bluuebunny/crossref_metadata_2025_split huggingface dataset:
ASSESSMENT OF RETINAL ARTERIOLAR TORTUOSITY IN PATIENTS WITH COL4A1 OR COL4A2 MUTATIONS
Authors: Krivosic Valérie , Goupillou Paul , Buffon-Porcher Frederic , Morel Hélène , Guey Stéphanie , Tadayoni Ramin , Lasserve Elisabeth Tournier , Chabriat Hugues , Gaudric Alain 
Published: October 2024

Purpose:
Qualitative and quantitative analyses of retinal arteriolar tortuosity in patients with COL4A1 and COL4A2 mutations to identify a tortuosity index (TI) threshold for detecting increased retinal arteriolar tortuosity.

Methods:
Fifty-two eyes of 28 patients were included. Group 1 included eyes with a normal arteriolar pattern (n = 19, 37%), Group 2 included eyes with moderately increased arteriolar tortuosity (n = 13, 25%), and Group 3 included eyes with typical abnormal arteriolar tortuosity (n = 20, 38%). The TI was measured by calculating the arc-to-chord ratio of arterioles and venules in the posterior pole.

Results:
The mean arteriolar TI was significantly higher in all groups with a COL4A1/A2 mutation compared with controls: 1.19 ± 0.03, 1.24 ± 0.05, and 1.57 ± 0.23 in Groups 1, 2 and 3, respectively, versus 1.12 ± 0.01 (all P < 0.0001). The TI threshold was 1.13, with a sensitivity of 98.1% and a specificity of 100%. The area under the curve was 0.995.

Conclusion:
Measuring the arteriolar TI allowed diagnosing increased retinal arteriolar tortuosity in all eyes with a COL4A1/A2 mutation, whereas the subjective assessment suspected or detected it in only 62% of eyes. In adult patients with cerebral microangiopathy, detecting increased retinal arteriolar tortuosity, even when mild, directs the diagnosis toward COL4A1/A2-related cerebroretinal angiopathy.
The Utility and Limitations of Remotely Delivered Feedback Messages Regarding Physical Activity in a 12-Month Weight Loss Intervention: Insights From the SMARTER Trial Focus Groups
Authors: Kariuki Jacob Kigo , Burke Lora E. , Zickmund Susan , Beatrice Britney , Kimball Elisabeth R. , Galyean Patrick , Cheng Jessica , Sereika Susan M. , Bizhanova Zhadyra , Cedillo Maribel , Wells Jessica , Conroy Molly B. 
Published: October 2024

Background
The increasing prevalence of obesity necessitates innovative interventions to address this grave public health concern. Standard behavioral therapy has been the mainstay for promoting weight loss, but its access and uptake are limited. The SMARTER randomized controlled trial aimed to explore the effects of self-monitoring with real-time, remotely delivered tailored feedback to recorded physical activity (PA) on weight loss.

Objective
This qualitative study examined the perceived utility and limitations of key intervention components in promoting PA and weight loss in the SMARTER trial.

Methods
Twenty-three participants who received feedback engaged in Zoom-based focus groups, providing insights into their interactions with the SMARTER app, Fitbit Charge 2 tracker, Aria II scale, and daily weighing. Participants' perspectives on feedback messages, personalized app experiences, and the impact of daily weighing on mental health emerged, providing nuanced insights into the multifaceted nature of success.

Results
Themes from the focus group emphasized the importance of tailoring feedback to individual preferences related to message timing, content, and engagement. The challenges that made the participants stop using the program as instructed included disappointment with not losing weight after several weeks of engagement, inability to open feedback messages within the 60-minute window, and environmental situations that prevented them from acting on the feedback received.

Conclusion
These findings contribute to ongoing efforts geared toward refining interventions targeting PA and weight loss among individuals with obesity and provide important insights for future studies seeking to optimize the design and delivery of remotely delivered feedback messages.
Primary signet ring cell carcinoma of the appendix presenting as gangrenous appendicitis with peritonitis: A case report
Authors: Liu Kuang-Ting , Chang Yueh-Ching , Lin Yu-Chieh , Chang Junn-Liang 
Published: October 2024

Introduction and clinical importance:
Primary signet ring cell carcinoma (SRCC) of the appendix is an exceedingly rare malignancy with a non-specific clinical manifestations, and it often masquerades as acute appendicitis. Case presentation
A 76-year-old man presented with acute abdominal pain and peritonitis. Abdominal computed tomography revealed relative acute appendicitis with peritonitis, and emergency laparoscopic partial cecectomy with appendectomy revealed gangrenous appendicitis with perforation. A histopathological examination revealed a primary appendiceal signet ring cell carcinoma (PASRCC).

Clinical discussion:
This case highlights the importance of considering appendiceal malignancies in the differential diagnosis of acute appendicitis. SRCC is a histological variant commonly associated with multiple malignancies of the gastrointestinal tract, particularly gastric and colorectal cancers.

Conclusion:
PASRCC is a rare malignancy presenting with symptoms indistinguishable from those of acute appendicitis. Clinicians should maintain a high index of suspicion for appendiceal malignancy, particularly in older patients with atypical clinical presentations. Early recognition, accurate diagnosis by histopathological and immunohistochemical examinations, and appropriate management are essential for optimizing the outcomes in these patients.
Breast reconstruction using the superficial circumflex iliac artery superficial branch perforator (SCISP) flap
Authors: Schwaiger Karl , Scharfetter Sandra , Russe Elisabeth , Köninger Fabian , Pumberger Peter , Wechselberger Gottfried 
Published: October 2024

Summary:
The deep inferior epigastric perforator (DIEP) flap is the gold standard for autologous breast reconstruction. One downside is its risk of postsurgical herniation and bulging due to the opening of the rectus fascia and intramuscular dissection of the rectus abdominis muscle. Additionally this part of the surgery is very time consuming. While the superficial inferior epigastric artery perforator (SIEA) flap has been thoroughly described for total autologous breast reconstruction, the use of the superficial circumflex iliac artery perforator flap in this field is limited. This series introduces the use of an extended superficial circumflex iliac artery (SCIA) perforator flap nourished solely by perforators of the superficial branch of the SCIA- artery for total autologous breast reconstruction.
Superficial preparation over the abdominal wall was performed without incising the rectus fascia, dissecting the superficial branch of the SCIA and its accompanying veins and the superficial inferior epigastric vein for additional venous drainage.
Four patients underwent successful autologous breast reconstruction with this extended SCIP (superficial circumflex iliac artery perforator)-flap-variation. The term superficial circumflex iliac artery superficial branch perforator (SCISP) flap was introduced to standardize the surgical technique for using only perforators of the superficial branch of the SCIA as free flaps.
The SCISP flap is safe and viable for total autologous breast reconstruction, particularly for women with small to medium sized breasts and with superficial dominance of the abdominal vascular system.
Selective colonization of microplastics, wood and glass by antimicrobial-resistant and pathogenic bacteria
Authors: Stevenson Emily M. , Rushby-Jones Owen , Buckling Angus , Cole Matthew , Lindeque Penelope K. , Murray Aimee K. 
Published: October 2024

Graphical abstract
Summary of key findings. Polystyrene and wood were selectively colonized by antimicrobial-resistant (AMR) bacteria, while bio-beads selected for potential Escherichia coli pathogens and surface weathering did not significantly influence AMR colonization. Created in BioRender. Stevenson, E. (2024) BioRender.com/r90g504
Effects of Home-Based EEG Neurofeedback Training as a Non-Pharmacological Intervention for Parkinson’s Disease
Authors: Cooke Andrew , Hindle John , Lawrence Catherine , Bellomo Eduardo , Pritchard Aaron W. , MacLeod Catherine A. , Martin-Forbes Pam , Jones Sally , Bracewell Martyn , Linden David E. J. , Mehler David M. A. 
Published: October 2024

AbstractAberrant movement-related cortical activity has been linked to impaired motor function in Parkinson’s disease (PD). Dopaminergic drug treatment can restore these, but dosages and long-term treatment are limited by adverse side-effects. This experiment reports the first study of home-based electroencephalographic (EEG) neurofeedback training as a non-pharmacological candidate treatment for PD. Sixteen people with PD received six home visits comprising symptomology self-reports, a standardised motor assessment, and a precision handgrip force production task while EEG was recorded (visits 1, 2 and 6); and 3 × 1-hr EEG neurofeedback training sessions to reduce EEG high-alpha power before initiating handgrip movements (visits 3 to 5). Participants successfully learned to self-regulate movement-related alpha rhythms, and this appeared to expedite the initiation of precision movements. There was no evidence of wider symptomology reduction. Interviews indicated that the intervention was well-received. We conclude that home-based neurofeedback for people with PD is feasible and warrants further research.
Detection of Nanoliter-Scale Cortical Perivascular Spaces Using Heavily T2-weighted MRI at 7T
Authors: Saib Gael , Demir Zeynep H. , Taylor Paul A. , Lalith Talagala S. , Koretsky Alan P. 
Published: October 2024

AbstractBackgroundThere is increasing interest in high-contrast cerebrospinal fluid (CSF) MRI to image perivascular spaces (PVSs). Dilated PVSs, associated with aging, dementia, and various other conditions, have been commonly detected within the white matter, basal ganglia, and midbrain. 7T MRI has enabled the early detection of smaller PVSs due to very high contrast and resolution. However, to date, PVSs in the cerebral cortex has received limited attention, despite that the identification of early changes in the cortical PVS could give valuable insight into neurological conditions.PurposeTo determine if PVSs can be detected within the cerebral cortex in healthy participants by using heavily T2-weighted MRI at 7T.Materials and MethodsA T2-weighted TSE sequence was optimized to detect CSF with high resolution and contrast at 7T while reducing the contribution from surrounding tissues. A semi-automated processing pipeline was used to extract PVSs and analyze their density in the whole brain including the cerebral cortex.ResultsA total of 17 healthy volunteers were scanned at 7T (10 Males and 7 Females, aged 40±14 years). The optimized 3D-TSE sequence (0.125 mm3volume, 0.5 mm isotropic resolution, 500 ms TE, 2.4 s TR and 10 min scan time) enabled a CNR of approximatively 180:1 after denoising, with a CSF volume detection limit of about 5 nL per voxel. At this sensitivity, average PVS density was found to be about 4.0% in white matter, 2.7% in deep gray matter and 1.3% in the cortex. Highest cortical PVS density was found to be in the insular cortex. Four characteristic classes of PVS morphology within the cortex or passing through the cortex were identified.ConclusionHigh-resolution CSF imaging using optimized 3D-TSE MRI at 7T allows nanoliter scale volume detection of cortical PVSs in healthy individuals. This lays the groundwork for exploring cortical PVSs and their potential for use in diagnosis or prognosis of neurological diseases.
Chikungunya Virus VLP Vaccine: Phase 3 Trial in Adolescents and Adults
Authors: Richardson Jason S. , Anderson Deborah M. , Mendy Jason , Tindale Lauren C. , Muhammad Sufia , Loreth Tobi , Tredo Sarah Royalty , Warfield Kelly L. , Ramanathan Roshan , Caso Jorge T. , Jenkins Victoria A. , Ajiboye Patrick , Bedell Lisa ,   the EBSI-CV-317-004 Study Group
Published: October 2024

1ABSTRACTBackgroundChikungunya disease is a growing global public health concern. Chikungunya virus (CHIKV) virus-like particle (VLP) vaccine is a single dose, pre-filled syringe for intramuscular injection.MethodsA pivotal phase 3 randomized, double-blind, placebo-controlled trial was conducted in healthy adolescents and adults 12-64 years of age. Participants received either CHIKV VLP vaccine or placebo on Day 1. Immunogenicity objectives assessed CHIKV serum neutralizing antibody (SNA) titers (NT80) at selected timepoints. Safety was assessed through Day 183 postvaccination.ResultsA total of 2790 participants received CHIKV VLP vaccine and 464 received placebo (n=3454). Coprimary endpoints were met including 1) immunologic superiority to placebo and 2) geometric mean titer at Day 22. Results demonstrated that CHIKV VLP vaccine induced a protective seroresponse (SNA NT80≥100; considered the presumptive seroprotective antibody response), in 97% of individuals at Day 15 (2 weeks), in 98% of individuals at Day 22, and in 86% of individuals at Day 183 (6 months). CHIKV VLP vaccine demonstrated a favorable safety profile. The majority of adverse events were self-limited and grade 1 or 2 in severity. The most common adverse events were injection site pain, fatigue, headache, and myalgia.ConclusionsCHIKV VLP vaccine induces a rapid and robust immune response by Day 15 that lasts through Day 183 postvaccination. These findings support the potential for this vaccine to protect individuals 12-64 years of age from disease caused by CHIKV. (Funded by Emergent BioSolutions Inc. and Bavarian Nordic A/S [as successor in interest to Emergent BioSolutions Inc.];ClinicalTrials.govnumber,NCT05072080).
A novel DNA methylation-based surrogate biomarker for chronic systemic inflammation (InfLaMeS): results from the Health and Retirement Study
Authors: Meier Helen C.S. , Klopack Eric T. , Farnia Mateo P. , Hernandez Belinda , Mitchell Colter , Faul Jessica D. , McCrory Cathal , Kenny Rose Anne , Crimmins Eileen M. 
Published: October 2024

ABSTRACTChronic low-grade systemic inflammation is a risk factor for chronic diseases and mortality and is an important biomarker in health research. DNA methylation (DNAm) surrogate biomarkers are valuable exposure, risk factor and health outcome predictors in studies where the measures cannot be measured directly and often perform as well or better than direct measure. We generated a DNAm surrogate biomarker for chronic, systemic inflammation from a systemic inflammation latent variable of seven inflammatory markers and evaluated its performance relative to measured inflammatory biomarkers in predicting several age-associated outcomes of interest, including mortality, activities of daily living and multimorbidity in the Health and Retirement Study (HRS). The DNAm surrogate, Inflammation Latent Variable Methylation Surrogate (InfLaMeS), correlated with seven individual inflammation markers (r= −0.2-0.6) and performed as well or better to the systemic inflammation latent variable measure when predicting multimorbidity, disability, and 4-year mortality in HRS. Findings were validated in an external cohort, The Irish Longitudinal Study of Ageing. These results suggest that InfLaMeS provides a robust alternative to measured blood-chemistry measures of inflammation with broad applicability in instances where values of inflammatory markers are not measured but DNAm data is available.
Association Between Angiotensin Receptor-Neprilysin Inhibitor Use and Clinical Outcomes in Concurrent Heart Failure with Reduced Ejection Fraction and End-Stage Renal Disease
Authors: Jung Mi-Hyang , Cho Dong-Hyuk , Choi Jimi , Kim Mi-Na , Lee Chan Joo , Son Jung-Woo , Youn Jong-Chan , Yoo Byung-Su 
Published: October 2024

AbstractBackgroundAlthough angiotensin receptor-neprilysin inhibitor (ARNI) therapy has been shown to improve outcomes in heart failure with reduced ejection fraction (HFrEF), its benefits in patients with end-stage renal disease (ESRD) on dialysis remain uncertain. This study investigated the clinical outcomes of ARNI compared to renin-angiotensin system (RAS) blockers in HFrEF patients with concomitant ESRD on dialysis.MethodsUsing the Korean National Health Insurance Service database, we identified individuals with HFrEF and ESRD on dialysis who were prescribed either ARNI or RAS blockers between 2017 and 2021. After applying inverse probability of treatment weighting, we compared 2,104 patients on ARNI with 2,191 on RAS blockers. The primary endpoint was a composite of all-cause mortality and any hospitalization over 2 years.ResultsBaseline characteristics were balanced between the groups. ARNI use was associated with a significantly lower risk of the primary endpoint (hazard ratio [HR] 0.86, 95% confidence interval [CI] 0.75–0.97) compared to RAS blockers. Additionally, ARNI was associated with a lower risk of all-cause mortality (HR 0.68, 95% CI 0.54–0.86) and any hospitalization (HR 0.86, 95% CI 0.75–0.98). Subgroup analyses demonstrated consistent associations between ARNI use and reduced risk across all subgroups (age, sex, comorbidities, and medications). Good adherence to ARNI was associated with a lower risk of the primary outcome, whereas non-adherence showed no such benefit.ConclusionIn a real-world population with HFrEF and ESRD on dialysis, ARNI use was associated with a lower risk of all-cause mortality and hospitalization compared to RAS blockers, particularly in those with good adherence to therapy.Abstract FigureGraphical Abstract. Association between Angiotensin Receptor-Neprilysin Inhibitor Use and Clinical Outcomes in Patients with Concurrent Heart Failure with Reduced Ejection Fraction and End-Stage Renal Disease on DialysisIn this real-world study of patients with heart failure with reduced ejection fraction (HFrEF) and end-stage renal disease (ESRD) on dialysis, the use of angiotensin receptor-neprilysin inhibitor (ARNI) was associated with a significant reduction in the risk of all-cause mortality and any hospitalization compared to renin-angiotensin system (RAS) blockers. These benefits were particularly evident in patients who adhered well to their medication.
CytoLNCpred - A computational method for predicting cytoplasm associated long-coding RNAs in 15 cell-lines
Authors: Choudhury Shubham , Mehta Naman Kumar , Raghava Gajendra P. S. 
Published: October 2024

ABSTRACTThe function of long non-coding RNA (lncRNA) is largely determined by its specific location within a cell. Previous methods have used noisy datasets, including mRNA transcripts in tools intended for lncRNAs, and excluded lncRNAs lacking significant differential localization between the cytoplasm and nucleus. In order to overcome these shortcomings, a method has been developed for predicting cytoplasm-associated lncRNAs in 15 human cell-lines, identifying which lncRNAs are more abundant in the cytoplasm compared to the nucleus. All models in this study were trained using five-fold cross validation and tested on an independent dataset. Initially, we developed machine and deep learning based models using traditional features like composition and correlation. Using composition and correlation based features, machine learning algorithms achieved an average AUC of 0.7049 and 0.7089, respectively for 15 cell-lines. Secondly, we developed machine based models developed using embedding features obtained from the large language model DNABERT-2. The average AUC for all the cell-lines achieved by this approach was 0.6604. Subsequently, we also fine-tuned DNABERT-2 on our training dataset and evaluated the fine-tuned DNABERT-2 model on the independent dataset. The fine-tuned DNABERT-2 model achieved an average AUC of 0.6336. Correlation-based features combined with ML algorithms outperform LLM-based models, in the case of predicting differential lncRNA localization. These cell-line specific models as well as web-based service are available to the public from our web server (https://webs.iiitd.edu.in/raghava/cytolncpred/) .HIGHLIGHTSPrediction of cytoplasm-associated lncRNAs in 15 human cell linesMachine learning using composition and correlation featuresDNABERT-2 embeddings for lncRNA localization predictionCorrelation-based models outperform LLM-based modelsWeb server and models available for public useAUTHOR’S BIOGRAPHYShubham Choudhury is currently working as Ph.D. in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.Naman Kumar Mehta is currently working as Ph.D. in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.Gajendra P. S. Raghava is currently working as Professor and Head of Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
Cell tracking with accurate error prediction
Authors: Betjes Max A. , Tans Sander J. , van Zon Jeroen S. 
Published: October 2024

AbstractCell tracking is an indispensable tool for studying development by time-lapse imaging. However, existing cell trackers cannot assign confidence to predicted tracks, which prohibits fully automated analysis without manual curation. We present a fundamental advance: an algorithm that combines neural networks with statistical physics to determine cell tracks with error probabilities for each step in the track. From these we can obtain error probabilities for any tracking feature, from cell cycles to lineage trees, that function like p-values in data interpretation. Our method greatly speeds up tracking analysis by limiting manual curation to rare low-confidence tracking steps. Importantly, it also enables fully-automated analysis by retaining only high-confidence track segments, which we demonstrate by analyzing cell cycles and differentiation events at scale, for thousands of cells in multiple intestinal organoids. Our approach brings cell dynamics-based organoid screening within reach, and enables transparent reporting of cell tracking results and associated scientific claims.
Manipulation of thebrown glume and internode 1gene leads to alterations in lignified tissue coloration, lignification, and pathogen resistance in wheat
Authors: Hua Lei , Song Rui , Hao Xiaohua , Zhang Jing , Liu Yanna , Luo Jing , Ren Xiaopeng , Li Hongna , Wang Guiping , Rehman Shams ur , Wu Jiajie , Fu Daolin , Dong Yuxiu , Wang Xiaodong , Zhang Chaozhong , Chen Shisheng 
Published: October 2024

AbstractLignin is a crucial component of the cell wall, providing mechanical support and protection against biotic and abiotic stresses. However, little is known about wheat lignin-related mutants and their roles in pathogen defense. In this study, we identified an ethyl methanesulfonate (EMS)-derivedAegilops tauschiimutant namedbrown glume and internode 1(bgi1), which exhibits reddish-brown pigmentation in various tissues, including internodes, spikes, and glumes. Using map-based cloning and single nucleotide polymorphism (SNP) analysis, we identifiedAET6Gv20438400(BGI1) as the leading candidate gene, encoding the TaCAD1 protein. The mutation occurred in the splice acceptor site of the first intron, resulting in a premature stop codon inBGI1. We validated the function ofBGI1using loss-of-function EMS and gene editing knockout mutants, both of which displayed reddish-brown pigmentation in lignified tissues.BGI1knockout mutants exhibited reduced lignin content and shearing force relative to wild type, whileBGI1overexpression transgenic plants showed increased lignin content and enhanced disease resistance against common root rot andFusariumcrown rot. We confirmed that BGI1 exhibits CAD activity bothin vitroandin vivo, playing an important role in lignin biosynthesis.BGI1was highly expressed in the stem and spike and localized in the cytoplasm. Transcriptome analysis revealed the regulatory networks associated withBGI1. Finally, we demonstrated that BGI1 interacts with TaPYL-1D, potentially involved in the abscisic acid signaling pathway. The identification and functional characterization ofBGI1significantly advance our understanding of CAD proteins in lignin biosynthesis and plant defense against pathogen infection in wheat.