bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using Kamishibai Cards to Identify Barriers and Display Adherence to the Central Line–Associated Bloodstream Infection Prevention Bundle
Authors: Brown Shelly L. , Klemanski Dori L. , Tornwall Joni , Ross Michelle M. , Browning Kristine K. 
Published: February 2025

Purpose
Central line–associated bloodstream infection (CLABSI) rates have been consistently high at an academic comprehensive cancer hospital. CLABSI prevention bundles can mitigate central line infections, and many components focus on nursing practice. Identification of barriers to maintaining adherence to these elements is not always assessed or addressed. The purpose of this project was to increase adherence to CLABSI prevention nursing practices and to implement a sustainable program to elevate nurses’ skills and documentation of CLABSI prevention bundle components.

Description
Pre-implementation/post-implementation chart reviews, post-implementation visual audits, and a survey for nurses post project were completed over a 9-week period. This project identified and addressed barriers to CLABSI prevention bundle compliance. Audits assessed nursing practice elements of the CLABSI prevention bundle. Evidence-based Kamishibai cards (K-cards) were used as a visual audit tool to display compliance of CLABSI bundle elements.

Outcomes
Compliant documentation of daily chlorhexidine gluconate (CHG) bathing increased to 75%. Inconsistent communication practices and knowledge gaps were frequent barriers to compliance. Seventy-five percent of nurses reported the K-card display changed their own CLABSI prevention practices.

Conclusion
This project increased knowledge, adherence to CLABSI prevention practices, and awareness of components most often missed.
Implementing the Clinical Nurse Specialist Role in Hospital Settings
Authors: Bachiller-Barquín Alejandra , Martín-Martín Jesús , Vázquez-Calatayud Mónica 
Published: February 2025

Purpose/Aims
To understand, based on the literature, how to implement the role of a clinical nurse specialist (CNS) in the hospital setting.

Design
A scoping review was conducted following the methodological framework of Arksey and O’Malley and the Joanna Briggs Institute.

Method
The search was conducted during March and April 2023 and was updated in November 2023. Electronic searches were conducted in the following major databases: PubMed, CINAHL, Web of Science, Scopus, PsycINFO, and Cochrane Library. Additionally, a “snowballing” strategy was used. A critical reading was conducted using the Joanna Briggs Institute methodological quality criteria. The Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for the Scoping Review guidelines were used.

Results
Eleven relevant studies were included in this review. The primary results are presented in 4 sections related to the framework, process, components, and evaluation of the implementation of the CNS role. The findings of the reviewed studies suggest that the implementation process of the CNS is cyclical, variable, context-dependent, and multifactorial and can be assessed using the indicators of structure, process, and outcome.

Conclusions
This scoping review provides relevant information to support the design of implementation and evaluation strategies for the role of the CNS in the hospital context. Based on the findings of the reviewed studies, a comprehensive strategy is suggested for implementing the role of the CNS in a hospital setting.
Disseminated Mycobacterium tuberculosis from Infected Bone Graft Source
Authors: Herb Thomas , Jentzen Jeffrey , Schmidt Carl 
Published: February 2025

Abstract
Iatrogenic infections of cadaveric bone grafts have led to 2 outbreaks of Mycobacterium tuberculosis (Mtb) infection in the United States that have resulted in multiple fatalities. We report a case of one of the bone graft recipients from the 2023 outbreak. A 57-year-old immunocompromised female with a history of renal failure status post 3 kidney transplants underwent a laminectomy with a cadaveric bone graft due to spinal stenosis. She was later hospitalized with diffuse lymphadenopathy and surgical site purulent ulceration. The workup included positive cultures for Mtb. Despite appropriate therapy, the patient died in the hospital. Autopsy findings included purulent discharge from the surgical site, medullary abscesses of one of the transplanted kidneys, diffuse pinpoint areas of softening in the liver, and lung congestion. Histology of the liver and right lung demonstrated loose granulomas with abundant acid-fast organisms. The kidney abscesses were due to Candida species infection. Overall, findings were consistent with disseminated Mtb infection. Additional investigation found similar infections in recipients of the same bone graft source. We compare the Mtb outbreaks to similar outbreaks, including cases of fungal meningitis due to steroid injections, and discuss our approach and strategy in cases of iatrogenic infection.
Evaluating a User-centered Redesign of the NYC Environment and Health Data Portal Website
Authors: Montesano Matthew , Gettings Chris , Torem Emily 
Published: February 2025

Context:
Public health agencies publish data so that data can influence public health policy and practice and improve the public health. But when these websites are difficult to use, they present barriers to this goal. Working to make data websites easier to use can add value to public health work.

Program:
In 2022, the NYC Department of Health and Mental Hygiene redesigned the Environment and Health Data Portal website to communicate data more effectively by improving usability. The redesigned website lets users browse datasets, visualize them, and includes companion explanatory material to communicate key public health findings.

Implementation:
We evaluated the usability as an outcome of the redesign and compared it to the usability of the prior website. Using a cross-over design, participants did simple tasks on both old and new websites, then filled out the Post-Study System Usability Questionnaire, a standard usability instrument.

Evaluation:
Participants scored the new site better than the old site, with statistically significant improvements in overall usability, system usefulness, and information. Additionally, web analytics show steadily increasing traffic to the new site, indicating that improved usability might have led to increased use.

Discussion:
This evaluation indicates a successful redesign: a measurable increase in usability and a substantial increase in web traffic. It suggests that designing data products for a wide range of users can be a successful strategy and demonstrate a viable method for evaluating public health data communication websites using a standard usability instrument.
“A Comparative Study of Septal Extension Graft versus Derotation Graft for Short Nose Correction in Asian Rhinoplasty”
Authors: Namgoong Sik , Yoon Yukyeong , Park Sangjun , Suh Man-Koon 
Published: February 2025

Background:
Precise nasal tip refinement is a cornerstone of Asian rhinoplasty that addresses characteristics such as bulbous tips, short columellas, and flared nostrils. Septal extension grafts (SEG) and derotation grafts (DRG) are commonly employed to enhance tip projection; however, comparative analyses are lacking. We assessed the outcomes of SEGs and DRGs in Asian patients who underwent tip-plasty.

Methods:
In this retrospective study, we analyzed 729 patients who underwent nasal tip-plasty using SEG or DRG between January 2011 and December 2017. Postoperative complications were assessed after a minimum follow-up of 6 months. For patients with long-term follow-up (≥24 months), nasal tip projection (NTP) and columellar-labial angle (CLA) were measured preoperatively and postoperatively using Goode’s and Byrd’s methods.

Results:
Among 287 SEG and 142 DRG cases, both techniques showed significant postoperative improvements: SEG (Δ NTP-Goode=0.036, p=0.001; ΔNTP-Byrd=0.036, p<0.001) and DRG (ΔNTP-Goode=0.047, p=0.005; ΔNTP-Byrd=0.053, p<0.001). No significant differences were noted for NTP ratios (Goode: p=0.954; Byrd: p=0.452) or CLA (p=0.116). Complications included more tip-columella deviations in SEG (5.23% vs. 1.41%) and higher tip drooping (4.53% vs. 8.45%; adjusted p=0.040) and supratip deformity (0% vs. 2.82%; adjusted p=0.010) in DRG.

Conclusions:
Longitudinal analysis shows that both SEG and DRG effectively preserve tip projection over time. SEG is more prone to tip and columellar deviations, while DRG is associated with tip drooping and supratip deformity, with no difference in tip shortening relapse. Technique selection should be customized to the patient’s anatomical features and the surgeon’s experience to minimize complications.

Level of Evidence:
IV
“Accessible Presurgical Orthopedics: Nasal Elevator and Lip Taping as a Cost-Effective Solution for Cleft Care in Low-Resource Settings.”
Authors: Tanikawa Daniela Y. S. 
Published: February 2025

Background:
This study evaluates the use of a nasal elevator plus lip taping as an option for presurgical infant orthopedics (PSIO) in patients with complete unilateral cleft lip with or without cleft palate (CL±P).

Methods:
From 2014 to 2019, 112 patients with unilateral CL±P underwent the studied presurgical treatment. Anthropometric measures from pre- and post-PSIO were compared within the treatment group. Postsurgical nasal morphology was compared to patients who did not receive presurgical treatment (N=62). The dental arch relationship for both groups was assessed using the 5-year-olds’ index.

Results:
The nostril width ratio and the columellar angle significantly improved after PSIO (p<0.001). Post-surgically, nasal asymmetry was observed in 20% of the treatment group compared to 59.7% in the control group (p<0.001). Dental arch relationship analysis in 78 patients showed no significant difference between the treatment and control groups (p=0.271 for CL+P, p=0.545 for CL-P).

Conclusions:
Nasal elevator plus lip taping is an effective, reliable, and simple PSIO method. It is less invasive, easier for parents to manage, cost-effective, and allows for monthly follow-up by the surgeon. Thus, it provides an effective alternative for teams without access to Nasoalveolar Molding (NAM) therapy.
“Do Surgeons Treat Their Patients’ Upper Extremity Nerve Palsies, Like They Would Treat Their Own?”
Authors: Krijnen Nienke A. , Arellano Jose Antonio , Wu Kitty Y. , Ring David , Teunis Teun ,   Science of Variation Group
Published: February 2025

Background:
Early surgical intervention in nerve palsies with a high probability of nerve integrity and natural recovery risks unnecessary surgery. Understanding the variables influencing surgeons to offer surgery might provide insight into variations in surgeon beliefs and guide treatment recommendations.

Methods:
Sixty-nine surgeons of the Science of Variation Group participated in a survey consisting of six traumatic and three non-traumatic nerve palsy scenarios. Participants were asked what their preferred treatment was and how likely they were to offer surgery on a scale from 0 to 10. Participants were randomized to choose for themselves (n=31) or for a patient of their age and gender (n=38).

Results:
There was no difference in the overall likelihood of offering surgery or in the types of treatment offered to patients compared to oneself. Surgery was least recommended for idiopathic palsies and most for ulnar (β 0.91 95% CI 0.10-1.7, p=0.027) or radial (β 0.92, 95% CI 0.12-1.7, p=0.025) nerve palsy following closed distal radius or humerus fractures. Longer symptom duration increased the likelihood of offering surgery.

Conclusions:
Surgeons were moderately likely to recommend surgery for nerve palsies, with notable variation in opinions regardless of whether they were deciding for themselves or for patients. For specific nerve palsies with a documented benign natural history this likely represents overtreatment. Future studies can assess if balancing awareness of a benign natural history with the pressure to act and the sense that recovery is “taking too long” might limit the rate of unnecessary surgery.
Adolescent boys’ sociocultural beliefs and attitudes toward menstruation in selected high schools in Ghana: Mediation and moderation effect of knowledge
Authors: Wuresah Israel , Klutse Priscilla , Mantey Sarah Odi , Agorinya Isaiah , Hennegan Julie , Gbogbo Sitsofe 
Published: February 2025

AbstractAdolescent boys can reinforce negative societal attitudes towards menstruation and make it difficult for adolescent girls to achieve optimal menstrual health and hygiene (MHH) which defeats Sustainable Development Goals 3, 5.1, 5.2 and 5.6. This study investigated how knowledge mediates/moderates the association between sociocultural beliefs (SB) and attitudes of adolescent boys regarding menstruation in senior high schools in Ghana. A cross-sectional study was conducted in five mix-sex public senior high schools (SHS) in Volta region, Ghana. Probability proportional to size was used to distribute 431 study subjects among the schools, and surveys were conducted using structured questionnaires. Structural equation modeling (SEM) and generalized least square (GLS) modeling were conducted. The mean age of the sample was 17.3 (±1.0). Majority (60.6%) were between 15-17 years old, and Christians (95.4%). Half of them had low knowledge; 38% had moderate, and 11% had high knowledge. Meanwhile, negative SB (55.2%) outweighed positive SB, which reflected in their attitudes towards menstruation with 52.7% exhibiting poor attitudes. The SEM revealed that knowledge had a significant negative effect on SB and attitudes, with coefficients of -0.06 (SE = 0.01, p < 0.001), and -0.28 (SE = 0.06, p < 0.001) respectively. The GLS model indicated that knowledge also moderates the relationship between SB and attitudes. Male students in Ghana have a tendency to stigmatize menstruation among their female counterparts because they have inadequate knowledge about it and this may affect the achievement of optimal MHH by their female colleagues. It is evident that effective menstrual education reduces negative attitudes.
StarTrace: A Multiplex Organoid Avatar Drug Testing Platform for Personalized Medicine
Authors: Khalili Sana , Patel Shrey , Patel Nidhi , Moy Victoria , Lyons Sawyer , Gray Emma , Brents Riley , Banister Carolyn E. , Morrison Sidney E. , Buckhaults Phillip J. 
Published: February 2025

AbstractThe goal of precision medicine is to improve clinical outcomes of cancer patients by choosing treatments most likely to work. One idea is to match tumor response to cancer-causing somatic mutations, but this strategy still faces limitations in colorectal cancer due to poorly understood genetic influences on drug resistance. We describe here a simple direct drug sensitivity assay platform applied to mixtures of patient-derived organoid avatars as a practical solution for choosing therapy, sidestepping the need for exhaustive knowledge of drug-genetic interactions. This approach rank orders individual patient’ organoid avatars’ responses to various drugs to be used to guide treatment choices. The platform multiplexes organoids using a clonal barcoding method, called StarTrace, which simultaneously tests pools of multiple patients’ organoid avatars for sensitivity or resistance to small molecule inhibitors. We utilized both quantitative real-time PCR-based and single-molecule sequencing assays to track the relative Darwinian fitness of each barcoded organoid within the pool. StarTrace offers a rapid, cost effective and sensitive testing platform that could be useful for either preclinical drug development or tailoring personalized therapy.
The cellular state space of AML unveils novelNPM1subtypes with distinct clinical outcomes and immune evasion properties
Authors: Lilljebjörn Henrik , Peña-Martínez Pablo , Thorsson Hanna , Henningsson Rasmus , Rissler Marianne , Landberg Niklas , Puente-Moncada Noelia , von Palffy Sofia , Rissler Vendela , Stanek Petr , Desponds Jonathan , Zhong Xiangfu , Juliusson Gunnar , Lazarevic Vladimir , Lehmann Sören , Fontes Magnus , Ågerstam Helena , Sandén Carl , Orsmark-Pietras Christina , Fioretos Thoas 
Published: February 2025

AbstractAcute myeloid leukemia (AML) is a genetically and cellularly heterogeneous disease. We characterized 120 AMLs using genomic and transcriptomic analyses, including single-cell RNA sequencing. Our results reveal an extensive cellular heterogeneity that distorts the bulk transcriptomic profiles. Selective examination of the transcriptional signatures of >90,000 immature AML cells identified four main clusters, thereby extending current genomic classification of AML. Notably,NPM1mutated AML could be stratified into two novel, clinically relevant classes, withNPM1classIassociated with downregulation of MHC class II and excellent survival following hematopoietic stem cell transplantation (HSCT).NPM1classIIwas instead associated with resistance to allogeneic T cells in anex vivoco culture assay, and importantly, dismal survival following HSCT. These findings provide new insights into the cellular state space of AML, define new diagnostic entities, and highlight potential therapeutic intervention points.Key PointsThe bulk transcriptional profiles of AML are mainly driven by a diverse set of cellular signatures.Single cell RNA-sequencing of the most common AML subtypes reveals marked heterogeneity extending beyond current genomic classification schemes.NPM1-mutated AML can be divided into two new classes, with distinct immune evasion mechanisms and survival after transplantation.
ClusterApp to visualize, organize, and navigate metabolomics data
Authors: Hansel Vinicius , Karunarathne Pothuvilage , Borelli Tiago Cabral , Quinn Robert , da Silva Ricardo R. 
Published: February 2025

AbstractBackgroundClustering analysis is a foundational step in exploratory data analysis workflows, with dimensionality reduction methods commonly used to visualize multidimensional data in lower-dimensional spaces and infer sample clustering. Principal Component Analysis (PCA) is widely applied in metabolomics but is often suboptimal for clustering visualization. Metabolomics data often require specialized manipulations such as blank removal, quality control adjustments, and data transformations that demand efficient visualization tools. However, the lack of user-friendly tools for clustering without computational expertise presents a challenge for metabolomics researchers. ClusterApp addresses this gap as a web application that performs Principal Coordinate Analysis (PCoA), expanding clustering alternatives in metabolomics. Built on a QIIME 2 Docker image, it enables PCoA computation and Emperor plot visualization. The app supports data input from GNPS, GNPS2, or user-provided spreadsheets. Freely available, ClusterApp can be locally installed as a Docker image or integrated into Jupyter notebooks, offering accessibility and flexibility to diverse users.ResultsTo demonstrate the data preprocessing techniques available in ClusterApp, we analyzed two Liquid Chromatography coupled to Tandem Mass Spectrometry (LC-MS/MS) metabolomics datasets: one exploring metabolomic differences in mouse tissue samples and another investigating coral life history stages. Among the dissimilarity measures available, the Bray-Curtis measure effectively highlighted key metabolomic variations and patterns across both datasets. Targeted filtering significantly enhanced data reliability by retaining biologically relevant features, 10,617 in the coral dataset and 7,341 in the mouse dataset while eliminating noise. The combination of Total Ion Current (TIC) normalization and auto-scaling improved clustering resolution, revealing distinct separations in tissue types and life stages. ClusterApp’s flexible features, such as customizable blank removal and group selection, provided tailored analyses, enhancing visualization and interpretation of metabolomic profiles.ConclusionClusterApp addresses the need for accessible, dynamic tools for exploratory data analysis in metabolomics. By coupling data transformation capabilities with PCoA on multiple dissimilarity matrices, it provides a versatile solution for clustering analysis. Its web interface and Docker-based deployment offer flexibility, accommodating a wide range of use cases through graphical or programmatic interactions. ClusterApp empowers researchers to uncover meaningful patterns and relationships in metabolomics data without requiring cumbersome data manipulation or advanced bioinformatics expertise.
DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs
Authors: Ghaffaari Ali , Schönhuth Alexander , Marschall Tobias 
Published: February 2025

AbstractDetermining the distance between two loci within a genomic region is a recurrent operation in various tasks in computational genomics. A notable example of this task arises in paired-end read mapping as a form of validation of distances between multiple alignments. While straightforward for a single genome, graph-based reference structures render the operation considerably more involved. Given the sheer number of such queries in a typical read mapping experiment, an efficient algorithm for answering distance queries is crucial. In this paper, we introduce DiVerG, a compact data structure as well as a fast and scalable algorithm, for constructing distance indexes for general sequence graphs on multi-core CPU and many-core GPU architectures. DiVerG is based on PairG [26], but overcomes the limitations of PairG by exploiting the extensive potential for improvements in terms of scalability and space efficiency. As a consequence, DiVerG can process substantially larger datasets, such as whole human genomes, which are unmanageable by PairG. DiVerG offers faster index construction time and consistently faster query time with gains proportional to the size of the underlying compact data structure. We demonstrate that our method performs favorably on multiple real datasets at various scales. DiVerG achieves superior performance over PairG; e.g. resulting to 2.5–4x speed-up in query time, 44–340x smaller index size, and 3–50x faster construction time for the genome graph of the MHC region, as a particularly variable region of the human genome.The implementation is available at:https://github.com/cartoonist/diverg
Sidechain conditioning and modeling for full-atom protein sequence design with FAMPNN
Authors: Shuai Richard W. , Widatalla Talal , Huang Po-Ssu , Hie Brian L. 
Published: February 2025

AbstractLeading deep learning-based methods for fixed-backbone protein sequence design do not model protein sidechain conformation during sequence generation despite the large role the three-dimensional arrangement of sidechain atoms play in protein conformation, stability, and overall protein function. Instead, these models implicitly reason about crucial sidechain interactions based on backbone geometry and known amino acid sequence labels. To address this, we present FAMPNN (Full-Atom MPNN), a sequence design method that explicitly models both sequence identity and sidechain conformation for each residue, where the per-token distribution of a residue’s discrete amino acid identity and its continuous sidechain conformation are learned with a combined categorical cross-entropy and diffusion loss objective. We demonstrate that learning these distributions jointly is a highly synergistic task that both improves sequence recovery while achieving state-of-the-art sidechain packing. Furthermore, benefits from explicit full-atom modeling generalize from sequence recovery to practical protein design applications, such as zero-shot prediction of experimental binding and stability measurements.