bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decomposing sibling correlations: a new measure of group-specific intergenerational persistence in socioeconomic outcomes
Authors: Karlson Kristian Bernt , In Jung 
Published: October 2024

Abstract
We introduce a novel approach for decomposing sibling correlations in socioeconomic attainment into group-specific components. These groups are defined at the family level, based on factors such as parental income, marital status, race, or the gender composition of siblings. Unlike existing studies that compare sibling correlations across different groups, our method accounts for differences in average outcomes between groups in the overall outcome distribution. This approach results in a group-specific measure of persistence in the overall outcome distribution, contrasting with the ‘within-group’ measure commonly used in the literature. Additionally, we propose a straightforward ‘counterfactual’ framework to identify which groups have a greater impact on trends or country differences in sibling correlations. We present three examples that demonstrate the utility of our method.
Bioinformatic Resources for Exploring Human–virus Protein–protein Interactions Based on Binding Modes
Authors: Chen Huimin , Liu Jiaxin , Tang Gege , Hao Gefei , Yang Guangfu 
Published: October 2024

Abstract
Historically, there have been many outbreaks of viral diseases that have continued to claim millions of lives. Research on human–virus protein–protein interactions (PPIs) is vital to understanding the principles of human–virus relationships, providing an essential foundation for developing virus control strategies to combat diseases. The rapidly accumulating data on human–virus PPIs offer unprecedented opportunities for bioinformatics research around human–virus PPIs. However, available detailed analyses and summaries to help use these resources systematically and efficiently are lacking. Here, we comprehensively review the bioinformatic resources used in human–virus PPI research, and discuss and compare their functions, performance, and limitations. This review aims to provide researchers with a bioinformatic toolbox that will hopefully better facilitate the exploration of human–virus PPIs based on binding modes.
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins
Authors: Zeng Yu-Hao , Yin Zhen-Ning , Luo Hao , Gao Feng 
Published: October 2024

Abstract
DNA replication is a complex and crucial biological process in eukaryotes. To facilitate the study of eukaryotic replication events, we present a database of eukaryotic DNA replication origins (DeOri), which collects genome-wide data on eukaryotic DNA replication origins currently available. With the rapid development of high-throughput experimental technology in recent years, the number of datasets in the new release of DeOri 10.0 increased from 10 to 151 and the number of sequences increased from 16,145 to 9,742,396. Besides nucleotide sequences and browser extensible data (BED) files, corresponding annotation files, such as coding sequences (CDSs), mRNAs, and other biological elements within replication origins, are also provided. The experimental techniques used for each dataset, as well as related statistical data, are also presented on web page. Differences in experimental methods, cell lines, and sequencing technologies have resulted in distinct replication origins, making it challenging to differentiate between cell-specific and non-specific replication origins. Based on multiple replication origin datasets at the species level, we scored and screened replication origins in Homo sapiens, Gallus gallus, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans. The screened regions with high scores were considered as species-conservative origins, which are integrated and presented as reference replication origins (rORIs). Additionally, we analyzed the distribution of relevant genomic elements associated with replication origins at the genome level, such as CpG island (CGI), transcription start site (TSS), and G-quadruplex (G4). These analysis results can be browsed and downloaded as needed at http://tubic.tju.edu.cn/deori/.
The political economy of national health insurance schemes: evidence from Zambia
Authors: Osei Afriyie Doris , Titi-Ofei Regina , Masiye Felix , Chansa Collins , Fink Günther 
Published: October 2024

Abstract
Governments in low and middle-income countries (LMICs) are increasingly considering the introduction of national health insurance scheme (NHIS) as a strategy to achieve universal health coverage (UHC) targets. The literature has widely documented the technical challenges associated with implementing UHC policies in LMICs but much less is known about the political process necessary to pass UHC legislation. In this article, we document the political economy issues surrounding the establishment of the Zambia NHIS in 2018. We adapted a political economy framework incorporating, semi-structured interviews with diverse stakeholders and document analysis of policies, operational reports and legislatures from 1991 and 2018. Our findings show the 26-year journey towards the establishment of the NHIS in Zambia involved a long sequence of policy dialogue, technical review and stakeholder engagement. Our interviews with key stakeholders suggest that the act was eventually passed due to strong political will and dominant leadership of the Ministry of Health. Passing the law required trade-offs between choices influenced by stakeholder pressures and recommendations from research and actuarial studies. Another equally critical factor was the high public support and legacies of past policies, such as the removal of user fees that had created quality gaps and inequities in the health system. Furthermore, global ideas about UHC and initiatives implemented by other countries also generated support for Zambia’s NHIS. Overall, this study highlights the complex set of political economy factors that need to align in order for governments to be able to adopt health insurance in low-income settings. We show that political leadership and commitment to getting reforms passed is crucial. We also highlight how certain narratives about countries in the global health sphere can shape policies in other countries.
Understanding freshwater to marine transitional scale growth in Atlantic salmon (Salmo salar)
Authors: Ellingson Brandon , Haas-Castro Ruth E , Sigourney Douglas , Kocik John F , Sheehan Timothy F 
Published: October 2024

Abstract
The first marine circulus is the scale feature associated with marine entry and has been used to support research evaluating the relationships between size, growth, and survival for Atlantic salmon. Ambiguity in growth rates and circulus deposition during the transition from freshwater to the marine environment leads to difficulty in the correct identification of the first marine circulus. In this study, scale growth occurring after the last freshwater annulus (plus-growth) was characterized for Atlantic salmon smolts migrating out of the Narraguagus River in Maine. Plus-growth was present in over 95% of scales from smolts leaving the river and represented on average 12.2% of total freshwater growth. These findings suggest plus-growth presents a significant source of error in growth analyses, if ignored, and the characterization of this scale feature helps to inform accurate identification of marine entry for future studies. Run day was a driver of plus-growth, suggesting extended freshwater residency provides opportunity for growth prior to smolt emigration. The negative association between fork length and plus-growth suggests smaller smolts that delay migration are demonstrating compensatory growth. Cumulative air temperature was positively associated with plus-growth, suggesting warming spring temperatures driven by climate change may influence size at marine entry for smolts.
Staggered interventions with no control groups
Authors: Batomen Brice , Benmarhnia Tarik 
Published: October 2024

Abstract
The limitations of the two-way fixed effects for the impact evaluation of interventions that occur at different times for each group have meant that ‘staggered interventions’ have been highlighted in recent years in the econometric literature and, more recently, in epidemiology. Although many alternative strategies (such as staggered difference-in-differences) have been proposed, the focus has predominantly been on scenarios in which one or more control groups are available. However, control groups are often unavailable, due to limitations in the available data or because all units eventually receive the intervention. In this context, interrupted time series (ITS) designs can constitute an appropriate alternative. The extent to which common model specifications for ITS analyses are limited in the case of staggered interventions remains an underexplored area in the methodological literature. In this work, we aim to demonstrate that standard ITS model specifications typically yield biased results for staggered interventions and we propose alternative model specifications that were inspired by recent developments in the difference-in-differences literature to propose adapted analytical strategies.
Polynomial Analogs of Theta Functions and Rational Solutions of the KP Equation
Authors: Agostini Daniele , Çelik Türkü Özlüm , Little John B 
Published: October 2024

Abstract
In this paper we classify the singular curves whose theta divisors in their generalized Jacobians are algebraic, meaning that they are cut out by polynomial analogs of theta functions. We also determine the degree of an algebraic theta divisor in terms of the singularities of the curve. Furthermore, we show a precise relation between such algebraic theta functions and the corresponding tau functions for the KP hierarchy.
Polygenic risk scores stratify breast cancer risk among women with benign breast disease
Authors: Sherman Mark E , Winham Stacey J , Vierkant Robert A , McCauley Bryan M , Scott Christopher G , Schrup Sarah , Gaudet Mia M , Troester Melissa A , Pruthi Sandhya , Radisky Derek C , Degnim Amy C , Couch Fergus J , Bolla Manjeet K , Wang Qin , Dennis Joe , Michailidou Kyriaki , Guenel Pascal , Truong Therese , Chang-Claude Jenny , Obi Nadia , Aronson Kristan J , Murphy Rachel , Garcia-Closas Montserrat , Chanock Stephen , Ahearn Thomas , Yang Xiaohong , Dunning Alison M , Mavaddat Nasim , Pharoah Paul D P , Easton Douglas F , Vachon Celine M 
Published: October 2024

Abstract

Background
Most breast biopsies are diagnosed as benign breast disease, with 1.5- to 4-fold increased breast cancer risk. Apart from pathologic diagnoses of atypical hyperplasia, few factors aid in breast cancer risk assessment of these patients. We assessed whether a 313–single nucleotide variation (formerly single-nucleotide polymorphism) polygenic risk score stratifies risk of benign breast disease patients.

Methods
We pooled data from 5 Breast Cancer Association Consortium case-control studies (mean age = 59.9 years), including 6706 participants with breast cancer and 8488 participants without breast cancer. Using logistic regression, we estimated breast cancer risk associations by self-reported benign breast disease history and strata of polygenic risk score, with median polygenic risk score category among women without benign breast disease as the referent. We assessed interactions and mediation of benign breast disease and polygenic risk score with breast cancer risk.

Results
Benign breast disease history was associated with increased breast cancer risk (odds ratio [OR] = 1.48, 95% confidence interval [CI] = 1.37 to 1.60; P &lt; .001). Polygenic risk score increased breast cancer risk, irrespective of benign breast disease history (Pinteraction = .48), with minimal evidence of mediation of either factor by the other. Women with benign breast disease and polygenic risk score in the highest tertile had more than twofold increased odds of breast cancer (OR = 2.73, 95% CI = 2.41 to 3.09), and those with benign breast disease and polygenic risk score in the lowest tertile experienced reduced breast cancer risk (OR = 0.79, 95% CI = 0.70 to 0.91) compared with the referent group. Women with benign breast disease and polygenic risk score in the highest decile had a 3.7-fold increase (95% CI = 3.00 to 4.61) compared with those with median polygenic risk score without benign breast disease.

Conclusion
Breast cancer risks are elevated among women with benign breast disease and increase progressively with polygenic risk score, suggesting that optimal combinations of these factors may improve risk stratification.
Pyrazolone-nicotinic acid derivative (4Z)-4-(2-hydroxybenzylidine)-5-methyl-2-(pyridine-3-ylcarbonyl)-2, 4-dihydro-3H-pyrazole-3-one (IIc) as multitarget inhibitor of neurodegeneration and behavioural impairment in Dementia
Authors: Kanwal Madiha , Sarwar Sadia , Nadeem Humaira , Alghamdi Suad A , Alamro Abir Abdullah , Malik Sumra , Maqsood Saima , Alghamdi Amani A , Tariq Muhammad Junaid , Malik Imran , Khan Arif Ullah , Muskan Aleena 
Published: October 2024

Abstract

Objective
The study was aimed at the synthesis and pharmacological investigation of (4Z)-4-(2-hydroxybenzylidine)-5-methyl-2-(pyridine-3-ylcarbonyl)-2, 4-dihydro-3H-pyrazole-3-one (IIc) in mice model of scopolamine-induced neurodegeneration and cognition impairment.

Methods
The behavioural studies included Y-Maze Test, Water Morris Test, and Novel Object Recognition Test in Albino mice (20–25 g). Scopalamine was used as an inducing agent. The acetylcholinesterase (AChE) inhibitory assay was used to assess the role of the test compounds in vitro. The Crystal Violet Staining (Nissl staining) was used to assess the neuroprotective and antiapoptotic effect through quantifying the number of neurons and viability. The expression of the anti-inflammatory enzyme cyclooxygenase-2 (COX-2), cytokine tumour necrotic factor (TNF-α), key transcription factor producing pro-inflammatory signals nuclear factor kappa B (P-NFkB), and apoptosis marker p-JNK was validated through enzyme-linked immunosorbent assay (ELISA) and immunohistochemical (IHC) analysis. The tested compound reverted cognitive and behavioural impairment through inhibiting scopolamine-induced inflammation and oxidative stress.

Key findings
We found that the compound IIc improved the short-term memory and learning behaviour of the experimental animals. Further investigation into molecular mechanisms showed that this effect was the manifestation of immunomodulatory, antioxidant, and consequently, of downsizing of inflammatory cytokines. These results were further validated through docking analysis.

Conclusion
Finally, we conclude that the pyrazolone-nicotinic acid derivative IIc reversed the scopolamine-induced cognitive and behavioural deficits, attributed to acetylcholinesterase inhibition, neuronal recovery, antioxidant potential, and through downregulating the neuroinflammatory mediators p-NF-kB, cytokine TNF-α, and anti-inflammatory enzyme COX-2.
Successful surgical treatment of a right atrial myxoma with hypothermic circulatory arrest and venous cannulation in pulmonary artery
Authors: Miki Takao , Ohki Satoshi , Yamaguchi Ryo , Nagasawa Ayako , Okonogi Shuichi , Yasuhara Kiyomitsu , Obayashi Tamiyuki 
Published: October 2024

Abstract
Myxomas are the most common type of benign cardiac tumors, and the right atrium is the second most common location among them, with an incidence ranging from 8.6% to 20% of all cardiac myxomas. Herein, we described a rare case of right atrial myxoma originating from the inferior vena cava orifice. In this case, main pulmonary artery cannulation and moderate hypothermic circulatory arrest were helpful to obtain a clear and simple view of the operative field without blood, which led to complete resection of the tumor with safety and better outcomes with no future recurrence.
Cybersecurity risks of automated (and autonomous) offshore oil and gas units—the IMO cybersecurity rules framework
Authors: Jao Juei-Cheng , Chuah Jason C T 
Published: October 2024

Abstract
Automated and/or autonomous offshore platforms or units are becoming more important in the energy sector, whether they are being used for oil and gas extraction or for carbon storage purposes. Automation means that harsh working conditions and risks of personal injury to crew could be cut to virtually zero. Automation also provides significant cost savings and helps make less attractive oil and gas fields more economically viable to exploit. However, automation does come with its own set of challenges—the notable one being the cybersecurity threat. Any regulation or international standard dealing with the cybersecurity risk which is relevant to automated offshore units is usually framed within those rules that apply to ships. This article examines to what extent that regulatory approach, especially that of the International Maritime Organisation’s (IMO) regime, could and should apply to automated or autonomous offshore platforms. It argues that whilst, for now, the IMO cybersecurity guidelines are relevant, a more targeted regulatory approach is needed.
Intermittent Fasting Ameliorates Age-Induced Morphological Changes in Aged Albino Rat Kidney via Autophagy Activation and Reduction of Apoptosis and Inflammation
Authors: Rifaai Rehab Ahmed , El-Tahawy Nashwa Fathy Gamal , Abozaid Samah Mohammed Mahmoud , Abdelwahab Alzahraa 
Published: October 2024

Abstract
Aging is a biological process with gradual decrease of cell function. Kidneys are one of the organs with higher susceptibility to the development of age-dependent tissue damage. Intermittent fasting has several beneficial effects on age-related degenerative changes. The aim of this study was to investigate the possible beneficial effect of intermittent fasting in delaying age-related renal changes and the possible mechanisms of this effect. Thirty male albino rats were classified into three groups: control, adult rats aged 3 months; aged group, 15-month-old rats and maintained until the age of 18 months; and intermittent fasting-aged groups, 15-month-old rats maintained on intermittent fasting for 3 months. Kidneys were processed for histological and immunohistochemical study. Aging resulted in a significant reduction in renal function and significant several degenerative changes in renal corpuscles and tubules which showed abnormal histological structure with increased collagen deposition. Aging caused significant reduction in the expression of autophagic marker light chain 3 with increased expression of active caspase-3 and inducible nitric oxide synthase. Intermittent fasting significantly improved these age-related renal changes. Intermittent fasting effectively prevents age-related renal changes through the reduction of age-related oxidative stress, inflammation, apoptosis, and activation of autophagy.
Cytological Effects of Cadmium Poisoning and the Protective Effect of Quercetin: A Mechanism Exploration based on the Testicular Lamina Propria
Authors: Wang Dian , Xiang Yi , Zhu Zhaoxuan , Liu Jiyue , Wang Yisheng , Xu Zeyu , Chen Si , Dai Chunyuan , Feng Jiasen , Chen Jie , Ma Qianhui , Yang Ping 
Published: October 2024

Abstract
This comprehensive study delved into the detrimental effects of cadmium (Cd), a toxic heavy metal, on the testicular lamina propria (LP), a key player in spermatogenesis, and the maintenance of testicular stem cell niches. Utilizing transmission electron microscopy, immunohistochemistry, and double-labeling immunofluorescence, the research characterized the structural and cellular components of mouse testicular LP under Cd exposure and investigated the protective effects of quercetin. The findings illustrated that Cd exposure results in significant morphological and cellular modifications within the LP, including the apoptosis of peritubular myoid cells, an upsurge in CD34+ stromal cells displaying anti-apoptotic behaviors, and an excessive production of collagen Type I fibers and extracellular matrix. Remarkably, quercetin effectively counteracted these adverse changes by reversing apoptosis, reducing the proliferation of CD34+ stromal cells, and addressing fibrosis markers, thereby mitigating the cellular damage induced by Cd. This study not only highlighted the critical impact of apoptosis and fibrosis in Cd-related testicular damage but also elucidated the protective mechanism of quercetin, laying the groundwork for future clinical applications in addressing testicular damage from heavy metal poisoning through cellular therapeutics and pharmacological interventions.
Machine Learning Reveals the Diversity of Human 3D Chromatin Contact Patterns
Authors: Gilbertson Erin N , Brand Colin M , McArthur Evonne , Rinker David C , Kuang Shuzhen , Pollard Katherine S , Capra John A 
Published: October 2024

Abstract
Understanding variation in chromatin contact patterns across diverse humans is critical for interpreting noncoding variants and their effects on gene expression and phenotypes. However, experimental determination of chromatin contact patterns across large samples is prohibitively expensive. To overcome this challenge, we develop and validate a machine learning method to quantify the variation in 3D chromatin contacts at 2 kilobase resolution from genome sequence alone. We apply this approach to thousands of human genomes from the 1000 Genomes Project and the inferred hominin ancestral genome. While patterns of 3D contact divergence genome wide are qualitatively similar to patterns of sequence divergence, we find substantial differences in 3D divergence and sequence divergence in local 1 megabase genomic windows. In particular, we identify 392 windows with significantly greater 3D divergence than expected from sequence. Moreover, for 31% of genomic windows, a single individual has a rare divergent 3D contact map pattern. Using in silico mutagenesis, we find that most single nucleotide sequence changes do not result in changes to 3D chromatin contacts. However, in windows with substantial 3D divergence just one or a few variants can lead to divergent 3D chromatin contacts without the individuals carrying those variants having high sequence divergence. In summary, inferring 3D chromatin contact maps across human populations reveals variable contact patterns. We anticipate that these genetically diverse maps of 3D chromatin contact will provide a reference for future work on the function and evolution of 3D chromatin contact variation across human populations.