bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Single-Cell Sequencing and Machine Learning to Uncover the Role of Mitophagy in Subtyping and Prognosis of Esophageal Cancer
Authors: Tian Feng , He Xinyang , Wang Saiwei , Liang Yiwei , Wang Zijie , Hu Minxuan , Gao Yaxian 
Published: October 2024

Abstract

Globally, esophageal cancer stands as a prominent contributor to cancer-related fatalities, distinguished by its grim prognosis. Mitophagy has a significant impact on the process of cancer progression. This study investigates the prognostic significance of mitophagy-related genes (MRGs) in esophageal carcinoma (ESCA) with the aim of elucidating molecular subtypes. By analyzing RNA-seq data from The Cancer Genome Atlas (TCGA), 6451 differentially expressed genes (DEGs) were identified. Cox regression analysis narrowed this list to 14 MRGs with notable prognostic implications. ESCA patients were classified into two distinct subtypes (C1 and C2) based on these genes. Furthermore, leveraging the differentially expressed genes between Cluster 1 and Cluster 2, ESCA patients were classified into two novel subtypes (CA and CB). Notably, patients in C2 and CA subtypes exhibited inferior prognosis compared to those in C1 and CB (p < 0.05). Functional enrichments and immune microenvironments varied significantly among these subtypes, with C1 and CB demonstrating higher immune checkpoint expression levels. Employing machine learning algorithms like LASSO regression and Random Forest, alongside multivariate COX regression analysis, two core genes: HSPD1 and MAP1LC3B were identified. A robust prognostic model based on these genes was developed and validated in two external cohorts. Additionally, single-cell sequencing analysis provided novel insights into esophageal cancer microenvironment heterogeneity. Through Coremine database screening, Icaritin emerged as a potential therapeutic candidate to improve esophageal cancer prognosis. Molecular docking results indicated favorable binding efficacies of Icaritin with HSPD1 and MAP1LC3B, enhancing the comprehension of the underlying molecular mechanisms of esophageal cancer and offering therapeutic avenues.
Incidence of death and its predictors among/HIV co-infected adult patients on anti-retro viral therapy at Gambelia referral hospital, Southwest, Ethiopia
Authors: Habtamu Endeshaw , Hiruy Endalk Getasew , Mulatu Kebadnew , Mohammed Asiya 
Published: October 2024

Abstract

Background: In patients who have tuberculosis and the human immunodeficiency virus, tuberculosis is the most prevalent opportunistic illness and the main killer. However, little is currently known about time to death and its predictors, particularly among individuals with coinfection in the study area. Therefore, this study was aimed at filling this gap in the region. Objective: To assess incidence of death and its predictors among tuberculosis and human immunodeficiency virus co-infected adult patients on anti-retroviral therapy in Gambella Referral Hospital, Southwest Ethiopia, 2023.
Methods: Retrospective cohort study was conducted in 320 co-infected adult patients on antiretroviral therapy from June 2017 to June 2022. Data were extracted from the document by using structured checklist those adapted and prepared based on the charts. Death is the event, whereas not having experienced death is censored. Data was entered in to Epi-data version 3.1 then export to STATA version 14. Kaplan Meier curve and log rank test was used to compare the survival curves and estimate survival time. Cox regression model was used to identify significant predictors of death. Cox-Snell residual plot was used to measure cox model goodness of fit.
Results: A total of 320 co-infected patients were followed with cumulative incidence of death are 14.7% and 6.7 deaths per 1000 person-months as the incidence rate (95%CI: 5.0-8.9). Patients who are being female (AHR 2.1, 95%CI: 1.05-4.21), with poor adherence to ART (AHR=5.88, 95%CI: 2.69-12.86), non-cotrimoxazole therapy users (AHR=4.03, 95%CI: 1.99- 8.16) and viral load >1000copes/ml (AHR: 3.18, 95%CI: 1.19-8.52) were at higher risk of death.
Conclusion and Recommendation: In the study area, the incidence rate of mortality was high compared to incidence rate of mortality in Ethiopia 2021. Patients on ART who are being female, had poor ART adherence, had an opportunistic infection other than tuberculosis, had a viral load value between 50 and 1000 copies per milliliter and greater than 1000 copies per milliliter, and non-cotrimoxazole prophylaxis therapy users were increased risk of deaths. As a result, patients with viral loads >000copes/ml, non-CPT users, who are being female, and who had poor ART adherence can benefit from intensive monitoring and counseling.
Spatiotemporal Analysis of Plasmodium falciparum Erythrocyte Binding Antigen (Pf EBA) 175 Gene Dimorphism in Ghana
Authors: Kpirikai Abraham Y. , Ofosu Belinda , Okai Josie , Kornu Victor , Kassim Abdul Rashid , Donkor Esther , Malm Frederica , Ahmed Osumanu , Sakyi Mona-Liza E. , Saiid Samirah , Kudakpo Albert Yao , Mensah Charles , Dzabeng Francis , Morang’a Collins , Awandare Gordon A. , Aniweh Yaw , Amenga-Etego Lucas N. 
Published: October 2024

Abstract

Background Malaria remains a leading cause of death worldwide, claiming over 600,000 lives each year. Over 90% of these deaths, mostly among children under five years, occur in sub-Saharan Africa and are caused by Plasmodium falciparum. The merozoites stage of the parasite, crucial for asexual development invade erythrocytes through ligand-receptor interactions. Erythrocyte binding antigen (EBA)-175 is one of the key ligands facilitating invasion via interaction with glycoprotein A (GpA) receptors on the erythrocytes. EBA-175 is known to exist in two dimorphic allelic (F and C) forms with each found to infer different virulence. There is paucity of data on the prevalence of these alleles and their epidemiology in the Ghanaian malaria landscape and hence this study.Methods Parasite gDNA was extracted from archived Dried Blood Spots (DBS) prepared from 700 confirmed malaria-infected individuals and analysed for Pf EBA-175 dimorphism. Selective EBA-175 gene amplification via nested PCR and allele scoring using agarose gel electrophoresis for F, C and F/C alleles.Results Of the total 632 successfully genotyped samples, we found a prevalence of F, C, and F/C allelic forms were 61.2% (n = 387), 20.7% (n = 131), 18.0% (n = 114) respectively. Seasonality analysis did not reveal a statistically significant difference in the prevalence of dimorphic forms between the wet (n = 475) and dry (n = 157) seasons (p = 0.051). The prevalence ratio (wet/dry) for C, F and F/C were determined to be 1.0, 1.1 and 1.4 respectively. Between 2019 and 2022, the prevalence of the alleles changed significantly (χ² = 6.5427, p = 0.03). Geometric mean parasite density for the C, F, and F/C alleles were 21477.1 [95%CI: 15749.2 -29288.1], 18308.0 [95%CI: 15149.9-22124.5] and 22690.4[95% CI: 16891.9–30479.2] respectively.Conclusion The F-allele was the most prevalent form across all age groups, followed by the C allele and mixed F/C alleles. No significant difference in allele prevalence was observed between the high malaria season (wet) and low malaria season (dry). However, we observed a statistically significant difference (p = 0.03) in the temporal prevalence of pure alleles (F & C) between two time points.
Assessment of Health-related Quality of Life of Children with Idiopathic Nephrotic Syndrome and their caregivers in China
Authors: Wang Xia , Tan Danny Junyi , Guan Lejing , Shao Yifei , Wang Jingjing , Feng Chunyue , Fu Haidong , Shen Huijun , Zhu Xiujuan , Rafay Abdul , Mao Jianhua , Bai Guannan 
Published: October 2024

Abstract

Aims: The primary aim of this study was to characterize the health-related quality of life (HRQoL) and identify the associated factors among children aged 2 to 18 years in China diagnosed with idiopathic nephrotic syndrome (INS). Additionally, the study aimed to evaluate the HRQoL and caregiving burden of their caregivers, as well as to investigate the correlation between the HRQoL of the children and that of their caregivers.
Methods: This study recruited 181 children with a diagnosis of INS from Children’s Hospital, Zhejiang University School of Medicine in China. The proxy-reported PedsQL Generic Core Module (PedsQL GCM) was used to measure the HRQoL of children, and the five-level EuroQol five-dimensional questionnaire (EQ-5D-5L) was applied to measure caregivers’ HRQoL. Differences in scale scores and total scores of PedsQL GCM were assessed using t tests and one-way ANOVA. Multivariate linear regression analysis was used to identify the associated factors of children’s HRQoL. Pearson correlation analysis was performed to assess the correlation between children’s HRQoL and caregiver’s HRQoL.
Results: HRQoL of Children with INS declines with increasing age, and children aged 5-18 years had lower scores in physical functioning, emotional functioning, school functioning, psychosocial health summary score, and total PedsQL GCM score compared to healthy children. Various factors, including the mother filling out the questionnaire, the father being unemployed, and use of other medications except for steroids were associated with worse HRQoL of children (p values < 0.05). Additionally, there is a correlation between children's HRQoL and their caregivers' HRQoL.
Conclusion: This study evaluated the HRQoL of children aged 2-18 years diagnosed with INS in China, along with the HRQoL of their caregivers. HRQoL of children was potentially influenced by multiple factors. A significant correlation was observed between the HRQoL of the children and that of their caregivers, who frequently experienced varying levels of caregiving burden. Therefore, it is recommended that healthcare professionals prioritize the optimization of HRQoL for both children with INS and their caregivers.
Using Bivariate Latent Growth Model to Better Understand the Anxiety Symptom in Parkinson's Patients
Authors: wang qiushuang , Li Pugang , Sun Yi , Shi YaoZhou , Bian Jing , Zhao Hua-Shuo 
Published: October 2024

Abstract

Objective
This study utilizes the Bivariate Latent Growth Model to explore the developmental trajectories of trait anxiety and state anxiety, as well as the interrelationships between the trait anxiety and state anxiety.
Methods
We obtained six-year follow-up data from 475 Parkinson's disease patients through the Parkinson's Progression Markers Initiative. We employed latent growth models to explore the trajectories of anxiety, trait anxiety, and state anxiety. Subsequently, we used the Bivariate Latent Growth Model to investigate the longitudinal relationships between state anxiety and trait anxiety.
Results
The trajectories of anxiety, trait anxiety, and state anxiety were best described by a linear growth model. The intercept and slope of each were significantly correlated with the intercept, and the variance of both intercepts and the correlation between them were all significant (P < 0.05). Only the slopes of the total anxiety score and state anxiety were not significant, but the variance of their slopes was significant, indicating significant variability among individuals. The variance of the trait anxiety slope was also significant. The results of the Bivariate Latent Growth Model show significant associations among all intercept and slope factors (P < 0.018). Specifically, the intercept of trait anxiety is positively correlated with the intercept of state anxiety, and the slope of trait anxiety is positively correlated with the slope of state anxiety. The remaining path covariances between intercepts and slopes are negative.
Conclusion
Our research results indicate that among individuals with Parkinson's disease, those showing a higher growth trend in trait anxiety are more likely to experience a higher growth trend in state anxiety at a particular time point. Individuals scoring higher on trait anxiety are more likely to experience elevated levels of state anxiety at a specific time point. Individuals with higher initial levels may undergo smaller growth. For instance, individuals with higher levels of trait anxiety may exhibit lower growth in state anxiety or vice versa. It is evident that there is a close and reciprocal relationship between trait anxiety and state anxiety, with mutual influences.
AI and Entrepreneurship: Facial Recognition Technology Detects Entrepreneurs, Outperforming Human Experts
Authors: Obschonka Martin , Fisch Christian , Fernando Tharindu , Fookes Clinton 
Published: October 2024

Abstract

Occupational outcomes like entrepreneurship are generally considered personal information that individuals should have the autonomy to disclose. With the advancing capability of artificial intelligence (AI) to infer private details from widely available human-centric data, such as social media, it is crucial to investigate whether AI can accurately extract private occupational information from such data. In this study, we demonstrate that deep neural networks can classify individuals as entrepreneurs based on a single facial image with high accuracy in data sourced from Crunchbase, a premier source for entrepreneurship data. Utilizing a dataset comprising facial images of 40,728 individuals, including both entrepreneurs and non-entrepreneurs, we trained a Convolutional Neural Network (CNN) and evaluated its classification performance. While human experts (n = 650) and trained participants (n = 133) were unable to classify entrepreneurs with accuracy above chance levels (> 50%), the AI model achieved a classification accuracy of 79.51%. Several robustness tests show that this high level of accuracy is maintained under various conditions.
Inter-Center Variations in Inpatient Outcomes for Infants with Gastroschisis from the Children's Hospitals Neonatal Consortium
Authors: Ling Con Yee , Zaniletti Isabella , Riddle Stefanie , Jacobson Elizabeth , Korff Stephanie , Chandler Angela , Downey L , Padula Michael , Evens Jacquelyn , Grover Theresa , Murthy Karna 
Published: October 2024

Abstract

Objective:
To estimate inter-center variation (ICV) in hospital length of stay (LOS) and oral feeding at discharge among infants with gastroschisis.
Study Design:
Children's Hospitals Neonatal Consortium's (CHNC) database was used to identify hospitalized survivors with gastroschisis. Two outcomes were evaluated: LOS and discharge without tube feedings. Hospital outcomes were evaluated in unadjusted and adjusted analyses. Generalized linear models with log link for gamma distribution was used to model LOS and logistic regression for discharge without tube feeds.
Results:
For 3987 surviving infants with gastroschisis, LOS and discharge within 70 days with exclusively oral feeding, both exhibited significant ICV. Differences persisted in multivariable analyses. Risk adjusted LOS (68% difference) and oral feeding at discharge (6.4-fold difference) varied significantly between centers.
Conclusion:
Hospital of care was independently associated with LOS and exclusive oral feeding at discharge rates for infants with gastroschisis. Management differences, potentially influenced by parental preferences, contributed to variation.
Integrated the analysis of single-cell and bulk RNA-sequencing to predict renal cell carcinoma by identifying signature based on Mitophagy-related Genes
Authors: Tang Guanbao , Li Shuai , Yang Jiwei , Chen Dongdong , Guo Xuewen , Chen Hao , wang Lizhun , Men Tongyi 
Published: October 2024

Abstract

Background
The features of resistance to mitophagy contribute significantly to invasion, malignancy and cell survival. But the mechanism of mitophagy in clear cell renal cell carcinoma (ccRCC) remains unclear It is valuable to estimate mitophagy molecular characters as a clinical factor for prognosis and immune phenotypes in ccRCC.
Methods
Clinical data of ccRCC patients, including genome and transcriptome data, were downloaded from The Cancer Gene Atlas (TCGA) and International Cancer Genome Consortium (ICGC) database. The differentially expressed genes (DEGs) of patient clusters determined by mitophagy gene expression and univariate Cox regression analysis were identified and used to classify patient clusters for constructing mitophagy scores via PCA analysis. Immune cell infiltration and immune cell function were analyzed by ssGSEA algorithm and TIDE algorithm.
Results
Based on the expression of mitophagy marker genes, ccRCC patients were divided into three mitophagy clusters with different gene expression patterns, prognosis and immune niches. 1,356 DEGs of mitophagy clusters related with prognosis were screened out for building mitophagy score. ccRCC patients with high mitophagy scores have better prognosis. Meanwhile, lower mitophagy patients with high expressed several immune-checkpoint proteins and had high immunophenoscore after immune-checkpoint blockers treatment, indicating better responsiveness to immune therapy.
Conclusions
mitophagy features are tightly correlated with ccRCC prognosis and immune responsiveness. mitophagy score built here is able to predict the prognosis and immune features of ccRCC patients and be indicative for immunotherapy.
Preventing effect of angiotensin-receptor-blocker for moderate to severe cerebral vasospasm after aneurysmal subarachnoid hemorrhage.
Authors: Lim Jeong-Wook , Lee Si Un , Byoun Hyoung Soo 
Published: October 2024

Abstract

Purpose
To verify the effectiveness of angiotensin-receptor blockers (ARBs) in preventing moderate to severe cerebral vasospasm, which may influence patient outcomes in cases of subarachnoid hemorrhage resulting from aneurysmal rupture.
Methods
Between 2016 and 2020, we treated a total of 210 patients. We obtained the clinical and radiological characteristics of patients through medical records and divided them into two groups: those who were administered ARBs (ARB group) and those who were not (no ARB group).
Results
One hundred eighty-one patients enrolled in this study. ARB group were 29 and no ARB group were 152. The overall incidence of moderate to severe vasospasm was 33.7%. The incidence of moderate to severe vasospasm in each group was 13.8% (4 patients) and 37.5% (57 patients), respectively. The independent risk factors for moderate to severe vasospasm included Fisher grade (III-IV) with an odds ratio (OR) of 2.732 (95% confidence interval [CI]: 1.343–5.560; P = 0.006), older age (OR = 0.963; 95% CI: 0.938–0.989; P = 0.006), and ARB administration (OR = 0.246; 95% CI: 0.079–0.771; P = 0.016).
Conclusions
Despite the potential adverse impacts associated with hypotension, the administration of ARBs may provide therapeutic benefits in preventing moderate to severe vasospasm. Age and volume of hemorrhage should be taken into consideration because of their association with the development of moderate to severe cerebral vasospasm.
A tough semi-dry hydrogel electrode with anti-bacterial properties for long-term repeatable non-invasive EEG acquisition
Authors: Lin Jiaqi , Wang Dongyang , Xue Hailing , Xia Long , Li Zongqi , Sun kai , Wang Huanan , Hamalainen Timo , Li Yanhua , Song Fei 
Published: October 2024

Abstract

Non-invasive brain-computer interfaces (NI-BCIs) have garnered significant attention due to their safety and wide range of applications. However, developing non-invasive electroencephalogram (EEG) electrodes that are highly sensitive, comfortable to wear, and reusable has been challenging due to the limitations of conventional electrodes. Here, we introduce a simple method for fabricating semi-dry hydrogel EEG sensors with antibacterial properties, enabling long-term, repeatable acquisition of EEG. By utilizing N-acryloyl glycinamide and hydroxypropyltrimethyl ammonium chloride chitosan, we have prepared electrodes that not only possess good mechanical properties (compression modulus 65 kPa) and anti-fatigue properties but also exhibit superior antibacterial properties. These electrodes effectively inhibit the growth of both Gram-negative (E. coli) and Gram-positive (S. epidermidis) bacteria. Furthermore, the hydrogel maintains stable water retention properties, resulting in an average contact impedance of less than 400 Ω measured over 12 hours, and an ionic conductivity of 0.39 mS/cm. Cytotoxicity and skin irritation tests have confirmed the high biocompatibility of the hydrogel electrodes. In N170 event-related potential (ERP) tests conducted on human volunteers, we successfully captured the expected ERP signal waveform, comparable to that of traditional wet electrodes. Moreover, contact impedance on the scalps remained below 100 kΩ for 12 hours, while wet electrodes became unable to detect signals after 7–8 hours due to dehydration. In summary, our hydrogel electrodes are capable of detecting ERPs over extended periods in an easy-to-use manner with antibacterial properties. This reduces the risk of bacterial infections associated with prolonged reuse and expands the potential of NI-BCIs in daily life.
Fast parallel index-based GPU particle collision detection for science and engineering.
Authors: Bell Jackie 
Published: October 2024

Abstract

A fast particle collision detection method by rounding and indexing particle and cell locations. The two part process is performed in compute and render pipelines exclusively on the GPU. The method is GPU-Driven in that detection and rendering are simultaneous and all logic resides on the GPU. The application can process 1 million particles in less than 1/30th of a second, (30 frames per second) on an inexpensive laptop workstation. This speed provides a basis for scientists and engineers accustomed to computational fluid dynamics, to consider particle systems for thremo-fluid flow including rarefied gases. It presents an opportunity for students and educators to explore massive particle systems (greater than 1 million particles). Also, in order to encourage comparative analysis, we have developed a light-weight benchmarking method where test data is generated by software.
Adaptive long-read and transcriptome sequencing detail a submicroscopic inv(15)(q14q15), generating fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency
Authors: Ek Marlene , Kvarnung Malin , Pettersson Maria , Soller Maria Johansson , Anderlid Britt-Marie , Thonberg Håkan , Eisfeldt Jesper , Lindstrand Anna 
Published: October 2024

Abstract

Inversions are balanced structural variants that often remain undetected in genetic diagnostics. We present a female proband with a de novo Chromosome 15 paracentric inversion, disrupting MEIS2 and NUSAP1. The inversion was detected by short-read genome sequencing and confirmed with adaptive long-read sequencing. The breakpoint junction analysis revealed a 96 base pair (bp) deletion and an 18 bp insertion in the two junctions, suggesting that the rearrangement arose through a replicative error. Transcriptome sequencing of cultured fibroblasts revealed normal MEIS2 levels and 0.61-fold decreased expression of NUSAP1. Furthermore, two fusion transcripts were detected and confirmed by Sanger sequencing.
Heterozygous loss of MEIS2 (MIM# 600987) is associated with a cleft palate, heart malformations, and intellectual impairment, which overlap with the clinical symptoms observed in the proband. The observed fusion transcripts are likely non-functional, and MEIS2haploinsufficiency is the likely disease causative mechanism. Altogether, this study findings illustrate the importance of including inversions in rare disease diagnostic testing and highlight the value of long read sequencing for the validation and characterization of such variants.