bluuebunny/crossref_metadata_2025_split huggingface dataset:
Skeletal facial asymmetry: reliability of manual and artificial intelligence-driven analysis
Authors: Kazimierczak Natalia , Kazimierczak Wojciech , Serafin Zbigniew , Nowicki Paweł , Jankowski Tomasz , Jankowska Agnieszka , Janiszewska-Olszowska Joanna 
Published: January 2024

Abstract

Objectives
To compare artificial intelligence (AI)-driven web-based platform and manual measurements for analysing facial asymmetry in craniofacial CT examinations.

Methods
The study included 95 craniofacial CT scans from patients aged 18-30 years. The degree of asymmetry was measured based on AI platform-predefined anatomical landmarks: sella (S), condylion (Co), anterior nasal spine (ANS), and menton (Me). The concordance between the results of automatic asymmetry reports and manual linear 3D measurements was calculated. The asymmetry rate (AR) indicator was determined for both automatic and manual measurements, and the concordance between them was calculated. The repeatability of manual measurements in 20 randomly selected subjects was assessed. The concordance of measurements of quantitative variables was assessed with interclass correlation coefficient (ICC) according to the Shrout and Fleiss classification.

Results
Erroneous AI tracings were found in 16.8% of cases, reducing the analysed cases to 79. The agreement between automatic and manual asymmetry measurements was very low (ICC &lt; 0.3). A lack of agreement between AI and manual AR analysis (ICC type 3 = 0) was found. The repeatability of manual measurements and AR calculations showed excellent correlation (ICC type 2 &gt; 0.947).

Conclusions
The results indicate that the rate of tracing errors and lack of agreement with manual AR analysis make it impossible to use the tested AI platform to assess the degree of facial asymmetry.
Mineralocorticoid receptor antagonists and atrial fibrillation: a meta-analysis of clinical trials
Authors: Oraii Alireza , Healey Jeff S , Kowalik Krzysztof , Pandey Avinash K , Benz Alexander P , Wong Jorge A , Conen David , McIntyre William F 
Published: January 2024

Abstract

Background and Aims
Mineralocorticoid receptor antagonists (MRAs) improve cardiovascular outcomes in a variety of settings. This study aimed to assess whether cardioprotective effects of MRAs are modified by heart failure (HF) and atrial fibrillation (AF) status and to study their impact on AF events.

Methods
MEDLINE, Embase, and Cochrane Central databases were searched to 24 March 2023 for randomized controlled trials evaluating the efficacy of MRAs as compared with placebo or usual care in reducing cardiovascular outcomes and AF events in patients with or at risk for cardiovascular diseases. Random-effects models and interaction analyses were used to test for effect modification.

Results
Meta-analysis of seven trials (20 741 participants, mean age: 65.6 years, 32% women) showed that the efficacy of MRAs, as compared with placebo, in reducing a composite of cardiovascular death or HF hospitalization remains consistent across patients with HF [risk ratio = 0.81; 95% confidence interval (CI): 0.67–0.98] and without HF (risk ratio = 0.84; 95% CI: 0.75–0.93; interaction P = .77). Among patients with HF, MRAs reduced cardiovascular death or HF hospitalization in patients with AF (hazard ratio = 0.95; 95% CI: 0.54–1.66) to a similar extent as in those without AF (hazard ratio = 0.82; 95% CI: 0.63–1.07; interaction P = .65). Pooled data from 20 trials (21 791 participants, mean age: 65.2 years, 31.3% women) showed that MRAs reduce AF events (risk ratio = 0.76; 95% CI: 0.67–0.87) in both patients with and without prior AF.

Conclusions
Mineralocorticoid receptor antagonists are similarly effective in preventing cardiovascular events in patients with and without HF and most likely retain their efficacy regardless of AF status. Mineralocorticoid receptor antagonists may also be moderately effective in preventing incident or recurrent AF events.
Long-term impact of parenting-related leave policies on adolescents’ well-being: a systematic review of quasi-experiments
Authors: Tugrul Hande , Stuckler David , Aassve Arnstein 
Published: January 2024

Abstract

Background
Parenting-related leave policies have gained increasing endorsement across Organisation for Economic Co-operation and Development (OECD) countries in recent decades. Previous reviews have focused on the short-term impacts and found predominantly positive effects on children. Although there is a growing interest in the long-term impact during adolescence and young adulthood, a comprehensive assessment of this aspect is currently lacking.

Methods
We systematically reviewed studies from three electronic databases (Scopus, Web of Science and PubMed), which used quasi-experimental design and examined policies legislating the introduction or expansion of parenting-related leave policies in North America or Europe. We looked at studies focused on well-being beyond the age of 12 and analyzed the findings across different domains of well-being: health, education and labour market outcomes.

Results
The quasi-experimental evidence is rather limited. The introduction of leave policies or gender-specific quotas produces substantial benefits in the long run. Further, maternal socioeconomic and educational background appears to play a substantial moderating role between leave and adolescents’ well-being. Adolescents with mothers who have higher levels of education have demonstrated a more pronounced advantage from the extended time spent together, thereby accentuating pre-existing disparities.

Conclusions
Though the expansion of already long leaves might not generate significant outcomes, the introduction of leave policies or gender-specific quotas produces substantial long-term benefits. This evidence entails considerable policy implications for countries that lack a national leave policy or offer only short durations of paid leave, such as the USA.
A new hybrid incompatibility locus between Drosophila melanogaster and Drosophila sechellia
Authors: Bladen Jackson , Cooper Jacob C , Ridges Jackson T , Guo Ping , Phadnis Nitin 
Published: January 2024

Abstract
Despite the fundamental importance of hybrid incompatibilities to the process of speciation, there are few cases where the evolution and genetic architecture of hybrid incompatibilities are understood. One of the longest studied hybrid incompatibilities causes F1 hybrid male inviability in crosses between Drosophila melanogaster females and males from the Drosophila simulans clade of species—Drosophila simulans, Drosophila mauritiana, and Drosophila sechellia. Here, we discover dramatic differences in the manifestation of this lethal hybrid incompatibility among the D. simulans clade of species. In particular, F1 hybrid males between D. melanogaster and D. sechellia are resistant to hybrid rescue through RNAi knockdown of an essential hybrid incompatibility gene. To understand the genetic basis of this inter-species difference in hybrid rescue, we developed a triple-hybrid mapping method. Our results show that 2 discrete large effect loci and many dispersed small effect changes across the genome underlie D. sechellia aversion to hybrid rescue. The large effect loci encompass a known incompatibility gene Lethal hybrid rescue (Lhr) and previously unknown factor, Sechellia aversion to hybrid rescue (Satyr). These results show that the genetic architecture of F1 hybrid male inviability is overlapping but not identical in the 3 inter-species crosses. Our results raise questions about whether new hybrid incompatibility genes can integrate into an existing hybrid incompatibility thus increasing in complexity over time, or if the continued evolution of genes can gradually strengthen an existing hybrid incompatibility.
Identification of Reduced mTOR T1262 Phosphorylation as a Novel Mechanism and Therapeutic Target of Apoptosis in Senescent Cardiomyocytes: Aging and Cardiomyocyte Apoptosis
Authors: Li Qiuyu , Lin Xiaolong , Bo Xiaowen , Chen Siyuan , Zhao Donghui , Ma Qin , Zhao Yuhao , Yang Hong , Liu Jinghua , Fan Qian 
Published: January 2024

Abstract
The mechanisms through which aging increases heart injury remain partially understood. Protein phosphorylation plays a critical regulatory role in cell survival and death. Using an unbiased phosphoproteomics approach, we aimed to identify the proteins whose phosphorylation could be causatively related to aging-related cardiomyocyte apoptosis and elucidate the underlying mechanisms. Comparative phosphoproteomics was conducted on cardiac tissues obtained from young (8 weeks) and aged (24 months) mice. Our findings revealed that the Mammalian Target of Rapamycin phosphorylation at T1262 (mTORT1262) was reduced in the aging heart. Immunohistochemical and Western blot analyses confirmed these findings in aging myocardia and D-galactose-induced senescent AC16 cardiomyocytes. In hypoxia/reoxygenation cardiomyocytes, mTORT1262 phosphorylation deficiency (mTORT1262A, lentivirus-mediated transfection) inhibited AKT1, suppressed NF-κB, activated FOXO1/3a signaling, and ultimately exacerbated apoptosis. Conversely, mTORT1262 pseudophosphorylation (mTORT1262E) exhibited opposite effects. Through bioinformatics and CO-IP, purinergic receptor P2X4 (P2X4R) was found to be the possible receptor responsible for mTORT1262 phosphorylation. Knockdown of P2X4R increased apoptosis, whereas its overexpression decreased it. In senescent cardiomyocytes, P2X4R expression and mTORT1262 and AKT1S473 phosphorylation were reduced, NF-κB signaling was suppressed, and FOXO1/3a signaling was activated. We demonstrated that P2X4R downregulation and the subsequent reduction of mTORT1262 phosphorylation is a novel mechanism contributing to cardiomyocyte apoptosis in aging hearts. The P2X4R-mTOR-AKT1 signaling pathway represents a potential therapeutic target against accelerated cardiac injury in aging.
Whole-genome Sequencing Reveals Autooctoploidy in Chinese Sturgeon and Its Evolutionary Trajectories
Authors: Wang Binzhong , Wu Bin , Liu Xueqing , Hu Yacheng , Ming Yao , Bai Mingzhou , Liu Juanjuan , Xiao Kan , Zeng Qingkai , Yang Jing , Wang Hongqi , Guo Baifu , Tan Chun , Hu Zixuan , Zhao Xun , Li Yanhong , Yue Zhen , Mei Junpu , Jiang Wei , Yang Yuanjin , Li Zhiyuan , Gao Yong , Chen Lei , Jian Jianbo , Du Hejun 
Published: January 2024

Abstract
The order Acipenseriformes, which includes sturgeons and paddlefishes, represents “living fossils” with complex genomes that are good models for understanding whole-genome duplication (WGD) and ploidy evolution in fishes. Here, we sequenced and assembled the first high-quality chromosome-level genome for the complex octoploid Acipenser sinensis (Chinese sturgeon), a critically endangered species that also represents a poorly understood ploidy group in Acipenseriformes. Our results show that A. sinensis is a complex autooctoploid species containing four kinds of octovalents (8n), a hexavalent (6n), two tetravalents (4n), and a divalent (2n). An analysis taking into account delayed rediploidization reveals that the octoploid genome composition of Chinese sturgeon results from two rounds of homologous WGDs, and further provides insights into the timing of its ploidy evolution. This study provides the first octoploid genome resource of Acipenseriformes for understanding ploidy compositions and evolutionary trajectories of polyploid fishes.
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice
Authors: An Jianting , Wang Jing , Kong Siming , Song Shi , Chen Wei , Yuan Peng , He Qilong , Chen Yidong , Li Ye , Yang Yi , Wang Wei , Li Rong , Yan Liying , Yan Zhiqiang , Qiao Jie 
Published: January 2024

Abstract
Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.
The Twist for Electrical Networks and the Inverse Problem
Authors: George Terrence 
Published: January 2024

Abstract
We construct an electrical-network version of the twist map for the positive Grassmannian, and use it to solve the inverse problem of recovering conductances from the response matrix. Each conductance is expressed as a biratio of Pfaffians as in the inverse map of Kenyon and Wilson; however, our Pfaffians are the more canonical $B$ variables instead of their tripod variables, and are coordinates on the positive orthogonal Grassmannian studied by Henriques and Speyer.
Competition for iron shapes metabolic antagonism betweenBacillus subtilisandPseudomonas marginalis
Authors: Lyng Mark , Jørgensen Johan P B , Schostag Morten D , Jarmusch Scott A , Aguilar Diana K C , Lozano-Andrade Carlos N , Kovács Ákos T 
Published: January 2024

AbstractSiderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly influenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of fluorescent Pseudomonas spp. and found that the Bacillus–Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria.
Protist predation selects for the soil resistome
Authors: Jiang Gaofei , Liu Chen , Xiong Wu , Shen Qirong , Wei Zhong 
Published: January 2024

Abstract
A key aspect of “One Health” is to comprehend how antibiotic resistomes evolve naturally. In this issue, Nguyen and colleagues pioneered an in situ investigation on the impact of protist predations on the soil microbial community and its antibiotic resistance genes (ARGs). They found that bacterivorous protists consistently increased the abundance of ARGs, such as tetracycline resistant genes. Indeed, antibiotic production is a common strategy for bacteria to evade protist predation. The rise of ARGs can be explained by the balance between antibiotic producers and resisters shaped by predatory selection. This work suggests that ARG enrichment due to biotic interactions may be less worrisome than previously thought. Unless, these ARGs are carried by or disseminated among pathogens. Therefore, it is essential to monitor the occurrence, dissemination and pathogenic hosts of ARGs, enhancing our capacity to combat antibiotic resistance.
Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments
Authors: Yin Xiuran , Zhou Guowei , Wang Haihua , Han Dukki , Maeke Mara , Richter-Heitmann Tim , Wunder Lea C , Aromokeye David A , Zhu Qing-Zeng , Nimzyk Rolf , Elvert Marcus , Friedrich Michael W 
Published: January 2024

Abstract
Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15–30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.
Inter-plasmid transfer of antibiotic resistance genes accelerates antibiotic resistance in bacterial pathogens
Authors: Wang Xiaolong , Zhang Hanhui , Yu Shenbo , Li Donghang , Gillings Michael R , Ren Hongqiang , Mao Daqing , Guo Jianhua , Luo Yi 
Published: January 2024

Abstract
Antimicrobial resistance is a major threat for public health. Plasmids play a critical role in the spread of antimicrobial resistance via horizontal gene transfer between bacterial species. However, it remains unclear how plasmids originally recruit and assemble various antibiotic resistance genes (ARGs). Here, we track ARG recruitment and assembly in clinically relevant plasmids by combining a systematic analysis of 2420 complete plasmid genomes and experimental validation. Results showed that ARG transfer across plasmids is prevalent, and 87% ARGs were observed to potentially transfer among various plasmids among 8229 plasmid-borne ARGs. Interestingly, recruitment and assembly of ARGs occur mostly among compatible plasmids within the same bacterial cell, with over 88% of ARG transfers occurring between compatible plasmids. Integron and insertion sequences drive the ongoing ARG acquisition by plasmids, especially in which IS26 facilitates 63.1% of ARG transfer events among plasmids. In vitro experiment validated the important role of IS26 involved in transferring gentamicin resistance gene aacC1 between compatible plasmids. Network analysis showed four beta-lactam genes (blaTEM-1, blaNDM-4, blaKPC-2, and blaSHV-1) shuffling among 1029 plasmids and 45 clinical pathogens, suggesting that clinically alarming ARGs transferred accelerate the propagation of antibiotic resistance in clinical pathogens. ARGs in plasmids are also able to transmit across clinical and environmental boundaries, in terms of the high-sequence similarities of plasmid-borne ARGs between clinical and environmental plasmids. This study demonstrated that inter-plasmid ARG transfer is a universal mechanism for plasmid to recruit various ARGs, thus advancing our understanding of the emergence of multidrug-resistant plasmids.
Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea
Authors: Zhao Dahe , Zhang Shengjie , Chen Junyu , Zhao Juanjuan , An Peng , Xiang Hua 
Published: January 2024

Abstract
The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria–Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.