bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues
Authors: Zhang Ying , Wang Zhikang , Zhang Yiwen , Li Shanshan , Guo Yuming , Song Jiangning , Yu Dong-Jun 
Published: November 2023

Abstract

Motivation
RNA N6-methyladenosine (m6A) in Homo sapiens plays vital roles in a variety of biological functions. Precise identification of m6A modifications is thus essential to elucidation of their biological functions and underlying molecular-level mechanisms. Currently available high-throughput single-nucleotide-resolution m6A modification data considerably accelerated the identification of RNA modification sites through the development of data-driven computational methods. Nevertheless, existing methods have limitations in terms of the coverage of single-nucleotide-resolution cell lines and have poor capability in model interpretations, thereby having limited applicability.

Results
In this study, we present CLSM6A, comprising a set of deep learning-based models designed for predicting single-nucleotide-resolution m6A RNA modification sites across eight different cell lines and three tissues. Extensive benchmarking experiments are conducted on well-curated datasets and accordingly, CLSM6A achieves superior performance than current state-of-the-art methods. Furthermore, CLSM6A is capable of interpreting the prediction decision-making process by excavating critical motifs activated by filters and pinpointing highly concerned positions in both forward and backward propagations. CLSM6A exhibits better portability on similar cross-cell line/tissue datasets, reveals a strong association between highly activated motifs and high-impact motifs, and demonstrates complementary attributes of different interpretation strategies.

Availability and implementation
The webserver is available at http://csbio.njust.edu.cn/bioinf/clsm6a. The datasets and code are available at https://github.com/zhangying-njust/CLSM6A/.
Seeing, Sharing and Supporting: Assertive Outreach as a Partial Solution to Rough Sleeping
Authors: Stambe Rose , Kuskoff Ella , Parsell Cameron , Plage Stefanie , Ablaza Christine , Perales Francisco 
Published: November 2023

Abstract
Assertive outreach is becoming an increasingly salient feature of policy responses to homelessness—and particularly rough sleeping—with the aim of supporting people to access secure housing. Despite its demonstrated successes, existing research points to structural challenges practitioners face in navigating complex and fragmented service systems to provide people sleeping rough with a continuum of care. This study examines an Australian organisation’s efforts to collaboratively and systematically overcome these challenges by bringing together government, community and service practitioners from multiple sectors in their delivery of an assertive outreach programme. Using an ethnographic research design, this article draws on observations of outreach practices and service provider administrative quantitative data, as well as qualitative interviews and focus groups conducted with assertive outreach service providers. Our findings demonstrate that through flexible and collaborative social work practices, practitioners were able to see people sleeping rough, share information across services and support people into a range of housing, health and other forms of services. Critically, however, structural barriers such as a lack of affordable and social housing prevented assertive outreach from ending people’s homelessness. We foreground the critical implications of these findings for social work.
Effectiveness and safety of direct oral anticoagulation vs. warfarin in frail patients with atrial fibrillation
Authors: Søgaard Mette , Ording Anne Gulbech , Skjøth Flemming , Larsen Torben Bjerregaard , Nielsen Peter Brønnum 
Published: November 2023

Abstract

Aims
Although frail patients with atrial fibrillation (AF) carry a high risk of stroke and treatment-related bleeding complications, evidence for the safety and effectiveness of anticoagulation remains sparse. This study investigated the effectiveness and safety of direct oral anticoagulant (DOAC) vs. warfarin in frail AF patients.

Methods and results
Nationwide registry-based cohort study including 32 048 anticoagulation naïve frail patients (median age 80 years, 53% female) with incident AF during 2012–20. Frailty was assessed using the hospital frailty risk score. To address baseline confounding, we applied inverse probability of treatment weighting (IPTW) and marginal structural models with weighted pooled regression to compute weighted hazard ratios (wHRs) and risk differences for thromboembolism and major bleeding comparing specific DOAC doses with warfarin. After AF diagnosis, 6747 (21.1%) initiated warfarin, 17 076 (50.3%) initiated standard-dose DOAC, and 9179 (28.6%) initiated reduced-dose DOAC. Comparative effectiveness analyses in the IPTW pseudo-populations revealed similar thromboembolism risk between standard-dose DOAC and warfarin [wHR 0.95, 95% confidence interval (CI) 0.80–1.13] and between reduced-dose DOAC and warfarin (wHR 0.97, 95% CI 0.77–1.23). The 1-year thromboembolic event-free survival difference was −0.2% for DOAC, regardless of dosing, vs. warfarin. Major bleeding risk was significantly lower with standard-dose DOAC (wHR 0.69, 95% CI 0.59–0.87) and reduced-dose DOAC (wHR 0.67, 95% CI 0.55–0.81) vs. warfarin. The 1-year bleeding risk difference with DOAC ranged from −1.3% to −3.0%.

Conclusion
Our findings indicate comparable thromboembolism risk and significantly lower bleeding risk with both standard and reduced DOAC regimens compared with warfarin in frail AF patients in routine care.
Stroke and bleeding risk in atrial fibrillation with CHA2DS2-VASC risk score of one: the Norwegian AFNOR study
Authors: Anjum Mariam , Ariansen Inger , Hjellvik Vidar , Selmer Randi , Kjerpeseth Lars J , Skovlund Eva , Myrstad Marius , Ellekjær Hanne , Christophersen Ingrid E , Tveit Arnljot , Berge Trygve 
Published: November 2023

Abstract

Background and Aims
The benefit of oral anticoagulant (OAC) therapy in atrial fibrillation (AF) and intermediate stroke risk is debated. In a nationwide Norwegian cohort with a non-sex CHA2DS2-VASc risk score of one, this study aimed to investigate (i) stroke and bleeding risk in AF patients with and without OAC treatment, and (ii) the risk of stroke in non-anticoagulated individuals with and without AF.

Methods
A total of 1 118 762 individuals including 34 460 AF patients were followed during 2011–18 until ischaemic stroke, intracranial haemorrhage, increased CHA2DS2-VASc score, or study end. One-year incidence rates (IRs) were calculated as events per 100 person-years (%/py). Cox regression models provided adjusted hazard ratios (aHRs [95% confidence intervals]).

Results
Among AF patients, the ischaemic stroke IR was 0.51%/py in OAC users and 1.05%/py in non-users (aHR 0.47 [0.37–0.59]). Intracranial haemorrhage IR was 0.28%/py in OAC users and 0.19%/py in non-users (aHR 1.23 [0.88–1.72]). Oral anticoagulant use was associated with an increased risk of major bleeding (aHR 1.37 [1.16–1.63]) but lower risk of the combined outcome of ischaemic stroke, major bleeding, and mortality (aHR 0.57 [0.51–0.63]). Non-anticoagulated individuals with AF had higher risk of ischaemic stroke compared to non-AF individuals with the same risk profile (aHR 2.47 [2.17–2.81]).

Conclusions
In AF patients at intermediate risk of stroke, OAC use was associated with overall favourable clinical outcomes. Non-anticoagulated AF patients had higher risk of ischaemic stroke compared to the general population without AF with the same risk profile.
Transitive Courant Algebroids and Double Symplectic Groupoids
Authors: Alvarez Daniel 
Published: November 2023

Abstract
In this work, we extend the Lu–Weinstein construction of double symplectic groupoids to any Lie bialgebroid such that its associated Courant algebroid is transitive and its Atiyah algebroid integrable. We illustrate this result by showing how it generalises many of the examples of double symplectic groupoids that have appeared in the literature. As preliminary steps for this construction, we give a classification of exact twisted Courant algebroids over Lie groupoids (CA-groupoids for short) and we show the existence of a foliation by twisted Courant algebroids on the base of a twisted CA-groupoid.
The Full Renormalization Horseshoe for Real Box Maps With Minimal Post-Critical Sets
Authors: Wang Yimin 
Published: November 2023

Abstract
In this paper, we consider the renormalization operator $\mathcal R$ for real box maps with minimal post-critical sets. We show the existence of the full renormalization horseshoe for real box maps with minimal post-critical sets. Moreover, the renormalization operator is exponentially contracting along the hybrid leaves.
Cutavirus Infection in Large-Plaque Parapsoriasis, a Premalignant Condition of Mycosis Fungoides
Authors: Hashida Yumiko , Nakajima Kimiko , Higuchi Tomonori , Ujihara Takako , Nakai Kozo , Daibata Masanori 
Published: November 2023

Abstract

Background
Cutavirus (CuV) is associated with mycosis fungoides; however, the CuV status in parapsoriasis en plaques (PP), a premalignant inflammatory condition of mycosis fungoides, has not been fully delineated.

Methods
Fifty-five Japanese patients with chronic inflammatory skin diseases, including 13 patients with PP, were studied.

Results
CuV DNA was detected significantly more frequently in biopsies of the lesional skin from patients with PP (38%; 4 of 13) than in those from patients with other inflammatory skin diseases (2%; 1 of 42; P = .009). All CuV-positive PP cases were of the large-plaque parapsoriasis (LPP) subtype. The viral loads ranged from 83 450 to 2 164 170 copies/103 cells. We recovered near–full-length CuV sequences from the CuV-positive LPP biopsies, all of which were of the Japanese/Asian genotype. The CuV genome appeared to be present within lymphoid cells infiltrating the epidermis and dermis. CuV NS1 and VP1 gene transcripts were also detected in the affected tissues.

Conclusions
The detection of high levels of CuV DNA with the expression of viral mRNA suggests a potential role for CuV in the pathogenesis of LPP, making it necessary to study further the impact of CuV, especially regarding the viral genotype, on the outcomes of patients with CuV-positive LPP.
Innovative approaches to COVID-19 medical countermeasure development
Authors: Harris Gavin H , Adalja Amesh A 
Published: November 2023

Abstract

Background
The COVID-19 pandemic, while unfortunately notable for immense strain and death throughout the world, has also shown great promise in the development of medical countermeasures. As the global scientific community shifted almost entirely towards vaccines, diagnostics and therapeutics, new trial designs most significantly adaptive platform trials, began to be used with greater speed and broader reach. These designs allowed for deploying and investigating new therapeutics, repurposing currently existing therapeutics and flexibly removing or adding additional medications as data appeared in real-time. Moreover, public–private sector partnering occurred at a level not seen before, contributing greatly to the rapid development and deployment of vaccines.

Objectives
To provide a brief overview of the advances in preventative and therapeutic medical countermeasure development for COVID-19.

Methods
A narrative review of relevant major medical countermeasure trials was conducted using the date range February 2020–December 2022, representing the period of greatest productivity in research to investigate COVID-19.

Results
Among the most influential trial designs are the adaptive platform designs, which have been applied to the development of initial COVID-19 antivirals, monoclonal antibodies, repurposing of existing immunomodulatory therapy and assisted in the disproof of ineffective medical therapies. Some of the most prominent examples include the REMAP-CAP, RECOVERY and TOGETHER trials.

Conclusions
Adaptive platform trial designs hold great promise for utility in future pandemics and mass casualty events. Additionally, public–private sectoring is essential for rapid medical countermeasure development and should be further enhanced for future biopreparedness.
A hidden gem in multidisciplinary antimicrobial stewardship: a systematic review on bedside nurses’ activities in daily practice regarding antibiotic use
Authors: Bos Maria , Schouten Jeroen , De Bot Cindy , Vermeulen Hester , Hulscher Marlies 
Published: November 2023

Abstract

Background
Antimicrobial stewardship (AMS), the set of actions to ensure antibiotics are used appropriately, is increasingly targeted at all those involved in the antimicrobial pathway, including nurses. Several healthcare organizations have issued position statements on how bedside nurses can be involved in AMS. However, it remains unclear how nurses, in reality, contribute to appropriate antibiotic use.

Objectives
To systematically search the literature to describe the activities bedside nurses perform regarding antibiotic use in daily clinical practice, in relation to the activities proposed by the aforementioned position statements.

Methods
We searched MEDLINE, Embase, CINAHL and grey literature until March 2021. Studies were included if they described activities regarding antibiotic use performed by bedside nurses. Methodological rigour was assessed by applying the Mixed Method Appraisal Tool.

Results
A total of 118 studies were included. The majority of the proposed nurses’ activities were found in daily practice, categorized into assessment of clinical status, collection of specimens, management of antimicrobial medication, prompting review and educating patient and relatives. Nurses may take the lead in these clinical processes and are communicators in all aspects of the antimicrobial pathway. Patient advocacy appears to be a strong driver of bedside nurses’ activities.

Conclusions
Nurses’ activities are already integrated in the day-to-day nursing practice and are grounded in the essence of nursing, being a patient advocate and showing nursing leadership in safeguarding the antimicrobial treatment process. An essential element of the nursing role is communication with other stakeholders in the patient-centred antimicrobial pathway. Educating, engaging and empowering nurses in this already integrated role, could lead to a solid, impactful nursing contribution to AMS.
Clonal spread of non-O157 Shiga toxigenic Escherichia coli O21:H25 in raw water buffalo milks
Authors: Uyanik Tolga , Gücükoğlu Ali , Gürler Hande , Kanat Sibel , Bölükbaş Ayşegül , Çadirci Özgür 
Published: November 2023

Abstract

Aims
This study was conducted to investigate the presence of Shiga toxin-producing O157 and non-O157 E. coli in raw water buffalo milk, as well as to determine the virulence gene profiles, phylogroups, sequence types, and serotypes of the isolated strains.

Methods and results
A total of 200 hand-milked raw water buffalo milk samples were collected from 200 different water buffaloes over a period of three months from 20 different farms. Isolation of STEC was performed using CHROMagar STEC. Presence of stx1, stx2, and eaeA genes were investigated by mPCR. Phylogroups and sequence types of E. coli strains were determined by Clermont phylotyping and MLST. Serotyping was performed using PCR or WGS. According to the results, two milk samples obtained from two different farms were found as STEC-positive. All Stx-positive E. coli isolates belonged to phylogenetic group A and were assigned to ST10. WGS results indicated that serotype of two isolates was O21:H25 and average nucleotide identity was detected at 99.99%. Thirteen additional registered E. coli O21:H25 assembled WGS data were obtained from EnteroBase and a phylogenetic tree was constructed.

Conclusions
With this study, the presence of stx2 harboring E. coli O21:H25 in milk was identified for the first time. Although the identified serotype is considered a non-pathogen seropathotype, we conclude it could play an important role in the environmental circulation of Stx-phages and consequently contribute to the emergence of new STEC-related outbreaks.
Work engagement among older workers: a systematic review
Authors: Mori Koji , Odagami Kiminori , Inagaki Mizuho , Moriya Kenta , Fujiwara Hidenori , Eguchi Hisashi 
Published: November 2023

Abstract
Objectives: Given current labor force conditions, including population aging, keeping older workers engaged in work and motivated is important. Aging may alter the effects that psychological and environmental factors have on work engagement. We conducted a systematic review to understand the features of work engagement among older workers.
Methods: A systematic search was conducted in July 2022 using 4 databases. The review included relevant articles that focused on participants aged 40 years and older.
Results: Fifty articles were selected for our review, which were grouped into 5 categories: (1) studies examining the relationship between chronological age and work engagement, (2) studies investigating the moderating effects of age on the relationship between job-related psychological factors and work environment factors and work engagement, (3) studies comparing the relationship of job-related psychological factors and work environment factors with work engagement across different age groups, (4) studies exploring the relationship between work engagement and retirement intentions or continued employment beyond retirement age, and (5) other studies discussing work engagement in the context of older workers. Most articles focused on workers in Europe and the United States and used observational study designs.
Conclusions: Work engagement increases with age, and is mainly mediated by increased emotional regulation. In addition, age moderates the relationships between various job-related psychological and work-environmental factors and work engagement. Work engagement is associated with working beyond retirement age. Organizations should understand the characteristics of work engagement among older workers and make age-conscious efforts to support them in adapting to social changes.
Breathing from the neck: Tracheostomy emergencies
Authors: Crawford Paul , Hypes Cameron 
Published: November 2023

Abstract
This chapter reviews commonly encountered tracheostomy emergencies. It briefly discusses tracheostomy placement and anatomy, including the anatomy of the innominate artery and the ideal location for tracheostomy placement. It then covers the various emergent presentations related to tracheostomies, focusing on tracheostomy bleeding and tracheo-innominate artery fistulas. It discusses etiologies of bleeding, concerning signs and features, and methods of evaluation as well as initial management. It includes figures demonstrating techniques used to control bleeding. The definitive management and disposition of these patients are also discussed. Finally, airway considerations for emergent ventilation are discussed. Specifically discussed are anatomic alterations and the possibility of laryngectomy and discontinuity of the oropharynx and the trachea.
The challenge down under: Subglottic airway access issues
Authors: Eppich Christopher I. , Mosier Jarrod M. 
Published: November 2023

Abstract
This chapter reviews a number of important points on how emergency physicians can recognize and manage subglottic airway access issues, such as tracheal stenosis, that occur in the emergency department. The authors review the common causes and possible presentations of patients with tracheal stenosis and provide guidance on how to manage the airway of these patients in the emergency setting. It also touches on other causes of subglottic airway access problems, including patients with laryngectomies and those with Montgomery T-tubes. The authors also discuss the anatomic challenges and complications as well as management options for patients presenting in respiratory distress.
Problems outside the lung: Pneumothorax and pleural effusions
Authors: Bruno John , Axelband Jennifer 
Published: November 2023

Abstract
Pleural diseases, including pleural effusion and pneumothorax, are widely prevalent in critically ill patients and contribute significantly to the morbidity and mortality of patients admitted to ICUs. Management often includes thoracentesis or tube thoracostomy, and drained pleural fluid can be analyzed for further diagnostics and evaluation using Light’s criteria. Lung ultrasound to facilitate pleural drainage or tube thoracostomy may decrease the rate of procedure-related complications. Infected pleural collections, including parapneumonic effusion and empyema, have a high rate of treatment failure and are particularly challenging to manage, often requiring several bedside and/or surgical procedures. They are best managed by a multidisciplinary team of intensivists, pulmonologists, and thoracic surgeons.
Intubated and boarded in the ED: Ventilator 101
Authors: Fozard Jessica , Shafer Krystle 
Published: November 2023

Abstract
Emergency physicians can be empowered by knowing the basics of how to safely ventilate patients with the mechanical ventilator. Learning how to initiate mechanical ventilation with appropriate settings is an important skill to learn, as inappropriate settings can increase length of stay, lengthen time on the ventilator, and negatively impact mortality. After choosing the mode of ventilator (the authors recommend volume-control mode), the four settings that must be set are respiratory rate, tidal volume, positive end-expiratory pressure, and fraction of inspired oxygen. A lung-protective ventilation strategy should be used for all patients. Additional parameters are titrated based on the patient’s comorbidities and indication for mechanical ventilation.
Too slow to go: Symptomatic bradycardia
Authors: VanDyck Tyler , Simpson Scott 
Published: November 2023

Abstract
The approach to bradycardia in the emergency department necessitates prompt, early recognition of the stability of the patient to guide treatment. For the unstable patient, treatment should proceed quickly from medications to pacing modalities, which include transcutaneous and transvenous approaches. Transcutaneous pacing can be provided in a quick, straightforward manner with most modern defibrillators. Progression to the use of temporary transvenous pacing is often required when the underlying etiology is not easily reversible. Emergency physicians must be familiar with the technical aspects of transvenous pacemaker insertion so that they can perform this procedure even if specialist consultation is not immediately available.
Brain on fire: Status epilepticus
Authors: Bux Michael , Niehaus Matthew T. 
Published: November 2023

Abstract
Status epilepticus (SE) is a diagnosis with a high morbidity and mortality rate, particularly in adults. It becomes increasingly difficult to treat with every delay in recognition or initiation care. SE is defined as a seizure lasting longer than 5 minutes or more than one seizure between which there is not full recovery of cognition. Treatment algorithms define four phases of care that should occur within the first hour of seizure: stabilization (first 5 minutes), initial therapy (emergent—benzodiazepine), second-tier therapies (urgent), and third-tier therapies (for refractory cases). The causes of SE are broad but will require investigation in order to correct the underlying etiology if possible. By recognizing patients and stabilizing them early with timely treatment, the astute emergency physician can reduce the risk of morbidity and mortality.