bluuebunny/crossref_metadata_2025_split huggingface dataset:
The combined focal loss and dice loss function improves the segmentation of beta-sheets in medium-resolution cryo-electron-microscopy density maps
Authors: Mu Yongcheng , Nguyen Thu , Hawickhorst Bryan , Wriggers Willy , Sun Jiangwen , He Jing 
Published: November 2024

Abstract

Summary
Although multiple neural networks have been proposed for detecting secondary structures from medium-resolution (5–10 Å) cryo-electron microscopy (cryo-EM) maps, the loss functions used in the existing deep learning networks are primarily based on cross-entropy loss, which is known to be sensitive to class imbalances. We investigated five loss functions: cross-entropy, Focal loss, Dice loss, and two combined loss functions. Using a U-Net architecture in our DeepSSETracer method and a dataset composed of 1355 box-cropped atomic-structure/density-map pairs, we found that a newly designed loss function that combines Focal loss and Dice loss provides the best overall detection accuracy for secondary structures. For β-sheet voxels, which are generally much harder to detect than helix voxels, the combined loss function achieved a significant improvement (an 8.8% increase in the F1 score) compared to the cross-entropy loss function and a noticeable improvement from the Dice loss function. This study demonstrates the potential for designing more effective loss functions for hard cases in the segmentation of secondary structures. The newly trained model was incorporated into DeepSSETracer 1.1 for the segmentation of protein secondary structures in medium-resolution cryo-EM map components. DeepSSETracer can be integrated into ChimeraX, a popular molecular visualization software.

Availability and implementation
https://www.cs.odu.edu/~bioinfo/B2I_Tools/.
FungiFun3: systemic gene set enrichment analysis for fungal species
Authors: Garcia Lopez Albert , Albrecht-Eckardt Daniela , Panagiotou Gianni , Schäuble Sascha 
Published: November 2024

Abstract

Summary
The ever-growing amount of genome-wide omics data paved the way for solving life science problems in a data-driven manner. Among others, enrichment analysis is part of the standard analysis arsenal to determine systemic signals in any given transcriptomic or proteomic data. Only a part of the members of the fungal kingdom, however, can be analyzed via public web applications, despite the global rise of fungal pathogens and their increasing resistance to antimycotics. We present FungiFun3, a major update of our user-friendly gene set enrichment web application dedicated to fungi. FungiFun3 was rebuilt from scratch to support a modern and easy-to-use web interface and supports &gt;4-fold more fungal strains (n = 1287 in total) than its predecessor. In addition, it also allows ranked gene set enrichment analysis at the genomic scale. FungiFun3 thus serves as a starting hub for identifying molecular signals in omics datasets related to a vast amount of available fungal strains including human fungal pathogens of the WHO’s priority list and far beyond.

Availability and implementation
FungiFun3, including sample data and FAQ, is freely available at https://fungifun3.hki-jena.de/.
Expert-guided protein language models enable accurate and blazingly fast fitness prediction
Authors: Marquet Céline , Schlensok Julius , Abakarova Marina , Rost Burkhard , Laine Elodie 
Published: November 2024

Abstract

Motivation
Exhaustive experimental annotation of the effect of all known protein variants remains daunting and expensive, stressing the need for scalable effect predictions. We introduce VespaG, a blazingly fast missense amino acid variant effect predictor, leveraging protein language model (pLM) embeddings as input to a minimal deep learning model.

Results
To overcome the sparsity of experimental training data, we created a dataset of 39 million single amino acid variants from the human proteome applying the multiple sequence alignment-based effect predictor GEMME as a pseudo standard-of-truth. This setup increases interpretability compared to the baseline pLM and is easily retrainable with novel or updated pLMs. Assessed against the ProteinGym benchmark (217 multiplex assays of variant effect—MAVE—with 2.5 million variants), VespaG achieved a mean Spearman correlation of 0.48 ± 0.02, matching top-performing methods evaluated on the same data. VespaG has the advantage of being orders of magnitude faster, predicting all mutational landscapes of all proteins in proteomes such as Homo sapiens or Drosophila melanogaster in under 30 min on a consumer laptop (12-core CPU, 16 GB RAM).

Availability and implementation
VespaG is available freely at https://github.com/jschlensok/vespag. The associated training data and predictions are available at https://doi.org/10.5281/zenodo.11085958.
Torticollis in incomplete Kawasaki disease: a case of atlantoaxial rotatory fixation
Authors: Ryu Keisho 
Published: November 2024

Abstract
Various respiratory, musculoskeletal, gastrointestinal, neurological, and urinary complications have been reported in Kawasaki disease. Here, we describe a rare case of atlantoaxial rotatory fixation (AARF) associated with incomplete Kawasaki disease. The case is of a healthy 4-year-old Japanese boy who had a high-grade fever, lymphadenopathy, and torticollis diagnosed with incomplete Kawasaki disease. Intravenous high-dose immunoglobulin and oral aspirin quickly resolved his fever and improved his lymphadenopathy, but torticollis remained. On orthopaedic examination, torticollis was observed with a marked restriction of rotation, and an open-mouth anteroposterior cervical radiograph and a CT scan confirmed rotational dislocation at the dens axis (AARF). Cervical collar fixation was immediately started, and the torticollis gradually normalized within a week. AARF is defined as torticollis due to dislocation or subluxation of the atlantoaxial joint. The diagnosis of AARF is difficult with routine plain cervical radiographs in 2 directions alone, and an additional cervical open-mouth anteroposterior radiograph and a CT scan aid the diagnosis. AARF associated with Kawasaki disease is uncommon, and only 24 cases have been reported in the literature. AARF may occur in Kawasaki disease patients with cervical lymphadenopathy. Still, torticollis is often transient and may not be recognized or ignored by family doctors and paediatricians. Reduction of the atlantoaxial joint can often be achieved spontaneously or with conservative treatment such as a collar or neck traction, but treatment is difficult if the diagnosis is delayed. Therefore, family doctors and paediatricians need to suspect the onset of AARF if torticollis is observed during treatment for Kawasaki disease, perform plain cervical radiographs including open-mouth anteroposterior view and a CT scan of the cervical spine, and have orthopaedists immediately intervene to avoid invasive surgery.
My body is a short-circuit that doesn’t need fixing: a disabled remediation of Zoom
Authors: Melling Rowan 
Published: November 2024

Abstract
During COVID-19 lockdowns, I started doing watercolor paintings of the interface of the videoconferencing program Zoom. Because I have a neurological disability, Zoom feels horrible for me to use; painting focused me and helped me cope. Using disability and these painting “remediations” as methods, I argue that digital interfaces function by sensorially training users to smoothly integrate as part of their operation. Disability is merely a word for the failure of a medium to properly interpellate a subject into the orientation necessary to facilitate its smooth functionality. Instead of suggesting accommodating upgrades to Zoom, I refuse the ableist demands of increased productivity that Zoom turns into requirements, and that require Zoom in order to register as norms. Using Zoom as a case study, my goal is to push back against the expectation that bodies passively adapt to the roll-out of technical systems, and the norms they operationalize.
Clinicopathological characteristics and favourable prognosis of paediatric cutaneous nodular fasciitis: a case series
Authors: Zhao Mutong , Han Xiaofeng , Wei Li , Sun Juan , Li Xu , Liang Yuan 
Published: November 2024

Abstract
Cutaneous nodular fasciitis (cNF) is a rare, benign myofibroblastic proliferation commonly misdiagnosed as a malignancy due to its rapid growth and histological features. We reviewed 15 paediatric patients with cNF, highlighting clinical, histological and molecular characteristics. The patients’ median age was 6 years, and there was a predilection for cNF in the head and neck region. Histologically, cNF showed plump spindle cells and myxoid stromal changes. USP6 rearrangement, particularly MYH9–USP6 fusion, was present in the majority of patients. Spontaneous resolution was observed in nonsurgically managed cases. Accurate diagnosis by screening for USP6 rearrangement is essential to avoid overtreatment. This study underscores the benign nature of cNF and the importance of conservative management, especially in cosmetically sensitive areas.
New approaches to acute kidney injury
Authors: Noel Sanjeev , Kapoor Radhika , Rabb Hamid 
Published: November 2024

ABSTRACT
Acute kidney injury (AKI) is a common and serious clinical syndrome that involves complex interplay between different cellular, molecular, metabolic and immunologic mechanisms. Elucidating these pathophysiologic mechanisms is crucial to identify novel biomarkers and therapies. Recent innovative methodologies and the advancement of existing technologies has accelerated our understanding of AKI and led to unexpected new therapeutic candidates. The aim of this review is to introduce and update the reader about recent developments applying novel technologies in omics, imaging, nanomedicine and artificial intelligence to AKI research, plus to provide examples where this can be translated to improve patient care.
Approaches to patients with obesity and CKD: focus on nutrition and surgery
Authors: Bellizzi Vincenzo , Annunziata Giuseppe , Albanese Alice , D'Alessandro Claudia , Garofalo Carlo , Foletto Mirto , Barrea Luigi , Cupisti Adamasco , Zoccali Carmine , De Nicola Luca 
Published: November 2024

ABSTRACT
Obesity is recognized as a public health challenge. During the last three decades, the global age-standardized prevalence increased from 8.8% to 18.5% in women and from 4.8% to 14.0% in men, with an absolute current number of 878 million obese subjects. Obesity significantly increases per se the risk of developing disability and chronic diseases, including chronic kidney disease (CKD). Specifically, obesity acts as a major, modifiable cause of CKD onset and progression toward kidney failure; as such, it is considered by the International Society of Nephrology a major health priority. This review analyses the effectiveness, safety and practicability of non-pharmacological anti-obesity interventions in CKD as the different patient phenotypes that may take advantage of personalized approaches.
Change in adiposity indices after 1 year of peritoneal dialysis: a single-center cohort study
Authors: Yang Zhikai , Ng Jack Kit-Chung , Fung Winston Wing-Shing , Chan Gordon Chun-Kau , Chow Kai-Ming , Szeto Cheuk-Chun 
Published: November 2024

ABSTRACT

Background
Weight gain is common after starting peritoneal dialysis (PD). Several adiposity indices have been developed recently as potential indicators of visceral adiposity and lipid accumulation. We aim to investigate the prevalence and prognostic implications of the change in adiposity indices after 1 year of PD.

Methods
We recruited 110 patients treated with PD for 12 months. Adiposity indices, including triglyceride glucose index, lipid accumulation product, visceral adiposity index and conicity index, were measured at baseline and then 1 year after PD started. The relation between their changes (Δ) and other clinical and biochemical parameters, as well as survival and hospitalization rates were analyzed.

Results
After 1 year of PD, more than half of the patients had increased adiposity indices. The change in adipose tissue mass significantly correlated with the concomitant changes in triglyceride glucose index (ΔTyGI) (r = 0.25, P = .01), lipid accumulation product (ΔLAP) (r = 0.27, P = .007) and visceral adiposity index (ΔVAI) (r = 0.26, P = .01). ΔTyGI significantly correlated with the change in insulin resistance as represented by homeostasis model assessment of insulin resistance (HOMA-IR) (r = 0.22, P = .02), while ΔLAP and change in conicity index (ΔCI) correlated with the changes in various anthropometric parameters. However, no indices variation was associated with patient survival, technique survival or hospitalization rate.

Conclusions
Increased adiposity indices were common after 1 year of PD. The changes in adiposity indices had variable correlation with the change in adipose tissue mass, insulin resistance and anthropometric parameters. Further studies are required to identify simple metabolic parameters with a prognostic impact that could be suitable for serial monitoring.
Low Incidence of Macular Edema and Other Ocular Events in the Etrasimod Development Program
Authors: Dubinsky Marla C , Wu Joseph , McDonnell Aoibhinn , Lazin Krisztina , Goetsch Martina , Branquinho Diogo , Modesto Irene , Armuzzi Alessandro 
Published: November 2024

Abstract

Background and Aims
Sphingosine 1-phosphate receptor modulators have been associated with an increased risk of macular edema. Etrasimod is an oral, once-daily, selective sphingosine 1-phosphate1,4,5 receptor modulator.

Methods
We report the proportions and incidence rates (per 100 patient-years of exposure) of Macular edema and other ocular adverse events in the etrasimod clinical program, including patients with ulcerative colitis, Crohn’s disease, eosinophilic esophagitis, alopecia areata, and atopic dermatitis. Ulcerative colitis data were analyzed in 2 cohorts: Placebo-controlled ulcerative colitis and All ulcerative colitis (comprising the Placebo-controlled ulcerative colitis cohort plus open-label extension studies).

Results
In the Placebo-controlled ulcerative colitis cohort, Macular edema was reported in 2 patients receiving etrasimod (0.3%; incidence rate: 0.70) and 1 receiving placebo (0.3%; incidence rate: 0.84). In the All ulcerative colitis cohort, 1 patient (0.1%; incidence rate: 0.13) receiving etrasimod reported 2 events of Cystoid macular edema. All events were nonserious, and 1 led to treatment discontinuation. No events of Macular edema were reported in other conditions. Nine and 4 patients receiving etrasimod reported Vision blurred and Visual impairment adverse events, respectively. All events were nonserious and most did not require any intervention.

Conclusions
Macular edema and other ocular events were uncommon in patients treated with etrasimod across multiple conditions. Incidence of Macular edema was comparable with placebo.

Clinical Trials.gov identifiers
NCT02447302; NCT03945188; NCT03996369; NCT02536404; NCT03950232; NCT04176588; NCT04173273; NCT04682639; NCT04556734; NCT04162769
Development and Validation of a Sexual Quality of Life Score for Youths With Inflammatory Bowel Disease
Authors: Mancheron Alexandre , Dumas Agnès , Nion Larmurier Isabelle , Landman Cecilia , Peyrin Biroulet Laurent , Caron Bénédicte , Baudry Clotilde , Allez Matthieu , Serrero Mélanie , Yahioune Dalal , Nancey Stéphane , Roman Céline , Ducleau-Loras Rémi , Coopman Stéphanie , Boizeau Priscilla , Husson Mathilde , Sable Shaya , Tarbet Iona , Devos Corinne , Bourmaud Aurelie , Martinez-Vinson Christine 
Published: November 2024

Abstract

Background and Aims
Inflammatory Bowel Disease (IBD) is known to impact patients' sexual lives. The aim of this study is to create and validate a sexual quality of life (QoL) designed for youth with IBD.

Methods
This study was conducted in 2 phases: development of the score and validation of the items. A multidisciplinary team created a score called BLOOMI, based on 2 validated scores: the International Index of Erectile Function (IIEF) and the Sexual Function Questionnaire 28 (SFQ28). It was validated through a French multicentric cross-sectional study among patients aged 15-25 years with IBD by comparison with IIEF and SFQ28 gold standard scores.

Results
BLOOMI is a sexual QoL designed with 10 items and formatted as a disk. The score was validated through the participation of 104 patients with a median age of 23.2 years. BLOOMI was well correlated with both gold standards and had a strong internal consistency. In total, 19.1% of IIEF-responders have erectile dysfunction and median scores for the SFQ domains Desire, Arousal sensation and cognition, and orgasm are below the threshold for the absence of sexual dysfunction. Fatigue, abdominal pain, body image concerns, or fear of anal leakages are correlated to a poorer sexual QoL.

Conclusions
The BLOOMI score is a newly validated score to assess the sexual QoL in 15-25 years with IBD. This tool may improve the screening for sexual challenges encountered by youths with IBD and may support future research into the impact of IBD on young patients’ lives.
Sodium–glucose cotransporter-2 inhibitors and clinical outcomes in patients with hypertrophic cardiomyopathy and diabetes: A population-based cohort study
Authors: Jung Mi-Hyang , Cho Jung Sun , Lee So-Young , Youn Jong-Chan , Choi Young , Chung Woo-Baek , Lee Jungkuk , Kang Dongwoo , Kwon Woojin , Kim Tae-Seok , Ihm Sang-Hyun , Jung Hae Ok 
Published: November 2024

Abstract

Aims
Hypertrophic cardiomyopathy (HCM) is associated with a significant risk of arrhythmia and heart failure (HF), yet treatment options for patients with HCM have remained limited. We aimed to investigate the relationship between sodium–glucose cotransporter-2 inhibitor (SGLT2i) use and clinical outcomes among patients with concurrent HCM and diabetes in real-world settings.

Methods and results
Using the Korean National Health Insurance Service database, we identified patients with a confirmed diagnosis of HCM and prescriptions for antidiabetic drugs from 2018 to 2022. After propensity matching, we compared 2063 patients who received SGLT2i with 2063 patients who did not for clinical outcomes. The primary outcome was a composite of all-cause death and HF hospitalization. Secondary outcomes included individual outcomes of all-cause death, HF hospitalization, sudden cardiac death, and ischaemic stroke. During a median follow-up period of 3.1 years, patients with HCM on SGLT2i had a significantly lower risk of the primary outcome [hazard ratio (HR) 0.76, 95% confidence interval (CI) 0.67–0.86]. Specifically, SGLT2i use was associated with reduced all-cause mortality (HR 0.56, 95% CI 0.46–0.68) and fewer HF hospitalizations (HR 0.82, 95% CI 0.72–0.94). Additionally, SGLT2i use was linked to a decreased risk of sudden cardiac death (HR 0.50, 95% CI 0.33–0.77) and ischaemic stroke (HR 0.74, 95% CI 0.62–0.88). Subgroup analyses by age, sex, and atrial fibrillation did not reveal any significant interactions.

Conclusion
The use of SGLT2i was associated with a decreased risk of adverse clinical outcomes among patients with HCM with concurrent diabetes on antidiabetic drugs.

Lay Summary
This population-based cohort study examined the association between sodium–glucose cotransporter-2 inhibitors (SGLT2is) and clinical outcomes in patients with hypertrophic cardiomyopathy (HCM) and diabetes. Patients with HCM and diabetes who used SGLT2i had a significantly lower risk of all-cause death and heart failure hospitalization compared with those who did not use SGLT2i.These associations were consistent across various subgroups, including sex, age, atrial fibrillation, and income levels.
Correlated evolution of categorical characters under a simple model
Authors: Grundler Michael C 
Published: November 2024

Abstract
I describe a simple model for quantifying the strength of association between two categorical characters evolving on a phylogenetic tree. The model can be used to estimate a correlation statistic that asks whether or not the two characters tend to change at the same time (positive correlation) or at different times (no correlation). This is different than asking if changes in one character are associated with a particular state in another character, which has been the focus of most prior tests for phylogenetic correlation in categorical characters. Analyses of simulated data indicate that positive correlations can be accurately estimated over a range of different tree sizes and phylogenetic signals.
Global genotype by environment prediction competition reveals that diverse modeling strategies can deliver satisfactory maize yield estimates
Authors: Washburn Jacob D , Varela José Ignacio , Xavier Alencar , Chen Qiuyue , Ertl David , Gage Joseph L , Holland James B , Lima Dayane Cristina , Romay Maria Cinta , Lopez-Cruz Marco , de los Campos Gustavo , Barber Wesley , Zimmer Cristiano , Trucillo Silva Ignacio , Rocha Fabiani , Rincent Renaud , Ali Baber , Hu Haixiao , Runcie Daniel E , Gusev Kirill , Slabodkin Andrei , Bax Phillip , Aubert Julie , Gangloff Hugo , Mary-Huard Tristan , Vanrenterghem Theodore , Quesada-Traver Carles , Yates Steven , Ariza-Suárez Daniel , Ulrich Argeo , Wyler Michele , Kick Daniel R , Bellis Emily S , Causey Jason L , Soriano Chavez Emilio , Wang Yixing , Piyush Ved , Fernando Gayara D , Hu Robert K , Kumar Rachit , Timon Annan J , Venkatesh Rasika , Segura Abá Kenia , Chen Huan , Ranaweera Thilanka , Shiu Shin-Han , Wang Peiran , Gordon Max J , Amos B Kirtley , Busato Sebastiano , Perondi Daniel , Gogna Abhishek , Psaroudakis Dennis , Chen Chun-Peng James , Al-Mamun Hawlader A , Danilevicz Monica F , Upadhyaya Shriprabha R , Edwards David , de Leon Natalia 
Published: November 2024

Abstract
Predicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023, the first open-to-the-public Genomes to Fields initiative Genotype by Environment prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements, and field management notes gathered by the project over 9 years. The competition attracted registrants from around the world with representation from academic, government, industry, and nonprofit institutions as well as unaffiliated. These participants came from diverse disciplines, including plant science, animal science, breeding, statistics, computational biology, and others. Some participants had no formal genetics or plant-related training, and some were just beginning their graduate education. The teams applied varied methods and strategies, providing a wealth of modeling knowledge based on a common dataset. The winner's strategy involved 2 models combining machine learning and traditional breeding tools: 1 model emphasized environment using features extracted by random forest, ridge regression, and least squares, and 1 focused on genetics. Other high-performing teams’ methods included quantitative genetics, machine learning/deep learning, mechanistic models, and model ensembles. The dataset factors used, such as genetics, weather, and management data, were also diverse, demonstrating that no single model or strategy is far superior to all others within the context of this competition.