bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid prediction of wall shear stress in stenosed coronary arteries based on deep learning
Authors: Alamir Salwa Husam , Tufaro Vincenzo , Trilli Matilde , Kitslaar Pieter , Mathur Anthony , Baumbach Andreas , Jacob Joseph , Bourantas Christos V. , Torii Ryo 
Published: August 2024

There is increasing evidence that coronary artery wall shear stress (WSS) measurement provides useful prognostic information that allows prediction of adverse cardiovascular events. Computational Fluid Dynamics (CFD) has been extensively used in research to measure vessel physiology and examine the role of the local haemodynamic forces on the evolution of atherosclerosis. Nonetheless, CFD modelling remains computationally expensive and time-consuming, making its direct use in clinical practice inconvenient. A number of studies have investigated the use of deep learning (DL) approaches for fast WSS prediction. However, in these reports, patient data were limited and most of them used synthetic data generation methods for developing the training set. In this paper, we implement 2 approaches for synthetic data generation and combine their output with real patient data in order to train a DL model with a U-net architecture for prediction of WSS in the coronary arteries. The model achieved 6.03% Normalised Mean Absolute Error (NMAE) with inference taking only 0.35 s; making this solution time-efficient and clinically relevant.
Four novel variants identified in the ACADVL gene causing very-long-chain acyl-coenzyme A dehydrogenase deficiency in four unrelated Chinese families
Authors: Li Lulu , Tang Yue , Zhao Jinqi , Gong Lifei , Yang Nan , Wang Shunan , Yang Haihe , Kong Yuanyuan 
Published: August 2024

Background: The biochemical and genetic characteristics of four very-long-chain acyl-coenzyme A dehydrogenase deficiency (VLCADD) patients, clarifying their pathogenic genetic factors and evaluating the application value of genetic diagnosis in the early diagnosis of VLCADD, are reported and discussed in this article.Methods: Patients underwent blood tandem mass spectrometry (MS/MS), urine gas chromatography (GC/MS), and high-throughput sequencing technology. New variants were analyzed for pathogenicity using bioinformatics software. Swiss-PdbViewer software was used to predict the effect of variants on the structure of the very-long-chain acyl-CoA dehydrogenase (VLCAD) protein.Result: A total of four VLCADD patients were diagnosed. They revealed elevated levels of C14, C14:1, C14:2, C14:1/C2, C14:1/C10, and C14:1/C12:1. Two patients were early-onset neonatal cases and died during infancy and the neonatal period, respectively. Seven kinds of variants were detected, including four novel variants. Bioinformatics software revealed that the variants were harmful, and the Swiss-PdbViewer results suggest that variation affects protein conformation.Conclusion: This study identified four novel ACADVL gene variants. These findings contribute to the understanding of the genetic basis and pathogenesis of VLCADD. Meanwhile, the study enriches the genetic mutation spectrum and the correlation between genotypes and phenotypes of VLCADD, indicating that genetic diagnosis plays an essential role in the early diagnosis and treatment of VLCADD.
Predictors of long-acting contraceptive utilization hot spots in Ethiopia: using geographical weighted regression analysis
Authors: Abate Hailemichael Kindie , Azagew Abere Woretaw , Kassahun Chanyalew Worku , Wassie Mulugeta , Mekonnen Chilot Kassa , Wassie Yilkal Abebaw , Zegeye Alebachew Ferede 
Published: August 2024

BackgroundThe use of long-acting contraceptives is a common health challenge in Ethiopia. Therefore, the current study aimed to assess the determinants of using long-acting contraceptive hot spots in Ethiopia using data from the Ethiopian Mini Demographic and Health Survey for 2019.MethodsThis study used data from the Ethiopia Mini Demographic and Health Survey 2019 and included a total weighted sample of 8,885 women in the analysis. The geographical variation of long-acting contraceptive usage was initially observed using hot spot analysis. Arc GIS version 10.7 was used for geographically weighted regression. Ordinarily, least squares regression was performed to identify predictors that explain the geographical variation in the use of long-acting contraceptives. Geographic weighted regression was used to predict the hot spot area of long-acting contraceptive methods.ResultsThe overall prevalence of long-acting contraceptive utilization use was 6.9% (95% confidence interval: 6.4–7.45). Most of the statistically significant hot spots for long-acting contraceptives were found in lactated areas of the Oromia part of Amhara and Dire Dawa. Primary education, followers of the Muslim religion, marital status, and women with &gt;4 children were the determinants of spatial variation use of hot spot areas for long-acting contraceptive methods.ConclusionsA detailed map of long-acting contraceptive use hot spots and their determinants will enable decisions to target their sociodemographic-related predictors of women.
The JAK1/JAK2 inhibitor ruxolitinib inhibits mediator release from human basophils and mast cells
Authors: Poto Remo , Cristinziano Leonardo , Criscuolo Gjada , Strisciuglio Caterina , Palestra Francesco , Lagnese Gianluca , Di Salvatore Antonio , Marone Gianni , Spadaro Giuseppe , Loffredo Stefania , Varricchi Gilda 
Published: August 2024

IntroductionThe Janus kinase (JAK) family includes four cytoplasmic tyrosine kinases (JAK1, JAK2, JAK3, and TYK2) constitutively bound to several cytokine receptors. JAKs phosphorylate downstream signal transducers and activators of transcription (STAT). JAK-STAT5 pathways play a critical role in basophil and mast cell activation. Previous studies have demonstrated that inhibitors of JAK-STAT pathway blocked the activation of mast cells and basophils.MethodsIn this study, we investigated the in vitro effects of ruxolitinib, a JAK1/2 inhibitor, on IgE- and IL-3-mediated release of mediators from human basophils, as well as substance P-induced mediator release from skin mast cells (HSMCs).ResultsRuxolitinib concentration-dependently inhibited IgE-mediated release of preformed (histamine) and de novo synthesized mediators (leukotriene C4) from human basophils. Ruxolitinib also inhibited anti-IgE- and IL-3-mediated cytokine (IL-4 and IL-13) release from basophils, as well as the secretion of preformed mediators (histamine, tryptase, and chymase) from substance P-activated HSMCs.DiscussionThese results indicate that ruxolitinib, inhibiting the release of several mediators from human basophils and mast cells, is a potential candidate for the treatment of inflammatory disorders.
A bibliometric analysis of drug resistance in immunotherapy for breast cancer: trends, themes, and research focus
Authors: Zhang Rendong , Jiang Qiongzhi , Zhuang Zhemin , Zeng Huancheng , Li Yaochen 
Published: August 2024

While breast cancer treatments have advanced significantly nowadays, yet metastatic, especially triple-negative breast cancer (TNBC), remains challenging with low survival. Cancer immunotherapy, a promising approach for HER2-positive and TNBC, still faces resistance hurdles. Recently, numerous studies have set their sights on the resistance of immunotherapy for breast cancer. Our study provides a thorough comprehension of the current research landscape, hotspots, and emerging breakthroughs in this critical area through a meticulous bibliometric analysis. As of March 26, 2024, a total of 1341 articles on immunology resistance in breast cancer have been gathered from Web of Science Core Collection, including 765 articles and 576 reviews. Bibliometrix, CiteSpace and VOSviewer software were utilized to examine publications and citations per year, prolific countries, contributive institutions, high-level journals and scholars, as well as highly cited articles, references and keywords. The research of immunotherapy resistance in breast cancer has witnessed a remarkable surge over the past seven years. The United States and China have made significant contributions, with Harvard Medical School being the most prolific institution and actively engaging in collaborations. The most contributive author is Curigliano, G from the European Institute of Oncology in Italy, while Wucherpfennig, K. W. from the Dana-Farber Cancer Institute in the USA, had the highest citations. Journals highly productive primarily focus on clinical, immunology and oncology research. Common keywords include “resistance”, “expression”, “tumor microenvironment”, “cancer”, “T cell”, “therapy”, “chemotherapy” and “cell”. Current research endeavors to unravel the mechanisms of immune resistance in breast cancer through the integration of bioinformatics, basic experiments, and clinical trials. Efforts are underway to develop strategies that improve the effectiveness of immunotherapy, including the exploration of combination therapies and advancements in drug delivery systems. Additionally, there is a strong focus on identifying novel biomarkers that can predict patient response to immunology. This study will provide researchers with an up-to-date overview of the present knowledge in drug resistance of immunology for breast cancer, serving as a valuable resource for informed decision-making and further research on innovative approaches to address immunotherapy resistance.
A non-enhanced CT-based deep learning diagnostic system for COVID-19 infection at high risk among lung cancer patients
Authors: Du Tianming , Sun Yihao , Wang Xinghao , Jiang Tao , Xu Ning , Boukhers Zeyd , Grzegorzek Marcin , Sun Hongzan , Li Chen 
Published: August 2024

BackgroundPneumonia and lung cancer have a mutually reinforcing relationship. Lung cancer patients are prone to contracting COVID-19, with poorer prognoses. Additionally, COVID-19 infection can impact anticancer treatments for lung cancer patients. Developing an early diagnostic system for COVID-19 pneumonia can help improve the prognosis of lung cancer patients with COVID-19 infection.MethodThis study proposes a neural network for COVID-19 diagnosis based on non-enhanced CT scans, consisting of two 3D convolutional neural networks (CNN) connected in series to form two diagnostic modules. The first diagnostic module classifies COVID-19 pneumonia patients from other pneumonia patients, while the second diagnostic module distinguishes severe COVID-19 patients from ordinary COVID-19 patients. We also analyzed the correlation between the deep learning features of the two diagnostic modules and various laboratory parameters, including KL-6.ResultThe first diagnostic module achieved an accuracy of 0.9669 on the training set and 0.8884 on the test set, while the second diagnostic module achieved an accuracy of 0.9722 on the training set and 0.9184 on the test set. Strong correlation was observed between the deep learning parameters of the second diagnostic module and KL-6.ConclusionOur neural network can differentiate between COVID-19 pneumonia and other pneumonias on CT images, while also distinguishing between ordinary COVID-19 patients and those with white lung. Patients with white lung in COVID-19 have greater alveolar damage compared to ordinary COVID-19 patients, and our deep learning features can serve as an imaging biomarker.
Characterizing the clinical heterogeneity of early symptomatic Alzheimer’s disease: a data-driven machine learning approach
Authors: Wang Xiwu , Ye Teng , Jiang Deguo , Zhou Wenjun , Zhang Jie ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: August 2024

IntroductionAlzheimer’s disease (AD) is highly heterogeneous, with substantial individual variabilities in clinical progression and neurobiology. Amyloid deposition has been thought to drive cognitive decline and thus a major contributor to the variations in cognitive deterioration in AD. However, the clinical heterogeneity of patients with early symptomatic AD (mild cognitive impairment or mild dementia due to AD) already with evidence of amyloid abnormality in the brain is still unknown.MethodsParticipants with a baseline diagnosis of mild cognitive impairment or mild dementia, a positive amyloid-PET scan, and more than one follow-up Alzheimer’s Disease Assessment Scale-Cognitive Subscale-13 (ADAS-Cog-13) administration within a period of 5-year follow-up were selected from the Alzheimer’s Disease Neuroimaging Initiative database (n = 421; age = 73±7; years of education = 16 ± 3; percentage of female gender = 43%; distribution of APOE4 carriers = 68%). A non-parametric k-means longitudinal clustering analysis in the context of the ADAS-Cog-13 data was performed to identify cognitive subtypes.ResultsWe found a highly variable profile of cognitive decline among patients with early AD and identified 4 clusters characterized by distinct rates of cognitive progression. Among the groups there were significant differences in the magnitude of rates of changes in other cognitive and functional outcomes, clinical progression from mild cognitive impairment to dementia, and changes in markers presumed to reflect neurodegeneration and neuronal injury. A nomogram based on a simplified logistic regression model predicted steep cognitive trajectory with an AUC of 0.912 (95% CI: 0.88 – 0.94). Simulation of clinical trials suggested that the incorporation of the nomogram into enrichment strategies would reduce the required sample sizes from 926.8 (95% CI: 822.6 – 1057.5) to 400.9 (95% CI: 306.9 – 516.8).DiscussionOur findings show usefulness in the stratification of patients in early AD and may thus increase the chances of finding a treatment for future AD clinical trials.
Association of hemoglobin-to-red cell distribution width ratio with the three-month outcomes in patients with acute ischemic stroke
Authors: Xie Xiaorui , He Keli , Zhang Yao , Wu Jianhua 
Published: August 2024

AimTo explore the association of Hemoglobin-to-Red Cell Distribution Width Ratio (HRR) with the risk of three-month unfavorable outcomes in acute ischemic stroke (AIS).MethodsA secondary analysis was conducted based on a prospective cohort study. A total of 1,889 patients with AIS treated in South Korea from January 2010 to December 2016 were enrolled. Multivariable logistic regression was conducted to investigated the independent relationship between HRR and risk of three-month unfavorable outcomes in AIS. Fitted smoothing curves were used to determine non-linear correlations. The recursive method was employed to explore the turning point and build a two-piece linear regression model. In addition, a set of subgroup analyses were carried out to evaluate the relationship between HRR and risk of three-month unfavorable outcomes.ResultsMultivariate analysis in which potential confounders were adjusted for indicated that the risk of unfavorable outcomes was reduced by 10% for each unit increased of HRR [OR = 0.90, 95% CI: 0.84–0.96, p = 0.0024]. In addition, a non-linear relationship was observed between HRR and risk of three-month unfavorable outcomes, which had an inflection point of HRR was 10.57. The effect sizes and the confidence intervals on the left side of the inflection point were 0.83 (0.75, 0.91), p = 0.0001. On the right side of the inflection point, no association was found between HRR and the risk of three-month unfavorable outcomes.ConclusionThis study demonstrates a negative association between HRR and risk of three-month unfavorable outcomes. The relationship between HRR and risk of three-month unfavorable outcomes is non-linear. The correlation is negative for HRR values less than 10.57. For, HRR higher than 10.57, HRR is not associated with the risk of three-month unfavorable outcomes.
Clinical management of children with tic disorder: insights from therapeutic visits in China—a real-world study
Authors: Wang Jing , Luo Changyong , Wang Zhendong , Liu Tiegang , Bai Chen , Wang Yang , Tian Yuanshuo , Li Qianqian , Wang Zhaoxin , Wu Liqun , Wang Sumei , Gu Xiaohong 
Published: August 2024

ObjectiveThis retrospective study aims to investigate the treatment of tic disorder (TD) in Dongfang Hospital affiliated with Beijing University of Chinese Medicine, explore its underlying mechanism, and provide valuable insights for future research and clinical management of TD.MethodsThe electronic medical records of children with TD, from 2015 to 2021, were extracted from the information system of Dongfang Hospital affiliated with Beijing University of Chinese Medicine. The clinical characteristics of TD, utilization patterns of Chinese herbal medicine and synthetic drugs in prescriptions, as well as their pharmacological effects, were statistically described and categorized. In addition, association rules and network pharmacology were employed to identify core prescriptions (CPs) and elucidate their microscopic molecular mechanisms in treating TD.ResultsThe age range of the children was from 6 to 11 years, with a higher proportion of male participants than female ones. The average duration of treatment was 6 weeks. Regimen Z for the treatment of TD can be summarized as follows: Chinese herbal medicine [Saposhnikoviae Radix (FangFeng), Puerariae Lobatae Radix (GeGen), Uncariae Ramulus cum Uncis (GouTeng), Acori Tatarinowii Rhizoma (ShiChangPu), Chuanxiong Rhizoma (ChuanXiong)] and vitamins [lysine, inosite, and vitamin B12 oral solution] form the basic treatment, combined with immunomodulators, antibiotics, electrolyte-balancing agents, and antiallergic agents. CPs primarily exerted their effects through the modulation of gene expression (transcription), the immune system, and signal transduction pathways, with interleukin-4 and interleukin-13 pathways being particularly crucial. Among the lysine synthetic drugs used, inosite and vitamin B12 oral solution were the most frequently prescribed.ConclusionThe regimen Z drug treatment holds significant importance in the field, as it exerts its therapeutic effects through a multitude of pathways and intricate interventions. Chinese herbal medicine primarily regulates immune system–related pathways, while synthetic drugs predominantly consist of vitamins.
An infant with testicular Fetus-in-fetu in the abdominal cavity: rare case report
Authors: Luo Mingshuang , Li Geng , Gao Heyun , Zhang Wen 
Published: August 2024

BackgroundFetus-in-fetu (FIF) represents an exceedingly rare disease, characterized as an encapsulated and pedunculated vertebrate neoplasm, typically lacking cerebral tissue. The prevalence shows no gender preference. Notably, FIF can cause compressive damage to adjacent organs and tissues, potentially impeding the host's development and maturation.Case presentationA four-month-old male infant was identified, during pregnancy, to have a left-sided pelvic mass on ultrasound. Subsequent evaluations suggested the mass could be a FIF, exhibiting active movement. Surgical exploration revealed that the mass's left boundary was connected to the left spermatic cord and vas deferens. Pathological analysis post-surgery showed the absence of testicular tissue, but the presence of skin tissue, cartilage-like structures, and gastrointestinal elements. Additionally, localized tissue resembling vertebrae confirmed the diagnosis of testicular FIF.ConclusionAn intraperitoneal testicular FIF is extremely rare, with its cause still unknown. This groundbreaking report details the diagnosis and management of such a case. Following a FIF diagnosis, prompt surgical removal is crucial, along with regular follow-up using ultrasound and tumor markers.
The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd (Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination
Authors: Qin Nannan , Yang Shanjie , Wang Yunan , Cheng Hui , Gao Yang , Cheng Xiaojing , Li Sen 
Published: August 2024

IntroductionBottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding.MethodsA hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes.ResultsThe length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing.ConclusionIn conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.
Foliar application of sodium selenite affects the growth, antioxidant system, and fruit quality of strawberry
Authors: Lin Yuanxiu , Cao Shuaipeng , Wang Xiao , Liu Yin , Sun Ziqing , Zhang Yunting , Li Mengyao , Wang Yan , He Wen , Zhang Yong , Chen Qing , Wang Xiaorong , Luo Ya , Tang Haoru 
Published: August 2024

IntroductionSelenium (Se) plays a vital role in various physiological processes in plants and is regarded as an essential micronutrient for human health as well.MethodsIn this study, sodium selenite solution at 10, 40, 70, and 100 mg·L-1 concentrations was foliar sprayed, and the strawberry plant growth, antioxidant system, and fruit quality with an emphasis on sugar and acid content were assessed.ResultsThe results showed that 10 mg·L-1 of sodium selenite treatment promoted plant growth, while all the treated concentrations could enhance photosynthesis, the antioxidant system in leaves, the content of Se, and ascorbic acid in fruits. More importantly, 40 mg·L-1 sodium selenite treatment significantly increased fruit weight, total soluble solid, total phenolic content, and anthocyanins, as well as improved the shape index. Furthermore, it decreased the total flavonoid and proanthocyanidin content. Particularly, sodium selenite treatment at 40 and 70 mg·L-1 largely increased the ratio of soluble sugars to titratable acid. The changes of predominant sugars and organic acids during fruit development were further investigated. The sucrose, fructose, and glucose content was upregulated by sodium selenite treatment through upregulating the activities of sucrose phosphate synthase (SPS) and acid invertase, as well as the FaSPS expression. In addition, sodium selenite treatment inhibited the activity of citrate synthase and phosphoenolpyruvate carboxylase, rather than modulating their transcript levels to reduce the citric acid content.ConclusionsThis work presented a potentially efficient approach to enhance plant growth and fruit quality and supplement Se in strawberry, providing insights into the mechanism of regulating sugar and acid metabolism by Se.