bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of night shift work and biological ageing: the mediating role of body mass index
Authors: Shen Wenqi , Cai Lingli , Li Jiang , Sun Ying , Wang Bin , Wang Ningjian , Lu Yingli 
Published: November 2024

Abstract

Background
We aimed to examine whether current and lifetime night shift work is associated with accelerated biological ageing and the potential role of body mass index (BMI) in mediating the association.

Methods
Data were sourced from the UK Biobank cohort. This study included participants who reported detailed information on their current work schedule and had complete data to calculate PhenoAge. The outcome of interest was biological ageing, measured by PhenoAge acceleration. Multivariable linear regression models were conducted to test the relationship between night shift work and biological ageing. Mediation analyses were performed.

Results
Of the 182 064 participants included, the mean age was 52.6 years, and 51.1% were male. After adjustment for chronological age and sex, compared with day workers, shift workers without night shift, irregular night shift workers and permanent night shift workers were associated with 0.59-, 0.87- and 1.30-year increase in biological ageing, respectively (P for trend &lt;.001). Considering the lifetime work schedule, participants who worked night shifts &gt;10 years and participants who worked &gt;8 night shifts each month showed increased biological age acceleration [&gt;10 years: β = 0.54, 95% confidence interval (CI) 0.29–0.79; &gt;8 times/month: β = 0.29, 95% CI 0.07–0.50]. The mediation analysis showed that BMI mediated the associations between night shift work and biological age acceleration by 36%–53%.

Conclusions
We showed that night shift work was associated with accelerated biological ageing. Our findings highlight the interventions on appropriate shift work schedules and weight management in night shift workers, which may slow the biological ageing process and ultimately reduce the burden of age-related diseases.
SpecGMM: Integrating Spectral analysis and Gaussian Mixture Models for taxonomic classification and identification of discriminative DNA regions
Authors: Jaiswal Saish , Murthy Hema A , Narayanan Manikandan 
Published: November 2024

Abstract

Motivation
Genomic signal processing (GSP), which transforms biomolecular sequences into discrete signals for spectral analysis, has provided valuable insights into DNA sequence, structure, and evolution. However, challenges persist with spectral representations of variable-length sequences for tasks like species classification and in interpreting these spectra to identify discriminative DNA regions.

Results
We introduce SpecGMM, a novel framework that integrates sliding window-based Spectral analysis with a Gaussian Mixture Model to transform variable-length DNA sequences into fixed-dimensional spectral representations for taxonomic classification. SpecGMM’s hyperparameters were selected using a dataset of plant sequences, and applied unchanged across diverse datasets, including mitochondrial DNA, viral and bacterial genome, and 16S rRNA sequences. Across these datasets, SpecGMM outperformed a baseline method, with 9.45% average and 35.55% maximum improvement in test accuracies for a Linear Discriminant classifier. Regarding interpretability, SpecGMM revealed discriminative hypervariable regions in 16S rRNA sequences—particularly V3/V4 for discriminating higher taxa and V2/V3 for lower taxa—corroborating their known classification relevance. SpecGMM’s spectrogram video analysis helped visualize species-specific DNA signatures. SpecGMM thus provides a robust and interpretable method for spectral DNA analysis, opening new avenues in GSP research.

Availability and implementation
SpecGMM’s source code is available at https://github.com/BIRDSgroup/SpecGMM.
MitoMAMMAL: a genome scale model of mammalian mitochondria predicts cardiac and BAT metabolism
Authors: Chapman Stephen , Brunet Theo , Mourier Arnaud , Habermann Bianca H 
Published: November 2024

Abstract

Motivation
Mitochondria are essential for cellular metabolism and are inherently flexible to allow correct function in a wide range of tissues. Consequently, dysregulated mitochondrial metabolism affects different tissues in different ways leading to challenges in understanding the pathology of mitochondrial diseases. System-level metabolic modelling is useful in studying tissue-specific mitochondrial metabolism, yet despite the mouse being a common model organism in research, no mouse specific mitochondrial metabolic model is currently available.

Results
Building upon the similarity between human and mouse mitochondrial metabolism, we present mitoMammal, a genome-scale metabolic model that contains human and mouse specific gene-product reaction rules. MitoMammal is able to model mouse and human mitochondrial metabolism. To demonstrate this, using an adapted E-Flux algorithm, we integrated proteomic data from mitochondria of isolated mouse cardiomyocytes and mouse brown adipocyte tissue, as well as transcriptomic data from in vitro differentiated human brown adipocytes and modelled the context specific metabolism using flux balance analysis. In all three simulations, mitoMammal made mostly accurate, and some novel predictions relating to energy metabolism in the context of cardiomyocytes and brown adipocytes. This demonstrates its usefulness in research in cardiac disease and diabetes in both mouse and human contexts.

Availability and implementation
The MitoMammal Jupyter Notebook is available at: https://gitlab.com/habermann_lab/mitomammal.
Afpdb: an efficient structure manipulation package for AI protein design
Authors: Zhou Yingyao , Cox Jiayi , Zhou Bin , Zhu Steven , Zhong Yang , Spraggon Glen 
Published: November 2024

Abstract

Motivation
The advent of AlphaFold and other protein Artificial Intelligence (AI) models has transformed protein design, necessitating efficient handling of large-scale data and complex workflows. Using existing programming packages that predate recent AI advancements often leads to inefficiencies in human coding and slow code execution. To address this gap, we developed the Afpdb package.

Results
Afpdb, built on AlphaFold’s NumPy architecture, offers a high-performance core. It uses RFDiffusion's contig syntax to streamline residue and atom selection, making coding simpler and more readable. Integrating PyMOL’s visualization capabilities, Afpdb allows automatic visual quality control. With over 180 methods commonly used in protein AI design, which are otherwise hard to find, Afpdb enhances productivity in structural biology by supporting the development of concise, high-performance code.

Availability and implementation
Code and documentation are available on GitHub (https://github.com/data2code/afpdb) and PyPI (https://pypi.org/project/afpdb). An interactive tutorial is accessible through Google Colab.
InterLabelGO+: unraveling label correlations in protein function prediction
Authors: Liu Quancheng , Zhang Chengxin , Freddolino Lydia 
Published: November 2024

Abstract

Motivation
Accurate protein function prediction is crucial for understanding biological processes and advancing biomedical research. However, the rapid growth of protein sequences far outpaces the experimental characterization of their functions, necessitating the development of automated computational methods.

Results
We present InterLabelGO+, a hybrid approach that integrates a deep learning-based method with an alignment-based method for improved protein function prediction. InterLabelGO+ incorporates a novel loss function that addresses label dependency and imbalance and further enhances performance through dynamic weighting of the alignment-based component. A preliminary version of InterLabelGO+ achieved a strong performance in the CAFA5 challenge, ranking sixth out of 1625 participating teams. Comprehensive evaluations on large-scale protein function prediction tasks demonstrate InterLabelGO+’s ability to accurately predict Gene Ontology terms across various functional categories and evaluation metrics.

Availability and implementation
The source code and datasets for InterLabelGO+ are freely available on GitHub at https://github.com/QuanEvans/InterLabelGO. A web-server is available at https://seq2fun.dcmb.med.umich.edu/InterLabelGO/. The software is implemented in Python and PyTorch, and is supported on Linux and macOS.
Evolutionary history written in tandem arrays – satellite repeats in the Lagoseris lineage of Crepis sensu lato (Asteraceae)
Authors: Yücel Gülru , Borowska-Zuchowska Natalia , Bisaga Maciej , Nowak Teresa , Kolano Bozena 
Published: November 2024

Abstract
Satellite DNA families are excellent markers in evolutionary studies of plant karyotypes. Together with phylogenetic background, they can provide additonal information on different scenarios accompanying the speciation and diversification of related species. The Lagoseris lineage of Crepis sensu lato constitutes an interesting model in such studies, mainly due to: (i) the presence of large chromosomes; (ii) several base chromosome numbers; and (iii) variation in genome sizes. We aimed to characterize the satellite families and compare their genomic and chromosomal organization to better understand the evolutionary pathways that shaped the genomes of the Lagoseris lineage. Eight different families of satellite repeats were identified in Crepis palaestina based on RepeatExplorer raw Illumina read analyses. Most of these satellites were present in five species studied from the Lagoseris lineage and organized in tandem arrays. If the particular repeat was present in the genome of the related species, its genomic organization showed similarity to the one observed in C. palaestina. This similar genomic organization was not often reflected at the chromosomal level, where many distinct distribution patterns were shown, from several major loci to numerous minor ones spread throughout the chromosomal arms. The evolution of satellite repeats is discussed in phylogenetic context.
Smaller cingulate grey matter mediates the association between dual-task gait and incident dementia
Authors: Ali Pauline , Pieruccini-Faria Frederico , Annweiler Cédric , Dinomais Mickaël , Son Surim , Wilson Scott K , Camicioli Richard , Muir-Hunter Susan , Bartha Robert , Montero-Odasso Manuel 
Published: November 2024

Abstract
Individuals with mild cognitive impairment that have high dual-task gait cost (≥20% slowing in gait speed while performing a cognitive brain demanding task), are three-fold more likely to progress to dementia. However, the cortical regions that may explain this association are unknown, which may identify potentially treatable areas.
The aim of the current study is to investigate whether brain grey matter volume loss and motor cortex metabolite levels explain the association between dual-task cost and incident dementia in individuals with mild cognitive impairment.
We included participants with mild cognitive impairment from the Gait&Brain Study Cohort, who had a baseline MRI and were followed-up for 9 years with cognitive and gait assessments every 6 months. Gait performance was investigated under four conditions: usual gait, counting backwards by ones, naming animals and subtracting serial sevens. Dual-task cost was calculated as the percentage change in gait speed under dual-task conditions relative to usual gait speed. Data were collected from July 2007 to June 2023.
From the 139 individuals with mild cognitive impairment included at baseline (mean [SD] age, 73[6] years, 62 (44%) women), and 33 (24%) progressed to dementia. Baseline high dual-task cost (≥20%) under counting backwards by ones and naming animals conditions were associated with smaller grey matter volume in several brain structures. A higher ratio of choline to creatine in the primary motor cortex was associated with higher serial sevens DTC. High dual-task cost while counting backwards by ones and naming animals was associated with a three-fold risk of incident dementia (P=0.02). Mediation analyses revealed that grey matter volume clusters localized in the right anterior and middle cingulate cortices mediated the association between counting backwards by ones dual-task cost and incident dementia (effect: 48%, P=0.045) with no mediation observed in grey matter loss in other brain regions or through motor cortex metabolite levels.
Smaller grey matter volume of the right anterior and middle cingulate cortices explained the association between high dual-task cost and incident dementia in mild cognitive impairment. This result sheds light on the neural mechanisms of cognitive-motor interaction linked with cognitive decline and dementia in mild cognitive impairment and support the use of gait under dual-tasking as a motor biomarker of dementia.
The CSF lipid profile in patients with probable idiopathic normal pressure hydrocephalus differs from control but does not differ between shunt responders and non-responders
Authors: Toft-Bertelsen Trine L , Andreassen Søren Norge , Simonsen Anja Hviid , Hasselbalch Steen Gregers , MacAulay Nanna 
Published: November 2024

Abstract
Idiopathic normal pressure hydrocephalus is a common form of hydrocephalus in the elderly, characterized by enlarged ventricles combined with clinical symptoms presenting as gait impairment, urinary incontinence, and dementia. Idiopathic normal pressure hydrocephalus may be difficult to differentiate clinically from other neurodegenerative disorders, and up to 80% of cases may remain unrecognized and thus untreated. Consequently, there is a pressing demand for biomarkers that can confirm the diagnosis of idiopathic normal pressure hydrocephalus. In this exploratory study, CSF was sampled from the lumbar compartment of 21 control individuals and 19 probable idiopathic normal pressure hydrocephalus patients and analyzed by an untargeted mass spectroscopy-based platform to reveal a complete CSF lipid profile in these samples. Two hundred forty-four lipids from 17 lipid classes were detected in CSF. Various lipid classes, and select individual lipids, were reduced in the CSF obtained from patients with probable idiopathic normal pressure hydrocephalus, whereas a range of lipids belonging to the class of triacylglycerols was elevated. We detected no difference in the CSF lipid profile between probable idiopathic normal pressure hydrocephalus patients with and without clinical improvement following CSF shunting. In conclusion, the lipidomic profile of the CSF in patients with probable idiopathic normal pressure hydrocephalus, therefore, may serve as a sought after biomarker of the pathology, which may be employed to complement the clinical diagnosis.
Rapid Characterization and Identification of the Chemical Constituents in San-Huang-Xie-Xin-Tang, a Traditional Chinese Medicine Formula, by High Performance Liquid Chromatography Coupled to Electrospray Ionization and Quadrupole Time-of-Flight Mass Spectrometry
Authors: Liu Lei , Hu Pei , Chen Mengmo , Huang Jiasi , Zhang Qing , Ling Yun 
Published: November 2024

Abstract
San-Huang-Xie-Xin-Tang (SHXXT), a traditional Chinese medicine formula composed of Coptidis rhizome (CR), Scutellariae radix (SR) and Rhei rhizome (RR), is widely used to treat hypertension, gastritis and peptic ulcer clinically. However, the chemical constituent of SHXXT is still unclear due to its complexity, which hindered the discovery of effective compounds and quality control. Thus, an in-depth understanding of its chemical constituents is very essential. To address this problem, comprehensive analysis of chemical constituents of SHXXT was performed by high performance liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry (HPLC-ESI-QTOF-MS/MS). As a result, 45 compounds were identified, including 8 phenolic acids, 15 flavonoids, 13 alkaloids, 8 anthraquinones and 1 lignan. Among them, 17 compounds were from CR, 17 compounds were from SR and 11 compounds were from RR. This established method can systematically and rapidly analyze the chemical constituents in SHXXT, which provides chemical foundation for further research on effective substances and action mechanism of SHXXT.
Fatal Borealpox in an Immunosuppressed Patient Treated With Antivirals and Vaccinia Immunoglobulin—Alaska, 2023
Authors: Rogers Julia H , Westley Benjamin , Mego Thomas , Newell Katherine G , Laurance John , Smith Lisa , Parker Jayme , Park Sarah Y , Venkatasubrahmanyam Shivkumar , Noll Nicholas , Bercovici Sivan , Rao Agam K , McCollum Andrea M , Davidson Whitni , Carson William C , Townsend Michael B , Doty Jeffrey B , Hutson Christina , Li Yu , Wilkins Kimberly , Deng Jiusheng , Gigante Crystal M , Satheshkumar Panayampalli S , Tuttle Alexandra , Villalba Julian A , Bhatnagar Julu , Reagan-Steiner Sarah , Castrodale Louisa J , McLaughlin Joseph B 
Published: November 2024

Abstract

Background
Borealpox virus (BRPV, formerly known as Alaskapox virus) is a zoonotic member of the Orthopoxvirus genus first identified in a person in 2015. In the 6 patients with infection previously observed, BRPV involved mild and self-limiting illness. We report the first fatal BRPV infection in an immunosuppressed patient.

Methods
A man aged 69 years from Alaska's Kenai Peninsula was receiving anti-CD20 therapy for chronic lymphocytic leukemia. He presented to care for a tender, red papule in his right axilla with increasing induration and pain. The patient failed to respond to multiple prescribed antibiotic regimens and was hospitalized 65 days after symptom onset for progression of presumed infectious cellulitis. BRPV was eventually detected through orthopoxvirus real-time polymerase chain reaction testing of mucosal swabs. He received combination antiviral therapy, including 21 days of intravenous tecovirimat, intravenous vaccinia immunoglobulin, and oral brincidofovir. Serial serology was conducted on specimens obtained posttreatment initiation.

Findings
The patient's condition initially improved with plaque recession, reduced erythema, and epithelization around the axillary lesion beginning 1 week posttherapy. He later exhibited delayed wound healing, malnutrition, acute renal failure, and respiratory failure. He died 138 days after symptom onset. Serologic testing revealed no evidence the patient generated a humoral immune response. No secondary cases were detected.

Conclusions
This report demonstrates that BRPV can cause overwhelming disseminated infection in certain immunocompromised patients. Based on the patient's initial response, early BRPV identification and antiviral therapies might have been beneficial. These therapies, in combination with optimized immune function, should be considered for patients at risk for manifestations of BRPV.
A novel approach to detecting epileptic patients: complex network-based EEG classification
Authors: Olgun Nevzat , Özkaynak Emrah 
Published: November 2024

Abstract
Detection of epileptic seizures is important for early diagnosis and treatment. It is known that the behavioral patterns of the brain in electroencephalogram (EEG) signals have huge and complex fluctuations. Diagnosing epilepsy by analyzing signals are costly process. Various methods are used to classify epileptic seizures. However, the inadequacy of these approaches in classifying signals makes it difficult to diagnose epilepsy. Complex network science produces effective solutions for analyzing interrelated structures. Using methods based on complex network analysis, it is possible to EEG signals analyze the relationship between signals and perform a classification process. In this study proposes a novel approach for classifying epileptic seizures by utilizing complex network science. In addition, unlike the studies in the literature, classification processes were carried out with lower dimensional signals by using 1-s EEG signals instead of 23.6-s full-size EEG signals. Using the topological properties of the EEG signal converted into a complex network, the classification process has been performed with the Jaccard Index method. The success of the classification process with the Jaccard Index was evaluated using Accuracy, F1 Score, Recall, and K-Fold metrics. In the results obtained, the signals of individuals with epileptic seizures were separated with an accuracy rate of 98.15%.
Incremental prognostic value of left ventricular and left atrial strains in moderate aortic stenosis
Authors: Lee Hyun-Jung , Kim Kyu , Gwak Seo-Yeon , Cho Iksung , Hong Geu-Ru , Ha Jong-Won , Shim Chi Young 
Published: November 2024

Abstract

Aims
Patients with moderate aortic stenosis (AS) show a poor prognosis if they have high-risk features. We investigated herein the incremental prognostic value of left ventricular (LV) and left atrial (LA) strain in patients with moderate AS.

Methods and results
In a cohort of 923 patients with moderate AS (median age 74 years, men 55%, aortic valve area 1.18 [interquartile range (IQR) 1.08–1.30] cm2, mean pressure gradient 25 [IQR 23–30] mmHg), the LV global longitudinal strain (LV-GLS) and LA reservoir strain (LARS) were measured using speckle-tracking echocardiography. Absolute values of myocardial strain were used. The primary endpoint was a composite of all-cause mortality and heart failure hospitalization. During a median of 5.9 years, the primary endpoint occurred in 186 patients (20.2%). The median LV-GLS and LARS were 17.7% (IQR 14.8–19.7%) and 24.5% (IQR 18.7–29.3%), respectively. LV-GLS [adjusted hazard ratio (HR) 0.92, 95% confidence interval (CI) 0.87–0.97] and LARS (adjusted HR 0.97, 95% CI 0.95–0.99) were significant predictors of the primary outcome, independent of clinical and echocardiographic variables, including LV ejection fraction. Notably, the prognostic value of LV-GLS was stronger than that of LARS, remaining significant after further adjustment for LARS. LV-GLS &lt; 17% and LARS &lt; 22% were identified as optimal cut-offs for the primary outcome. Patients with both reduced LV-GLS and LARS had the worst outcomes (log-rank P &lt; 0.001). LV-GLS &lt; 17% and LARS &lt; 22% had incremental prognostic values on top of other clinical and echocardiographic variables.

Conclusion
In moderate AS, reduced LV-GLS and LARS have incremental prognostic values and can refine risk stratification to identify high-risk patients.