bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality Improvement Identifies Healthcare Transition Disparities in Adolescents with Congenital Heart Disease and Disabilities
Authors: Allen Catherine C. , Swanson Briana L. , Zhang Xiao , Coller Ryan J. , Olson Krisjon R. 
Published: May 2024

Introduction:
We aim to implement healthcare transition (HCT) education for youth with congenital heart disease (CHD) and assess HCT preparedness for cardiac self-care.

Methods:
An HCT clinic was implemented at an academic pediatric cardiology clinic for CHD youth 17 years of age and older. An educator used transition readiness assessment questionnaires and discussed HCT material. The percentage of eligible youth who received HCT education and the cause for missed occurrences were tracked. Plan-do-study-act cycles began in August 2020 to improve the number of youths reached. Secondary analyses assessed improvement differences among those without cardiac procedures or disabilities.

Results:
HCT education provision improved from a mean of 38% to 73% in the 17-year and older age group by December 2022. Communication failure was the leading cause of missed visits in 2021 (30%), reduced to 0 by 2022 following plan-do-study-act cycles. Other missed HCT visits included clinic add-ons after screening, limited staff availability, and unidentified eligibility. Readiness assessments were similar for youth with and without prior cardiac procedures, for example, confidence in taking charge of their health care (P = 0.47) and moving to adult care (P = 0.22). Adolescents with disabilities were significantly less confident than those without disabilities in taking charge of their heart health care (6.3 versus 7.5, P = 0.04) and moving to adult care (4.9 versus 7.4, P < 0.001).

Conclusions:
Implementation of a CHD HCT clinic improved successful education delivery. Provider engagement and clinic staffing are important for sustainability. HCT knowledge gaps exist for all adolescents, yet those with disabilities had the greatest deficits.
Comparison and Influence of a Multicomponent Educational Program on the Patient-Reported Outcomes of a Group of Patients With Rheumatoid Arthritis
Authors: Santos-Moreno Pedro , Rodríguez-Vargas Gabriel-Santiago , Rodríguez-Florido Fernando , Rubio-Rubio Jaime-Andrés , Rodríguez Pedro A. , Rojas-Villarraga Adriana 
Published: May 2024

Background
Rheumatoid arthritis (RA) is a chronic disease that affects different areas of the patient's body. Patient education and health literacy is essential for them to participate actively in follow-up.

Objectives
The aim of this study was to assess differences between clinimetric measurements done by a medical team and patient-reported outcome measures (PROMs) in RA and understand the impact of patient education strategies in order to identify differences between RA assessment methods.

Methods
This is a longitudinal cohort study. It included adult patients with RA and access to digital tools. These were divided into 3 groups by type of education. Group 1 included patients who participated in a multicomponent RA educational program. Group 2 did not have this multicomponent RA education. Group 3 did not receive any education. The 3 groups performed PROMs. Disease activity scales, functional class, and quality of life were measured. Univariate and bivariate analysis (χ2 and Wilcoxon for paired data) were done.

Results
Twenty-eight patients were included in group 1, 26 in group 2, and 37 in group 3. All were women. In group 1, there were no significant differences in clinimetrics between the medical team and patient's PROMs except for fatigue. In group 2 and group 3, significant differences were found. The RAPID3 and PAS variables did not show significant differences when analyzed by intervention subgroups.

Conclusions
This study shows no differences between clinimetrics/PROMs for patients with a high-level education on RA and physicians. On the other hand, when patient did not have any RA education, the clinimetric results differed from physician measurement.
An Atypical Spindle Cell/Pleomorphic Lipomatous Tumor of the Thigh With a Difficult Imaging Diagnosis That Mimicked a Malignant Lipomatous Tumor
Authors: Fujibuchi Taketsugu , Ichikawa Jiro , Kawasaki Tomonori , Onohara Kojiro , Aoki Kaoru 
Published: May 2024

Abstract
Atypical spindle cell/pleomorphic lipomatous tumor is categorized as a benign lipomatous tumor, but various MRI findings pose accurate diagnostic challenges. In our case, both MRI and PET/CT scans indicated the possibility of atypical lipomatous tumor/well-differentiated liposarcoma or dedifferentiated liposarcoma. Needle biopsy suggested benign to low-grade malignancy; hence, we opted for the wide resection. The final diagnosis of atypical spindle cell/pleomorphic lipomatous tumor was confirmed through histopathology analysis, including immunohistochemistry and fluorescence in situ hybridization. Since achieving an accurate diagnosis solely through imaging can be challenging, histopathology remains essential.
68Ga-DOTATATE PET/CT Imaging of a Solitary Nasopharyngeal Metastasis of Merkel Cell Carcinoma
Authors: Ding Haoyuan , Wang Yudi , He Kaixiang , Liu Ya , Chen Yue 
Published: May 2024

Abstract
Merkel cell carcinoma (MCC) is an uncommon highly aggressive cutaneous neuroendocrine neoplasm with high mortality. Rarer still is nasopharyngeal metastasis of MCC. Herein, we report the 68Ga-DOTATATE PET/CT findings of MCC with metastasis to the nasopharynx in a 53-year-old man who underwent surgery for MCC in his thigh 2 years ago.
Focal Nodular Hyperplasia of the Liver Detected on Myocardial Perfusion PET/CT
Authors: van der Zant Friso M. , Lazarenko Sergiy V. , Knol Remco J.J. 
Published: May 2024

Abstract
A 65-year-old woman with a few episodes of chest pain and progressive dyspnea on exertion was sent to the department of nuclear medicine for myocardial PET/CT. Pharmacological stress was performed with adenosine. During pharmacological stress, neither anginal complaints nor changes in electrocardiogram were observed. The PET/CT showed normal tracer uptake in the myocardium with normal myocardial flow and normal flow reserve. Furthermore, normal wall motion and left ventricle ejection fraction of 74% were observed. Incidentally, four 13N-NH3–avid liver lesions were detected. An additional MRI of the liver showed that these lesions were typical for focal nodular hyperplasia.
Current international tools and guidance for the implementation of hand hygiene recommendations in community settings: a scoping review
Authors: MacLeod Clara , Esteves Mills Joanna , Caruso Bethany A , Chase Claire , Chidziwisano Kondwani , Chipungu Jenala , Dreibelbis Robert , Ejemot-Nwadiaro Regina , Gordon Bruce , Thomas Ann , Cumming Oliver , Braun Laura 
Published: May 2024

AbstractBackgroundHand hygiene is an important measure to prevent disease transmission. This scoping review identifies and summarises current tools and guidance for the implementation of hand hygiene recommendations in community settings.MethodsWe conducted a scoping review following the Arksey and O’Malley framework. To identify relevant documents, we searched: 1) a grey literature database, 2) Google search engine, and 3) the websites of international organisations in August 2023. We included tools and implementation guidance relevant to hand hygiene in community settings, categorised as domestic, public, or institutional, and published in English by international organisations between January 1990 and August 2023. Tools and implementation guidance were mapped to an existing conceptual framework adapted for this review that includes a six-step implementation approach.ResultsWe included a total of 35 documents, comprising 30 implementation guidance documents and 5 stand-alone tools. Among these 35 documents, we identified 207 implementation recommendations and a total of 21 tools for the six implementation steps. The 21 tools include 5 stand-alone tools and 16 tools embedded within guidance documents. Most implementation guidance was mapped to steps 1 (prepare for action), 2 (analyse the situation), 3 (develop an action plan), and 5 (monitor, evaluate, and course correct) of the conceptual framework, with limited guidance for step 4 (executing the action plan) and step 6 (cross-cutting themes). Over half of identified tools are for step 2 (analyse the situation) and primarily for undertaking a situation analysis. Only two documents provided guidance or a tool across the six steps.ConclusionImplementation guidance is available, yet inconsistently spread across the different implementation steps. There is also a limited number of tools to support implementation. Future work should focus on developing comprehensive practical tools for the implementation of hand hygiene recommendations in community settings, in line with international guidelines.
Glutathione Effects on Liver Enzymes and Serum Electrolyte in Mice Exposed to 850–1900 MHz Mobile Phone Radiation
Authors: Binhambali Abdulhakeem , Umar Abdullahi Hussein , Aliyah Ahmed Temitayo , Mukhtar Abubakar Ibrahim , Tekanyi Amat Abdoulie , Pate Aisha Ahmad , Nuhu Amina , Ipinlaiye Tolulope , Muhammad Haruna Kolo , Ismail Ummulkhairi , Magaji Rabiu AbduSSALAM 
Published: May 2024

AbstractThe widespread presence of electromagnetic fields (EMF) produced by modern technologies may pose a significant threat to animal health. Ionizing radiation, a byproduct of EMF exposure, has the potential to contribute to serious diseases, including cancer. This study examines the impact of chronic exposure to 900-1800 MHz GSM-EMF-induced electromagnetic radiation on liver enzymes and serum electrolytes in mice, and the potential mitigating effects of exogenous glutathione (GSH) administration. Thirty-five adult male mice were randomly divided into seven groups and exposed to various modes of mobile phone radiation for five weeks, with or without GSH administration. Liver enzymes, Alkaline phosphates (ALP), Alanine transaminase (ALT), Aspartate aminotransferase (AST) and, serum electrolytes, sodium, potassium and bicarbonate were analyzed. Results showed significant increases in ALP levels in the Silent, Ringtone + GSH, and Silent + GSH groups compared to control group, while ALT and AST levels remained largely unchanged with the exception of some groups across the experimental cohorts. Serum electrolyte concentrations did not significantly differ across the control group. Our study found that chronic mobile phone radiation exposure in mice generally does not significantly affect liver enzyme levels or serum electrolyte concentrations. However, certain combinations with GSH administration notably increased some biochemical markers like ALP, ALT, and AST levels. Our study concluded that chronic mobile phone radiation had no significant impact on liver enzymes or serum electrolytes in mice. However, glutathione administration in combination with radiation increased liver enzyme levels, suggesting a potential role in oxidative stress mitigation. Further research is needed to explore these findings.
Bone marrow by day, lymph nodes by night: Undernutrition imparts a distinct circadian rhythm to T cells in mice
Authors: Foster Takesha R. , Dadzie Kwesi A. , Dunn Sydney , Gubbels Bupp Melanie R. 
Published: May 2024

AbstractIn well-nourished organisms, T cells migrate between the blood and secondary lymphoid organs, conducting surveillance for invading pathogens. T cell surveillance is under circadian control via diurnal fluctuations in corticosterone levels and undernutrition is associated with increased corticosterone. Therefore, we hypothesized that undernutrition disrupts the circadian migratory patterns of T cells. We report that compared to well-nourished controls, undernourished mice demonstrate enhanced T cell relocation to the bone marrow throughout the 24-hour period, but especially during the light phase, and diminished T cell migration to the lymph nodes only during the light phase. Undernutrition-related changes in T cell expression of key migration proteins are also mostly limited to the light phase. For example, undernourished naïve CD4+ T cells exhibited higher levels of CXCR4 and CCR7 as well as reduced levels of S1P1 compared to controls; with all changes, except for CXCR4 expression, being restricted to the light phase. These results suggest that naïve CD4+ T cells in the lymph nodes upregulate CXCR4 during the dark phase, enabling their migration to the bone marrow where they remain for the light phase. Once there, CCR7 is upregulated, presumably sending them back to the lymph node, thereby preserving immunosurveillance during the dark phase. Naïve CD4+ T cell disengagement from S1P1-related egress signals may further contribute to increased retention of cells within each compartment during the appropriate phase. Undernutrition-related increases in T cell residency of the bone marrow likely preserve T cell numbers until nutrition is restored.
Maggot : An ecosystem for sharing metadata within the web of FAIR Data
Authors: Jacob Daniel , Ehrenmann François , David Romain , Tran Joseph , Mirande-Ney Cathleen , Chaumeil Philippe 
Published: May 2024

AbstractBackgroundDescriptive metadata are crucial for the discovery, reporting and mobilisation of research datasets. Addressing all metadata issues within the Data Management Plan often poses challenges for data producers. Organising and documenting data within data storage entails creating various descriptive metadata. Subsequently, data sharing involves ensuring metadata interoperability in alignment with FAIR principles. Given the tangible nature of these challenges, a real need for management tools has to be addressed to assist data managers to the fullest extent. Moreover, these tools have to meet data producers requirements and be user-friendly as well with minimal training as prerequisites.ResultsWe developed Maggot which stands for Metadata Aggregation on Data Storage, specifically designed to annotate datasets by generating metadata files to be linked into storage spaces. Maggot enables users to seamlessly generate and attach comprehensible metadata to datasets within a collaborative environment. This approach seamlessly integrates into a data management plan, effectively tackling challenges related to data organisation, documentation, storage, and frictionless FAIR metadata sharing within the collaborative group and beyond. Furthermore, for enabling metadata crosswalk, metadata generated with Maggot can be converted for a specific data repository or configured to be exported into a suitable format for data harvesting by third-party applications.ConclusionThe primary feature of Maggot is to ease metadata capture based on a carefully selected schema and standards. Then, it greatly eases access to data through metadata as requested nowadays in projects funded by public institutions and entities such as Europe Commission. Thus, Maggot can be used on one hand to promote good local versus global data management with open data sharing in mind while respecting FAIR principles, and on the other hand to prepare the future EOSC FAIR Web of Data within the framework of the European Open Science Cloud.
Serum Proteome Profiling Identifies N-Cadherin and C-Met as Early Marker Candidates of Therapeutic Response to Neoadjuvant Chemotherapy in Breast Cancer
Authors: Steenbuck Ines Derya , Cosenza-Contreras Miguel , Fröhlich Klemens , Mayer Bettina , Kurowski Konrad , Werner Tilman , Reinold Meike , Fahrner Matthias , Hause Frank , Seredynska Adrianna , Feilen Tobias , Ritter Andrea , Guénégou-Arnoux Armelle , Biniossek Martin L. , Weiss Daniela , Nöthling Claudia , Jäger Markus , Erbes Thalia , Schilling Oliver 
Published: May 2024

AbstractBreast cancer remains the most common cancer in women worldwide. Neoadjuvant chemotherapy (NACT) is often preferred to adjuvant chemotherapy to achieve tumour shrinkage, monitor response to therapy and facilitate surgical removal in the absence of metastases. In addition, there is strong evidence that pathological complete remission (pCR) is associated with prolonged survival. In this study, we sought to identify candidate markers that signal response or resistance to therapy. We present a retrospective longitudinal serum proteomic study of 22 breast cancer patients (11 with pCR and 11 with non-pCR) matched with 21 healthy controls. Serum was analysed by LC-MS/MS after depletion of abundant proteins by immunoaffinity, trypsinisation, isobaric labelling and fractionation by reversed-phase HPLC. We observed an inverse behaviour of the serum proteins c-Met and N-cadherin after the second cycle of chemotherapy with a high predictive value (AUC 0.93). More pronounced changes were observed after the 6th cycle of NACT, with significant changes in the intensity of the proteins contactin-1, centrosomal protein, sex hormone-binding globuline and cholinesterase. Our study highlights the possibility of monitoring response to NACT using serum as a liquid biopsy.
micronuclAI: Automated quantification of micronuclei for assessment of chromosomal instability
Authors: Ibarra-Arellano Miguel A. , Caprio Lindsay A. , Hada Aroj , Stotzem Niklas , Cai Luke , Shah Shivem , Melms Johannes C. , Wünneman Florian , Izar Benjamin , Schapiro Denis 
Published: May 2024

AbstractChromosomal instability (CIN) is a hallmark of cancer that drives metastasis, immune evasion and treatment resistance. CIN results from chromosome mis-segregation events during anaphase, as excessive chromatin is packaged in micronuclei (MN), that can be enumerated to quantify CIN. Despite recent advancements in automation through computer vision and machine learning, the assessment of CIN remains a predominantly manual and time-consuming task, thus hampering important work in the field. Here, we presentmicronuclAI, a novel pipeline for automated and reliable quantification of MN of varying size, morphology and location from DNA-only stained images. InmicronucleAI, single-cell crops are extracted from high-resolution microscopy images with the help of segmentation masks, which are then used to train a convolutional neural network (CNN) to output the number of MN associated with each cell. The pipeline was evaluated against manual single-cell level counts by experts and against routinely used MN ratio within the complete image. The classifier was able to achieve a weighted F1 score of 0.937 on the test dataset and the complete pipeline can achieve close to human-level performance on various datasets derived from multiple human and murine cancer cell lines. The pipeline achieved a root-mean-square deviation (RMSE) value of 0.0041, an R2of 0.87 and a Pearson’s correlation of 0.938 on images obtained at 10X magnification. We tested the approach in otherwise isogenic cell lines in which we genetically dialed up or down CIN rates, and also on a publicly available image data set (obtained at 100X) and achieved an RMSE value of 0.0159, an R2of 0.90, and a Pearson’s correlation of 0.951. Given the increasing interest in developing therapies for CIN-driven cancers, this method provides an important, scalable, and rapid approach to quantifying CIN on routinely obtained images. We release a GUI-implementation for easy access and utilization of the pipeline.
Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project
Authors: Ge Yuchen , Lu Jennifer , Puiu Daniela , Revsine Mahler , Salzberg Steven L. 
Published: May 2024

AbstractIn recent years, a growing number of publications have reported the presence of microbial species in human tumors and of mixtures of microbes that appear to be highly specific to different cancer types. Our recent re-analysis of data from three cancer types revealed that technical errors have caused erroneous reports of numerous microbial species found in sequencing data from The Cancer Genome Atlas (TCGA) project. Here we have expanded our analysis to cover all 5,734 whole-genome sequencing (WGS) data sets currently available from TCGA, covering 25 distinct types of cancer. We analyzed the microbial content using updated computational methods and databases, and compared our results to those from two major recent studies that focused on bacteria, viruses, and fungi in cancer. Our results expand upon and reinforce our recent findings, which showed that the presence of microbes is far smaller than had been previously reported, and that many species identified in TCGA data are either not present at all, or are known contaminants rather than microbes residing within tumors. As part of this expanded analysis, and to help others avoid being misled by flawed data, we have released a dataset that contains detailed read counts for bacteria, viruses, archaea, and fungi detected in all 5,734 TCGA samples, which can serve as a public reference for future investigations.One-sentence summaryAnalysis of microbial content in 5,734 whole-genome sequencing samples from TCGA yields a comprehensive new resource for investigating the role of microbes in cancer.
DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture
Authors: Eskndir Nebiyat , Hossain Manseeb , Currey Marilena L , Pho Mai , Berrada Yasmin , Stephens Andrew D 
Published: May 2024

AbstractThe nucleus must maintain stiffness to protect the shape and integrity of the nucleus to ensure proper function. Defects in nuclear stiffness caused from chromatin and lamin perturbations produce abnormal nuclear shapes common in aging, heart disease, and cancer. Loss of nuclear shape via protrusions called blebs leads to nuclear rupture that is well-established to cause nuclear dysfunction, including DNA damage. However, it remains unknown how increased DNA damage affects nuclear stiffness, shape, and ruptures, which could create a negative feedback loop. To determine if increased DNA damage alters nuclear physical properties, we treated MEF cells with DNA damage drugs cisplatin and bleomycin. DNA damage drugs caused increased nuclear blebbing and rupture in interphase nuclei within a few hours and independent of mitosis. Micromanipulation force measurements reveal that DNA damage decreased chromatin-based nuclear mechanics but did not change lamin-based strain stiffening at long extensions relative to wild type. Immunofluorescence measurements of DNA damage treatments reveal the mechanism is an ATM-dependent decrease in heterochromatin leading to nuclear weaken, blebbing, and rupture which can be rescued upon ATM inhibition treatment. Thus, DNA damage drugs cause ATM-dependent heterochromatin loss resulting in nuclear softening, blebbing, and rupture.