bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using convolutional neural networks for stereological characterization of 3D hetero-aggregates based on synthetic STEM data
Authors: Fuchs Lukas , Kirstein Tom , Mahr Christoph , Furat Orkun , Baric Valentin , Rosenauer Andreas , Mädler Lutz , Schmidt Volker 
Published: March 2024

Abstract
The 3D nano/microstructure of materials can significantly influence their macroscopic properties. In order to enable a better understanding of such structure-property relationships, 3D microscopy techniques can be deployed, which are however often expensive in both time and costs. Often 2D imaging techniques are more accessible, yet they have the disadvantage that the 3D nano/microstructure of materials cannot be directly retrieved from such measurements. The motivation of this work is to overcome the issues of characterizing 3D structures from 2D measurements for hetero-aggregate materials. For this purpose, a method is presented that relies on machine learning combined with methods of spatial stochastic modeling for characterizing the 3D nano/microstructure of materials from 2D data. More precisely, a stochastic model is utilized for the generation of synthetic training data. This kind of training data has the advantage that time-consuming experiments for the synthesis of differently structured materials followed by their 3D imaging can be avoided. More precisely, a parametric stochastic 3D model is presented, from which a wide spectrum of virtual hetero-aggregates can be generated. Additionally, the virtual structures are passed to a physics-based simulation tool in order to generate virtual scanning transmission electron microscopy (STEM) images. The preset parameters of the 3D model together with the simulated STEM images serve as a database for the training of convolutional neural networks, which can be used to determine the parameters of the underlying 3D model and, consequently, to predict 3D structures of hetero-aggregates from 2D STEM images. Furthermore, an error analysis is performed with respect to structural descriptors, e.g. the hetero-coordination number. The proposed method is applied to image data of TiO2-WO3 hetero-aggregates, which are highly relevant in photocatalysis processes. However, the proposed method can be transferred to other types of aggregates and to different 2D microscopy techniques. Consequently, the method is relevant for industrial or laboratory setups in which product quality is to be quantified by means of inexpensive 2D image acquisition.
Prediction of mild cognitive impairment using EEG signal and BiLSTM network
Authors: Alahmadi Tahani Jaser , Rahman Atta Ur , Alhababi Zaid Ali , Ali Sania , Alkahtani Hend Khalid 
Published: March 2024

Abstract
Mild cognitive impairment (MCI) is a cognitive disease that primarily affects elderly persons. Patients with MCI have impairments in one or more cognitive areas, such as memory, attention, language, and problem-solving. The risk of Alzheimer’s disease development is 10 times higher among individuals who meet the MCI diagnosis than in those who do not have such a diagnosis. Identifying the primary neurophysiological variations between those who are suffering from cognitive impairment and those who are ageing normally may provide helpful techniques to assess the effectiveness of therapies. Event-related Potentials (ERPs) are utilized to investigate the processing of sensory, cognitive, and motor information in the brain. ERPs enable excellent temporal resolution of underlying brain activity. ERP data is complex due to the temporal variation that occurs in the time domain. It is actually a type of electroencephalography (EEG) signal that is time-locked to a specific event or behavior. To remove artifacts from the data, this work utilizes Independent component analysis, finite impulse response filter, and fast Fourier transformation as preprocessing techniques. The bidirectional long short-term memory network is utilized to retain the spatial relationships between the ERP data while learning changes in temporal information for a long time. This network performed well both in modeling and information extraction from the signals. To validate the model performance, the proposed framework is tested on two benchmark datasets. The proposed framework achieved a state-of-the-art accuracy of 96.03% on the SJTU Emotion EEG Dataset dataset and 97.31% on the Chung–Ang University Hospital EEG dataset for the classification tasks.
Rapid multiple protein sequence search by parallel and heterogeneous computation
Authors: Li Jiefu , Wang Ziyuan , Fan Xuwei , Yao Ruijie , Zhang Guoqing , Fan Rui , Wang Zefeng 
Published: March 2024

Abstract

Motivation
Protein sequence database search and multiple sequence alignment generation is a fundamental task in many bioinformatics analyses. As the data volume of sequences continues to grow rapidly, there is an increasing need for efficient and scalable multiple sequence query algorithms for super-large databases without expensive time and computational costs.

Results
We introduce Chorus, a novel protein sequence query system that leverages parallel model and heterogeneous computation architecture to enable users to query thousands of protein sequences concurrently against large protein databases on a desktop workstation. Chorus achieves over 100× speedup over BLASTP without sacrificing sensitivity. We demonstrate the utility of Chorus through a case study of analyzing a ∼1.5-TB large-scale metagenomic datasets for novel CRISPR-Cas protein discovery within 30 min.

Availability and implementation
Chorus is open-source and its code repository is available at https://github.com/Bio-Acc/Chorus.
Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning
Authors: Chen Fuqun , Zou Guanhua , Wu Yongxian , Ou-Yang Le 
Published: March 2024

Abstract

Motivation
Single-cell clustering plays a crucial role in distinguishing between cell types, facilitating the analysis of cell heterogeneity mechanisms. While many existing clustering methods rely solely on gene expression data obtained from single-cell RNA sequencing techniques to identify cell clusters, the information contained in mono-omic data is often limited, leading to suboptimal clustering performance. The emergence of single-cell multi-omics sequencing technologies enables the integration of multiple omics data for identifying cell clusters, but how to integrate different omics data effectively remains challenging. In addition, designing a clustering method that performs well across various types of multi-omics data poses a persistent challenge due to the data’s inherent characteristics.

Results
In this paper, we propose a graph-regularized multi-view ensemble clustering (GRMEC-SC) model for single-cell clustering. Our proposed approach can adaptively integrate multiple omics data and leverage insights from multiple base clustering results. We extensively evaluate our method on five multi-omics datasets through a series of rigorous experiments. The results of these experiments demonstrate that our GRMEC-SC model achieves competitive performance across diverse multi-omics datasets with varying characteristics.

Availability and implementation
Implementation of GRMEC-SC, along with examples, can be found on the GitHub repository: https://github.com/polarisChen/GRMEC-SC.
Insertional effect following electrode implantation: an underreported but important phenomenon
Authors: Hamani Clement , Davidson Benjamin , Lipsman Nir , Abrahao Agessandro , Nestor Sean M , Rabin Jennifer S , Giacobbe Peter , Pagano Rosana L , Campos Ana Carolina P 
Published: March 2024

Abstract
Deep brain stimulation has revolutionized the treatment of movement disorders and is gaining momentum in the treatment of several other neuropsychiatric disorders. In almost all applications of this therapy, the insertion of electrodes into the target has been shown to induce some degree of clinical improvement prior to stimulation onset. Disregarding this phenomenon, commonly referred to as ‘insertional effect’, can lead to biased results in clinical trials, as patients receiving sham stimulation may still experience some degree of symptom amelioration. Similar to the clinical scenario, an improvement in behavioural performance following electrode implantation has also been reported in preclinical models. From a neurohistopathologic perspective, the insertion of electrodes into the brain causes an initial trauma and inflammatory response, the activation of astrocytes, a focal release of gliotransmitters, the hyperexcitability of neurons in the vicinity of the implants, as well as neuroplastic and circuitry changes at a distance from the target. Taken together, it would appear that electrode insertion is not an inert process, but rather triggers a cascade of biological processes, and, as such, should be considered alongside the active delivery of stimulation as an active part of the deep brain stimulation therapy.
Age-dependent effects of metformin on human oligodendrocyte lineage cell ensheathment capacity
Authors: Mohammadnia Abdulshakour , Cui Qiao-Ling , Weng Chao , Yaqubi Moein , Fernandes Milton G F , Hall Jeffery A , Dudley Roy , Srour Myriam , Kennedy Timothy E , Stratton Jo Anne , Antel Jack P 
Published: March 2024

Abstract
Metformin restores the myelination potential of aged rat A2B5+ oligodendrocyte progenitor cells and may enhance recovery in children with post-radiation brain injury. Human late progenitor cells (O4+A2B5+) have a superior capacity to ensheath nanofibres compared to mature oligodendrocytes, with cells from paediatric sources exceeding adults. In this study, we assessed the effects of metformin on ensheathment capacity of human adult and paediatric progenitors and mature oligodendrocytes and related differences to transcriptional changes. A2B5+ progenitors and mature cells, derived from surgical tissues by immune-magnetic separation, were assessed for ensheathment capacity in nanofibre plates over 2 weeks. Metformin (10 µM every other day) was added to selected cultures. RNA was extracted from treated and control cultures after 2 days. For all ages, ensheathment by progenitors exceeded mature oligodendrocytes. Metformin enhanced ensheathment by adult donor cells but reduced ensheathment by paediatric cells. Metformin marginally increased cell death in paediatric progenitors. Metformin-induced changes in gene expression are distinct for each cell type. Adult progenitors showed up-regulation of pathways involved in the process of outgrowth and promoting lipid biosynthesis. Paediatric progenitors showed a relatively greater proportion of down- versus up-regulated pathways, these involved cell morphology, development and synaptic transmission. Metformin-induced AMP-activated protein kinase activation in all cell types; AMP-activated protein kinase inhibitor BML-275 reduced functional metformin effects only with adult cells. Our results indicate age and differentiation stage-related differences in human oligodendroglia lineage cells in response to metformin. Clinical trials for demyelinating conditions will indicate how these differences translate in vivo.
The “aroma of citrus” as transnational queer digital culture: Girls’ Love webtoons in contemporary China
Authors: Zhao Jamie J 
Published: March 2024

Abstract
This commentary focuses on a rising transnational queer Chinese digital culture—Girls’ Love (GL) webtoons. I consider this queer women-focused entertainment as an epitome of the queer convergence of transnational flows, women’s cultures, and digital platform technologies in today’s Asia. My discussion sheds light on its multilayered queer-transnational characteristics, as well as the controversies surrounding its transcultural mediation of queer women. Rather than simplifying it as an anti-heterocentric Chinese convergence culture in an age of globalization and digitization, I highlight GL webtoons’ role in stimulating various voices concerning women during transnational encounters of gender and sexual knowledge.
Association of deprivation and its individual domains on outcomes in people with chronic kidney disease
Authors: Al-Chalabi Saif , Parkinson Eleanor , Chinnadurai Rajkumar , Kalra Philip A , Sinha Smeeta 
Published: March 2024

ABSTRACT

Background
Due to the high correlation of chronic kidney disease (CKD) with other comorbidities, the sole effect of CKD on deprived people is not clear. In addition, there is a paucity of evidence in the literature linking isolated domains of deprivation to outcomes. This study aimed to examine whether deprivation was associated with adverse outcomes in patients with CKD, independent of cardiometabolic morbidities. Individual domains of deprivation were also evaluated.

Methods
A retrospective study of patients with non-dialysis-dependent CKD (ND-CKD) in the Salford Kidney Study to investigate the association of deprivation with outcomes. The English Indices of Deprivation was used for the comparative analysis of the five quintiles of deprivation. Two propensity score methods were used to attenuate the confounding effect of cardiometabolic morbidities between the least and the most deprived groups.

Results
People living in the least deprived areas (n = 319) had a lower risk of combined outcomes (all-cause mortality and renal replacement therapy) when compared with the most deprived group (n = 813) [hazard ratio (HR) 0.83; 95% confidence interval (CI) 0.71–0.98]. The negative association of deprivation remained after matching but with mixed statistical significance when using different propensity methods (HR 0.85; 95% CI 0.70–1.03 for propensity score matching and HR 0.77; 95% CI 0.61–0.98 for inverse probability weighting). The association of combined outcomes varied across component index of multiple deprivation domains with wide CIs. However, areas with lower scores for education, income and employment were significantly associated with a higher risk.

Conclusions
This study has identified that in people with ND-CKD, unemployment, poor educational attainment and lower household income were associated with poor outcomes. The association of deprivation with adverse outcomes persists despite adjustment for cardiometabolic morbidities.
Non-surgical interventions to control bleeding from arteriovenous fistulas and grafts inside and outside the hemodialysis unit: a scoping review
Authors: Milosevic Elizabeth , Forster Adam , Moist Louise , Rehman Faisal , Thomson Benjamin 
Published: March 2024

ABSTRACTBackgroundProlonged bleeding from arteriovenous fistulas (AVF) and arteriovenous grafts (AVG) associates with worse outcomes; Within the hemodialysis unit these outcomes include anemia and quality of life disruptions, and outside the hemodialysis unit includes fatal hemorrhage. However, various guidelines for AVF/AVG bleeding management inside and outside the hemodialysis unit lack consensus.MethodsA scoping review was conducted of four databases, from inception to 17 February 2024. The study population was hemodialysis patients experiencing bleeding from AVF or AVG. Studies that assessed non-operative management were included.ResultsSixteen studies met inclusion criteria. Most (14/16) addressed post-cannulation bleeding from AVF/AVG within the dialysis unit. Compared with standard dressings, hemostatic dressings (chitosan-, cellulose- or thrombin-based) decreased post-cannulation bleeding time at arterial and venous site 35.7%–84.0% (P &lt; .05) and 38.5%–78.7% (P &lt; .05), respectively. Use of chitosan-based dressings decreased percentage of patients bleeding 4-min post-cannulation by 16.3%–39.2%. One pilot observational study demonstrated no access thromboses or infections with short-term use of a compression device within the hemodialysis unit. However, the role of compression devices and tourniquets within the dialysis unit remains unclear, despite widespread use. Long-term AVF/AVG survival was not reported in any study. Limited research confirms that devices are effective in prevention of catastrophic out-of-hospital bleeding. It remains uncertain if device availability enhances patient confidence in managing out-of-hospital bleeding. This may impact patient choices around dialysis modality, access and transplant, but this remains uncertain.ConclusionsIn hemodialysis patents with bleeding from AVF/AVG, several alternative dressings or devices decrease post-cannulation bleeding time within the hemodialysis unit. Existing research has not established criteria on when it might be appropriate to use specialized dressings. There is very limited research on methods to control bleeding from AVF/AVG outside the hemodialysis unit. More data are required before evidence-based guidelines can be made. Recommendations for future research are provided.
Heterogeneity of coronary vascular function and myocardial oxygenation in women with angina and non-obstructive coronary artery disease
Authors: Hillier Elizabeth , Elharram Malik , White James A , Anderson Todd , Luu Judy , Labib Dina , Alhussein Muhammad , Friedrich Matthias G , Pilote Louise 
Published: March 2024

Abstract

Aims
Women with angina and non-obstructive coronary artery disease (ANOCA) have a heightened risk for cardiovascular events, and the pathophysiology for ischaemic symptoms may be related to alterations in microvascular structure and function. We examined the use of breathing-enhanced oxygenation-sensitive cardiac magnetic resonance imaging (OS-CMR) using vasoactive breathing manoeuvres to assess myocardial oxygenation in women with ANOCA.

Methods and results
We recruited women (aged 40–65 years) from two sites in Canada who presented to healthcare with persistent retrosternal chest pain and found to have ANOCA, or without a history of cardiovascular disease. All participants were scanned using a clinical 3T MRI scanner, and OS-CMR images were acquired over a breath hold following paced hyperventilation to measure global and regional measurements of heterogeneity. Fifty-four women with ANOCA (age: 55 ± 6.2 years) and 48 healthy controls (age: 51.2 ± 4.8 years) were recruited. There was no significant difference in volume, function, mass, or global myocardial oxygenation between the two groups [mean %Δ in signal intensity (SI): 4.9 (±7.3) vs. 4.5 (±10.1), P = 0.82]. Women with ANOCA had higher regional variations in myocardial oxygenation in circumferential [median %Δ in SI: 5.1 (2.0–7.6) vs. 2.2 (1.4–3.5), P = 0.0004] and longitudinal directions [median %Δ in SI: 11.4 (5.4–16.7) vs. 6.0 (3.0–7.0), P = 0.001], which remained present in a multivariate model.

Conclusion
Heterogeneous myocardial oxygenation may explain ischaemic symptoms without any associated epicardial obstructive coronary artery disease. Regional variations in myocardial oxygenation on OS-CMR could serve as an important diagnostic marker for microvascular dysfunction in women with ANOCA.
Long-term rate of ventricular arrhythmia in autoimmune disease
Authors: Sun Guoli , Fosbøl Emil L , Schou Morten , Faurschou Mikkel , Yafasova Adelina , Petersen Jeppe K , Haugan Ketil J , Mogensen Ulrik Madvig , Svendsen Jesper H , Køber Lars , Butt Jawad H 
Published: March 2024

Abstract

Aims
Although selected autoimmune diseases (AIDs) have been linked to an increased risk of ventricular arrhythmias (VAs), data on the long-term rate of VAs across the spectrum of AIDs are lacking. The aim of this study was to investigate the long-term rate of VAs (a composite of ventricular tachycardia, ventricular fibrillation, ventricular flutter, or cardiac arrest) in individuals with a history of 28 different AIDs.

Methods and results
Individuals diagnosed with an AID (2005–18) were identified through Danish nationwide registries. Each patient with an AID was matched with four individuals from the background population by age and sex. Multivariable Cox regression was used to compare the rate of VAs between the AIDs and background population, overall and according to individual AIDs. In total, 186 733 patients diagnosed with AIDs were matched with 746 932 individuals without AIDs (median age 55 years; 63% female; median follow-up 6.0 years). The 5-year cumulative incidence of VAs was 0.5% for patients with AIDs and 0.3% for matched individuals. Patients with any AIDs had a higher associated rate of VAs than matched individuals {hazard ratio (HR) 1.39 [95% confidence interval (CI), 1.29–1.49]}. The highest HR was observed in patients with systemic sclerosis [3.86 (95% CI, 1.92–7.75)]. The higher rate of VAs in patients with AIDs, compared with individuals from the background population, was more pronounced in patients without ischaemic heart disease or heart failure/cardiomyopathy compared with those with these conditions (Pinteraction &lt;0.05).

Conclusion
Despite a low cumulative incidence, patients with a history of AIDs had a higher relative rate of VAs than matched individuals.
Cost-effectiveness of Mediterranean diet and physical activity in secondary cardiovascular disease prevention: results from the UCC-SMART cohort study
Authors: Bonekamp Nadia E , Visseren Frank L J , van der Schouw Yvonne T , van der Meer Manon G , Teraa Martin , Ruigrok Ynte M , Geleijnse Johanna M , Koopal Charlotte ,   UCC-SMART study group, Cramer M J , Nathoe H M , van der Harst P , van de Meer M G , de Borst G J , Teraa M , Bots M L , van Smeden M , Emmelot-Vonk M H , de Jong P A , Lely A T , van der Kaaij N P , Kappelle L J , Ruigrok Y M , Verhaar M C , Dorresteijn J A N , Visseren F L J 
Published: March 2024

Abstract

Aims
The efficacy of a healthy lifestyle in secondary prevention of cardiovascular disease (CVD) is well established and a first-line recommendation in CVD prevention guidelines. The aim of this study was to assess whether Mediterranean diet and physical activity are also cost-effective in patients with established CVD.

Methods and results
A cost–utility analysis (CUA) was performed comparing a combined Mediterranean diet and physical activity intervention to usual care in patients with CVD. The CUA had a healthcare perspective and lifetime horizon. Costs and utilities were estimated using a microsimulation on a cohort of 100 000 patients with CVD sampled from the Utrecht Cardiovascular Cohort—Secondary Manifestations of ARTerial disease study (n = 8947, mean age 62 ± 8.7 years, and 74% male). Cost-effectiveness was expressed as an incremental cost-effectiveness ratio (ICER), incremental net health benefit (INHB), and incremental net monetary benefit (INMB). Mediterranean diet and physical activity yielded 2.0 incremental quality-adjusted life years (QALYs) and cost reductions of €1236 per person compared with usual care, resulting in an ICER of €−626/QALY [95% confidence interval (CI) −1929 to 2673]. At a willingness-to-pay of €20 000/QALY, INHB was 2.04 (95% CI 0.99–3.58) QALYs and INMB was €40 757 (95% CI 19 819–71 605). The interventions remained cost-effective in a wide range of sensitivity analyses, including worst-case scenarios and scenarios with reimbursement for food and physical activity costs.

Conclusion
In patients with established CVD, a combined Mediterranean diet and physical activity intervention was cost-saving and highly cost-effective compared with usual care. These findings strongly advocate for the incorporation of lifestyle interventions as integral components of care for all patients with CVD.