bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating recommendation-based dietary and physical activity strategies for prostate cancer prevention: a target trial emulation in the Health Professionals Follow-up Study
Authors: Guo Fuyu , McGee Emma E , Chiu Yu-Han , Giovannucci Edward , Mucci Lorelei A , Dickerman Barbra A 
Published: July 2024

Abstract
The 2018 World Cancer Research Fund/American Institute for Cancer Research recommends sustained strategies of physical activity and diet for cancer prevention, but evidence for long-term prostate cancer risk is limited. Using observational data from 27 859 men in the Health Professionals Follow-up Study, we emulated a target trial of recommendation-based physical activity and dietary strategies and 26-year risks of prostate cancer, adjusting for risk factors via the parametric g-formula. Compared with no intervention, limiting sugar-sweetened beverages showed a 0.4% (0.0%-0.9%) lower risk of lethal (metastatic or fatal) disease and 0.5% (0.1%-0.9%) lower risk of fatal disease. Restricting consumption of processed foods showed a 0.4% to 0.9% higher risk of all prostate cancer outcomes. Estimated risk differences for clinically significant disease were close to null for strategies involving fruits and nonstarchy vegetables, whole grains and legumes, red meat, and processed meat, as well as under a joint strategy of physical activity and diet. Compared with a “low-adherence” strategy, maintaining recommended physical activity levels showed a 0.4% (0.1%-0.8%) lower risk of lethal and 0.5% (0.2%-0.8%) lower risk of fatal disease. Adhering to specific components of current physical activity and dietary recommendations may help to prevent lethal and fatal prostate cancer over 26 years.
A simple Cox approach to estimating risk ratios without sharing individual-level data in multisite studies
Authors: Shu Di , Zou Guangyong , Hou Laura , Petrone Andrew B , Maro Judith C , Fireman Bruce H , Toh Sengwee , Connolly John G 
Published: July 2024

Abstract
Epidemiologic studies frequently use risk ratios to quantify associations between exposures and binary outcomes. When the data are physically stored at the sites of multiple data partners, it can be challenging to perform individual-level analysis if data cannot be pooled centrally due to privacy constraints. Existing methods either require multiple file transfers between each data partner and an analysis center (eg, distributed regression) or only provide approximate estimation of the risk ratio (eg, meta-analysis). Here we develop a practical method that requires a single transfer of 8 summary-level quantities from each data partner. Our approach leverages an existing risk-set method and software originally developed for Cox regression. Sharing only summary-level information, the proposed method provides risk ratio estimates and 95% CIs identical to those that would be provided—if individual-level data were pooled—by the modified Poisson regression. We justify the method theoretically, confirm its performance using simulated data, and implement it in a distributed analysis of COVID-19 data from the US Food and Drug Administration’s Sentinel System.
This article is part of a Special Collection on Pharmacoepidemiology.
A rapid literature review of the effect of alcohol marketing on people with, or at increased risk of, an alcohol problem
Authors: Murray Rachael L , Leonardi-Bee Jo , Barker Alexander , Brown Olivia , Langley Tessa 
Published: July 2024

Abstract

Aims
To explore the effect or potential effect of alcohol marketing in people with an alcohol use disorder, in recovery from an alcohol use disorder, and hazardous and harmful drinkers.

Methods
Relevant literature was identified by searching Medline (OVID), EMBASE (OVID), and PsycINFO (OVID) and relevant websites. Both quantitative and qualitative studies were eligible for inclusion. A narrative approach was used to synthesize the findings.

Results
The review included 10 studies. Two quantitative and three qualitative studies focused on participants recovering from an alcohol use disorder and five quantitative studies on those with hazardous or harmful consumption levels of alcohol. The effect of alcohol advertising on alcohol use was only assessed in one study, a small experimental study of young adult heavy drinkers, which found no significant association. Studies looking at other outcomes found that people with or at risk of alcohol problems were likely to notice alcohol advertisements and find them appealing, and that advertisements may have an effect on positive alcohol-related emotions and cognitions. Among people in recovery from an alcohol use disorder, findings suggested that there could be an effect on craving, and that alcohol marketing may be perceived to trigger a desire to drink.

Conclusions
Alcohol marketing is likely to have an effect on alcohol consumption in people with, or at increased risk of, an alcohol problem. Studies have also found that alcohol marketing is perceived to act as a trigger by people in recovery from alcohol problems.

Summary
A rapid review explored the effect of alcohol marketing in people with an alcohol use disorder, in recovery from an alcohol use disorder, and hazardous and harmful drinkers. The findings of the 10 included studies suggest that an effect of alcohol marketing in these populations is likely.
Characterizing efficient feature selection for single-cell expression analysis
Authors: Cho Juok , Baik Bukyung , Nguyen Hai C T , Park Daeui , Nam Dougu 
Published: July 2024

Abstract
Unsupervised feature selection is a critical step for efficient and accurate analysis of single-cell RNA-seq data. Previous benchmarks used two different criteria to compare feature selection methods: (i) proportion of ground-truth marker genes included in the selected features and (ii) accuracy of cell clustering using ground-truth cell types. Here, we systematically compare the performance of 11 feature selection methods for both criteria. We first demonstrate the discordance between these criteria and suggest using the latter. We then compare the distribution of selected genes in their means between feature selection methods. We show that lowly expressed genes exhibit seriously high coefficients of variation and are mostly excluded by high-performance methods. In particular, high-deviation- and high-expression-based methods outperform the widely used in Seurat package in clustering cells and data visualization. We further show they also enable a clear separation of the same cell type from different tissues as well as accurate estimation of cell trajectories.
Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet
Authors: Gao Yuan , Ma Bin , Xu Qianshuai , Peng Yuna , Gong Huimin , Guan Aohan , Hua Kexin , Langford Paul R , Jin Hui , Luo Rui 
Published: July 2024

Abstract
Understanding the biological functions and processes of genes, particularly those not yet characterized, is crucial for advancing molecular biology and identifying therapeutic targets. The hypothesis guiding this study is that the 3D proximity of genes correlates with their functional interactions and relevance in prokaryotes. We introduced 3D-GeneNet, an innovative software tool that utilizes high-throughput sequencing data from chromosome conformation capture techniques and integrates topological metrics to construct gene association networks. Through a series of comparative analyses focused on spatial versus linear distances, we explored various dimensions such as topological structure, functional enrichment levels, distribution patterns of linear distances among gene pairs, and the area under the receiver operating characteristic curve by utilizing model organism Escherichia coli K-12. Furthermore, 3D-GeneNet was shown to maintain good accuracy compared to multiple algorithms (neighbourhood, co-occurrence, coexpression, and fusion) across multiple bacteria, including E. coli, Brucella abortus, and Vibrio cholerae. In addition, the accuracy of 3D-GeneNet’s prediction of long-distance gene interactions was identified by bacterial two-hybrid assays on E. coli K-12 MG1655, where 3D-GeneNet not only increased the accuracy of linear genomic distance tripled but also achieved 60% accuracy by running alone. Finally, it can be concluded that the applicability of 3D-GeneNet will extend to various bacterial forms, including Gram-negative, Gram-positive, single-, and multi-chromosomal bacteria through Hi-C sequencing and analysis. Such findings highlight the broad applicability and significant promise of this method in the realm of gene association network. 3D-GeneNet is freely accessible at https://github.com/gaoyuanccc/3D-GeneNet.
GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes
Authors: Pisarenco Vadim A , Vizueta Joel , Rozas Julio 
Published: July 2024

Abstract

Motivation
Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.

Results
To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.

Availability and implementation
GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon
scMaSigPro: differential expression analysis along single-cell trajectories
Authors: Srivastava Priyansh , Benegas Coll Marta , Götz Stefan , Nueda María José , Conesa Ana 
Published: July 2024

Abstract

Motivation
Understanding the dynamics of gene expression across different cellular states is crucial for discerning the mechanisms underneath cellular differentiation. Genes that exhibit variation in mean expression as a function of Pseudotime and between branching trajectories are expected to govern cell fate decisions. We introduce scMaSigPro, a method for the identification of differential gene expression patterns along Pseudotime and branching paths simultaneously.

Results
We assessed the performance of scMaSigPro using synthetic and public datasets. Our evaluation shows that scMaSigPro outperforms existing methods in controlling the False Positive Rate and is computationally efficient.

Availability and implementation
scMaSigPro is available as a free R package (version 4.0 or higher) under the GPL(≥2) license on GitHub at ‘github.com/BioBam/scMaSigPro’ and archived with version 0.03 on Zenodo at ‘zenodo.org/records/12568922’.
Testing independence for sparse longitudinal data
Authors: Zhu Changbo , Yao Junwen , Wang Jane-Ling 
Published: July 2024

Abstract
With the advance of science and technology, more and more data are collected in the form of functions. A fundamental question for a pair of random functions is to test whether they are independent. This problem becomes quite challenging when the random trajectories are sampled irregularly and sparsely for each subject. In other words, each random function is only sampled at a few time-points, and these time-points vary with subjects. Furthermore, the observed data may contain noise. To the best of our knowledge, there exists no consistent test in the literature to test the independence of sparsely observed functional data. We show in this work that testing pointwise independence simultaneously is feasible. The test statistics are constructed by integrating pointwise distance covariances (Székely et al., 2007) and are shown to converge, at a certain rate, to their corresponding population counterparts, which characterize the simultaneous pointwise independence of two random functions. The performance of the proposed methods is further verified by Monte Carlo simulations and analysis of real data.
Party Politics in Austria: From Proporz to Populism?
Authors: Roesel Felix 
Published: July 2024

Abstract
Party politics in Austria has two distinctive features: institutionalized power sharing between the two main parties, known as Proporz, and a longstanding tradition of far-right populism. I examine whether these two phenomena are connected: Does reduced political competition correlate with vote shares for the far right? The results do not support the hypothesis that populist parties are stronger in places with reduced political competition and with Proporz institutions. Instead, the results show that Austrian populism has very deep historical roots. Historical party preferences in the 1930s explain a substantial part of the variation in far-right populist vote shares across Austrian regions today. Populism may also have economic consequences. Descriptive evidence shows that economic growth was 2 percentage points lower in Austria when far-right populists were in the national government, whereas no partisan differences can be found for the two main parties.
In vitro accuracy of ultra-low dose cone-beam CT for detection of proximal caries
Authors: Taeby Aria , Seyyedi Seyyed Amir , Mostafavi Maryam 
Published: July 2024

Abstract

Objectives
This study aimed to assess the accuracy of ultra-low dose (ULD) cone-beam CT (CBCT) for detection of proximal caries.

Methods
This in vitro study evaluated 104 molar and premolar teeth. The teeth were mounted in dry skulls and underwent CBCT with 4 protocols of high-resolution (HR), normal (NORM), ULD-HR, and ULD-NORM; 78 CBCT images were scored by 3 observers for the presence and penetration depth of caries twice with a 2-week interval using a 5-point Likert scale. The teeth were then sectioned and observed under a stereomicroscope (gold standard). The 4 protocols were compared with each other and with the gold standard. The receiver operating characteristic curve was drawn, and the area under the curve (AUC) was calculated and compared by the Chi-square test (alpha = .05).

Results
The interobserver agreement ranged from 0.5233 to 0.6034 for ULD-NORM, 0.5380 to 0.6279 for NORM, 0.5856 to 0.6300 for ULD-HR, and 0.6614 to 0.7707 for HR images. The intra-observer agreement ranged from 0.6027 to 0.8812 for ULD-HR, 0.7083 to 0.7556 for HR, 0.6076 to 0.9452 for ULD-NORM, and 0.7012 to 0.9221 for NORM images. Comparison of AUC revealed no significant difference between NORM and ULD-NORM (P &gt; .05), or HR and ULD-HR (P &gt; .05). The highest AUC belonged to HR (0.8529) and the lowest to NORM (0.7774).

Conclusions
Considering the significant reduction in radiation dose in ULD CBCT and its acceptable diagnostic accuracy for detection of proximal caries, this protocol may be used for detection of proximal carious lesions and assessment of their depth.
Lumican promotes calcific aortic valve disease through H3 histone lactylation
Authors: Huang Yuming , Wang Chunli , Zhou Tingwen , Xie Fei , Liu Zongtao , Xu Haiying , Liu Ming , Wang Shunshun , Li Lanqing , Chi Qingjia , Shi Jiawei , Dong Nianguo , Xu Kang 
Published: July 2024

Abstract

Background and Aims
Valve interstitial cells (VICs) undergo a transition to intermediate state cells before ultimately transforming into the osteogenic cell population, which is a pivotal cellular process in calcific aortic valve disease (CAVD). Herein, this study successfully delineated the stages of VIC osteogenic transformation and elucidated a novel key regulatory role of lumican (LUM) in this process.

Methods
Single-cell RNA-sequencing (scRNA-seq) from nine human aortic valves was used to characterize the pathological switch process and identify key regulatory factors. The in vitro, ex vivo, in vivo, and double knockout mice were constructed to further unravel the calcification-promoting effect of LUM. Moreover, the multi-omic approaches were employed to analyse the molecular mechanism of LUM in CAVD.

Results
ScRNA-seq successfully delineated the process of VIC pathological transformation and highlighted the significance of LUM as a novel molecule in this process. The pro-calcification role of LUM is confirmed on the in vitro, ex vivo, in vivo level, and ApoE−/−//LUM−/− double knockout mice. The LUM induces osteogenesis in VICs via activation of inflammatory pathways and augmentation of cellular glycolysis, resulting in the accumulation of lactate. Subsequent investigation has unveiled a novel LUM driving histone modification, lactylation, which plays a role in facilitating valve calcification. More importantly, this study has identified two specific sites of histone lactylation, namely, H3K14la and H3K9la, which have been found to facilitate the process of calcification. The confirmation of these modification sites’ association with the expression of calcific genes Runx2 and BMP2 has been achieved through ChIP-PCR analysis.

Conclusions
The study presents novel findings, being the first to establish the involvement of lumican in mediating H3 histone lactylation, thus facilitating the development of aortic valve calcification. Consequently, lumican would be a promising therapeutic target for intervention in the treatment of CAVD.
Who cares? Elucidating parental care evolution in extant birds
Authors: Lavaniegos-Puebla Pablo , Rincón-Rubio Verónica A , Gonzalez-Voyer Alejandro 
Published: July 2024

Abstract
Extant birds stand out among vertebrates in the diversity of parental care types they present, spanning absence of care to uniparental care by either sex, biparental care, or even cooperative care. Despite years of research, key questions remain regarding parental care evolution in birds. Firstly, the parental care type in the most recent ancestor of extant birds is a matter of controversy, with proposed ancestral states including no care, uniparental male or female care, and biparental care. Another unsolved question is the direction, order, and frequency of transitions between parental care types. We address these key questions using a database of 5,438 bird species (~50% of extant diversity) and modern phylogenetic comparative methods controlling simultaneously for model and phylogenetic uncertainty as well as potential confounding effects of state-dependent diversification. Our results indicate that the most likely ancestral state for extant birds is male-only care, with a posterior probability of 0.8. Transition rates across parental care types were generally low and heterogeneous; loss of parental care virtually never occurs and transitions away from female-only or cooperative care most often lead to biparental care. Given the low transition rates, future research should analyze the factors favoring the maintenance of care types.
Total RNA analysis of the active microbiome on moving bed biofilm reactor carriers under incrementally increasing micropollutant concentrations
Authors: Martin Joseph Donald , Tisler Selina , Scheel Maria , Svendsen Sif , Anwar Muhammad Zohaib , Zervas Athanasios , Ekelund Flemming , Bester Kai , Hansen Lars Hestbjerg , Jacobsen Carsten Suhr , Ellegaard-Jensen Lea 
Published: July 2024

AbstractMicropollutants are increasingly prevalent in the aquatic environment. A major part of these originates from wastewater treatment plants since traditional treatment technologies do not remove micropollutants sufficiently. Moving bed biofilm reactors (MBBRs), however, have been shown to aid in micropollutant removal when applied to conventional wastewater treatment as a polishing step. Here, we used Total RNA sequencing to investigate both the active microbial community and functional dynamics of MBBR biofilms when these were exposed to increasing micropollutant concentrations over time. Concurrently, we conducted batch culture experiments using biofilm carriers from the MBBRs to assess micropollutant degradation potential. Our study showed that biofilm eukaryotes, in particular protozoa, were negatively influenced by micropollutant exposure, in contrast to prokaryotes that increased in relative abundance. Further, we found several functional genes that were differentially expressed between the MBBR with added micropollutants and the control. These include genes involved in aromatic and xenobiotic compound degradation. Moreover, the biofilm carrier batch experiment showed vastly different alterations in benzotriazole and diclofenac degradation following the increased micropollutant concentrations in the MBBR. Ultimately, this study provides essential insights into the microbial community and functional dynamics of MBBRs and how an increased load of micropollutants influences these dynamics.
Global Change in a Material World
Authors: Burnett Nicholas P , Moore Talia Y 
Published: July 2024

Synopsis
The biological structures that fill the environment around us are derived from materials produced by organisms. These biological materials are key to the mechanical function of organisms. The pathways and growth processes that produce biological materials can influence the mechanical properties of the materials, which can in turn shape the higher level function of the system into which the materials are incorporated. Characterizing a biological system requires thorough knowledge of the underlying materials, including their mechanical function, diversity, evolution, and sensitivity to the environment. Anthropogenic activity is driving rapid and widespread changes to the natural environment and global climate, which are influencing organismal growth and physiology in myriad ways. Here, we briefly introduce a collection of articles that focus on the intersection of anthropogenic activity and the mechanical function of biological materials, as part of the “Global Change in a Material World” bundle for Integrative and Comparative Biology. In addition, we provide an analysis of the current scientific literature in this field, highlighting an urgent need to better understand how changes to our world, driven by human activity, are influencing the fundamental architecture and mechanical performance of organisms across the globe.