bluuebunny/crossref_metadata_2025_split huggingface dataset:
MultiTax-human: an extensive and high-resolution human-related full-length 16S rRNA reference database and taxonomy
Authors: Bao Zhiwei , Zhang Bin , Yao Jianhua , Li Ming D. 
Published: January 2025

ABSTRACT

Considering that the human microbiota plays a critical role in health and disease, an accurate and high-resolution taxonomic classification is thus essential for meaningful microbiome analysis. In this study, we developed an automatic system, named MultiTax pipeline, for generating
de novo
taxonomy from full-length 16S rRNA sequences using the Genome Taxonomy Database and other existing reference databases. We first constructed the MultiTax-human database, a high-resolution resource specifically designed for human microbiome research and clinical applications. The database includes 842,649 high-quality full-length 16S rRNA sequences, extracted from multiple public repositories and human-related studies, offering a comprehensive and accurate portrayal of the human microbiome. To validate the MultiTax-human database, we profiled the human microbiome across various body sites, identified core microbial taxa, and tested its performance using an independent data set. Additionally, the database is equipped with a user-friendly web interface for easy querying and data exploration. The MultiTax-human database is poised to serve as a valuable tool for researchers, enhancing the precision of human microbiome studies and advancing our understanding of its impact on human health and diseases.

IMPORTANCE
Understanding the human microbiome, the collection of microorganisms in and on our bodies, is essential for advancing health research. Current methods often lack precision and consistency, hindering our ability to study these microorganisms effectively. Our study presents the MultiTax-human database, a high-resolution reference tool specifically designed for human microbiome research. By integrating data from multiple sources and employing advanced classification techniques, this database offers an accurate and detailed map of the human microbiome. This resource enhances the ability of researchers and clinicians to explore the roles of microorganisms in health and disease, potentially leading to improved diagnostics, treatments, and insights into various medical conditions.
Endotracheal tube as chest tube: a back-up alternative in resource limited settings
Authors: Schober Patrick , Giannakopoulos Georgios F , Loer Stephan A , Schwarte Lothar A 
Published: January 2025

Thoracostomies, and subsequent placements of chest tubes (CTs), are a standard procedure in several domains of medicine. In emergency medicine, thoracostomies are indicated to release a relevant hemothorax or pneumothorax, particularly a life-threatening tension pneumothorax. In many cases, an initial finger-assisted thoracostomy is followed by placement of a CT to ensure continuous decompression of blood and air. CTs prevent the reoccurrence of a hemothorax or pneumothorax, which may otherwise develop by closure of the initial thoracostomy incision. CTs are commercial, purpose-made products; however, in certain settings, those may not be readily available. Triggered by own experience, we review the use of endotracheal tubes as back-up alternatives to commercial CTs.On a structural base, commercial CTs may not be available in economically challenged regions. Furthermore, in settings with restricted capacity for equipment weight and volume, for example, in mountain rescue backpacks, it might not be feasible to carry CTs, even if the care provider is adequately trained. Finally, care providers may run out of stock of commercial CTs, for example, in civil mass casualty (‘MASCAL’) scenarios, natural disasters or on the battlefield with difficult resupply. Literature on this topic is very limited. In this manuscript, we discuss the advantages and disadvantages of standard endotracheal tubes as alternatives in settings, where commercial CTs are not readily available.Although certainly not advocated as standard, the use of endotracheal tubes as CTs may be a suitable alternative or back-up solution in settings where commercial CTs are not readily available. We assume that this technique will be particularly of interest in settings with a high risk for thoracic injuries and limited availability of commercial CTs, for example, in military conflicts. Given the virtual absence of scientific data, more research on risks, benefits and patient outcome is required.
Relationship between left ventricular shape and cardiovascular risk factors: comparison between the Multi-Ethnic Study of Atherosclerosis and UK Biobank
Authors: Suinesiaputra Avan , Gilbert Kathleen , Mauger Charlene , Bluemke David A , Wu Colin O , Aung Nay , Neubauer Stefan , Piechnik Stefan K , Petersen Steffen E , Lima Joao A C , Ambale Venkatesh Bharath , Young Alistair 
Published: January 2025

BackgroundStatistical shape atlases have been used in large-cohort studies to investigate relationships between heart shape and risk factors. The generalisability of these relationships between cohorts is unknown. The aims of this study were to compare left ventricular (LV) shapes in patients with differing cardiovascular risk factor profiles from two cohorts and to investigate whether LV shape scores generated with respect to a reference cohort can be directly used to study shape differences in another cohort.MethodsTwo cardiac MRI cohorts were included: 2106 participants (median age: 65 years, 54% women) from the Multi-Ethnic Study of Atherosclerosis (MESA) and 2960 participants (median age: 64 years, 52% women) from the UK Biobank (UKB) study. LV shape atlases were constructed from 3D LV models derived from expert-drawn contours from separate core labs. Atlases were considered generalisable for a risk factor if the area under the receiver operating characteristic curves (AUC) were not significantly different (p>0.05) between internal (within-cohort) and external (cross-cohort) cases.ResultsLV mass and volume indices were differed significantly between cohorts, even in age-matched and sex-matched cases without risk factors, partly reflecting different core lab analysis protocols. For the UKB atlas, internal and external discriminative performance were not significantly different for hypertension (AUC: 0.77 vs 0.76, p=0.37), diabetes (AUC: 0.79 vs 0.77, p=0.48), hypercholesterolaemia (AUC: 0.76 vs 0.79, p=0.38) and smoking (AUC: 0.69 vs 0.67, p=0.18). For the MESA atlas, diabetes (AUC: 0.79 vs 0.74, p=0.09) and hypercholesterolaemia (AUC: 0.75 vs 0.70, p=0.10) were not significantly different. Both atlases showed significant differences for obesity.ConclusionsThe MESA and UKB atlases demonstrated good generalisability for diabetes and hypercholesterolaemia, without requiring corrections for differences in mass and volume. Significant differences in obesity may be due to different relationships between obesity and heart shapes between cohorts.
Cost-effectiveness of digoxin versus beta blockers in permanent atrial fibrillation: the Rate Control Therapy Evaluation in Permanent Atrial Fibrillation (RATE-AF) randomised trial
Authors: Abdali Zainab , Bunting Karina V , Mehta Samir , Camm John , Rahimi Kazem , Stanbury Mary , Haynes Sandra , Kotecha Dipak , Jowett Sue 
Published: January 2025

BackgroundAtrial fibrillation (AF) is a major and increasing burden on health services. This study aimed to evaluate the cost-effectiveness of digoxin versus beta-blockers for heart rate control in patients with permanent AF and symptoms of heart failure.MethodsRAte control Therapy Evaluation in permanent Atrial Fibrillation (RATE-AF) was a randomised, open-label, blinded, endpoint trial embedded in the UK National Health Service (NHS) to directly compare low-dose digoxin with beta-blockers (ClinicalTrials.gov:NCT02391337). A trial-based cost-utility analysis was performed from a healthcare perspective over 12 months. Resource use in primary and secondary healthcare services, medications and patient-reported quality of life were prospectively collected to estimate differences in costs and quality-adjusted life years (QALYs).ResultsRATE-AF randomised 160 patients with mean age of 76 (SD 8) years and 46% women, of which 149 patients (n=73 digoxin, n=76 beta blockers) had complete data and survived to 12-month follow-up. Treatment with digoxin was significantly less costly, with a mean saving of £530.41 per patient per year (95% CI −£848.06 to −£249.38, p=0.001). This was principally due to substantially lower rates of adverse events, with less primary and secondary healthcare utilisation compared with beta-blocker therapy. There was no significant difference in QALYs (0.013; 95% CI −0.033 to 0.052, p=0.56). At the £20 000 per-QALY willingness to pay threshold, the probability of digoxin being cost-effective compared with beta-blockers was 94%, with potential annual savings to the NHS of £102 million/year (95% CI £48 million to £164 million saving, p=0.001).ConclusionsDigoxin is a less costly option when compared with beta-blockers for control of heart rate in suitable patients with permanent AF, with larger cost-effectiveness studies warranted to advise on national and global policy-making.Trial registration numberNCT02391337, EudraCT 2015-005043-13.
Mechanical circulatory support for patients with infarct-related cardiogenic shock: a state-of-the-art review
Authors: Moller Jacob Eifer , Thiele Holger , Zeymer Uwe , Proudfoot Alastair , Hassager Christian 
Published: January 2025

Acute myocardial infarction-related cardiogenic shock (AMI-CS) is a severe, life-threatening condition characterised by inadequate tissue perfusion due to the heart’s inability to pump blood effectively. The pathophysiology of AMI-CS usually arises from the sudden loss of myocardial contractility, leading to a decrease in cardiac output and systemic hypoperfusion. In approximately 90% of AMI-CS cases, the left ventricle is the primary site of dysfunction.Despite early recognition and the implementation of strategies such as primary percutaneous coronary intervention, the mortality rate associated with AMI-CS remains alarmingly high, reflecting significant unmet clinical needs. A major challenge lies in identifying the optimal patient population for mechanical circulatory support (MCS) devices, as these interventions are costly and can lead to serious complications.This review provides a comprehensive overview of the pathophysiological mechanisms underlying AMI-CS, explores the current range of MCS devices available and offers an in-depth discussion on the balance of benefits and risks associated with these devices. By highlighting key evidence from recent studies, we aim to shed light on the clinical decision-making process and improve outcomes in this high-risk patient population.
Transitioning to high-sensitivity troponin: 1-year mortality outcomes in patients with suspected acute coronary syndrome presenting to emergency departments
Authors: Hickling Siobhan , Sanfilippo Frank M , Cullen Louise , Chew Derek P , Hillis Graham S , Fatovich Daniel M , Karnon Jonathon , Rankin Jamie , Nedkoff Lee , Scanlan Samuel , Hickman Peter E , Stapleton Stuart , Knuiman Matthew , Parsonage William , Mitra Biswadev , Schneider Hans G , Wilkes Garry , Robinson Teagan , Briffa Tom 
Published: January 2025

BackgroundSwitching from a conventional to a high-sensitivity cardiac troponin (hs-cTn) assay enables detection of smaller amounts of myocardial damage, but the clinical benefit is unclear. We investigated whether switching to a hs-cTnI assay with a sex-specific 99th centile diagnostic threshold was associated with lower 1-year death or new myocardial infarction (MI) in patients with suspected acute coronary syndrome (ACS).MethodsThis pre–post study included nine tertiary hospitals in Australia. During the pre-hs-cTn period, all hospitals used conventional troponin assays, and during the postperiod, four switched to using hs-cTnI. Participants were ≥20 years old and presenting to emergency departments (EDs) with suspected ACS between March 2011 and November 2015. Outcomes were determined using linked administrative data and compared using Kaplan-Meier and Cox regression analyses.ResultsWe identified 179 681 consecutive patients (62 (SD 19) years, 47% women), 87 019 (48%) during the preperiod, and 92 662 (52%) during the postperiod. Following the switch to hs-TnI, the proportion of patients diagnosed with new MI was not significantly different (3.9% postperiod vs 4.2% preperiod; p=0.08) while diagnoses of unstable angina were lower (1.5% postperiod vs 2.5% preperiod; p<0.0001). In non-switching jurisdictions, rates of new MI remained stable, while diagnoses of unstable angina increased. Switching to hs-cTnI assay was associated with lower mortality at 30 days (adjusted HR 0.88 (0.82, 0.95)) and 1 year (aHR 0.90 (0.85, 0.94)). The corresponding aHRs for non-switching jurisdictions were not statistically different.ConclusionThe use of an hs-cTnI assay in an ED population with suspected ACS was associated with lower mortality at 1 year.
Phenotypic and transcriptomic changes in Acinetobacter baumannii in rich and minimal growth mediums
Authors: Kornelsen Vanessa , White Dawn , Kumar Ayush 
Published: January 2025

Acinetobacter baumannii is an opportunistic pathogen that is often studied in commonly used rich media in laboratories worldwide. Due to the metabolic versatility of A. baumannii, it can be cultured in different growth mediums; however, this can lead to genotypic and phenotypic variations. In this study, we compared phenotypic and transcriptomic changes in A. baumannii ATCC17978-VU cultured in M9 minimal media supplemented with 20 mmol/L sodium succinate and rich lysogeny broth media. Phenotypically, growth was significantly slowed, virulence in Galleria mellonella was attenuated, and susceptibility to a variety of antibiotic classes was reduced when A. baumannii ATCC17978-VU was grown in minimal media versus rich media. Transcriptomic analysis showed differential regulation of >700 genes—including those associated with energy production and ribosomal function—when the two growth conditions were compared, with the majority of the upregulated genes seen in minimal media of unknown function. This study showed that culture media has a profound effect on the phenotype and cellular workings of a bacteria, highlighting the need for more studies of pathogens like A. baumannii ATCC17978-VU in minimal media.
Seasonal changes in the movement rates and activity patterns of Canada lynx
Authors: Kynoch M.C. , Williams C.T. , Breed G.A. , Kielland K. 
Published: January 2025

In Subarctic and Arctic environments, daily patterns of activity and space-use are strongly influenced by interplay between seasonal abiotic factors and the corresponding responses of the biotic environment. Here, we combined accelerometry with GPS telemetry of Canada lynx ( Lynx canadensis Kerr, 1792, n = 12) in northern Alaska to test the hypotheses that lynx activity would peak during twilight throughout the year, coinciding with activity of their preferred prey, and that individuals with larger home ranges would have greater spatial displacement and expend more energy on movement. Lynx activity occurred throughout the 24 h day and peaked during twilight, but variation among individuals was high and diel rhythms were sometimes only detectable using the finer resolution accelerometer data. Surprisingly, home range size was not correlated with movement costs estimated via acceleration, but step length and acceleration were correlated in a positive curvilinear fashion. However, step length was sometimes disproportionately lower than predicted by acceleration. Such intervals of high activity with low spatial displacement were often followed by periods of rest, suggesting they may be indicative of hunting in a restricted patch of habitat. We conclude that accelerometers can provide additional information to supplement GPS data, providing a more complete picture of animal behavior.
Simulation of satellite and optical link dynamics in a quantum repeater constellation
Authors: Meister Jaspar , Kleinpaß Philipp , Orsucci Davide 
Published: January 2025

Abstract
Quantum repeaters and satellite-based optical links are complementary technological approaches to overcome the exponential photon loss in optical fibers and thus allow quantum communication on a global scale. We analyze architectures which combine these approaches and use satellites as quantum repeater nodes to distribute entanglement to distant optical ground stations. Here we simulate dynamic, three-dimensional ground station passes, going beyond previous studies that typically consider static satellite links. For this, we numerically solve the equations of motion of the dynamic system consisting of three satellites in low Earth orbit. The model of the optical link takes into account atmospheric attenuation, single-mode fiber coupling, beam wandering and broadening, as well as adaptive optics effects. We derive analytical expressions for the Bell state measurement and associated error rates for quantum memory assisted communications, including retrieval efficiency and state coherence. We consider downlink and uplink architectures for continental and intercontinental connections and evaluate the impact of satellite altitude and inter-satellite distance on the expected entanglement swapping rate. Our simulation model enables us to design different orbital configurations for the satellite constellation and analyze the annual performance of the quantum repeater under realistic conditions.
Maximizing Data and Hardware Reuse for HLS with Early-Stage Symbolic Partitioning
Authors: Juang Tzung-Han , Dubach Christophe 
Published: January 2025

While traditional HLS (High-Level Synthesis) converts “high-level” C-like programs into hardware automatically, producing high-performance designs still requires hardware expertise. Optimizations such as data partitioning can have a large impact on performance since they directly affect data reuse patterns and the ability to reuse hardware. However, optimizing partitioning is a difficult process since minor changes in the parameter choices can lead to totally unpredictable performance.
Functional array-based languages have been proposed instead of C-based approaches, as they offer stronger performance guarantees. This paper proposes to follow a similar approach and exposes a divide-and-conquer primitive at the algorithmic level to let users partition any arbitrary computation. The compiler is then free to explore different partition shapes to maximize both data and hardware reuse automatically. The main challenge remains that the impact of partitioning is only known much later in the compilation flow. This is due to the hard-to-predict effects of the many optimizations applied during compilation.
To solve this problem, the partitioning is expressed using a set of symbolic tunable parameters, introduced early in the compilation pipeline. A symbolic performance model is then used in the last compilation stage to predict performance based on the possible values of the tunable parameters. Using this approach, a design space exploration is conducted on an Intel Arria 10 FPGAs (Field Programmable Gate Arrays), and competitive performance is achieved on the classical VGG and TinyYolo neural networks.
Acrocyanosis: The Least Known Acrosyndrome Revisited With a Dermatologic Perspective
Authors: Demircioğlu Deniz , Öztürk Durmaz Emel 
Published: January 2025

Background: Acrocyanosis is a functional peripheral vascular disorder, currently categorized under the canopy of acrosyndromes, i.e., a group of clinically similar and significantly overlapping vascular disorders involving the acral skin. The disorder might be primary or secondary, depending on the cause. Recently, there has been a remarkable surge in acrocyanosis prevalence along with the COVID‐19 pandemic. Both COVID‐19 infection and vaccines for COVID‐19 have been affixed to the list of disorders instigating acrocyanosis.Objectives: The goal of this narrative review was to evaluate the existing literature, project acrocyanosis from the viewpoint of dermatologists in the face of the COVID‐19 pandemic, and assess the need for targeted research, education, and/or clinical practice.Methods: An English literature search was conducted using PubMed and Google. All abstracts on acrocyanosis, irrespective of the article type and publication date, were retrieved and reviewed and those most relevant for the focus of this article were selected and summarized.Discussion/Results: A narrative review was carried out. There is paucity of randomized, double‐blind, placebo‐controlled studies on acrocyanosis in the English literature, implicating the need for targeted research. Pertinent information still relies on anecdotal observations, case reports, case series, or scarce reviews, which are dated rather old and published in vascular‐oriented journals. The scarcity of published literature on acrocyanosis in dermatology‐oriented journals points to the necessity of professional education and improvement of clinical diagnostic skills for dermatologists.Conclusions: Although acrocyanosis is the least known and the least studied acrosyndrome, it is increasingly more commonly confronted in the COVID‐19 era. The diagnosis still largely relies on clinical findings. Accordingly, it has become a growing necessity for a dermatologist to remain updated on this peculiar disorder and be able to differentiate acrocyanosis from clinically similar cold‐induced or cold‐exacerbated acrosyndromes. Acrocyanosis is still misdiagnosed, underdiagnosed, underreported, and undertreated by the dermatology community.
Adopting a Dyadic Approach to Treating Chronic Cancer‐Related Fatigue: A Mixed Methods Study to Assess Patients’ and Partners’ Needs, Benefits, Barriers and Preferences
Authors: van Dongen Sophie I. , Müller Fabiola , van Woezik Rosalie A. M. , Hagedoorn Mariët , van der Lee Marije L. 
Published: January 2025

Introduction: Chronic cancer‐related fatigue (CCRF) is a common symptom among patients. Current therapies target the patient alone, while evidence suggests that targeting the dyad might be more beneficial.Method: Using a mixed methods design, we conducted two studies that together aimed to provide more insight into the needs, benefits, barriers and preferences regarding a couples therapy for CCRF. In a qualitative study, we conducted focus groups and semi‐structured interviews with a purposive sample of 10 patients and 10 partners with experience of CCRF care, followed by thematic analysis. In a subsequent quantitative study, a convenience sample of patients (n = 172) and partners (n = 55) completed an online survey developed based on the qualitative findings.Results: In the qualitative study, both patients and partners expressed that a couples therapy could help them. Perceived benefits included empowerment of partners to support patients and improved couples communication. In the online survey, the need for a dyadic approach to CCRF therapy was confirmed by both patients (39%) and partners (91%). The benefits reported by most patients and partners were that partners could get attention for their own problems related to the patients’ cancer and fatigue (patients: 72%, partners: 86%) and receive advice on coping with fatigue (66% and 90%, respectively). Participants in both studies identified barriers, such as a fear of burdening partners with a couples therapy (50%). Partner involvement was considered desirable for most therapy elements (e.g., psychoeducation, contact with the therapist, exercises and relapse prevention). Yet, individual preferences varied widely.Conclusion: Results of both studies support the potential acceptability of a couples therapy for CCRF among patients and partners. Based on divergent preferences, we determined that a couples therapy must provide flexibility regarding the degree, intensity and type of partner involvement. Dyadic psychoeducation can be used as a solid starting point to manage expectations and get relief from perceived barriers.