bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring suitability to electrical storm ablation in patients in waiting list for heart transplantation: A single center experience
Authors: Gigli Lorenzo , Preda Alberto , Varrenti Marisa , Baroni Matteo , Vargiu Sara , Guarracini Fabrizio , Ammirati Enrico , Mazzone Patrizio 
Published: July 2024

AbstractElectrical storm (ES) is among the most fearsome events in patients in waiting list for heart transplantation (HT) and catheter ablation (CA) demonstrated to be effective in reduce the arrhythmic burden. However, selection criteria for CA suitability in this specific population have never been addressed before. We retrospectively enrolled 36 patients (mean age 51 ± 8 years; 83% men) waiting HT referred to our department for ES resistant to antiarrhythmic drugs and percutaneous stellate ganglion blockade. Twenty patients were judged suitable for VT ablation according to specific criteria including absence of increased arrhythmic burden secondary to volume overload and hemodynamic decompensation; expected CA outcome favorable due to etiology of the cardiomyopathy, no need for coronary revascularization and technical feasibility of the procedure. The pre‐emptive use of mechanical circulatory supports (MCS) were discussed integrating the PAINESD score with additional clinical and hemodynamic parameters. Acute procedural success was accounted in 85% of cases with only two major complications. The CA group reported lower length of in‐hospital stay after CA suitability evaluation (56 ± 17 vs. 131 ± 64 days, p = .004). Furthermore, at a mean follow‐up of 703 ± 145 days, this group showed reduction of ventricular arrhythmia (VA) recurrence leading to implantable cardioverter defibrillator shock (4 vs. 8, p = .051) and underwent HT with a lower level of urgency (0 vs. 6 patients needed for UNOS1 status upgrade). Respectively, one patient of the CA group and two patients of the conservative group died (p = .839). At the end of follow‐up, eight patients underwent heart transplantation (p = .964) while four patients underwent Left Ventricular Assist device (LVAD) implantation (p = .440). This pilot study should be a proof for further studies exploring CA of VAs as a possible bridge therapy to HT.
Acute Kidney Injury Requiring Dialysis After Pediatric Heart Transplant
Authors: Lipman Amy R. , Lytrivi Irene D. , Fernandez Hilda E. , Lynch Aine M. , Yu Miko E. , Stevens Jacob S. , Mohan Sumit , Husain Syed Ali 
Published: July 2024

ABSTRACTBackgroundAcute kidney injury (AKI) is a common complication of pediatric heart transplant, with a subset of patients developing severe AKI requiring dialysis (AKI‐D). We aimed to identify the epidemiology, risk factors, and outcomes of postoperative AKI‐D in pediatric heart transplant recipients.MethodsWe retrospectively identified all pediatric first‐time, single‐organ heart transplants at our institution from 2014 to 2022. Postoperative AKI was defined as AKI within 2 weeks of transplant. Unadjusted and adjusted logistic regression were used to identify characteristics associated with AKI‐D, and unadjusted time‐to‐event analyses were used to determine the association between AKI‐D and survival free of kidney failure.ResultsAmong 177 patients included, 116 (66%) developed postoperative AKI of any stage, including 13 (7%) who developed AKI‐D with median time from transplant to dialysis initiation of 6 days (IQR 3–13). In adjusted models, increased cardiopulmonary bypass time (OR 1.19, 95% CI 1.04–1.37, per 15 min increase in bypass time) and higher weight at transplant were associated with higher odds of AKI‐D, whereas patient demographics and pretransplant kidney function were not associated with AKI‐D. AKI‐D was associated with greater mortality during initial hospitalization (46% vs. 1%, p < 0.001) and a lower rate of survival free of kidney failure.ConclusionsThe incidence of AKI‐D after pediatric heart transplant was 7%, with extended cardiopulmonary bypass time associated with postoperative AKI‐D even in adjusted models. Further research is needed to improve the prediction and management of AKI‐D in this population.
A causal modeler's guide to double effect reasoning
Authors: Rothfus Gerard J. 
Published: July 2024

AbstractTrolley problems and like cases are often thought to show the inadequacy of purely consequentialist moral theories. In particular, they are often taken to reveal that consequentialists unduly neglect the moral significance of the causal structure of decision problems. To precisify such critiques and one sort of deontological morality they motivate, I develop a formal modeling framework within which trolley problems can be represented as suitably supplemented structural causal models and various consequentialist and double effect‐inspired moral theories can be viewed as disagreeing over the inputs of a common decision rule.
Does leadership promote a cleaner climate?
Authors: Mideksa Torben 
Published: July 2024

AbstractThe Paris Agreement encourages developed countries to lead in reducing emissions. Using a model of national emissions, I examine whether leadership improves global welfare. The results suggest that leadership reduces global emissions when the leader's abatement generates cost‐reducing spillover effects or conveys private information about abatement costs. With spillover effects, the leader abates more to incentivize a greater reduction of emissions by followers. Under private information, the leader abates more to signal the abatement cost. If it has to choose between transparency and no transparency, the leader commits to transparency despite this being inefficient. Besides, I find sequential abatement stable against unilateral deviation.
Role of adaptor protein complexes in generating functionally distinct synaptic vesicle pools
Authors: Asmerian Hrach , Alberts Jacob , Sanetra Anna M. , Diaz Alexia J. , Silm Katlin 
Published: July 2024

AbstractThe synaptic vesicle (SV) cycle ensures the release of neurotransmitters and the replenishment of SVs to sustain neuronal activity. Multiple endocytosis and sorting pathways contribute to the recapture of the SV membrane and proteins after fusion. Adaptor protein (AP) complexes are among the critical components of the SV retrieval machinery. The canonical clathrin adaptor AP2 ensures the replenishment of most SVs across many neuronal populations. An alternative AP1/AP3‐dependent process mediates the formation of a subset of SVs that differ from AP2 vesicles in molecular composition and respond preferentially during higher frequency firing. Furthermore, recent studies show that vesicular transporters for different neurotransmitters depend to a different extent on the AP3 pathway and this affects the release properties of the respective neurotransmitters. This review focuses on the current understanding of the AP‐dependent molecular and functional diversity among SVs. We also discuss the contribution of these pathways to the regulation of neurotransmitter release across neuronal populations.
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Analytic Modeling of Two-Dimensional Transient Heat Conduction With Heat Source Under Mixed Boundary Constraints by Symplectic Superposition
Authors: Xu Dian , Li Jinbao , Wang Zixuan , Xiong Sijun , He Qianqiang , Li Rui 
Published: July 2024

Abstract
Many studies have been conducted on two-dimensional (2D) transient heat conduction, but analytic modeling is still uncommon for the cases with complex boundary constraints due to the mathematical challenge. With an unusual symplectic superposition method (SSM), this paper reports new analytic solutions to 2D isotropic transient heat conduction problems with heat source over a rectangular region under mixed boundary constraints at an edge. With the Laplace transform, the Hamiltonian governing equation is derived. The applicable mathematical treatments, e.g., the variable separation and the symplectic eigenvector expansion in the symplectic space, are implemented for the fundamental solutions whose superposition yields the ultimate solutions. Benchmark results obtained by the present method are tabulated, with verification by the finite element solutions. Instead of the conventional Euclidean space, the present symplectic-space solution framework has the superiority on rigorous derivations without predetermining solution forms, which may be extended to more issues with the complexity caused by mixed boundary constraints.
Draft genome of
Bacillus subtilis
strain YB955, prophage-cured derivative of strain 168
Authors: Perez Ryan King , Chavez Rios Jocelyn Sofia , Grifaldo Jessica , Regner Kurt , Pedraza-Reyes Mario , Robleto Eduardo A. 
Published: July 2024

ABSTRACT

We report the genome sequence of
Bacillus subtilis
strain YB955, a prophage-cured strain used as a model in DNA repair, bacterial physiology, and mutagenesis studies. The assembled and annotated draft genome contains 4,031 coding genes, 5 rRNAs, and 73 tRNAs. Compared to 168, YB955 has a 134,402 bp deletion.
Draft genome sequence of
Collimonas
sp. strain H4R21, an effective mineral-weathering bacterial strain isolated from the beech rhizosphere
Authors: E. Morin , S. Uroz , R. Kumar , M.W. Rey , J. Pham , F. Akum , J. H. J. Leveau 
Published: July 2024

ABSTRACT

We present the draft genome sequence of
Collimonas
sp. strain H4R21, isolated from the rhizosphere of
Fagus sylvatica
in the forest experimental site of Montiers (France). This genome features coding capacity for plant growth promotion, such as the ability to solubilize minerals, to produce siderophores and antifungal secondary metabolites.
Whole-genome sequence of
Enterobacter hormaechei
, isolate
jjbc
recovered from the gut of
Plutella xylostella
feeding on cabbage
Authors: Mugo-Kamiri Loretta , Schäfer Lea , Wennmann Jörg T. , Herniou Elisabeth A. , Raymond Ben 
Published: July 2024

ABSTRACT

We present the whole-genome sequence of
Enterobacter hormaechei
(previously
Enterobacter cloacae
) obtained from long and short reads. It is a dominant gut symbiont of the notorious crop pest
Plutella xylostella
, highly prevalent in lepidopteran midguts and a useful model for the evolution of resistance to antimicrobials.
Metagenome-assembled bacterial genomes derived from various aging flue-cured tobacco samples
Authors: Li Minghou , Dong Yingjie , Liu Chen , Liu Haoran , Wang Zhen , Ma Jingru , Wang Xinhui , Zhang Xiaojun 
Published: July 2024

ABSTRACT

We recovered 16 bacterial metagenome-assembled genomes from 11 flue-cured tobacco samples with different aging stage and various geographic origins. Their sizes range from 2.3 M to 5.4 M, with GC contents of 43.17%–74.45%, completeness of 78.80%–99.25%, and contamination of 0.47%–8.56%.
Draft genome sequence of multidrug-resistant
Kurthia gibsonii
strain Hakim RU_BHWE isolated from sewage water in Bangladesh
Authors: Romance M. , Polash Md. Arif-Uz-Zaman , Zahan Nusrat , Raihan Jafor , Ali Md. Sumon , khan Muhib Ullah , Sarker Subir , Haque Md. Hakimul 
Published: July 2024

ABSTRACT

We have sequenced the genome of Kurthia
gibsonii
strain Hakim RU_BHWE, isolated from sewage water. The assembled genome consists of 2.891 Mb with 58.6883× coverage, presenting an average GC content of 36.60%. This genome includes 8 CRISPR arrays, 3 prophages, 3 antibiotic resistance genes, and 12 virulence factor genes.
Whole-genome sequences of
Helicobacter pylori
isolated from patients with high risk of gastric cancer in the Andes of Nariño, Colombia
Authors: Guzman Kevin Andres , Daza Angi Paola , Gomez Rudy Viviana , Montenegro Lidia Madeline , Pazos Alvaro 
Published: July 2024

ABSTRACT

We sequenced the complete genomes of 16
Helicobacter pylori
isolates obtained from patients residing in Nariño, Colombia. These isolates were collected from patients presenting various gastric lesions classified according to the Correa cascade classification. The genomic characterization of these isolates provides valuable insights into the structure, composition, and pathogenicity.
Beav: a bacterial genome and mobile element annotation pipeline
Authors: Jung Jewell M. , Rahman Arafat , Schiffer Andrea M. , Weisberg Alexandra J. 
Published: July 2024

ABSTRACT

Comprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optional
Agrobacterium
-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download at
https://github.com/weisberglab/beav
.

IMPORTANCE
Annotation of genome features, such as the presence of genes and their predicted function, or larger loci encoding secretion systems or biosynthetic gene clusters, is necessary for understanding the functions encoded by an organism. Genomes can also host diverse mobile genetic elements, such as integrative and conjugative elements and/or phages, that are often not annotated by existing pipelines. These elements can horizontally mobilize genes encoding for virulence, antimicrobial resistance, or other adaptive functions and alter the phenotype of an organism. We developed a software pipeline, called Beav, that combines new and existing tools for the comprehensive annotation of these and other major features. Existing pipelines often misannotate loci important for virulence or mutualism in plant-associated bacteria. Beav includes custom databases and optional workflows for the improved annotation of plant-associated bacteria. Beav is designed to be easy to install and run, making comprehensive genome annotation broadly available to the research community.
Deep learning-based image quality assessment for optical coherence tomography macular scans: a multicentre study
Authors: Tang Ziqi , Wang Xi , Ran An Ran , Yang Dawei , Ling Anni , Yam Jason C , Zhang Xiujuan , Szeto Simon K H , Chan Jason , Wong Cherie Y K , Hui Vivian W K , Chan Carmen K M , Wong Tien Yin , Cheng Ching-Yu , Sabanayagam Charumathi , Tham Yih Chung , Liew Gerald , Anantharaman Giridhar , Raman Rajiv , Cai Yu , Che Haoxuan , Luo Luyang , Liu Quande , Wong Yiu Lun , Ngai Amanda K Y , Yuen Vincent L , Kei Nelson , Lai Timothy Y Y , Chen Hao , Tham Clement C , Heng Pheng-Ann , Cheung Carol Y 
Published: July 2024

Aims
To develop and externally test deep learning (DL) models for assessing the image quality of three-dimensional (3D) macular scans from Cirrus and Spectralis optical coherence tomography devices.

Methods
We retrospectively collected two data sets including 2277 Cirrus 3D scans and 1557 Spectralis 3D scans, respectively, for training (70%), fine-tuning (10%) and internal validation (20%) from electronic medical and research records at The Chinese University of Hong Kong Eye Centre and the Hong Kong Eye Hospital. Scans with various eye diseases (eg, diabetic macular oedema, age-related macular degeneration, polypoidal choroidal vasculopathy and pathological myopia), and scans of normal eyes from adults and children were included. Two graders labelled each 3D scan as gradable or ungradable, according to standardised criteria. We used a 3D version of the residual network (ResNet)-18 for Cirrus 3D scans and a multiple-instance learning pipline with ResNet-18 for Spectralis 3D scans. Two deep learning (DL) models were further tested via three unseen Cirrus data sets from Singapore and five unseen Spectralis data sets from India, Australia and Hong Kong, respectively.

Results
In the internal validation, the models achieved the area under curves (AUCs) of 0.930 (0.885–0.976) and 0.906 (0.863–0.948) for assessing the Cirrus 3D scans and Spectralis 3D scans, respectively. In the external testing, the models showed robust performance with AUCs ranging from 0.832 (0.730–0.934) to 0.930 (0.906–0.953) and 0.891 (0.836–0.945) to 0.962 (0.918–1.000), respectively.

Conclusions
Our models could be used for filtering out ungradable 3D scans and further incorporated with a disease-detection DL model, allowing a fully automated eye disease detection workflow.
Novel machine learning algorithm in risk prediction model for pan-cancer risk: application in a large prospective cohort
Authors: Wu Xifeng , Tu Huakang , Hu Qingfeng , Tsai Shan Pou , Ta-Wei Chu David , Wen Chi-Pang 
Published: July 2024

Objective
To develop and validate machine-learning models that predict the risk of pan-cancer incidence using demographic, questionnaire and routine health check-up data in a large Asian population.

Methods and analysis
This study is a prospective cohort study including 433 549 participants from the prospective MJ cohort including a male cohort (n=208 599) and a female cohort (n=224 950).

Results
During an 8-year median follow-up, 5143 cancers occurred in males and 4764 in females. Compared with Lasso-Cox and Random Survival Forests, XGBoost showed superior performance for both cohorts. The XGBoost model with all 155 features in males and 160 features in females achieved an area under the curve (AUC) of 0.877 and 0.750, respectively. Light models with 31 variables for males and 11 variables for females showed comparable performance: an AUC of 0.876 (95% CI 0.858 to 0.894) in the overall population and 0.818 (95% CI 0.795 to 0.841) in those aged ≥40 years in the male cohort and an AUC of 0.746 (95% CI 0.721 to 0.771) in the overall population and 0.641 (95% CI 0.605 to 0.677) in those aged ≥40 years in the female cohort. High-risk individuals have at least ninefold higher risk of pan-cancer incidence compared with low-risk groups.

Conclusion
We developed and internally validated the first machine-learning models based on routine health check-up data to predict pan-cancer risk in the general population and achieved generally good discriminatory ability with a small set of predictors. External validation is warranted before the implementation of our risk model in clinical practice.
Suicide in Hong Kong during the COVID-19 pandemic: an observational study
Authors: Bai Anying , Li Jinjian , Pan Yuhang , Jiang Yu 
Published: July 2024

IntroductionThe COVID-19 pandemic has exacerbated suicide risk factors in Hong Kong, which faces economic shocks and strict travel restrictions due to its unique economic structure and geographical location. However, there is a scarcity of reliable empirical evidence regarding the relationship between the pandemic and suicide mortality. This study examines whether changes in the suicide rate align with COVID-19 situations and anti-COVID-19 policy events in Hong Kong, focusing on vulnerable population groups based on demographic and socioeconomic characteristics.MethodsSuicide data spanning 1 January 2019 to 31 December 2022 were sourced from the Hong Kong Suicide Press Database. Case-level data were aggregated monthly by district. Population-weighted Poisson regression with district-level fixed effects was employed to analyse suicide patterns and their association with COVID-19 developments. Robustness checks and demographic-based heterogeneity analysis were conducted, distinguishing suicide risk among different population groups.ResultsA total of 4061 suicide cases were analysed, encompassing deaths and attempts. The first wave of the pandemic saw a 30% decline in suicide cases compared with the 2019 average, while the second and fifth waves witnessed increases of 33% and 51% in suicide rates, respectively. Older adults and individuals with lower socioeconomic status were particularly susceptible to the adverse effects, as evidenced by a significant rise in suicides during the fifth wave.ConclusionsThe findings underscore the importance of targeted interventions to address the mental health needs of vulnerable populations during pandemics, highlighting the impact of COVID-19 situations and antipandemic policies on the suicide rate.
Monitoring the progress and impact of a multicountry, interdisciplinary research project on childhood stunting: the UKRI GCRF Action Against Stunting Hub MEL protocol
Authors: D M Dinesh Yadav , Tata Darius Tetsa , Jobarteh Modou Lamin , Ndulu Ndolo Rose , Banjara Santosh Kumar , Augustine Little Flower , Manne Munikumar , Kulkarni Bharati , Diop Assana , Tairou Fassiatou , Fatou Ndiaye Diop Camara , Faye Babacar , Fahmida Umi , Htet Min Kyaw , Zahra Nur L , Sudibya Arienta R P , Naab Francis , Harder Marie K , Knott Chelsey Victoria , Waddington Hugh Sharma , Heffernan Claire 
Published: July 2024

IntroductionMonitoring, Evaluation and Learning (MEL) is an integral part of research, programme and policy development and implementation. However, MEL methods used to monitor and evaluate interdisciplinary research projects are often informal and under-reported. This article describes the MEL protocol of the UKRI GCRF Action Against Stunting Hub (AASH).Methods and analysisThe AASH conducts interdisciplinary research into childhood stunting in India, Indonesia and Senegal across 23 distinct work packages. Project-specific MEL framework and methods will be implemented. A logframe will be developed to monitor and evaluate the research activities across the field sites including the number of participants recruited, questionnaires, measurements and procedures completed. MEL dashboards using Tableau and Glasscubes will be used to track and report progress, milestones and outcomes of the project. Dashboard outputs will be reported as numbers and percentages, with additional graphs/charts for easy visualisation. A ‘learning’ framework will be developed to outline appropriate pipelines for the dissemination of the research findings. This includes a theory of change explicating the overarching ambitions of the project in influencing policy, practice and research, and strategic engagement of relevant stakeholders to evaluate knowledge, attitudes and best practices for impactful engagement and dissemination of the research findings.Ethics and disseminationEthical approval was granted by the Ethics Committee of the London School of Hygiene & Tropical Medicine (17915/RR/17513); National Institute of Nutrition (ICMR)–Ministry of Health and Family Welfare, Government of India (CR/04/I/2021); Health Research Ethics Committee, University of Indonesia and Cipto Mangunkusumo Hospital (KET-887/UN2.F1/ETIK/PPM.00.02/2019); and the National Ethics Committee for Health Research (CNERS), Senegal (Protocole SEN19/78). Findings from this work will be published in peer-reviewed journals, presented in conferences and disseminated to policy makers and research communities.