bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malate inhibits light-induced stomatal opening through SLAC1- and G-proteins-mediated pathway in grapevine and Arabidopsis
Authors: Yang Zhongyi , Gong Ruhai , Mimata Yoshiharu , Ye Shaosong , Ji Wei , Ye Wenxiu 
Published: February 2025

Abstract
A key tricarboxylic acid cycle metabolite, malate, accumulates in leaves during dehydration and induces stomatal closure by recruiting cytosolic Ca2+, activating a SLOW ANION CHANNEL-ASSOCIATED 1, and promoting reactive oxygen species. However, the effects of malate on stomatal opening and its underlying molecular mechanisms remain poorly understood. Our study revealed that, among TCA cycle metabolites, malate specifically inhibited light-induced stomatal opening in both grapevine and Arabidopsis. We demonstrated that SLAC1 was required for malate's inhibitory effects. The inhibition by malate was disrupted by Ca2+ signaling inhibitors. Additionally, malate signal was mediated by G-proteins, which regulate the production of second messengers. ROS production was abolished when G-proteins were inhibited. These findings show that malate efficiently maintains stomatal closure by not only inducing stomatal closure but also inhibiting stomatal opening. The inhibition of stomatal opening by malate is mediated through the activation of SLAC1 and the G-protein signaling cascade.
Privacy-Preserving Framework for Genomic Computations via Multi-Key Homomorphic Encryption
Authors: Namazi Mina , Farahpoor Mohammadali , Ayday Erman , Pérez-González Fernando 
Published: February 2025

Abstract

Motivation
The affordability of genome sequencing and the widespread availability of genomic data have opened up new medical possibilities. Nevertheless, they also raise significant concerns regarding privacy due to the sensitive information they encompass. These privacy implications act as barriers to medical research and data availability. Researchers have proposed privacy-preserving techniques to address this, with cryptography-based methods showing the most promise. However, existing cryptography-based designs lack i) interoperability, ii) scalability, iii) a high degree of privacy (i.e., compromise one to have the other), or (iv) multiparty analyses support (as most existing schemes process genomic information of each party individually). Overcoming these limitations is essential to unlocking the full potential of genomic data while ensuring privacy and data utility. Further research and development are needed to advance privacy-preserving techniques in genomics, focusing on achieving interoperability and scalability, preserving data utility, and enabling secure multiparty computation.

Results
This study aims to overcome the limitations of current cryptography-based techniques by employing a multi-key homomorphic encryption scheme. By utilizing this scheme, we have developed a comprehensive protocol capable of conducting diverse genomic analyses. Our protocol facilitates interoperability among individual genome processing and enables multiparty tests, analyses of genomic databases, and operations involving multiple databases. Consequently, our approach represents an innovative advancement in secure genomic data processing, offering enhanced protection and privacy measures.

Availability and Implementation
All associated code and documentation, is available at https://github.com/farahpoor/smkhe.
tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets
Authors: Brown Max R , Manuel Gonzalez de La Rosa Pablo , Blaxter Mark 
Published: February 2025

Abstract

Summary
“tidk” (short for telomere identification toolkit) uses a simple, fast algorithm to scan long DNA reads for the presence of short tandemly repeated DNA in runs, and to aggregate them based on canonical DNA string representation. These are telomeric repeat candidates. Our algorithm is shown to be accurate in genomes for which the telomeric repeat unit is known and is tested across a wide variety of newly assembled genomes to uncover new telomeric repeat units. Tools are provided to identify telomeric repeats de novo, scan genomes for known telomeric repeats, and to visualize telomeric repeats on the assembly. “tidk” is implemented in Rust and is available as a command line tool which can be compiled using the Rust toolchain or downloaded as a binary from bioconda.

Availability and implementation
The “tidk” Rust crate is freely available under the MIT license (https://crates.io/crates/tidk), and the source code is available at https://github.com/tolkit/telomeric-identifier.
Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations
Authors: Du Lin , Farooq Hammad , Delafrouz Pourya , Liang Jie 
Published: February 2025

Abstract

Motivation
Techniques such as high-throughput chromosome conformation capture (Hi-C) have provided a wealth of information on nucleus organization and genome important for understanding gene expression regulation. Genome-Wide Association Studies have identified numerous loci associated with complex traits. Expression quantitative trait loci (eQTL) studies have further linked the genetic variants to alteration in expression levels of associated target genes across individuals. However, the functional roles of many eQTLs in noncoding regions remain unclear. Current joint analyses of Hi-C and eQTLs data lack advanced computational tools, limiting what can be learned from these data.

Results
We developed a computational method for simultaneous analysis of Hi-C and eQTL data, capable of identifying a small set of nonrandom interactions from all Hi-C interactions. Using these nonrandom interactions, we reconstructed large ensembles (×105) of high-resolution single-cell 3D chromatin conformations with thorough sampling, accurately replicating Hi-C measurements. Our results revealed many-body interactions in chromatin conformation at the single-cell level within eQTL loci, providing a detailed view of how 3D chromatin structures form the physical foundation for gene regulation, including how genetic variants of eQTLs affect the expression of associated eGenes. Furthermore, our method can deconvolve chromatin heterogeneity and investigate the spatial associations of eQTLs and eGenes at subpopulation level, revealing their regulatory impacts on gene expression. Together, ensemble modeling of thoroughly sampled single-cell chromatin conformations combined with eQTL data, helps decipher how 3D chromatin structures provide the physical basis for gene regulation, expression control, and aid in understanding the overall structure-function relationships of genome organization.

Availability and implementation
It is available at https://github.com/uic-liang-lab/3DChromFolding-eQTL-Loci.
Instrumental variable estimation of complier casual treatment effects with interval-censored competing risks data
Authors: Lou Yichen , Ma Yuqing , Sun Jianguo , Wang Peijie , Ye Zhisheng 
Published: February 2025

ABSTRACT
This paper discusses the assessment of causal treatment effects on a time-to-event outcome, a crucial part of many scientific investigations. Although some methods have been developed for the problem, they are not applicable to situations where there exist both interval censoring and competing risks. We fill in this critical gap under a class of transformation models for cumulative incidence functions by developing an instrumented variable (IV) estimation approach. The IV is a valuable tool commonly used to mitigate the impact of endogenous treatment selection and to determine causal treatment effects in an unbiased manner. The proposed method is flexible as the model includes many commonly used models such as the sub-distributional proportional odds and hazards models (ie, the Fine–Gray model) as special cases. The resulting estimator for the regression parameter is shown to be consistent and asymptotically normal. A simulation study is conducted to evaluate finite sample performance of the proposed approach and suggests that it works well in practice. It is applied to a breast cancer screening study.
Neuropathological comorbidity, genetics and cognition in a Chinese community-based autopsy cohort
Authors: Wu Wei , Wang Xue , Xu Yuanyuan , Ma Chao , Qian Xiaojing , Qiu Wenying 
Published: February 2025

Abstract
Neurodegenerative comorbidities are common and critical, yet data specific to the Chinese population remains limited. The study aims to investigate the prevalence and associations of neuropathologic changes and comorbidities, and their correlation with genetics and cognition in a community-dwelling autopsy cohort in China.
Datasets of 610 participants were obtained from the National Human Brain Bank for Development and Function at the Chinese Academy of Medical Sciences/Peking Union Medical College. Neuropathological changes analysed included Alzheimer’s disease neuropathological change (ADNC) (n = 331); α-synucleinopathies (n = 124) with 120 Lewy body disease (LBD) and 4 multiple system atrophy; limbic-predominant age-related TDP-43 encephalopathy neuropathologic changes (LATE-NC) (n = 341); primary age-related tauopathy (PART) (n = 231); argyrophilic grain disease (AGD) (n = 107); age-related tau astrogliopathy (ARTAG) (n = 144); cerebral amyloid angiopathy (CAA) (n = 183); hippocampus sclerosis (HS) (n = 46). Frontotemporal lobar degeneration, amyotrophic lateral sclerosis, and amygdala-predominant LBD are rare. Descriptive statistics and logistic regression models were used to assess the neuropathological associations.
Increased age at death was correlated with increased severity in ADNC, LBD, and LATE-NC, as well as with a higher number of comorbidities. APOE ε4 allele frequency in the present autopsy cohort was 13.63%. The presence of the APOE ε4 allele was linked to an advanced ADNC stage and increased comorbidities. The co-pathology prevalence varied by pathologies, with notable increases in specific subgroups: within the ADNC subgroups, LBD, LATE-NC, CAA, and HS were more frequent in advanced stages; in the LATE-NC subgroups, ADNC, CAA, and ARTAG increased, while PART decreased in higher LATE-NC stages. PART cases presented the highest proportion of pure pathology (37.2%) compared to other groups. Advanced ADNC stages were significantly associated with higher LATE-NC stages, and vice versa. Neocortical LBD was correlated with elevated ADNC levels, and higher LATE-NC stages were associated with worsening LBD pathology. High level ADNC, neocortical LBD, and stage 3 of LATE-NC were identified as independent predictors of severe cognition status.
Our study suggests that older age at death and APOE ε4 presence are the risk factors for neuropathologic comorbidities in Chinese people. The findings underscore the importance of considering comorbid neurologic diagnoses and therapies in clinical practice.
What's Hot This Year in Infectious Diseases Clinical Science
Authors: Freiberg Jeffrey A , Wright Patty W 
Published: February 2025

Abstract
Clinical science in the field of infectious diseases (ID) moved at a rapid pace in 2024. Among the highlights were multiple trials of new antibiotics and new approaches to prevent infections. Concerning trends, with outbreaks of dengue, measles, mpox, and highly pathogenic avian influenza A in 2024, demonstrate the importance of ID and the continued need for further advances through clinical science. This review highlights some of the most important trials and clinical trends in ID over the past year.
Attraction of Lygus lineolaris (Hemiptera: Miridae) to a ubiquitous floral volatile in the field
Authors: Hetherington Matthew C , Weissner Morgan , Guédot Christelle 
Published: February 2025

Abstract
Herbivorous insects utilize olfactory and visual cues to orient on suitable host plants, and such cues can be employed to facilitate insect monitoring. Lygus lineolaris Palisot de Beauvois is a polyphagous pest throughout North America. Monitoring this pest as it moves between crop and non-crop hosts remains challenging, and a lack of effective monitoring tools complicates management of this insect. In this study, we examined the electrophysiological and behavioral responses of L. lineolaris to the volatile emissions of 2 crop hosts: alfalfa and strawberry. Gas chromatography with electroantennographic detection was applied to identify antennally active compounds in headspace extracts of flowering host plants, before responses to individual compounds were examined in the field. Five compounds consistently elicited antennal depolarizations in adults of L. lineolaris and, of these, (±)-linalool increased the capture rate of L. lineolaris females in the field. Subsequent experiments examined the influence of visual cues and stereochemistry on capture rate, revealing that lures containing (±)-linalool and (S)-(+)-linalool significantly increased the capture rate of L. lineolaris females compared with traps baited with (R)-(-)-linalool and controls, indicating that L. lineolaris is attracted to (S)-(+)-linalool. While lures increased capture on red traps, this was not the case for white traps, emphasizing the importance of visual cues in the movements and monitoring of L. lineolaris. This study demonstrates that L. lineolaris is attracted to (S)-(+)-linalool in the field, and that attraction depends on trap color. This knowledge is expected to improve monitoring strategies for L. lineolaris in agricultural systems.
Risk factors for prolonged air leak after uniportal anatomical segmentectomy
Authors: Gioutsos Konstantinos , Rieder Olga , Galanis Michail , Nguyen Thanh-Long , Senbaklavaci Ömer , Dorn Patrick 
Published: February 2025

Abstract

OBJECTIVES
Our aim was to investigate the incidence and risk factors for prolonged air leak in patients undergoing minimally invasive single-port pulmonary segmentectomy.

METHODS
A retrospective analysis of all patients undergoing uniportal segmentectomy in our department from March 2015 to September 2023 was performed. Univariable, multivariable logistic regression analyses and machine learning were used to investigate risk factors for prolonged air leak (&gt;5 days)

RESULTS
575 segmentectomies were performed using uniportal video-assisted thoracoscopic surgery. 333 patients (57.9%) were men and the mean age was 64.8 years.
Prolonged air leak occurred in 88 patients (15.3%). Length of stay and duration of chest drainage were 8.6 (SD 4.86) and 10.6 (SD 8.12) days in the subgroup with prolonged air leak, compared to 3.6 (SD 2.25) and 2.0 (SD 1.3) days in the subgroup without air leak (p &lt; 0.0001). Multivariable analysis revealed that upper lobe location, lower BMI, an additional wedge resection on another segment and hypertension were associated with increased risk of PAL.
Machine learning was used to develop models that predicted the occurrence of prolonged air leak with an accuracy of 70%. The first model detected the following parameters as significant: resection of segment 2, diabetes, inhalers, and squamous cell carcinoma. The second model recognized DLCO (%), pack-years, FEV1 (%) and surgery time respectively.

CONCLUSIONS
Low BMI, DLCO% or FEV1% values, increased pack-years, inhalers, diabetes, hypertension, histology of primary lung cancer, longer surgery time, an additional wedge resection, segment 2 removal and upper lobe surgery were identified as risk factors for prolonged air leak.
Real-life experience on efficacy and safety of setmelanotide treatment in prepubertal children
Authors: Kahveci Ahmet , Kurt Ilknur , Turan Serap , Guran Tulay , Bereket Abdullah , Haliloglu Belma 
Published: February 2025

Abstract
Monogenic obesity, characterized by severe, early-onset obesity due to single-gene defects, often resists traditional weight management strategies. This report presents real-life experiences on the efficacy and safety of setmelanotide, an MC4R agonist, in 4 prepubertal children (ages 3-9) with LEPR and POMC deficiencies. Findings indicate that setmelanotide is effective at lower doses in our patients with POMC deficiency (0.3-0.5 mg/day) than the patients with LEPR deficiency (2.5 mg/day). Treatment was generally well-tolerated, with injection site reactions and hyperpigmentation as common side effects. As novel findings, gonadotropin-related effects such as hypothalamo-pituitary-gonadal axis activation and testicular descent were observed in 2 patients. Growth deceleration was noted in 2 children, and recovery from central hypothyroidism in 1 patient with POMC deficiency. Overall, setmelanotide appears to be effective and well-tolerated in young children with monogenic obesity. However, further studies are necessary to evaluate the long-term effects of early intervention on growth and pubertal development.
When selection becomes selection bias
Authors: Laugesen Kristina , Dekkers Olaf M , Groenwold Rolf H H , Skajaa Nils 
Published: February 2025

Abstract
Selection in clinical research does not necessarily result in selection bias. To understand when selection leads to bias, we discuss collider-conditioning bias, which is a common and often self-inflicted type of selection bias. Collider-conditioning bias may be difficult to recognize, and paying more attention to the bias could therefore increase the quality of research. In this paper, we aim to increase awareness and understanding of the topic.
Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea
Authors: Locatelli Nicolas S , Baums Iliana B 
Published: February 2025

Abstract
Coral populations worldwide are declining rapidly due to elevated ocean temperatures and other human impacts. The Caribbean harbors a high number of threatened, endangered, and critically endangered coral species compared with reefs of the larger Indo-Pacific. The reef corals of the Caribbean are also long diverged from their Pacific counterparts and may have evolved different survival strategies. Most genomic resources have been developed for Pacific coral species which may impede our ability to study the changes in genetic composition of Caribbean reef communities in response to global change. To help fill the gap in genomic resources, we used PacBio HiFi sequencing to generate the first genome assemblies for 3 Caribbean reef-building corals, Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea. We also explore the genomic novelties that shape scleractinian genomes. Notably, we find abundant gene duplications of all classes (e.g. tandem and segmental), especially in S. siderea. This species has one of the largest genomes of any scleractinian coral (822 Mb) which seems to be driven by repetitive content and gene family expansion and diversification. As the genome size of S. siderea was double the size expected of stony corals, we also evaluated the possibility of an ancient whole-genome duplication using Ks tests and found no evidence of such an event in the species. By presenting these genome assemblies, we hope to develop a better understanding of coral evolution as a whole and to enable researchers to further investigate the population genetics and diversity of these 3 species.
Pakistan’s Judicial Engagement with International Refugee Law
Authors: Kazmi Arjumand Bano 
Published: February 2025

ABSTRACT
This article examines the case law at different tiers of Pakistan’s judiciary in order to map its engagement with international refugee law. Pakistan hosts one of the world’s largest refugee populations, with no national legislation dealing with refugees. Nor has it ratified the 1951 Convention relating to the Status of Refugees (Refugee Convention). Nevertheless, this article shows that Pakistan’s judicial engagement with the Refugee Convention has been meaningful and instructive. Rahil Azizi v The State is used to illustrate how domestic courts can utilize the principle of non-refoulement, as well as article 31 of the Refugee Convention, to deal with the situation of refugees unlawfully in the country of refuge. The judgment instructs the State that the application of existing domestic law for illegal foreigners or refugees should be nuanced and sensitive to their distinct vulnerabilities. Further, it is argued that, by creatively weaving together UNHCR–host State memoranda of understanding with constitutional and international law obligations, courts in non-signatory States can ensure stronger protection for refugees vis-à-vis ad hoc and regressive government policies.
Comparative analysis of routine clinical debriefings and incident reports: insights for patient safety and teamwork enhancement
Authors: Paquay Méryl , Kolbe Michaela , Klenkenberg Sophie , Buléon Clément , Bertrand Audrey , Simon Robert , Ghuysen Alexandre 
Published: February 2025

Abstract

Background
Routine clinical debriefings (RCDs) have been shown to improve communication, team reflexivity, and safety in clinical settings. When combined with incident reports (IRs), RCDs offer a potential tool for enhancing quality improvement frameworks. This study aimed to identify and compare healthcare safety-related information captured through RCDs and IRs in a Belgian emergency department operating across two distinct facilities.

Methods
This study employed a quasi-mixed-method design with a monostrand conversion approach. Information was collected from 90 RCDs and 263 IRs. Data were analyzed using two frameworks: the World Health Organization’s Incident Report Classification Grid and the Debriefing and Organizational Lessons Learned Grid.

Results
The findings revealed significant differences in the types of information captured by RCDs and IRs. RCDs predominantly highlighted teamwork, internal organization, and procedural issues, while IRs focused more on care processes, patient concerns, and patient flow. These complementary insights demonstrate the value of integrating RCDs and IRs to create a comprehensive understanding of patient and clinician safety.

Conclusions
This study highlights the complementary nature of RCDs and IRs in addressing healthcare safety. RCDs foster team reflexivity and promote open discussions about systemic challenges, directly improving team cohesion, resilience, and learning. Combining RCDs and IRs provides actionable insights for enhancing safety and driving organizational improvements.
Widespread yet Unreliable: A Systematic Analysis of the Use of Presence Questionnaires
Authors: Kukshinov Eugene , Tu Joseph , Szita Kata , Senthil Nathan Kaushall , Nacke Lennart E 
Published: February 2025

Abstract
Presence, as a psychological state, is typically assessed using questionnaires. While many researchers in this field assume that these self-report instruments are standardized, the reliability of such questionnaires remains uncertain. This knowledge gap challenges the accuracy and validity of data derived from studies assessing presence. Ensuring reliable and precise data collection and reporting is essential for the credibility of findings in presence research, because inaccuracies may cause errors in conclusions, which affects theoretical understandings, methodological approaches and practical applications. To address this issue, we conducted a systematic analysis of 397 empirical quantitative studies on presence. We investigated the use of presence scales, including applications, modifications, a variety of measures and reporting practices. We found that the majority of the presence studies modify questionnaires, do not re-validate them and improperly report their methods. Based on these findings, we propose solutions to enhance transparency and validation of the presence measurements.