bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interplay of cognitive control and feature integration: insights from theta oscillatory dynamics during conflict processing
Authors: Pastötter Bernhard , Haciahmet Céline C , Beste Christian , Münchau Alexander , Frings Christian 
Published: August 2024

Abstract
Adaptive behavior is fundamental to cognitive control and executive functioning. This study investigates how cognitive control mechanisms and episodic feature retrieval interact to influence adaptiveness, focusing particularly on theta (4 to 8 Hz) oscillatory dynamics. We conducted two variations of the Simon task, incorporating response-incompatible, response-compatible, and neutral trials. Experiment 1 demonstrated that cognitive adjustments—specifically, cognitive shielding following incompatible trials and cognitive relaxation following compatible ones—are reflected in midfrontal theta power modulations associated with the Simon effect. Experiment 2 showed that reducing feature overlap between trials leads to less pronounced sequential modulations in behavior and midfrontal theta activity, supporting the hypothesis that cognitive control and feature integration share a common neural mechanism. These findings highlight the interaction of cognitive control processes and episodic feature integration in modulating behavior. The results advocate for hybrid models that combine top–down and bottom–up processes as a comprehensive framework to understand cognitive control dynamics and adaptive behavior.
Antipredator decisions of male Trinidadian guppies (Poecilia reticulata) depend on social cues from females
Authors: Brusseau Alix J P , Feyten Laurence E A , Crane Adam L , Ramnarine Indar W , Ferrari Maud C O , Brown Grant E 
Published: August 2024

Abstract
Many prey species rely on publicly available personal and social information regarding local predation threats to assess risks and make context-appropriate behavioral decisions. However, in sexually dimorphic species, males and females are expected to differ in the perceived costs and/or benefits associated with predator avoidance decisions. Recent studies suggest that male Trinidadian guppies (Poecilia reticulata) show reduced or absent responses to acute personal information cues, placing them at greater risk of predation relative to females. Our goal here was to test the hypothesis that adult (reproductively active) male guppies rely on social information to limit potential costs associated with their lack of response to risky personal cues. Adult male guppies were exposed to personal chemosensory cues (either conspecific alarm cues (AC), a novel odor, or a water control) in the presence of a shoal of three females inside a holding container that allowed the transmission of visual but not chemical cues. At the same time, we exposed females to either risk from AC or no risk, resulting in the display of a range of female behavior, from calm to alarmed, available as social information for males. Alarmed females caused male fright activity to increase and male interest in females to decrease, regardless of the personal cue treatment. These results indicate that male guppies rely more on female information regarding predation risk than their own personal information, probably to balance trade-offs between reproduction and predator avoidance.
The overview of the BioRED (Biomedical Relation Extraction Dataset) track at BioCreative VIII
Authors: Islamaj Rezarta , Lai Po-Ting , Wei Chih-Hsuan , Luo Ling , Almeida Tiago , Jonker Richard A. A , Conceição Sofia I. R , Sousa Diana F , Phan Cong-Phuoc , Chiang Jung-Hsien , Li Jiru , Pan Dinghao , Meesawad Wilailack , Tsai Richard Tzong-Han , Sarol M. Janina , Hong Gibong , Valiev Airat , Tutubalina Elena , Lee Shao-Man , Hsu Yi-Yu , Li Mingjie , Verspoor Karin , Lu Zhiyong 
Published: August 2024

Abstract
The BioRED track at BioCreative VIII calls for a community effort to identify, semantically categorize, and highlight the novelty factor of the relationships between biomedical entities in unstructured text. Relation extraction is crucial for many biomedical natural language processing (NLP) applications, from drug discovery to custom medical solutions. The BioRED track simulates a real-world application of biomedical relationship extraction, and as such, considers multiple biomedical entity types, normalized to their specific corresponding database identifiers, as well as defines relationships between them in the documents. The challenge consisted of two subtasks: (i) in Subtask 1, participants were given the article text and human expert annotated entities, and were asked to extract the relation pairs, identify their semantic type and the novelty factor, and (ii) in Subtask 2, participants were given only the article text, and were asked to build an end-to-end system that could identify and categorize the relationships and their novelty. We received a total of 94 submissions from 14 teams worldwide. The highest F-score performances achieved for the Subtask 1 were: 77.17% for relation pair identification, 58.95% for relation type identification, 59.22% for novelty identification, and 44.55% when evaluating all of the above aspects of the comprehensive relation extraction. The highest F-score performances achieved for the Subtask 2 were: 55.84% for relation pair, 43.03% for relation type, 42.74% for novelty, and 32.75% for comprehensive relation extraction. The entire BioRED track dataset and other challenge materials are available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BC8-BioRED-track/ and https://codalab.lisn.upsaclay.fr/competitions/13377 and https://codalab.lisn.upsaclay.fr/competitions/13378.
Database URL: https://ftp.ncbi.nlm.nih.gov/pub/lu/BC8-BioRED-track/https://codalab.lisn.upsaclay.fr/competitions/13377https://codalab.lisn.upsaclay.fr/competitions/13378
Propagation path of a flowering cherry (Cerasus × yedoensis) cultivar ‘Somei-Yoshino’ traced by somatic mutations
Authors: Shirasawa Kenta , Esumi Tomoya , Itai Akihiro , Hatakeyama Katsunori , Takashina Tadashi , Yakuwa Takuji , Sumitomo Katsuhiko , Kurokura Takeshi , Fukai Eigo , Sato Keiichi , Shimada Takehiko , Shiratake Katsuhiro , Hosokawa Munetaka , Monden Yuki , Kusaba Makoto , Ikegami Hidetoshi , Isobe Sachiko 
Published: August 2024

Abstract
In the long history of human relations with flowering cherry trees in Japan, ‘Somei-Yoshino’ occupies an exceptional position among a variety of flowering trees: it is a self-incompatible interspecific hybrid but has been enthusiastically planted by grafting throughout Japan, due most likely to its flamboyant appearance upon full bloom. Thus, ‘Somei-Yoshino’ gives us a rare opportunity to trace and investigate the occurrence and distribution of somatic mutations within a single plant species through analysis of the genomes of the clonally propagated trees grown under a variety of geographical and artificial environments. In the studies presented here, a total of 46 samples of ‘Somei-Yoshino’ trees were collected and their genomes were analysed. We identified 684 single nucleotide mutations, of which 71 were present in more than two samples. Clustering analysis of the mutations indicated that the 46 samples were classified into eight groups, four of which included 36 of the 46 samples analysed. Interestingly, all the four tree samples collected in Ueno Park of Tokyo were members of the four groups mentioned above. Based on comparative analysis of their mutations, one of the four trees growing in Ueno Park was concluded to be the closest to the original ancestor. We propose that somatic mutations may be used as tracers to establish the ancestral relationship amongst clonally propagated individuals.
Cardiac fibromas in adult patients: a case series focusing on rhythmology and radiographic features
Authors: Finke Karl , Gietzen Thorsten , Steven Daniel , Baldus Stephan , ten Freyhaus Henrik , Maintz David , Pennig Lenhard , Gietzen Carsten 
Published: August 2024

Abstract

Background
Fibromas are rare primary benign cardiac tumours that can become symptomatic due to expansive growth, ventricular rhythm disturbances, and sudden cardiac death. Distinguishing fibromas from other (malign) cardiac masses is essential for accurate diagnosis and treatment. While there is some experience in management of cardiac fibromas in children, management of adult patients is unknown.

Case summary
We present three cases of cardiac fibroma in adult patients diagnosed by echocardiography, cardiovascular magnetic resonance (CMR), and computed tomography (CT): (1) a 55-year-old male with a left ventricular fibroma leading to reduced left ventricular ejection fraction and mitral regurgitation. He had family history of sudden cardiac death, showed premature ventricular contractions (PVCs), and was treated with a primary preventive subcutaneous implantable cardiac defibrillator (S-ICD); (2) a 39-year-old male with right ventricular fibroma as an incidental finding. He complained of episodes of PVC. Due to a low PVC burden, decision was made against ablation and the patient was planned for follow-up; and (3) an 18-year-old female with left ventricular apex fibroma detected by CMR shortly after birth and confirmed by surgical biopsy. Being asymptomatic, conservative management was pursued and follow-up by CMR planned.

Discussion
Cardiac fibromas can show various clinical presentations and hence being detected late in life. Given potential complications of surgical biopsy, diagnosis of cardiac fibromas is primarily based on echocardiography, CT, and CMR. Rhythm disturbances as PVCs are common. Due to association with ventricular arrhythmias and sudden cardiac death, preventive ICD placement might be appropriate on an individual basis.
The prognostic impact of unplanned invasive coronary angiography following coronary artery bypass grafting
Authors: Heuts Samuel , Bova Roberto , Romeo Jamie L R , Vriesendorp Pieter A , van der Horst Iwan C C , Segers Patrique , Maessen Jos G , Gollmann-Tepeköylü Can , van 't Hof Arnoud W J , Bidar Elham , Lux Arpad 
Published: August 2024

Abstract

OBJECTIVES
Myocardial ischaemia following coronary artery bypass grafting (CABG) is a potentially devastating complication. Nevertheless, the incidence, aetiology and prognostic relevance of unplanned coronary angiography (uCAG) remain understudied. We aimed to investigate the prevalence and outcome of patients undergoing urgent, uCAG in the postoperative period following CABG.

METHODS
We screened all patients undergoing isolated elective CABG in an academic referral centre between 2016 and 2021 and identified patients undergoing uCAG within 30 days of surgery. For uCAG patients, a distinction was made between patients undergoing re-revascularization (REV) and patients receiving conservative management (CON). The primary outcomes were 30-day mortality and unadjusted and adjusted long-term survival. Secondary outcomes were the indication for and prevalence of uCAG and urgent revascularization.

RESULTS
Of the 1918 patients undergoing isolated CABG, 78 individuals needed uCAG (4.1%), of whom 45 underwent immediate revascularization (REV group; 2.3% overall, 57% within the uCAG group, median age 69.9 years) and 33 were treated conservatively (CONS group; 1.7% overall, 42% within the uCAG group, median age 69.1 years). Patients undergoing uCAG (n = 78) had a higher 30-day mortality than patients not undergoing uCAG (n = 1840, 30-day mortality: 9.0% vs 0.4%, P &lt; 0.001). Long-term survival was significantly decreased in patients undergoing uCAG in both unadjusted (hazard ratio 2.20, 95% confidence interval 1.30–3.73) and EuroSCORE-, age- and sex-adjusted models (hazard ratio uCAG 2.03, 95% confidence interval 1.16–3.56).

CONCLUSIONS
Unplanned postoperative coronary angiography is performed in 4.1% of isolated CABG procedures, and patients in need of such urgent invasive evaluation are subjected to decreased short- and long-term survival.
The association of haemoglobin A1c variability with adverse outcomes in patients with atrial fibrillation prescribed anticoagulants
Authors: Huang Jia-Yi , Cai An-Ping , Tsang Christopher Tze Wei , Wu Mei-Zhen , Gu Wen-Li , Guo Ran , Zhang Jing-Nan , Zhu Ching-Yan , Hung Yik-Ming , Lip Gregory Y H , Yiu Kai-Hang 
Published: August 2024

Abstract

Aims
The association of haemoglobin A1c (HbA1c) variability with the risk of adverse outcomes in patients with atrial fibrillation (AF) prescribed anticoagulants remains unclear. This study aimed to evaluate the association of HbA1c variability with the risk of ischaemic stroke (IS)/systemic embolism (SE) and all-cause mortality among patients with non-valvular AF prescribed anticoagulants.

Methods and results
Patients newly diagnosed with AF from 2013 to 2018 were included. Variability in HbA1c, indexed by the coefficient of variation (CV), was determined for those with at least three HbA1c measurements available from the time of study enrolment to the end of follow-up. To evaluate whether prevalent diabetes would modify the relationship between HbA1c variability and outcomes, participants were divided into diabetes and non-diabetes groups. The study included 8790 patients (mean age 72.7% and 48.5% female). Over a median follow-up of 5.5 years (interquartile range 5.2, 5.8), the incident rate was 3.74 per 100 person-years for IS/SE and 4.89 for all-cause mortality in the diabetes group. The corresponding incident rates in the non-diabetes group were 2.41 and 2.42 per 100 person-years. In the diabetes group, after adjusting for covariates including mean HbA1c, greater HbA1c variability was significantly associated with increased risk of IS/SE [hazard ratio (HR) = 1.65, 95% confidence interval (CI): 1.27–2.13) and all-cause mortality (HR = 1.24, 95% CI: 1.05–1.47) compared with the lowest CV tertile. A similar pattern was evident in the non-diabetes group (IS/SE: HR = 1.58, 95% CI: 1.23–2.02; all-cause mortality: HR = 1.35, 95% CI: 1.10–1.64).

Conclusion
Greater HbA1c variability was independently associated with increased risk of IS/SE and all-cause mortality among patients with AF, regardless of diabetic status.
Hypnotic use and the risk of cardiovascular diseases in insomnia patients
Authors: Xie Yao , Zhu Shiyu , Wu Shuang , Liu Chang , Shen Jian , Jin Chunna , Ma Hong , Xiang Meixiang 
Published: August 2024

Abstract

Aims
We aimed to examine the association between hypnotic agents and cardiovascular outcomes in general individuals with insomnia.

Methods and results
In a propensity score matched cohort of UK Biobank (UKB) participants with insomnia, Cox proportional hazard model was used to estimate the association between regular use of hypnotic agents and predetermined cardiovascular outcomes including incident coronary heart diseases (CHD), heart failure (HF), stroke, and cardiovascular death. Inverse probability of treatment weighting, competing risk models, and shared frailty models were further performed during sensitivity analysis. Drug-target Mendelian randomization (MR) analyses were employed for further evaluation of the association between therapeutic targets of hypnotics and cardiovascular diseases. During a median follow-up of 14.3 years, the matched cohort documented a total of 929 CHD cases, 360 HF cases, 262 stroke cases, and 180 cardiovascular deaths. No significant association was detected between Z-meds and CHD, stroke, and cardiovascular mortality. Benzodiazepine use was significantly associated with the increased risk of CHD, HF, and cardiovascular mortality. The inverse probability of treatment weighting, competing risk models, and shared frailty models didn’t alter the above associations. Moreover, drug-target MR analyses corroborated the safety of Z-meds in the general population regarding cardiovascular health.

Conclusion
Our findings suggested the heterogeneous associations between different categories of hypnotics and incident cardiovascular events in individuals with insomnia. Both observational and genetic evidence raised safety concerns regarding the cardiovascular impact of benzodiazepines. No cardiovascular hazard of Z-meds was discovered in the UKB population with insomnia.
Adaptive radiation despite conserved modularity patterns in San Salvador Island Cyprinodon pupfishes and their hybrids
Authors: Chan HoWan , Colaco Emma , Martin Christopher H , Evans Kory M 
Published: August 2024

Abstract
Adaptive radiations are striking examples of rapid speciation along ecological lines. In adaptive radiations, fast rates of lineage diversification often pair with rapid rates of morphological diversification. Such diversification has often been documented through the lens of ecological drivers, overlooking the intrinsic structural constraints that may also have a key role in configuring patterns of trait diversification. Covariation within and between traits has been hypothesized to govern the axes of trait evolution, either by increasing the degree of covariation between traits (i.e. integration), which promotes morphological coordination, or by strengthening the degree of covariation within traits (i.e. modularity), which allows organisms to explore novel trait combinations and different regions of morphospace. Here, we study the modularity of the skull within an adaptive radiation of pupfishes that is endemic to San Salvador Island, Bahamas. This radiation exhibits divergent craniofacial morphologies, including generalist, snail-eating specialist, and scale-eating specialist species. We assessed morphological disparity, integration strength, and modularity patterns across the sympatric San Salvador Island pupfish radiation, lab-reared hybrids, and closely related outgroup species. Our findings revealed an unexpected uniformity in the pattern of modularity across diverse species, supporting a five-module functional hypothesis comprising the oral jaw, pharyngeal jaw, neurocranium, hyoid apparatus, and hyomandibula. Despite this conserved modularity pattern, all species exhibited weak but significantly varying strengths of overall between-module integration and significant disparity across all cranial regions. Our results suggest rapid morphological diversification can occur even with conserved patterns of modularity. We propose that broadscale patterns of modularity are more conserved while between-module associations are more evolvable between species.
Metabolic reprogramming in the food-borne pathogen Listeria monocytogenes as a critical defence against acid stress
Authors: Wu Jialun , Wang Chuhan , O'Byrne Conor 
Published: August 2024

Abstract
The ability to sense and respond effectively to acidic stress is important for microorganisms to survive and proliferate in fluctuating environments. As specific metabolic activities can serve to buffer the cytoplasmic pH, microorganisms rewire their metabolism to favour these reactions and thereby mitigate acid stress. The orally acquired pathogen Listeria monocytogenes exploits alternative metabolic activities to overcome the acidic stress encountered in the human stomach or food products. In this minireview, we discuss the metabolic processes in L. monocytogenes that mitigate acid stress, with an emphasis on the proton-depleting reactions, including glutamate decarboxylation, arginine/agmatine deimination, and fermentative acetoin production. We also summarize the recent findings on regulatory mechanisms that control the expression of genes that are responsible for these metabolic activities, including the general stress response regulator SigB, arginine repressor ArgR, and the recently discovered RofA-like transcriptional regulatory GadR. We further discuss the importance of this metabolic reprogramming in the context of food products and within the host. Finally, we highlight some outstanding challenges in the field, including an understanding of acid-sensing mechanisms, the role of intraspecies heterogeneity in acid resistance, and how a fundamental understanding of acid stress response can be exploited for food formulation to improve food safety and reduce food waste.
Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing
Authors: Johnson Hollie A , Rondeau Eric B , Sutherland Ben J G , Minkley David R , Leong Jong S , Whitehead Joanne , Despins Cody A , Gowen Brent E , Collyard Brian J , Whipps Christopher M , Farrell John M , Koop Ben F 
Published: August 2024

Abstract
The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here, we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g. Interior Alaska and St. Lawrence River have on average 181 and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = −1.07 and −1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(−) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g. amhby).
Association Between Adverse Early Life Factors and Telomere Length in Middle and Late Life
Authors: Lin Fengyu , Luo Jiefeng , Zhu Yiqun , Liang Huaying , Li Dianwu , Han Duoduo , Chang Qinyu , Pan Pinhua , Zhang Yan 
Published: August 2024

Abstract

Background and Objectives
Telomere length (TL) has been acknowledged as biomarker of biological aging. Numerous investigations have examined associations between individual early life factors and leukocyte TL; however, the findings were far from consistent.

Research Design and Methods
We evaluated the relationship between individual and combined early life factors and leukocytes TL in middle and late life using data from the UK Biobank. The early life factors (eg, maternal smoking, breastfeeding, birth weight, and comparative body size and height to peers at age 10) were measured. The regression coefficients (β) and 95% confidence interval (CI) were applied to assess the link of the early life factors and TL in adulthood. Flexible parametric survival models incorporated age to calculate the relationship between early life factors and life expectancy.

Results
Exposure to maternal smoking, lack of breastfeeding, low birth weight, and shorter height compared to peers at age 10 were identified to be associated with shorter TL in middle and older age according to the large population-based study with 197 504 participants. Individuals who experienced more than 3 adverse early life factors had the shortest TL in middle and late life (β = −0.053; 95% CI = −0.069 to −0.038; p &lt; .0001), as well as an average of 0.54 years of life loss at the age of 45 and 0.49 years of life loss at the age of 60, compared to those who were not exposed to any early life risk factors.

Discussion and Implications
Early life factors including maternal smoking, non-breastfed, low birth weight, and shorter height compared to peers at age 10 were associated with shorter TL in later life. In addition, an increased number of the aforementioned factors was associated with a greater likelihood of shorter TL in adulthood, as well as a reduced life expectancy.