bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors that influence the uptake of virtual care solutions in Australian primary care practice: a systematic scoping review
Authors: Delaforce Alana , Maddock Emma , Wheeler Pamela , Jayasena Rajiv , Parkinson Joy 
Published: October 2024

ABSTRACT

Introduction:
Uptake of virtual care solutions in primary care settings has increased exponentially, and current evidence suggests high patient satisfaction but mixed clinician views.

Aims:
This paper aimed to identify factors influencing its’ implementation to support delivery to the right patient, in the right clinical context, at the right time. Further, this paper evaluates how the updated Consolidated Framework for Implementation Research (CFIR) can be used to assess these factors that contribute to the uptake of virtual care innovations.

Methods:
This systematic scoping review identified empirical research on factors influencing the uptake of virtual care solutions in the Australian primary care setting. Searches were undertaken in Embase, PubMed, Scopus, and Web of Science. The CFIR was used to code factors influencing the implementation of virtual care solutions. Inductive coding was used to generate new constructs where no appropriate CFIR construct could be identified.

Results:
Fourteen eligible studies were identified as eligible for inclusion. Five common influencing factors were identified. Three are from the existing CFIR framework, and two are newly developed constructs. CFIR constructs included innovation relative advantage, capability, and IT infrastructure. New constructs included accessibility and suitability. A further six new constructs were identified (trust, privacy, governance, unintended consequences, preference, and choice) but these were not prominently mentioned.

Conclusions:
Common factors influence virtual care uptake in Australian primary care. The CFIR assisted in conceptualizing these but was not sufficient for capturing factors unique to virtual care. Newly developed constructs are noted to be of importance in the literature, but further research is needed to understand whether they are applicable in multiple contexts.

Spanish abstract:

http://links.lww.com/IJEBH/A286
Improving the nursing quality of non-pharmacological interventions for elderly constipation patients in the hospital: a best practice implementation project
Authors: Li Jingjing , Zhang Dahua , Zhang Yaqian , Li Chunyang , Fan Xueyan , Yu Qiushuang , Yang Ming , Du Jian , Li Xuejing , Hao Yufang , Han Liu 
Published: October 2024

ABSTRACT

Introduction:
Non-pharmacological interventions are the preferred treatment for constipation; however, health care professionals in clinical settings tend to focus more on pharmacological treatments.

Objectives:
This best practice implementation project aimed to integrate the best evidence on non-pharmacological interventions for elderly patients with constipation in clinical care practice and to promote the use of non-pharmacological interventions for such patients in the hospital setting.

Methods:
This project is based on the JBI Evidence Implementation Framework, which follows three stages. The first stage involved a baseline audit using two audit criteria derived from the best available evidence. This audit evaluated current clinical scenarios, guided by the i-PARIHS framework. The second stage involved analyzing the results of the baseline audit, identifying barriers to compliance, and developing and implementing strategies to overcome those barriers. Strategies included nursing education, development of constipation information booklets for nurses and patients, establishment of a nursing workflow, and modification of the department environment. In the third stage, a follow-up audit was conducted to evaluate the implementation, using the same data collection indicators and methods as in the baseline audit. Sixty patients participated in the project.

Results:
Compliance for Criterion 1 (patient education) increased from 0% to 60% (p < 0.001), while compliance for Criterion 2 (monitoring patients’ bowel health) increased from 0% to 100% (p < 0.001).

Conclusions:
The results indicate that this evidence-based implementation project facilitated the application of non-pharmacological interventions for elderly patients with constipation. Nurses played a significant role in developing regular defecation habits in patients and monitoring their defecation.

Spanish abstract:

http://links.lww.com/IJEBH/A284
Mechanisms of brain self-regulation: psychological factors, mechanistic models and neural substrates
Authors: Sitaram Ranganatha , Sanchez-Corzo Andrea , Vargas Gabriela , Cortese Aurelio , El-Deredy Wael , Jackson Andrew , Fetz Eberhard 
Published: October 2024

While neurofeedback represents a promising tool for neuroscience and a brain self-regulation approach to psychological rehabilitation, the field faces several problems and challenges. Current research has shown great variability and even failure among human participants in learning to self-regulate target features of brain activity with neurofeedback. A better understanding of cognitive mechanisms, psychological factors and neural substrates underlying self-regulation might help improve neurofeedback’s scientific and clinical practices. This article reviews the current understanding of the neural mechanisms of brain self-regulation by drawing on findings from human and animal studies in neurofeedback, brain–computer/machine interfaces and neuroprosthetics. In this article, we look closer at the following topics: cognitive processes and psychophysiological factors affecting self-regulation, theoretical models and neural substrates underlying self-regulation, and finally, we provide an outlook on the outstanding gaps in knowledge and technical challenges.
This article is part of the theme issue ‘Neurofeedback: new territories and neurocognitive mechanisms of endogenous neuromodulation’.
Has the design quality of randomized controlled trials of Acupotomy improved over the past 18 years? -- CONSORT statement-based literature study from 2006 to 2024
Authors: Li Junjie , Zhou Yantong , Lu Xinzhu , Bian Ying 
Published: October 2024

AbstractAcupotomy, originally named ‘Nine Needles’ inLing Shu, was invented as a new type of TCM instrument in 1976, an innovative combination of acupuncture and surgical treatment. Its forward development is related to the Clinical effectiveness and safety. RCTs are gold standards in clinical practice and were welcomed in Acupotomy recently. The CONSORT Statement is set to guide the designing, analysis and interpretation of trials. But there haven’t been many Acupotomy RCTs until now, with few on quality evaluation, therefore design quality of Acupotomy RCTs is still weakness. This study aims to assess design quality of acupotomy RCTs by CONSORT statement, to analyze the overall quality status and influencing factors.PubMed database was used to search keywords like ‘Acupotomy’ and ‘Randomized Controlled Trial’. All 48 Acupotomy RCTs published from January 2006 to January 2024 were included. The CONSORT(2010) was used for quality assessment.48 studies were included for analysis, with 39 articles from Grade 3A hospitals and 9 from non-Grade 3A hospitals. Scores of RCTs ranged from 33 to 82, the mean score of 53.1 and median of 49. Grade 3A and non-Grade 3A hospitals differed significantly only in item 8, no studies reported item 18, and items 11, 14, and 23 had the highest frequency of reporting as failed.Based on 48 Acupotomy RCTs included, the publication time associated with the quality of reports. The number of authors and possession of funding were the most important factors affecting the total score. Number of beds, hospitals’ grade, sample sizes, and region GDP/PP did not relate to the total score. Among 25 items, Ancillary analyses, Blinding, Recruitment were the worst-performing items. Therefore, updating and standardizing the use of CONSORT can help to improve quality of RCTs, and cross-team communication and cooperation could promote the use of CONSORT.
Dark Microglia Are Abundant in Normal Postnatal Development, where they Remodel Synapses via Phagocytosis and Trogocytosis, and Are Dependent on TREM2
Authors: Vecchiarelli Haley A. , Bisht Kanchan , Sharma Kaushik , Weiser Novak Sammy , Traetta Marianela E. , Garcia-Segura Monica Emili , St-Pierre Marie-Kim , Savage Julie C. , Willis Cory , Picard Katherine , Bordeleau Maude , Vernoux Nathalie , Khakpour Mohammadparsa , Garg Rishika , Loewen Sophia M. , Murray Colin J. , Grinberg Yelena Y. , Faustino Joel , Halvorson Torin , Lau Victor , Pluchino Stefano , Vexler Zinaida S. , Carson Monica J. , Manor Uri , Peruzzotti-Jametti Luca , Tremblay Marie-Ève 
Published: October 2024

AbstractThis study examined dark microglia—a state linked to central nervous system pathology and neurodegeneration—during postnatal development in the mouse ventral hippocampus, finding that dark microglia interact with blood vessels and synapses and perform trogocytosis of pre-synaptic axon terminals. Furthermore, we found that dark microglia in development notably expressed C-type lectin domain family 7 member A (CLEC7a), lipoprotein lipase (LPL) and triggering receptor expressed on myeloid cells 2 (TREM2) and required TREM2, differently from other microglia, suggesting a link between their role in remodeling during development and central nervous system pathology. Together, these results point towards a previously under-appreciated role for dark microglia in synaptic pruning and plasticity during normal postnatal development.
Adhesion G protein-coupled receptor ADGRG1 promotes protective microglial response in Alzheimer’s disease
Authors: Zhu Beika , Wangzhou Andi , Yu Diankun , Li Tao , Schmidt Rachael , De Florencio Stacy L. , Chao Lauren , Perez Yonatan , Grinberg Lea T. , Spina Salvatore , Ransohoff Richard M. , Kriegstein Arnold R. , Seeley William W. , Nowakowski Tomasz , Piao Xianhua 
Published: October 2024

AbstractGermline genetic architecture of Alzheimer’s disease (AD) indicates microglial mechanisms of disease susceptibility and outcomes. However, the mechanisms that enable microglia to mediate protective responses to AD pathology remain elusive.Adgrg1is specifically expressed in yolk-sac-derived microglia. This study reveals the role of yolk-sac-derived microglia in AD pathology, highlighting the function of ADGRG1 in modulating microglial protective responses to amyloid deposition. Utilizing both constitutive and inducible microglialAdgrg1knockout 5xFAD models, we demonstrate thatAdgrg1deficiency leads to increased amyloid deposition, exacerbated neuropathology, and accelerated cognitive impairment. Transcriptomic analyses reveal a distinct microglial state characterized by downregulated genes associated with homeostasis, phagocytosis, and lysosomal functions. Functional assays in mouse models and human embryonic stem cells-derived microglia support that microglial ADGRG1 is required for efficient Aβ phagocytosis. Together, these results uncover a GPCR-dependent microglial response to Aβ, pointing towards potential therapeutic strategies to alleviate disease progression by enhancing microglial functional competence.
DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing
Authors: Song Junwei , Lin Li-an , Tang Chao , Chen Chuan , Yang Qingxin , Zhang Dan , Zhao Yuancun , Wei Han-cheng , Linghu Kepan , Xu Zijie , Chen Tingfeng , He Zhifeng , Liu Defu , Zhong Yu , Zhu Weizhen , Zeng Wanqin , Chen Li , Song Guiqin , Chen Mutian , Jiang Juan , Zhou Juan , Wang Jing , Chen Bojiang , Ying Binwu , Wang Yuan , Geng Jia , Lin Jing-wen , Chen Lu 
Published: October 2024

AbstractNanopore direct RNA sequencing (DRS) advances RNA biology but is limited by relatively low basecalling accuracy, low throughput, yet high RNA input and costs. Here we introduce a novel DRS toolkit, DEMINERS, which integrates an RNA multiplexing experimental workflow, a machine-learning barcode classifier based on Random Forest and a novel basecaller built on an optimized convolutional neural network providing an additional species-specific training module. With the increased accuracy in barcode classification and basecalling, DEMINERS can demultiplex up to 24 samples and the required RNA input and running time are both substantially reduced. We demonstrated the applications of DEMINERS in clinical metagenomics, cancer transcriptomics and parallel comparison of transcriptomic features in different biological conditions, revealing altered airway microbial diversity in COVID-19 and a potential role of m6A in increasing transcriptomic diversity in glioma and the mature blood-stage of malaria parasites. Overall, DEMINERS is a simple, robust, high-throughput DRS method for accurately estimating transcript levels, poly(A) lengths, and mutation and RNA modification heterogeneity at single-read level, with minimal sequencing biases.
14C-age of carbon used to grow fine roots reflects tree carbon status
Authors: Hilman Boaz , Solly Emily F. , Hagedorn Frank , Kuhlman Iris , Herrera-Ramírez David , Trumbore Susan 
Published: October 2024

Summary“Bomb”14C ages in trees indicate the time elapsed between carbon fixation into nonstructural carbon (NSC) and its use for metabolism and growth. It remains unknown why newly grown aboveground tissues have a narrow range of young14C-ages, while fine root ages can span decades.We measured14C in tissues of two coniferous species along an alpine treeline ecotone and used a mixing model to estimate the fraction of NSC that is metabolically active. We expected that greater growth limitation higher in the ecotone would supply more freshly fixed NSC to respiration, active NSC, carbohydrates, and roots, resulting in younger14C-ages of NSC used to grow tissues.Results confirmed an increase in fresh NSC supply with elevation. Needle and branch growth was supported by young NSC (< 2 yr) with little elevation influence, while root growth was supported by older NSC that declined from 10 to 6 yr with elevation.Massive allocation of fresh NSC to needles and branches could explain their young14C-ages. Variable fine root14C-ages reflect tree C status, with older ages when aboveground growth limits the contribution of new C belowground, while young ages represent greater delivery of fresh NSC to roots.
How do gepotidacin and zoliflodacin stabilize DNA-cleavage complexes with bacterial type IIA topoisomerases? 1. Experimental definition of metal binding sites
Authors: Morgan Harry , Nicholls Robert A. , Warren Anna J. , Ward Simon E. , Evans Gwyndaf , Long Fei , Murshudov Garib N. , Duman Ramona , Bax Benjamin D. 
Published: October 2024

AbstractOne of the challenges for experimental structural biology in the 21st century is to see chemical reactions happen.Staphylococcus aureus(S. aureus) DNA gyrase is a type IIA topoisomerase that can create temporary double-stranded DNA breaks to regulate DNA topology. Drugs, such as gepotidacin, zoliflodacin and the quinolone moxifloxacin, can stabilize these normally transient DNA-strand breaks and kill bacteria. Crystal structures of uncleaved DNA with a gepotidacin precursor (2.1Å GSK2999423) or with doubly cleaved DNA and zoliflodacin (or with its progenitor QPT-1) have been solved in the same P61space-group (a=b≈93Å, c≈412Å). This suggests it may be possible to observe the two DNA-cleavage steps (and two DNA-religation steps) in this P61space-group. Here a 2.58Å anomalous manganese dataset in this crystal form is solved, and four previous crystal structures (1.98Å, 2.1Å, 2.5Å and 2.65Å) in this crystal form are re-refined to clarify crystal contacts. The structures clearly suggest a single moving metal mechanism - presented in an accompanying (2nd) paper. A previously published 2.98Å structure of a yeast topoisomerase II, which has static disorder around a crystallographic twofold axis, was published as containing two metals at one active site. Re-refined coordinates of this 2.98Å yeast structure are consistent with other type IIA topoisomerase structures in only having one metal ion at each of the two different active sites.
Benchmarking alternative polyadenylation detection in single-cell and spatial transcriptomes
Authors: Li Sida , Wang Zixuan , Hu Yanshi , Ni Qingyang , Feng Cong , Hu Yueming , Zhang Shilong , Chen Ming 
Published: October 2024

AbstractBackground3’-tag-based sequencing methods have become the predominant approach for single-cell and spatial transcriptomics, with some protocols proven effective in detecting alternative polyadenylation (APA). While numerous computational tools have been developed for APA detection from these sequencing data, the absence of comprehensive benchmarks and the diversity of sequencing protocols and tools make it challenging to select appropriate methods for APA analysis in these contexts.ResultsWe systematically compared seven 3’-tag-based sequencing protocols and identified key peak features affecting APA detection performance. We developed a simulation pipeline that generates realistic datasets preserving protocol-specific characteristics. Using simulated and real data, we comprehensively assessed six computational tools for their ability to identify polyA sites, quantify polyA site expression, detect differentially expressed (DE) APA genes, filter sequencing artifacts, and their computational efficiency. We also investigated factors influencing APA detection. Our evaluation revealed that SCAPE and scAPAtrap generally outperformed other tools across various performance metrics and protocols.ConclusionOur systematic evaluation provides guidance for tool selection, experiment design, and future tool development in APA analysis for singlecell and spatial transcriptomics, paving the way for investigating APA in these contexts.
How do gepotidacin and zolifodacin stabilize DNA-cleavage complexes with bacterial type IIA topoisomerases? 2. A Single Moving Metal Mechanism
Authors: Nicholls Robert A. , Morgan Harry , Warren Anna J. , Ward Simon E. , Long Fei , Murshudov Garib N. , Sutormin Dimitry , Bax Benjamin D. 
Published: October 2024

AbstractDNA gyrase is a type IIA topoisomerase that can create temporary double-stranded DNA breaks to regulate DNA topology and an archetypical target of antibiotics. The widely used quinolone class of drugs use a water-metal ion bridge in interacting with the GyrA subunit of DNA gyrase. Zoliflodacin sits in the same pocket as quinolones but interacts with the GyrB subunit and also stabilizes lethal double-stranded DNA-breaks. Gepotidacin had been observed to sit on the twofold axis of the complex, midway between the two four base-pair separated DNA-cleavage sites and has been observed to stabilize singe-stranded DNA-breaks. Here we use information from three crystal structures of complexes ofStaphlococcus aureusDNA gyrase (one with a precursor of gepotidacin and one with the progenitor of zoliflodacin) to propose a simple single moving metal-ion catalyzed DNA-cleavage mechanism. Our model explains why the catalytic tyrosine is in the tyrosinate (negatively charged) form for DNA-cleavage. Movement of a single catalytic metal-ion (Mg2+or Mn2+) guides water mediated protonation and cleavage of the scissile phosphate which is then accepted by the catalytic tyrosinate. Type IIA topoisomerases need to be able to rapidly cut the DNA when it becomes positively supercoiled (in front of replication forks and transcription bubbles) and we propose that the original purpose of the small Greek Key domain, common to all type IIA topoisomerases, was to allow access of the catalytic metal to the DNA-cleavage site. Although the proposed mechanism is consistent with published data, it is not proven and other mechanisms have been proposed. Finally how such mechanisms can be experimentally distinguished is considered.
Investigating the genetic architecture of biotic stress response in stone fruit tree orchards under natural infections with a multi-environment GWAS approach
Authors: Serrie Marie , Segura Vincent , Blanc Alain , Brun Laurent , Dlalah Naïma , Gilles Frédéric , Heurtevin Laure , Le-Pans Mathilde , Signoret Véronique , Viret Sabrina , Audergon Jean-Marc , Quilot Bénédicte , Roth Morgane 
Published: October 2024

AbstractThe mapping and introduction of sustainable plant immunity to pests and diseases in fruit tree is still a major challenge in modern breeding. This study aims at deciphering the genetic architecture underlying resistance or tolerance across environments for major pests and diseases in peach (P. persica) and apricot (P. armeniaca). We set up a multi-environment trial (MET) approach by studying two core collections of 206 peach and 150 apricot accessions deployed under low phytosanitary conditions in respectively three and two environmentally contrasted locations in South-East of France. To capture the complex dynamics of pest and disease spread in naturally infected orchards, visual scoring of symptoms was repeated within and between 3 years, for five and two pests and diseases respectively for peach and apricot, resulting in the maximum of damage score and the AUDPC. These traits were used as phenotypic inputs in our genome-wide association studies (GWAS) strategy, and leading to the identification of: i) non-additive genotype–phenotype associations, ii) environment-shared QTLs iii) environment-specific QTLs, and iv) interactive QTLs which changes in direction (‘antagonist’) or intensity (‘differential’) according to the environment. By conducting GWAS with multiple methods, we successfully identified a total of 60 high confidence QTLs, leading to the identification of 87 candidate genes, the majority belonging to the Leucine-rich repeat containing receptors (LRR-CRs) family gene. Finally, we provided a comparative analysis of our results on peach and apricot, two closely related species. The present results contribute to the development of genomics-assisted breeding to improve biotic resilience inPrunusvarieties.
Estimating the rate of sexual reproduction and the inbreeding rate inLeishmania
Authors: Nicoll Andrew G. , Kilford Hannah , Grace Cooper Alastair , Reis-Cunha João Luís , Jeffares Daniel C. , Constable George W. A. 
Published: October 2024

AbstractMany eukaryotic species undergo sexual reproduction facultatively, either in response to stress or in particular environments. For the remainder of their life cycle they reproduce by mitosis. This facultative sex may be rare, which alters features of their evolutionary dynamics. Both the frequency of sex and the degree of inbreeding have been challenging to estimate from genome-scale polymorphism data. Here, we describe a method to estimate both these parameters based on the Moran model of heterozygous sites. We apply this method to population genomic data fromLeishmaniaparasitic protozoans from theLeishmania donovanispecies complex, showing that these parasites undergo sexual reproduction approximately once per 10,000 generations and that populations vary considerably in the extent of their inbreeding.
Carafe enables high qualityin silicospectral library generation for data-independent acquisition proteomics
Authors: Wen Bo , Hsu Chris , Zeng Wen-Feng , Riffle Michael , Chang Alexis , Mudge Miranda , Nunn Brook , Berg Matthew D. , Villén Judit , MacCoss Michael J. , Noble William S. 
Published: October 2024

AbstractData-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use ofin silicogenerated spectral libraries. However, the generation of high-quality spectral libraries for DIA data analysis remains a challenge, particularly because most such libraries are generated directly from data-dependent acquisition (DDA) data or are fromin silicoprediction using models trained on DDA data. In this study, we developed Carafe, a tool that generates high-quality experiment-specificin silicospectral libraries by training deep learning models directly on DIA data. We demonstrate the performance of Carafe on a wide range of DIA datasets, where we observe improved fragment ion intensity prediction and peptide detection relative to existing pretrained DDA models.