bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analyzing trends and practices: A survey of procedures performed by nurse practitioners
Authors: D'Aoust Rita F. , McCamey Danielle , Russell Nancy G. , Fingerhood Marianne L. , Ling Catherine , Baker Deborah J. , Bianchi Carolanne , Slone Sarah 
Published: November 2024

ABSTRACT

Background:
Nurse practitioners (NPs) provide essential patient care services. Most (88%) are primary care certified, and 70% practice in primary care settings. National NP organizations and state practice authority regulations influence the training and level of independence of performing procedures common in primary care practice. National standards reference the ability to select and interpret appropriate diagnostic tests related to clinical reasoning or management functions, but not competency in the procedures. Although the blueprint for certification examinations includes procedures as part of evidence-informed practice, none are specifically named.

Purpose:
There are limited data concerning procedural training for NPs. The study aims were to describe the training practicing NPs received for procedures they perform, define areas of research concerning the development of uniform training, and identify advocacy initiatives for competency acquisition for procedures.

Methodology:
Practicing NPs completed a survey concerning the procedures they perform in their practice. In addition, they reported their level of perceived competency, independence in performing, and method of training.

Results:
The majority of respondents (87.8%) hold certifications in primary care specialties. In this sample of practicing NPs, 74% of the respondents perform procedures independently, but only 67% had procedure training as part of their initial NP education. Additional training (60%) was completed through professional development programs.

Conclusions:
Many NPs surveyed perform procedures independently. Training occurred in their NP programs and through continuing education.

Implications:
Further studies are needed concerning procedural training and the setting that is most appropriate for competency achievement.
Wear and use of prostheses in sport by adolescents with upper limb absence: A preliminary mixed-methods study
Authors: Chinn Natalie M. , Kenney Laurence P. J. , Chadwell Alix , Williams Anita E. , Head John 
Published: November 2024

Background:
There is minimal research on sports participation in adolescents with upper limb absence (ULA) and specifically on the impact of prosthesis provision.

Objectives:
This study explored using activity monitoring sensors and interviews to gain insight into levels of sport participation and associated prosthesis use in active adolescents with ULA.

Study design:
A mixed methods study using a convergent parallel design.

Methods:
Semi-structured interviews and activity diaries were used to investigate sports and related activities undertaken during a 2-week period. Prosthesis wear/use were determined via accelerometers worn on the anatomical and prosthetic wrists throughout; interview data added context. For comparison, accelerometer data and activity diaries were captured from similar aged anatomically intact (AI) participants.

Results:
Three adolescents with unilateral transradial ULA and 4 AI adolescents were recruited. Two ULA participants wore prostheses during sport (16.2% and 56.5% of the time). The third rarely wore their prosthesis. The ability to participate in sport has a powerful influence on participants' lives, and prostheses were used when participants felt they offered specific benefits. In contrast to AI participants, who showed similar reliance on each of their arms throughout, when wearing a prosthesis, users were heavily reliant on the anatomical arm, including during periods playing sports.

Conclusions:
Prosthesis use facilitated access to some sports, although they were only used by 2 out of 3 participants for short periods. The methods were acceptable to adolescent individuals with ULA.
A scoping review of digital fabrication techniques applied to prosthetics & orthotics: Part 2 of 2—orthotics
Authors: Oldfrey Ben M. , Morgado Ramirez Dafne Z. , Holloway Catherine , Wassall Matthew , Nester Christopher , Dickinson Alex , Wong Man S. , Danemayer Jamie , Kenney Laurence , Lemaire Edward , Ramstrand Nerrolyn , Gholizadeh Hossein , Diment Laura E. , Donovan-Hall Margaret K. , Miodownik Mark 
Published: November 2024

Introduction:
Traditionally, orthosis manufacturing is time and labor-intensive. Digitalization of some of the fabrication process is already ubiquitous, yet extension across device types could reduce the burden of manual labor and advance automation to help unblock access to assistive technologies globally. It seems, however, that appropriately strong evidence is holding this back. This review looks to thoroughly examine the current state of evidence to make this clear.

Objectives:
To identify gaps in the literature that create barriers to decision-making on either appropriate uptake by clinical teams or setting research directions, by identifying what forms of evidence the current research literature provides to the orthotics community.

Study design:
Scoping literature review.

Methods:
A comprehensive search was completed in the following databases: AMED, MEDLINE, EMBASE, Global Health Archive, CINAHL Plus, Cochrane Library, Web of Science, ACM, IEEE, and Engineering Village, resulting in 3487 articles to be screened.

Results:
After screening, 121 lower limb orthosis, 104 upper limb orthosis, and 30 spinal orthosis articles were included in this review. For some areas such as CAD/CAM-produced insoles and spinal orthoses, the evidence base is strong. For most additive manufacture articles, long-term, larger-scale studies as well as research into training requirements are lacking.

Conclusion:
The advantages of digital fabrication technology that could streamline orthotic device production in many cases are still blocked by a lack of strong formal evidence, ie large longitudinal studies with a range of evaluation measures. Increased collaboration between clinicians, patient/service users, academia, and industry could be a route to addressing these gaps and creating a better pathway to market for new technologies.
Strength profiles in patients with knee osteoarthritis with and without unilateral transfemoral amputation
Authors: Hannigan Lindsay Slater , Sudhir Shraddha , Jetanalin Pim , Foucher Kharma C. 
Published: November 2024

Background:
Individuals with lower limb amputation have increased risk of developing knee osteoarthritis (KOA) in the intact limb, however there is little information regarding strength profiles in individuals with KOA with and without amputation.

Objective:
To compare lower extremity strength in individuals with KOA with and without unilateral transfemoral (TF) amputation.

Study Design:
Descriptive laboratory study.

Methods:
Seven participants with unilateral TF amputation (3F/4M, 58.0 ± 11.0 years, 172.7 ± 12.8 cm, 90.8 ± 19.1 kg, 38.8 ± 14.4 years after amputation) and symptomatic KOA in the intact limb and 9 participants with unilateral KOA (control (CON)) without leg amputation (4F/5M, 66.0 ± 9.9 years, 170.5 ± 10.7 cm, 86.8 ± 18.1 kg) participated in this study. Both groups completed strength testing on the involved limb with KOA and the Knee Injury and Osteoarthritis Outcome Score (KOOS) questionnaire to meaure subjective function. Strength variables were mass-normalized.

Results:
There were no significant differences between groups in age, mass, or height. The CON group reported significantly reduced subjective function on the KOOS total score (P = 0.049; d = 1.03) and KOOS symptoms scores (P = 0.047, d = 0.95) compared with the TF amputation group. A lower subjective function score indicates worse function. There were no other significant differences between groups on KOOS subcategories. The TF amputation group had significantly greater average isokinetic quadriceps torque (P = 0.05; d = 1.10), peak isokinetic quadriceps torque (P = 0.02; d = 1.36), and average isokinetic quadriceps power (P = 0.02; d = 1.38) compared with the CON group. There were no differences between groups in isometric knee extensor strength or any differences in knee flexor isokinetic or isometric strength.

Conclusions:
The TF amputation group demonstrated greater isokinetic knee extensor strength in their intact limb with KOA compared with the CON group osteoarthritic limb; however, there were no differences in isometric strength. Furthermore, the differences in isokinetic strength may suggest that those with a history of leg amputation may require more strength and power in the intact limb to maintain daily activity and, therefore, may require greater thresholds of strength to protect the knee joint from cartilage degradation.
Exploring legitimacy in a municipal budget decision in Switzerland: empirical insights into citizens’ perceptions
Authors: Hänggli Fricker Regula , Wellings Thomas , Zai Florin , Yang Joshua C. , Majumdar Srijoni , Bernhard Laurent , Weil Leopold , Hausladen Carina I. , Pournaras Evangelos 
Published: November 2024

This study examines legitimacy in municipal budgeting decisions, focusing on input, throughput and output dimensions. Using data from four Swiss studies, we explore how citizens assess these dimensions across traditional and innovative decision-making processes and investigate the impact of different voting methods on legitimacy perceptions. Our findings reveal that in routine processes using traditional voting, legitimacy dimensions are considered collectively. Conversely, in innovative participatory budgeting, dimensions are judged separately, involving more active evaluation. Throughput legitimacy (perceived fairness) emerges as crucial in both contexts, while input and output legitimacy's importance varies by process type. The Method of Equal Shares voting system shifts focus towards procedural fairness, increases representation and is perceived as fairer than the traditional Greedy method. However, even fair processes cannot fully compensate for outcome dissatisfaction, highlighting the complex interplay of legitimacy dimensions. This research contributes to understanding legitimacy construction in municipal decision-making, offering insights into the relationship between voting methods and legitimacy perceptions. The findings have implications for policy-makers seeking to enhance the effectiveness and acceptance of budgeting processes.
This article is part of the theme issue ‘Co-creating the future: participatory cities and digital governance’.
Translocation of gutEnterococcus faecalistrains myeloid bone marrow progenitors via the C-type lectin receptor Mincle
Authors: Robles-Vera Iñaki , Jarit-Cabanillas Aitor , Brandi Paola , Martínez-López María , Martínez-Cano Sarai , González-Correa Cristina , Moleón Javier , Duarte Juan , Conejero Laura , Mata-Martínez Pablo , Díez-Rivero Carmen María , Bergón-Gutiérrez Marta , Fernández-López Iván , Gómez Manuel J. , Quintas Ana , Dopazo Ana , Sánchez-Cabo Fátima , Pariente Esther , del Fresno Carlos , Subiza José Luis , Iborra Salvador , Sancho David 
Published: November 2024

SummaryImpairment of the intestinal barrier allows the systemic translocation of commensal bacteria, inducing a pro-inflammatory state in the host. To address potential mechanisms underlying this link, we explored innate immune responses following increased gut permeability upon administration of dextran sulfate sodium (DSS) to mice. Microbiota translocation induced trained immunity (TI) in mouse myeloid bone marrow progenitors (BMPs).Enterococcus faecaliswas the predominant bacteria detected in the bone marrow (BM) following DSS treatment. Notably, live or heat-killedE. faecalisinduced reprogramming of mouse BMPsin vitroandin vivoand enhanced macrophage inflammatory activity, also training human monocytes.E. faecalissensing by the C-type lectin receptor Mincle (Clec4e−/-) is essential for TI induction in BMPs. Consequently,Clec4e−/-mice showed impaired TI uponE. faecalisor reduced pathology following DSS treatment. Our results identifyE. faecalisas inducer of TI-related inflammation that may contribute to pathologies associated with increased gut permeability.
The environmental impact of pharmaceuticals: an evidence-mapping review of recent data on aquatic concentrations and predictable effects
Authors: Francesca Renda , Valentina Giunchi , Matilde Bianconi , Rossana Matera , Emanuele Tandurella , Elisabetta Poluzzi , Giorgia Macedonio , Carlotta Lunghi 
Published: November 2024

ABSTRACTPharmaceuticals are recognised among emerging contaminants, particularly in water. They have the potential to alter ecosystem dynamics, with notable examples including hormone-induced feminization of male fish and disruptions to oogenesis in invertebrates. To assess the risk posed by pharmaceuticals, it is essential to understand their amount (via Measured Environmental Concentrations – MEC) and their actual effects on target species (via Predicted No Effect Concentrations – PNEC). Recently, many studies have aimed to collect MEC data from around the world, but a comprehensive overview is still lacking. Thus, the objective of this study is to provide a comprehensive overview by examining recently published literature on MEC data for a wide range of pharmaceuticals. Additionally, to enable risk assessment, this study also reviewed the published literature on PNEC data and integrated it with existing databases. A total of 315 substances were selected for MEC data extraction, with the inclusion of 56 articles. The most frequently monitored locations were Cadiz Bay in Spain (90 samples), the River Thames in the UK (51), and Hrdějovice in the Czech Republic (49). Most MEC samples were collected from surface water (N=325), influent wastewater treatment plants (WWTP) (205), and effluent WWTP (118). Based on PNEC values, risk analysis identified 81 pharmaceuticals as high-risk, with the highest risk values for propranolol (risk quotient [RQ]: 29,450,000), diclofenac (395,920), and 17alpha-ethinylestradiol (95,946). Additionally, the ATC classes with the most high-risk substances were anti-infectives (J), nervous system agents (N), cardiovascular agents (C), antineoplastic agents (L), analgesics (M), and sex hormones (G). The findings of this study highlight the widespread impact of pharmaceuticals across the globe and the involvement of multiple therapeutic classes. To move beyond the current point-in-time overview, which is limited to specific locations and sampling periods, systems for continuous monitoring of pharmaceuticals should be developed. This could involve the creation of resource-efficient methods and the integration of sampling data with estimation models. Furthermore, these results could serve as a starting point for developing and implementing actions to prevent and mitigate the environmental impact of pharmaceuticals.
TissueMosaic enables cross-sample differential analysis of spatial transcriptomics datasets through self-supervised representation learning
Authors: Kambhampati Sandeep , D’Alessio Luca , Grab Fedor , Fleming Stephen , Chen Fei , Babadi Mehrtash 
Published: November 2024

AbstractSpatial transcriptomics allows for the measurement of gene expression within native tissue context, thereby improving our understanding of how cell states are modulated by their microenvironment. Despite technological advancements, computational methods to link cell states with their microenvironment and perform comparative analysis across different samples and conditions are still underdeveloped. To address this, we introduce TissueMosaic (Tissue MOtif-based SpAtial Inference across Conditions), a self-supervised convolutional neural network designed to discover and represent tissue architectural motifs from multi-sample spatial transcriptomic datasets (https://github.com/broadinstitute/TissueMosaic). TissueMosaic effectively maps structurally similar tissue motifs close together in a learned latent space. TissueMosaic further links these motifs to gene expression, enabling the study of how changes in tissue structure impact function. TissueMosaic increases the signal-to-noise ratio of differential expression analysis through a motif enrichment strategy, resulting in more reliable detection of genes that covary with tissue structure. Here, we demonstrate TissueMosaic on high resolution spatial transcriptomics datasets across tissues, learning representations that outperform neighborhood cell-type composition baselines and existing methods on downstream tasks. We highlight genes and pathways in these tissues that are associated with changes in tissue structure across external conditions. These findings underscore the potential of self-supervised learning to significantly advance spatial transcriptomics research.
Single-Cell and Spatial Multi-omics Reveal Interferon Signaling in the Pathogenesis of Perianal Fistulizing Crohn’s Disease
Authors: Cao Siyan , Nguyen Khai M. , Ma Kaiming , Yao Xin , Liu Ta-Chiang , Ayoub Malek , Devi Jalpa , Liu Yizhou , Smith Radhika , Silviera Matthew , Hunt Steven R. , Wise Paul E. , Mutch Matthew G. , Glasgow Sean C. , Chapman William C. , Cowan Michelle , Ciorba Mathew A. , Colonna Marco , Deepak Parakkal 
Published: November 2024

ABSTRACTBackground & AimsPerianal fistulizing Crohn’s disease (PCD) is a common and debilitating complication with elusive pathophysiology. We examined mucosal cells from patients with PCD and related conditions using a multi-omics approach.MethodsWe recruited patients with PCD (n = 24), CD without perianal disease (NPCD, n = 10), and idiopathic perianal fistulas (IPF, n = 29). Biopsies were taken from fistula tracts, fistula opening, and rectal mucosa. Single-cell RNA-sequencing (scRNA-seq), mass cytometry (CyTOF), spatial transcriptomics (ST), immunohistochemistry, and integrated analysis were performed.ResultsScRNA-seq, CyTOF, and ST unraveled immune and non-immune cell compartments in PCD and IPF fistula tracts. PCD fistulas showed hyperactivated pathogenic pathways including interferon (IFN)G response and TNF signaling in myeloid and stromal cells. Intestinal cells from PCD patients also expressed greater levels of IFNG-responsive and EMT genes compared to NPCD patients. Furthermore, both fistula tracts and ileal mucosa from PCD patients harbored expanded IFNG+ pathogenic Th17 cells, which expressed elevated inflammatory mediators. CyTOF also identified skewed immune cell phenotypes in the fistula tracts, fistula opening, and rectum in PCD patients including expanded Th17 cells, increased pathogenic myeloid cells, and altered T cell exhaustion markers. Further analysis also revealed cellular modules associated with anti-TNF therapy in PCD patients.ConclusionMulti-omics analysis revealed immune, stromal, and epithelial cell landscapes of PCD, which highlight the pathogenic role of hyperactivated IFNG signaling in both fistula tracts and luminal mucosa. This study identified IFNG as a potential therapeutic target for PCD.
Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism
Authors: Woo Amelia Y. M. , Sandoval–Espinola Walter J. , Bollenbach Maud , Wong Alison , Sakanaka–Yokoyama Mariko , Zhang Qijun , Nieto Vincent , Rey Federico E. , Balskus Emily P. 
Published: November 2024

SummaryAnaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiome is a disease-associated pathway. The host’s impaired ability to oxidize TMA to trimethylamine-N-oxide (TMAO) results in trimethylaminuria (TMAU), while elevated serum TMAO levels have been positively correlated with cardiometabolic disease. Small molecule inhibition of gut bacterial choline metabolism attenuates the development of disease in mice, highlighting the therapeutic potential of modulating this metabolism. Inhibitors previously developed to target this pathway are often designed to mimic choline, the substrate of the key TMA-generating enzyme choline trimethylamine-lyase (CutC). Here, we use a growth-based phenotypic high-throughput screen and medicinal chemistry to identify distinct chemical scaffolds that can modulate anaerobic microbial choline metabolism and lower TMAO levelsin vivo. These results illustrate the potential of using phenotypic screening to rapidly discover new inhibitors of gut microbial metabolic activities.
Evaluating metagenomic analyses for undercharacterized environments: what’s needed to light up the microbial dark matter?
Authors: Nickols William A. , McIver Lauren J. , Walsh Aaron , Zhang Yancong , Nearing Jacob T. , Asnicar Francesco , Punčochář Michal , Segata Nicola , Nguyen Long H. , Hartmann Erica M. , Franzosa Eric A. , Huttenhower Curtis , Thompson Kelsey N. 
Published: November 2024

AbstractNon-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles.
Alternative EEG pre-processing pipelines can lead to conflicting conclusions regarding cortical excitation/inhibition ratio
Authors: Racz Frigyes Samuel , Mac-Auliffe Diego , Mukli Peter , Milton John , Cabrera Juan Luis , Millán José del R. 
Published: November 2024

AbstractConfluent recent evidence indicates that the spectral slope of1/fneurophysiological recordings is correspondent to cortical excitation/inhibition (E/I) ratio. In this framework, a steeper power spectrum (i.e., one with a larger spectral exponentβ) is indicative of stronger inhibitory tone and thus lower E/I ratio, and vice versa. While the tools commonly utilized for estimatingβare mostly consistent, there appears to be a lack of standardization among data processing protocols for slope analysis. In this work our goal is to draw attention to a fundamental consequence of this issue, namely that even in a confined, comparative research environment, applying different pre-processing steps to electroencephalography (EEG) data can lead to conflicting conclusions in terms of the E/I ratio. To this end, we analyzed resting-state EEG recordings in two independent datasets, containing data collected with eyes open (EO) and eyes closed (EC), with the latter considered as a physiological state with stronger inhibitory tone. Our analysis confirmed consistently in both cohorts that applying different spatial filtering schemes in an otherwise identical analytical pipeline indicated a decrease in E/I ratio over the prefrontal cortex in one case, but not the other when transitioning from EO to EC. In contrast, this same pattern was apparent over the occipital cortex regardless of the pre-processing scheme. This empirical evidence calls for the development of a standardized data processing protocol for EEG-based analyses of the E/I ratio.