bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolomic profiling reveals decreased serum cysteine levels during gestational diabetes mellitus progression
Authors: Lai Mengyu , Li Jiaomeng , Yang Jiaying , Zhang Qingli , Gong Yujia , Ma Yuhang , Fang Fang , Li Na , Zhai Yingxiang , Shen Tingting , Peng Yongde , Liu Jia , Wang Yufan 
Published: February 2024

Abstract
Gestational diabetes mellitus (GDM) is a pregnancy-related metabolic disorder associated with short-term and long-term adverse health outcomes, but its pathogenesis has not been clearly elucidated. Investigations of the dynamic changes in metabolomic markers in different trimesters may reveal the underlying pathophysiology of GDM progression. Therefore, in the present study, we analysed the metabolic profiles of 75 women with GDM and 75 women with normal glucose tolerance throughout the three trimesters. We found that the variation trends of 38 metabolites were significantly changed during GDM development. Specifically, longitudinal analyses revealed that cysteine (Cys) levels significantly decreased over the course of GDM progression. Further study showed that Cys alleviated GDM in female mice at gestational day 14.5, possibly by inhibiting phosphoenolpyruvate carboxykinase to suppress hepatic gluconeogenesis. Taken together, these findings suggest that the Cys metabolism pathway might play a crucial role in GDM and Cys supplementation represents a potential new treatment strategy for GDM patients.
Unfreedom or Mere Inability? The Case of Biomedical Enhancement
Authors: Lee Ji Young 
Published: February 2024

Abstract
Mere inability, which refers to what persons are naturally unable to do, is traditionally thought to be distinct from unfreedom, which is a social type of constraint. The advent of biomedical enhancement, however, challenges the idea that there is a clear division between mere inability and unfreedom. This is because bioenhancement makes it possible for some people’s mere inabilities to become matters of unfreedom. In this paper, I discuss several ways that this might occur: first, bioenhancement can exacerbate social pressures to enhance one’s abilities; second, people may face discrimination for not enhancing; third, the new abilities made possible due to bioenhancement may be accompanied by new inabilities for the enhanced and unenhanced; and finally, shifting values around abilities and inabilities due to bioenhancement may reinforce a pre-existing ableism about human abilities. As such, we must give careful consideration to these potential unfreedom-generating outcomes when it comes to our moral evaluations of bioenhancement.
Population-level incidence of human papillomavirus–positive oropharyngeal, cervical, and anal cancers, by smoking status
Authors: Gopalani Sameer V , Saraiya Mona , Huang Bin , Tucker Thomas C , Mix Jacqueline M , Chaturvedi Anil K 
Published: February 2024

Abstract
We estimated the population-level incidence of human papillomavirus (HPV)–positive oropharyngeal, cervical, and anal cancers by smoking status. We combined HPV DNA genotyping data from the Centers for Disease Control and Prevention’s Cancer Registry Sentinel Surveillance System with data from the Kentucky Cancer Registry and Behavioral Risk Factor Surveillance System across smoking status. During 2004-2005 and 2014-2015 in Kentucky, most cases of oropharyngeal (63.3%), anal (59.7%), and cervical (54.9%) cancer were among individuals who ever smoked. The population-level incidence rate was higher among individuals who ever smoked than among those who never smoked for HPV-positive oropharyngeal (7.8 vs 2.1; adjusted incidence rate ratio = 2.6), cervical (13.7 vs 6.8; adjusted incidence rate ratio = 2.0), and anal (3.9 vs 1.6; adjusted incidence rate ratio = 2.5) cancers. These findings indicate that smoking is associated with increased risk of HPV-positive oropharyngeal, cervical, and anal cancers, and the population-level burden of these cancers is higher among individuals who ever smoked.
CFD simulation analysis of air curtain applications in vulcanization machines
Authors: Hsieh Kun-Liang , Huang Pin-Quan , Lee Shi-Min , Lee Po-Cheng , Kuan Yean-Der 
Published: February 2024

Abstract
This study simulates the vulcanization gas generated during the processing of the vulcanizing machine. During the simulation process, the influence of different angles and flow rates of the gas curtain on its flow field is simulated. Since the rubber has to go through the vulcanization process of the vulcanizer during the manufacturing process, the original liquid rubber is turned into a viscoelastic rubber solid. During the process, toxic and high-temperature vulcanization gas will be generated due to high-temperature hot pressing. If a large amount of this gas is inhaled, it will cause harm to the human body. Therefore, this study uses the CFD software Flow Vision to simulate the opening of the vulcanizing machine, and observes the flow field with different air curtains to find the most suitable air curtain wind speed and angle. Then, make a simple model for actual experiments, using CO2 instead of sulfide gas and installing a CO2 sensor at the nose of the mannequin, using the sensor to observe whether there is excessive CO2 diffused to the mannequin to judge the air curtain. Whether the gas is successfully prevented from spreading to the position where the personnel is located, to facilitate the observation of the gas diffusion, a smoke machine and a ray generator are added so that the gas diffusion status can be observed in real-time. In the end, finding the 9 m/s flow rate and a 90° air curtain angle positioned near the machine can greatly reduce the inhalation of excessive sulfide gas by machine operators and reduce the potential harm to the human body during work.
Symmetry estimating R × C vote transfer matrices from aggregate data
Authors: Pavía Jose M , Romero Rafael 
Published: February 2024

Abstract
Ecological inference methods are devised to estimate unknown inner-cells of 2-way contingency tables by inferring conditional distribution probabilities. This outlines one of the more long-standing social science problems, chiefly frequent in political science and sociology. To solve the problem, ecological inference algorithms consider an asymmetric relationship, with a main characteristic (e.g. race or social class) mapped to rows impacting on a dependent variable, usually the vote, mapped to columns. The problem arises because different solutions are reached depending on how variables are assigned to rows and columns. The models are asymmetric. In this paper, we propose 2 new sets of ecological inference algorithms and explore if accuracy could be improved by handling the problem in a symmetric way. We assess the accuracy of the proposed methods using real data from more than 550 concurrent elections where the true district-level cross-classifications of votes (straight- and split-tickets) are known. Our empirical assessment clearly identifies the symmetric solutions as more accurate. They outperform asymmetric methods 90% of the time and reduce error, on average, by 11%. Our results are based on data from simultaneous elections, so further research is required to see whether our conclusions can be maintained in other ecological inference contexts. Interested readers can easily use the proposed methods as they are implemented in the R package lphom.
A doubly self-exciting Poisson model for describing scoring levels in NBA basketball
Authors: Briz-Redón Álvaro 
Published: February 2024

Abstract
In this article, Poisson time series models are considered to describe the number of field goals made by a basketball team or player at both the game (within-season) and the minute (within-game) level. The model is endowed with a doubly self-exciting structure, following the INGARCH(1,1) specification. To estimate the model at the within-game level, a divide-and-conquer procedure is carried out under a Bayesian framework. Then, we perform a clustering of the players in terms of their similarity according to the corresponding posterior distributions of key model parameters. The model is tested with National Basketball Association (NBA) teams and players from the 2018–2019 season.
A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops
Authors: Ji Gaoxiang , Long Ying , Cai Guangqin , Wang Aihua , Yan Guixin , Li Hao , Gao Guizhen , Xu Kun , Huang Qian , Chen Biyun , Li Lixia , Li Feng , Nishio Takeshi , Shen Jinxiong , Wu Xiaoming 
Published: February 2024

Abstract
The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.
Chromatin sensing: integration of environmental signals to reprogram plant development through chromatin regulators
Authors: Wang Wenli , Sung Sibum 
Published: February 2024

Abstract
Chromatin regulation in eukaryotes plays pivotal roles in controlling the developmental regulatory gene network. This review explores the intricate interplay between chromatin regulators and environmental signals, elucidating their roles in shaping plant development. As sessile organisms, plants have evolved sophisticated mechanisms to perceive and respond to environmental cues, orchestrating developmental programs that ensure adaptability and survival. A central aspect of this dynamic response lies in the modulation of versatile gene regulatory networks, mediated in part by various chromatin regulators. Here, we summarized current understanding of the molecular mechanisms through which chromatin regulators integrate environmental signals, influencing key aspects of plant development.
A clinical update of compound heterozygosity for hemoglobin Hekinan II [a27(B8)Glu–Asp; HBA1: c.84G&gt;T] variant in China
Authors: Pan Liqiu , Qiu Yuling , Ye Lihua , Li Linlin , Huang Yuanyuan , Mo Wuning , Lin Faquan 
Published: February 2024

Abstract

Background
Hemoglobin (Hb) Hekinan II (A27; Glu-Asp) is an α-chain variant, and its interaction with the common Southeast Asian (--SEA/) α-thalassemia (α-thal) deletion is rarely reported. This study provides a clinical update of Hb Hekinan II associated with (--SEA/) α-thal.

Methods
A total of 11 simple heterozygotes and 20 composite heterozygotes for Hb Hekinan II and (--SEA/) α-thal were included based on molecular diagnosis.

Results
Hb Hekinan II exhibited a significant increase in hemoglobin, mean corpuscular volume, and mean corpuscular hemoglobin content, but a decrease in red blood cell level compared with α+ thalassemia deletion. Compared with (--SEA/) α-thal, composite heterozygotes for Hb Hekinan II and (--SEA/) α-thal showed similar erythrocyte parameters. Both heterozygotes with and without (--SEA/) α-thal showed low Hb A2 level. Hb Hekinan II showed abnormal performance in high-performance liquid chromatography but not in capillary electrophoresis.

Conclusion
Hb Hekinan II is a benign Hb variant. The heterozygotes exhibit clinically asymptomatic coinheritance with (--SEA/) α-thal having comparable hematological phenotype to simple (--SEA/) α-thal. The combination of hematological and molecular analysis helped to improve the detection rate of this rare variant.
Myokines: metabolic regulation in obesity and type 2 diabetes
Authors: Chen Zhi-Tian , Weng Zhi-Xuan , Lin Jiandie D , Meng Zhuo-Xian 
Published: February 2024

Abstract
Skeletal muscle plays a vital role in the regulation of systemic metabolism, partly through its secretion of endocrine factors which are collectively known as myokines. Altered myokine levels are associated with metabolic diseases, such as type 2 diabetes (T2D). The significance of interorgan crosstalk, particularly through myokines, has emerged as a fundamental aspect of nutrient and energy homeostasis. However, a comprehensive understanding of myokine biology in the setting of obesity and T2D remains a major challenge. In this review, we discuss the regulation and biological functions of key myokines that have been extensively studied during the past two decades, namely interleukin 6 (IL-6), irisin, myostatin (MSTN), growth differentiation factor 11 (GDF11), fibroblast growth factor 21 (FGF21), apelin, brain-derived neurotrophic factor (BDNF), meteorin-like (Metrnl), secreted protein acidic and rich in cysteine (SPARC), β-aminoisobutyric acid (BAIBA), Musclin, and Dickkopf 3 (Dkk3). Related to these, we detail the role of exercise in myokine expression and secretion together with their contributions to metabolic physiology and disease. Despite significant advancements in myokine research, many myokines remain challenging to measure accurately and investigate thoroughly. Hence, new research techniques and detection methods should be developed and rigorously tested. Therefore, developing a comprehensive perspective on myokine biology is crucial, as this will likely offer new insights into the pathophysiological mechanisms underlying obesity and T2D and may reveal novel targets for therapeutic interventions.
Formation of Different Polyploids Through Disrupting Meiotic Crossover Frequencies Based oncntd1Knockout in Zebrafish
Authors: Ou Yuan , Li Huilin , Li Juan , Dai Xiangyan , He Jiaxin , Wang Shi , Liu Qingfeng , Yang Conghui , Wang Jing , Zhao Rurong , Yin Zhan , Shu Yuqin , Liu Shaojun 
Published: February 2024

AbstractPolyploidy, a significant catalyst for speciation and evolutionary processes in both plant and animal kingdoms, has been recognized for a long time. However, the exact molecular mechanism that leads to polyploid formation, especially in vertebrates, is not fully understood. Our study aimed to elucidate this phenomenon using the zebrafish model. We successfully achieved an effective knockout of the cyclin N-terminal domain containing 1 (cntd1) using CRISPR/Cas9 technology. This resulted in impaired formation of meiotic crossovers, leading to cell-cycle arrest during meiotic metaphase and triggering apoptosis of spermatocytes in the testes. Despite these defects, the mutant (cntd1−/−) males were still able to produce a limited amount of sperm with normal ploidy and function. Interestingly, in the mutant females, it was the ploidy not the capacity of egg production that was altered. This resulted in the production of haploid, aneuploid, and unreduced gametes. This alteration enabled us to successfully obtain triploid and tetraploid zebrafish from cntd1−/− and cntd1−/−/− females, respectively. Furthermore, the tetraploid-heterozygous zebrafish produced reduced-diploid gametes and yielded all-triploid or all-tetraploid offspring when crossed with wild-type (WT) or tetraploid zebrafish, respectively. Collectively, our findings provide direct evidence supporting the crucial role of meiotic crossover defects in the process of polyploidization. This is particularly evident in the generation of unreduced eggs in fish and, potentially, other vertebrate species.
The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples
Authors: Kuhn Christina Katharina , Stenzel Udo , Berndt Sandra , Liebscher Ines , Schöneberg Torsten , Horn Susanne 
Published: February 2024

Abstract
Alternative splicing and multiple transcription start and termination sites can produce a diverse repertoire of mRNA transcript variants from a given gene. While the full picture of the human transcriptome is still incomplete, publicly available RNA datasets have enabled the assembly of transcripts. Using publicly available deep sequencing data from 927 human samples across 48 tissues, we quantified known and new transcript variants, provide an interactive, browser-based application Splice-O-Mat and demonstrate its relevance using adhesion G protein-coupled receptors (aGPCRs) as an example. On average, 24 different transcript variants were detected for each of the 33 human aGPCR genes, and several dominant transcript variants were not yet annotated. Variable transcription starts and complex exon-intron structures encode a flexible protein domain architecture of the N- and C termini and the seven-transmembrane helix domain (7TMD). Notably, we discovered the first GPCR (ADGRG7/GPR128) with eight transmembrane helices. Both the N- and C terminus of this aGPCR were intracellularly oriented, anchoring the N terminus in the plasma membrane. Moreover, the assessment of tissue-specific transcript variants, also for other gene classes, in our application may change the evaluation of disease-causing mutations, as their position in different transcript variants may explain tissue-specific phenotypes.
Peptide nucleic acid-assisted generation of targeted double-stranded DNA breaks with T7 endonuclease I
Authors: Aman Rashid , Syed Muntjeeb M , Saleh Ahmed , Melliti Firdaws , Gundra Sivakrishna Rao , Wang Qiaochu , Marsic Tin , Mahas Ahmed , Mahfouz Magdy M 
Published: February 2024

Abstract
Gene-editing technologies have revolutionized biotechnology, but current gene editors suffer from several limitations. Here, we harnessed the power of gamma-modified peptide nucleic acids (γPNAs) to facilitate targeted, specific DNA invasion and used T7 endonuclease I (T7EI) to recognize and cleave the γPNA-invaded DNA. Our data show that T7EI can specifically target PNA-invaded linear and circular DNA to introduce double-strand breaks (DSBs). Our PNA-Guided T7EI (PG-T7EI) technology demonstrates that T7EI can be used as a programmable nuclease capable of generating single or multiple specific DSBs in vitro under a broad range of conditions and could be potentially applied for large-scale genomic manipulation. With no protospacer adjacent motif (PAM) constraints and featuring a compact protein size, our PG-T7EI system will facilitate and expand DNA manipulations both in vitro and in vivo, including cloning, large-fragment DNA assembly, and gene editing, with exciting applications in biotechnology, medicine, agriculture, and synthetic biology.
Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus
Authors: Rousseau Meghan , Oulavallickal Tifany , Williamson Adele , Arcus Vic , Patrick Wayne M , Hicks Joanna 
Published: February 2024

Abstract
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
Olivine-Hosted Melt Inclusions Track Progressive Dehydration Reactions in Subducting Slabs Across Volcanic Arcs
Authors: Brahm Raimundo , Coulthard Jr Daniel , Zellmer Georg , Kuritani Takeshi , Sakamoto Naoya , Taniuchi Hajime , Yurimoto Hisayoshi , Nakagawa Mitsuhiro , Sato Eiichi 
Published: February 2024

Abstract
The stability and breakdown of mineral phases in subducting slabs control the cycling of trace elements through subduction zones. Stability of key minerals and the partitioning of trace elements between these minerals and liquid phases of interests have been charted by natural sample analysis and experimental constraints. However, systematic study from arc front to far back arc has rarely shown that the expected geochemical variations of the slab liquid are actually recorded by natural samples. Complexities arise by uncertainties on the nature of the slab component (melts, fluids and supercritical liquids), source heterogeneities and transport processes. Using data from olivine-hosted melt inclusions sampled along and across the NE Japan and southern Kurile arcs, we demonstrate that experimentally and thermodynamically constrained phase stabilities in subducted materials indeed control the trace element signatures as predicted by these models and experiments. The main reactions that can be traced across arc are progressive breakdown of light rare earth element-rich accessory phases (e.g. allanite), enhanced dehydration of the lithospheric mantle (serpentine breakdown) and changes in the nature of the slab component. This work elucidates subduction zone elemental cycling in a well-characterized petrogenetic setting and provides important constraints on the interpretation of trace element ratios in arc magmas in terms of the prograde metamorphic reactions within the subducting slab.