Operation Provide Comfort’
Authors: İşleyen Beste 
Published: June 2024

Abstract
The evolution of refugee humanitarianism is commonly studied in terms of critical junctures. One such historical moment is the creation of a ‘safe zone’ for Iraqi Kurdish refugees above the 36th parallel of Northern Iraq through the 1991 United Nations (UN) mission known as ‘Operation Provide Comfort.’ The UN intervention is widely accepted as a critical juncture because it marked the beginning of international humanitarianism's extra-territorial phase. ‘Operation Provide Comfort’ brought a paradigm shift in the management of displaced populations by means of introducing “preventive protection” as a novel approach combining protection with control as the idea is to keep refugees in their own countries and offer them help without the need to cross an international border. The standard narrative underlines Western historical priority by attributing the preventive protection to a single source of ideas and processes stemming from the West. Drawing on postcolonial research, this paper argues for recognizing the agency of the non-West in the formulation and execution of the safe haven concept as a historical milestone. More specifically, it demonstrates the pioneering role that Turkey played through international debates and diplomatic action, which culminated into the new episode of refugee humanitarianism. The findings also invite us to revisit current explanations of the evolution of international humanitarian norms by showing the entanglement of refugee protection on the one hand, and domestic and regional questions of ethnicity and counter-insurgency on the other.