bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression
Authors: Shaw Timothy , Wagner Jessica , Tian Liqing , Wickman Elizabeth , Poudel Suresh , Wang Jian , Paul Robin , Koo Selene , Lu Meifen , Sheppard Heather , Fan Yiping , O’Neil Francis , Lau Ching , Zhou Xin , Zhang Jinghui , Gottschalk Stephen
Published: January 2024

Immunotherapy with CAR T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons (CSE) present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify CSE targets, we analyzed 1,532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We found 2,933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n=148) or the alternatively spliced (AS) isoform (n=9) level. Expression of selected AS targets, including the EDB domain of FN1 (EDB), and gene targets, such as COL11A1, were validated in pediatric PDX tumors. We generated CAR T cells specific to EDB or COL11A1 and demonstrated that COL11A1-CAR T-cells have potent antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.
Assessing the causal relationship between inflammatory cytokines and myasthenia gravis: A bidirectional and two-sample Mendelian randomization study
Authors: Wang Wenqiao , Li Min , Zhang Zengshan
Published: January 2024

Background:
Myasthenia gravis (MG) is categorized as an autoimmune disorder. A myriad of preceding investigations have elucidated the interrelation between inflammation and MG. Nevertheless, the precise array of inflammatory cytokines and their underlying mechanisms of action remain enigmatic.
Objective:
The primary intent of this research was to discern and elucidate the potential causal associations between 41 inflammatory cytokines and MG, employing a bidirectional and two-sample Mendelian randomization (MR) paradigm.
Methods:
Summary statistics pertaining to MG were procured from a genome-wide association study (GWAS) comprising 232 cases and 217,056 controls of European descent. Concurrently, genetic variants were sourced from an avant-garde GWAS centered on inflammatory cytokines, with an inclusive sample of 8,293 European subjects. An array of techniques including Inverse Variance Weighted (IVW), MR-Egger, weighted median, simple mode, and Weighted Mode were harnessed to assess the putative causal interlinkages between the 41 inflammatory cytokines and MG. Primarily, IVW outcomes formed the basis for deliberations on causality. Additionally, the MR-Egger approach was utilized to ascertain the potential horizontal pleiotropy of instrumental variables, and Cochran's Q statistics were employed to gauge the heterogeneity intrinsic to instrumental variables (IV).
Results:
Findings derived from the IVW model posited that IL-10 (OR=0.46, 95% CI=0.300.72, P=0.0006), IL-17 (OR=0.43, 95% CI=0.210.85, P=0.015), MIP1a (OR=2.24, 95% CI=1.014.97, P=0.048), MIP1b (OR=0.84, 95% CI=0.720.99, P=0.033), and SDF1a (OR=2.32, 95% CI=1.124.81, P=0.024) are potentially implicated in MG susceptibility. Concurrently, cytokines such as bNGF (OR=1.03, 95% CI=1.001.07, P=0.038, PFDR=0.778) and MIF (OR=0.97, 95% CI=0.95~1.00, P=0.033, PFDR=0.778) are ostensibly resultant sequelae of MG pathology. Upon the application of the False Discovery Rate (FDR) correction, a profound association was discerned solely for IL-10 in relation to MG (PFDR=0.025). Contrastingly, multiple inflammatory cytokines, including IL-17, MIP1a, MIP1b, and SDF1a, failed to meet the threshold post-FDR correction (with PFDR＞0.05), as did bNGF and MIF.
Conclusions:
The Mendelian randomization study, anchored in genetic variation methodologies, substantiates that IL-10 potentially holds significant relevance in the etiological landscape of MG. Contrarily, no discernible evidence was found to implicate other inflammatory cytokines in the post-onset progression of MG.
Community-based health education led by women’s groups significantly improved maternal health service utilization in southern Ethiopia: A cluster randomized controlled trial
Authors: Yoseph Amanuel , Teklesilasie Wondwosen , Guillen-Grima Francisco , Astatkie Ayalew
Published: January 2024

Introduction: Maternal health service utilization (MHSU) is cost-effective to reduce maternal mortality. One of the methods to increase its utilization is via health education intervention (HEI). Yet, the impact of HEI on MHSU had not been comprehensively investigated, and previous studies reported controversial findings. Thus, this study aimed to evaluate the effect of HEI on MHSU in southern Ethiopia.
Methods: From January 10 to August 1, 2023, a community-based, two-arm, parallel-group cRCT was conducted among pregnant mothers in the Northern Zone of Sidama National Regional State, Ethiopia. Pregnant mothers < 12 weeks of gestation were eligible for this study. The pregnant women in treatment clusters (kebeles) received standard and pre-prepared audio-based HEI led by women development team leaders, whereas comparator clusters received routine HEI for six months. Six months later, MHSU was assessed in both groups by data collectors who were masked from treatment allocation. The results of the two groups were compared using the intention-to-treat analysis. We utilized multilevel mixed-effects modified Poisson regression with robust variance to control for the effects of clustering and potential confounders. The level of significance was adjusted for multiple comparisons.
Results: The overall utilization of at least one antenatal care (ANC) visit was 90.2% in the treatment group and 59.5% in the comparator group (c2 = 89.22, df =1, p < 0.001). Health facility delivery (HFD) utilization was considerably different between the treatment group (74.3%) and the comparator group (50.8%) (c2 = 70.50, df =1, p < 0.001). HEI significantly increased ANC utilization (adjusted risk ratio [ARR]: 1.32; 99% CI: 1.12-1.56) and HFD utilization (ARR: 1.24; 99% CI: 1.06-1.46). The utilization of at least one postnatal care (PNC) was 65.4% in the treatment group and 52.1% in the comparator group (c2 = 19.51, df =1, p = 0.01). However, after controlling for the effects of confounders and clustering, the impact of HEI on PNC utilization was insignificant between the two groups (ARR: 1.15; 99% CI: 0.89-1.48).
Conclusion: A community-based HEI significantly increased ANC and HFD utilization but did not increase PNC utilization. Expanding the HEI with certain modifications will have a superior effect on improving MHSU.
Trial registration number: NCT05865873.
A New Nomogram for Predicting Extrahepatic Metastases in Patients With Hepatocellular Carcinoma： A population-based study of the SEER database and a Chinese single-institutional cohort
Authors: Xu Li , Li Zhi-Lei , Zhang Na , Sun Quan-Quan , Liu Peng
Published: January 2024

Purpose
This study aimed to identify risk factors associated with the occurrence of extrahepatic metastases (EHM) in patients with hepatocellular carcinoma (HCC) and to establish an effective predictive nomogram.
Methods
We extracted eligible data of HCC patients from the Surveillance, Epidemiology, and End Results (SEER) database. This study also included 196 HCC patients from the Zhejiang Cancer Hospital in China. A nomogram for predicting extrahepatic metastases in patients with hepatocellular carcinoma was developed according to the independent variables that were found by univariate and multivariate logistic analysis analyses. The effective performance of the nomogram was evaluated using the areas under the curves (AUC), receiver operating characteristic curve (ROC), and calibration curves. The clinical practicability was evaluated using decision curve analysis (DCA).
Results
Sex, N stage, histological grade, tumor size, AFP, vascular Invasion (VI), and surgery were all included as independent predictors in a nomogram to predict HCC patients for extrahepatic metastases. In the training cohort, internal validation cohort, and external validation cohort, the AUC of the prediction model were 0.830, 0.834, and 0.831, respectively, while the AUC of the AJCC Stage were 0.692, 0.693, and 0.650. Among patients with extrahepatic metastases, the most common metastasis site was lung (37.38%), followed by bone (36.0%), and lymph nodes (30.6%).
Conclusion
Based on the SEER database and the Chinese single-institutional cohort, we have developed and validated a nomogram to forecast EHM in HCC patients. The AUC indicated that the nomogram showed adequate accuracy in discriminating EHM. Additionally, the nomogram fared well in the validation cohort and could support clinical decision-making.
Clinicopathological analysis of primary central nervous system lymphoma in patients with or without AIDS
Authors: Li Man , Chen Jia-min , Feng En-shan , Chen Xiang-mei , Gao Hai-li , Ma Zhi-yuan , Wang Peng , Zhou Xin-gang
Published: January 2024

Background AIDS-related primary central nervous system lymphoma (AR-PCNSL) differs from immunocompetent-primary central nervous system lymphoma (IC-PCNSL) in certain features. The main objective of this study was to investigate the differences in clinicopathological features between AR-PCNSL and IC-PCNSL.
Methods Thirty-seven AR-PCNSL patients and thirty IC-PCNSL patients were included. hematoxylin & eosin staining; immunohistochemical detection using CD20, Bcl-2, Bcl-6, p53, C-MYC, Ki67, and METTL3 antibodies; and Epstein–Barr encoding region (EBER) in situ hybridization were performed.
Results All of the observed patients were classified as the DLBCL histological type. AR-PCNSL were younger (37.7 vs. 60.5 years) and had a higher likelihood of being male (86.5% vs. 63.3%) than non-AIDS patients were. Elevated LDH and low sugar content in cerebrospinal fluid (CSF) were more common among AR-PCNSL. The expression levels of METTL3, Bcl-2 and p53 expressions were significantly higher in AR-PCNSL patients than in PCNSL patients without AIDS. In contrast, AR-PCNSL patients exhibited lower levels of Bcl-6 expression. AR-PCNSL patients were more likely to be positive for EBER, accounting for 81.1% of these patients. Furthermore, we also found that the expression of METTL3 was lower in GCB-like DLBCL (n=7) than in ABC-like DLBCL (n=32) in AR-PCNSL (p=0.041); however, in IC-PCNSL patients, the expression of METTL3 was not significantly different between GCB-like DLBCL and ABC-like DLBCL (p=0.710).
Conclusions Our study of Chinese AR-PCNSL and IC-PCNSL patients revealed new findings, indicating that METTL3, Bcl-2 and p53 were increased in AR-PCNSL patients compared to IC-PCNSL patients and that METTL3 was higher in ABC-like DLBCL patients than in GCB-like DLBCL in AR-PCNSL patients, suggesting a notable distinction in the pathological characteristics between PCNSL patients with or without AIDS.
Plasma Metabolomics and Olink Proteomics Profiling Predict Outcome of Fufang Duzhong Jiangu Granules in Kashin-beck Disease
Authors: Deng Xingxing , Niu Hui , Zhang Qian , Wen Jinfeng , Zhao Yijun , Naren Gaowa , Liu Huan , Guo Xiong , Zhang Feng , Wu Cuiyan
Published: January 2024

Objectives
To investigate predictive biomarkers that could be used to identify patients’ response to treatment, plasma metabolomics and proteomics analyses were performed in Kashin-beck disease (KBD) patients treated with Fufang Duzhong Jiangu Granules (FDJG).
Methods
Plasma were collected from twelve KBD patients before treatment and one month after FDJG treatment. LC-MS was employed for plasma metabolomics profiling, while the olink inflammatory protein panel was used for obtaining inflammatory protein profiles. Patients were classified into responders and non-responders based on drug efficacy after one-month treatment. Enrichment analyses of differential metabolites and proteins of the responders at baseline and after treatment were conducted to study the mechanism of drug action. Differential metabolites and proteins between the two groups were screened as biomarkers to predict drug efficacy. ROC curve was used to evaluate the prediction accuracy of biomarkers.
Results
The changes of metabolites and inflammatory proteins in responders after treatment reflected the mechanism of FDJG treatment for KBD, which may act on glycerophospholipid metabolism, D-glutamine and D-glutamate metabolism, nitrogen metabolism, and NF-kappa B signaling pathway. We identified three metabolites as potential predictors: N-undecanoylglycine, beta-aminopropionitrile, and PC (18:3(6Z,9Z,12Z)/20:4(8Z,11Z,14Z,17Z)). For inflammatory protein, IL-8 was identified as predictive biomarkers to detect responders. Additionally, IL-8 persisted significant in comparison responders to non-responders after one month of therapy. Combined use of these four biomarkers had high predictive ability (AUC = 0.972).
Conclusion
Metabolomics and olink proteomics provide new insights for precision therapy. In our study, IL-8 may be a novel stable potential biomarker for predicting the efficacy of FDJG in KBD treatment.
Analysis of Immune Cell Infiltration Characteristics in Severe Acute Pancreatitis through Integrated Bioinformatics
Authors: Chen Rui , Xiao Shuai , Xiao Han , Bai Shuhui
Published: January 2024

Objective: The etiopathogenesisof severe acute pancreatitis(SAP) remains poorly understood.We aim to investigate the role of immune cells Infiltration Characteristics during SAP progression.
Methods/Design:Gene expression profiles of the GSE194331 dataset were retrieved from the GEO. Lasso regression and random forest algorithms were employed to select feature genes from genes related to SAP progression and immune responses. CIBERSORT was utilized to estimate differences in immune cell types and proportions and the relationship between immune cells and gene expression. We performed pathway enrichment analysis using GSEA to examine disparities in KEGG signaling pathways when comparing the two groups. Additionally, CMap analysis was executed to identify prospective small molecular compounds.
Results: The three hub genes (CBLB,JADE2,RNF144A) were identified that can predict SAP progression. Analysis of CIBERSORT and TISIDB databases has shown that there are significant differences in immune cell expression levels between the normal and SAP groups, and three hub genes (CBLB,JADE2,RNF144A) were highly correlated with multiple immune cells, regulating the characteristics of immune cell infiltration in the microenvironment.Finally,drug prediction through the Connectivity Map database suggested that compounds such as Entecavir, KU-0063794, Y-27632, and Antipyrine have certain effects as potential targeted drugs for the treatment of SAP.
Conclusion: CBLB, JADE2, and RNF144A are hub genes in SAP, potentially playing important roles in SAP progression. This finding further broadens the understanding of the etiopathogenesis of SAP and provides a feasible basis for future research on diagnostic and immunotherapeutic targets for SAP.
Strengths and limitations of this study:
To find new hub genes related to severe pancreatitis and to suggest the key role of immunoinfiltrating cells in the occurrence and development of severe acute pancreatitis.
There is a lack of relevant basic experiments to further verify the pathogenesis of severe acute pancreatitis
Single-cell Data Unveil the Multifaceted Role of LRP1 in Alzheimer’s Disease Pathogenesis
Authors: Chen Kang , Wei ZiLin , Wei AiLi , Qin YingKai , Liu Chen , Xin Haolin , Chen Shisheng , Ge Yi , Li Bin , Wang Kun , Wang TianHui
Published: January 2024

Background
The role of low-density lipoprotein receptor-related protein 1 (LRP1) in Alzheimer’s disease (AD) has been a focal point of research, highlighting its crucial function in amyloid-beta (Aβ) metabolism in the central nervous system. Despite these significant findings, the detailed mechanisms of LRP1 in neuronal Aβ handling and its systemic effects in AD have not been fully elucidated. Here, we employ innovative single-cell data analysis and temporal analysis complemented by multi-tissue data integration to shed light on the specific roles and systemic impact of LRP1 in AD.
Methods
We conducted in-depth single-cell data mining and analysis using publicly available datasets from the GSE181279, GSE174367, and GSE173429. These findings were augmented with complementary in vivo and in vitro experiments aimed at substantiating the function of LRP1 in the phagocytosis of Aβ by hepatic macrophages.
Results
Detailed data mining and analysis of public datasets have revealed the nuanced role of LRP1 in AD, notably impacting the brain, blood, and liver. Our findings demonstrated pronounced upregulation of LRP1 in brain astrocyte, microglia, and oligodendrocyte progenitor cells (OPCs), establishing a direct correlation with the neurological manifestations of AD. In peripheral blood mononuclear cells (PBMC), LRP1 exhibited unique expression patterns, underscoring its systemic influence on AD pathology. Critically, our data reveal that physical exercise modulates LRP1 expression in Kupffer cells, identifying lifestyle factors as key modulators of the molecular processes involved in AD. Experimental evidence further confirms that reduced LRP1 expression is associated with impaired amyloid-beta clearance, highlighting its pivotal role in the progression of AD. Collectively, these insights position LRP1 as a central molecular player in AD, suggesting novel avenues for therapeutic intervention.
Conclusions
This study, which involved leveraging multi-tissue single-cell analyses of human and mice samples, investigated the multifaceted functionality and molecular dynamics of LRP1 in AD progression. Additionally, this study unveiled the modulatory effects of physical exercise on LRP1 expression, paving the way for novel therapeutic approaches for AD management.
The exploration of the pathogenesis and causative relationship of hypertrophic cardiomyopathy mediated by STAT3 through bioinformatics and Mendelian randomization
Authors: LI yaling , TANG LIANG , FAN Ouyang
Published: January 2024

Purpose
Hypertrophic cardiomyopathy (HCM) is a prevalent condition posing a severe threat to human health. This study aims to investigate the expression of STAT3 in HCM and its potential mechanisms.
Methods
Two sets of data from hypertrophic cardiomyopathy patients and healthy individuals were downloaded from the Gene Expression Omnibus (GEO) database. After batch effect removal and merging, differential analysis of STAT3 between healthy individuals and HCM such as limma and Weighted correlation network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed for gene function enrichment. In vitro experiments involved constructing angiotensin II (Ang II)-induced H9c2 cardiomyocytes to validate STAT3 expression and explore the impact of hydrogen sulfide(H2S) intervention on improving drug targets for H9c2 cardiomyocyte hypertrophy. Lastly, MR was utilized to explore the causal relationship between STAT3 and HCM.
Results
STAT3 exhibited high expression in HCM patients. GO analysis indicated enrichment in immune responses, cell proliferation, and transcription. KEGG analysis suggested associations between HCM and pathways like JAK/STAT and NF-kβ. In vitro experiments demonstrated no significant change in STAT3 within Ang II-induced H9c2 cardiomyocytes, with an upregulation of P-STAT3 and hypertrophy-related proteins ANP and BNP. However, these changes were attenuated following H2S intervention. MR showed no causal relationship between STAT3 and HCM. In conclusion, while STAT3 may be associated with HCM occurrence, its expression doesn't exhibit a causal relationship with HCM. The mechanism for STAT3-induced HCM might be linked to increased P-STAT3 levels, and H2S might ameliorate HCM by inhibiting STAT3 phosphorylation.
Echocardiographic Strain imaging to assess immediate and short term effects of successful percutaneous balloon mitral valvotomy on Left Atrial and Right Ventricular Mechanics
Authors: Ranjan Rout Smarak , Sudeep Kumar , Aditya Kapoor , Ankit Sahu , Roopali Khanna , Naveen Garg , Satyendra Tewari
Published: January 2024

Background
Strain imaging for Left atrium and Right Ventricle has been used as a novel assessment tool to evaluate LA and RV functional status. However, their implication is not fully established regarding the effect of percutaneous balloon mitral valvotomy (BMV) in patients with rheumatic severe mitral stenosis (MS). In the present study, we sought to assess the Global LA Strain and RV Strain in this patient population.
Methods
It is an observational study and was conducted in a tertiary health care centre of North India from the Year 2018 to 2020. 66 consecutive patients with suitable mitral valve anatomy for BMV procedure were taken, out of which 38 patients could be followed up till 3 months. Global LA strain and RV Strain were being calculated using special software (GE Healthcare, ECHO PAC Version 203) at three temporal sequences.
Results
The mean age of the study population was 31.63 ± 10.15 years. Both Peak Left atrial longitudinal strain (PALS) and Global RV Longitudinal strain (GLSRV) were impaired in patients with severe MS and both significantly improved both at 24 hrs and 3 months following BMV. There was a significant positive correlation of LA strain and RV strain both at 24 hours and 3 months of follow up. (Pearson r = 0.9142).
Conclusions
Peak LA strain (PALS) and Global RV strain (GLS RV ) can be considered as an indicator of respectively left atrial and Right ventricular function, and its improvement may be taken as a good indicator of successful BMV.
PDIA6 promotes immune escape of head and neck squamous cell carcinoma by regulating TIGIT/CD155 axis
Authors: Jiang Weiwei , Wang Ji , Song Kai , Gong Zhengpeng , Yu Ming
Published: January 2024

BACKGROUND
Protein disulfide isomerases A6 (PDIA6) is a family member of the PDI enzymes. Recently, it was found that PDIA6 is closely associated with a variety of cancers. Here, we studied the role of PDIA6 in pan-cancer and further verified the results in head and neck squamous cell carcinoma (HNSCC) through in vitro experiments.
METHODS
The TCGA database and GEPIA2 were used to assess PDIA6's potential as a diagnostic and prognostic biomarker in pan-cancer. The cBioPortal database was used to examine the PDIA6 mutation character. PDIA6 function analysis was carried out using the LinkedOmics and CancerSEA databases. The TIMER and TISIDB websites were used to investigate the role of PDIA6 in immunological infiltration.PDIA6 mRNA and protein expression were identified in HNSCC tissues. PDIA6 expression was detected in primary HNSCC tissues and cell lines using RT-qPCR, Western blotting, and immunohistochemistry. Furthermore, PDIA6 deletion and overexpression cell lines were developed to investigate the interaction of PDIA6 and TIGIT/CD155, as well as the influence of PDIA6 on cell proliferation and metastasis in vitro.
RESULTS
PDIA6 was elevated in the majority of malignancies. In numerous malignancies, the overexpression and mutation of PDIA6 were associated with a poorer prognosis. In the majority of malignancies, the results revealed a strong positive association between PDIA6 and myeloid-derived suppressor cell (MDSC) infiltration and a significant negative correlation between PDIA6 and T-cell natural killer (NK) infiltration. Experiments in vitro revealed that PDIA6 levels were elevated in HNSCC tissues and cell lines. The connection between PDIA6 expression and CD8 + T-cell infiltration was negative. In addition, PDIA6 was found to be co-expressed with immune-related genes and immune-checkpoints. The effect of PDIA6 on immune evasion of head and neck cancers may be mediated by the TIGIT/CD155 signal pathway.
CONCLUSION
PDIA6 could be a biomarker and an oncogene in HNSCC and other types of cancer. Also, PDIA6 was linked to immune cell infiltration in pan-cancer, which could be a target for immune therapy to treat tumors.
Chaperonin Containing TCP-1 subunit 6A (CCT6A) is involved in development of colon cancer
Authors: Jiang Ze-Kun , Wu Yi-Xiang , Chen Gao-Min , Yang Xiao , Huang Jiong-Qiang , Chen Jing-Song
Published: January 2024

Purpose
Worldwide, colon cancer (CC) is one of the most commonly occurring malignancies. However, the molecular basis of the pathogenesis of CRC needs to be further explored. Studies have demonstrated that the chaperonin-containing TCP1 (CCT) complex contributes to the development and progression of various tumors. However, the functional significance of CCT in CC is unclear.
Methods
This study explored the potential functions of CCT family genes in CC by bioinformatics analysis. In addition, we established a risk score model based on the CCT family genes, which was validated to effectively predict the prognosis of CC patients.
Results
We found that CCTA6, one of the CCT family genes, was significantly more highly expressed in CC tissues than in normal tissues, and that increased expression of CCT6A was associated with a lower survival rate in CC patients. These findings were validated by real-world data.
Conclusion
Through the preliminary exploration of the role of CCT family genes in CC in this study, we found that CCT6A may contribute significantly in CC, and thus this gene may be an attractive therapeutic target for CC patients.
Applying Protein Language Models Using Limited Dataset. Sequence-Based Hot Spot Prediction in Protein Interactions Using AutoGluon
Authors: Sargsyan Karen , Lim Carmay
Published: January 2024

Background
Protein language models, inspired by the success of large language models in deciphering human language, have emerged as powerful tools for unraveling the intricate code of life inscribed within protein sequences. They have gained significant attention for their promising applications across various areas, including the sequence-based prediction of secondary and tertiary protein structure, the discovery of new functional protein sequences/folds, and the assessment of mutational impact on protein fitness. However, their utility in learning to predict protein residue properties based on scant datasets, such as protein-protein interaction (PPI)-hotspots whose mutations significantly impair PPIs, remained unclear. Here, we explore the feasibility of using protein language-learned representations as features for machine learning to predict PPI hotspots using a dataset containing 414 experimentally confirmed PPI-hot spots and 504 PPI-nonhot spots.
Results
Our findings showcase the capacity of unsupervised learning with protein language models in capturing critical functional attributes of protein residues derived from the evolutionary information encoded within amino acid sequences. We show that methods relying on protein language models can compete with methods employing sequence and structure-based features to predict PPI hotspots from the free protein structure. We observed an optimal number of features for model precision, suggesting a balance between information and overfitting.
Conclusions
This study underscores the potential of transformer-based protein language models to extract critical knowledge from sparse datasets, exemplified here by the challenging realm of predicting PPI hotspots. These models offer a cost-effective and time-efficient alternative to traditional experimental methods for predicting certain residue properties. However, the challenge of explaining the importance of specific features in determining residue properties remains.
In situ electrospun three-dimensional polyacrylonitrile nanofiber reinforced silica aerogels via ambient pressure drying for efficient oil/water separation
Authors: Li Yi-Ming , Liu Fang , jia Zhen-Zhen , Cheng Xuan , Zheng Yu-Ming , Shao Zai-Dong
Published: January 2024

In situ electrospun 3D polyacrylonitrile (PAN) nanofiber-reinforced (EPNR) silica aerogel monoliths were prepared through methyltriethoxysilane–trimethylchlorosilane modification followed by ambient pressure drying (APD). The 3D PAN nanofiber network was built into silica sol by liquid-assisted collection. Homodispersed and intertwined PAN nanofibers were well incorporated into the silica aerogel matrix. The APD-EPNR silica aerogel had a porosity of 90.9% and a BJH pore volume of 2.15 cm3⋅g− 1. Furthermore, the APD-EPNR silica aerogel monolith showed excellent flexibility and revealed a highly hydrophobic surface with a water contact angle of 145º. The APD-EPNR aerogel was suitable for removal of oil from water. The static mass of the APD-EPNR silica aerogel achieved 700–1500% to various solvents and recovered without obvious performance decline. The APD-EPNR silica aerogel mat also achieved continuous oil/water separation with separation efficiency of more than 99%. Hence, the prepared APD-EPNR silica aerogel has promising application for treatment of oil pollution.
Refractive EEG classification joint singular spectrum analysis and tunable Q factor wavelet transform
Authors: Ren Hongyi , Fan Chixuan , Zhang Ruyi , Ma Qingkai , Gong Jianyang , Han Yishi
Published: January 2024

Compared with the traditional methods, the application of electroencephalogram(EEG) in refractive classification is more portable and more suitable for daily environment. However, there is still a lack of research on refractive classification based on EEG signals. Therefore, this paper proposes a multi-classification of refractive EEG based on single-channel joint singular spectrum analysis and tunable Q factor wavelet transform(SSA-TQWT). In order to improve the classification accuracy of refractive EEG signals and better adapt to the characteristics of nonlinear EEGs, this paper proposes a time-frequency analysis method of SSA-TQWT to denoise EEG signals. Firstly, this method uses SSA algorithm to decompose, and uses component selection algorithm to quickly and automatically screen useful signals, which reduces the labor loss and avoids the loss of useful signals. Then, TQWT algorithm is used to adaptively process the refractive EEG signal through flexible and adjustable Q and r. At the same time, multi-domain features are extracted for fusion. Include nonlinear dynamic features, statistical features and frequency domain features. Finally, machine learning is used to classify them. The experimental results show that the average classification accuracy of this method is 90.61%, which is 10.29% higher than SSA method and 8.05% higher than TQWT method. At the same time, the sensitivity and specificity for low, medium and high refractive states are 93.94%, 81.82% and 80%, 93.75%, 92.11% and 93.48% respectively.
In silico Functional Annotation and Characterization of Hypothetical Proteins in Cedecea neteri SSMD04: Insights into Pathogenicity and Antibiotic Resistance
Authors: Sharma Shubhangi , Pandey Pallavi , Kaur Jaspreet
Published: January 2024

Cedecea neteri strain SSMD04 is a rare gram-negative pathogenic bacterium belonging to the Enterobacteriaceae family. It is known to cause sporadic acute infections, particularly in immunocompromised individuals, but understanding of its antibiotic resistance and virulence factors is limited. This study aims to shed light on the functional roles of its hypothetical proteins (HPs) and identifying the ones that are responsible for the resilient and pathogenic nature of the bacterium. Using bioinformatic tools, we conducted a comprehensive analysis of 30 HPs out of a total of 244 HPs in C. neteri SSMD04. The systematic analysis began with the prediction of their functional domains and molecular functions, followed by analyzing their physicochemical properties, including molecular weight, charge distribution, stability, and hydrophobicity. We also determined the subcellular locations of HPs, identifying membranous and cytoplasmic proteins that could serve as potential drug and vaccine targets. Followed by localization, the incidence of their virulence was assessed. Tertiary structure analysis of the proteins revealed some interesting insights into the structures of HPs, such as the presence of active ligand-binding sites which can be targeted to alter the antibiotic resistance ability of C. neteri SSMD04. Overall, the results of our analyses revealed that several HPs play crucial roles in the bacterium owing to its virulence and survival within the host. The insights gained from this study will be helpful for developing targeted therapies against bacterial infections and combating antibiotic resistance.
Synthesis and characterization of silver nanoparticles using the Shrub Solanum betaceum and evaluation of their anticancer activity
Authors: Subbaian Aejitha , Babu Kaviya , Ali Apshana Mubarak , Mani Neelakandan , Arumugam Ramakrishnan , Thilagar Gobinath
Published: January 2024

The biological activity of Solanum betaceum leaves and its nanoparticles has been poorly studied in the field of anticancer science. In this research, the synthesis of silver nanoparticles was accomplished by the new effortless green synthesis process, using S.betaceum leaves extract as reducing and capping agent. The effects of various parameters i.e., pH, reactants ratio, and temperature on the synthesis of AgNPs were studied. The production of S.betaceum leaves extract AgNO3 NPs was characterized by powder X-ray diffraction (XRD), UV-visible, Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM). The S.betaceum leaves fabricated AgNO3 NPs were tested for their cytotoxicity action against cancer cells (Leukaemia cell line (K562), Bone cancer - MG63, Breast cancer - MCF7). It was found that the formation of AgNPs enhanced with time at a higher temperature and alkaline pH. The UV visible absorbance spectrum of AgNO3 NPs exhibited the absorbance band at 280 nm and SEM studied highlighted average crystalline sizes of nanoparticles of 0.2µm to 0.5µm. The in vitro cytotoxic effect of .betaceum leaves fabricated AgNO3 NPs inhibited the proliferation of Leukaemia cell line (K562), Bone cancer - MG63, Breast cancer - MCF7 with IC50 concentration. Overall, based on our results, we strongly believe that the synthesis of AgNO3 NPs using commonly used S.betaceum leaves can be promoted as a potential eco-friendly option to chemical methods currently used for nanoparticle synthesis of anticancer compounds.
Imagining Sport as a Social Space in Thimlich Ohinga Society: Multivariate Approach
Authors: Muthegethi David Maina , Wagura Kennedy Gitu , Ndiiri Washington
Published: January 2024

The article examines sports in antiquity as a social institution, just like religion, family, and others in the Thimlich Ohinga archaeological site. Its re-centers sports in exploring past societies in East Africa, emphasizing the Thimlich Ohinga society that existed from the 15th to the 20th century. The study employs multivariate strategies of data collection and subsequent analysis. They include archaeological, historical, and ethnographic methods. Key findings show that the Thimlich Ohinga incorporated various sports through time and space. They include bao, wrestling, swimming, spear throwing, and running, which can be categorized as games that lie under chance and physical skills. To that end, these games fall under societies that were not complex in the past. Interestingly, these games were practiced for survival, defense, and spaces for expressing gender, especially masculinity, in the above society. Namely, spear throwing acted as defense and raiding other communities for livestock, especially among the Luo community. However, the bao game was based on chance, a possibility of expression of luck, which is in line with religious activities. The study demonstrates that sports were part of Thimlich Ohinga’s social institutions. Therefore, these findings warrant further interrogation of sports as a social institution in wider East African past and contemporary indigenous societies.
Evaluating the Impact of Training and Skill Development Programs on Employee Performance in Private Banks
Authors: Dewi Lutfiana , Utomo Nadira , Puspitasari Fitriani
Published: January 2024

In the ever-evolving landscape of the banking industry, the imperative of maintaining a highly skilled and adaptable workforce is paramount. This research undertakes a comprehensive examination of the influence exerted by training and skill development programs on employee performance within private banks. The study endeavors to unravel the intricacies of the relationship between training initiatives, skill enhancement, and overall organizational outcomes. Employing a meticulously crafted mixed-methods approach, combining quantitative surveys and qualitative interviews, this research seeks to provide a nuanced and holistic understanding of the multifaceted dynamics at play. The literature review situates this study within the broader context of research on training programs and employee performance. While existing studies demonstrate a positive correlation between employee training and improved performance, it is acknowledged that the effectiveness of such programs is contingent upon factors such as program design, delivery methods, and organizational culture. The specific nuances within the private banking sector necessitate a dedicated exploration to bridge the current gap in the literature. Methodologically, a mixed-methods approach was employed to capture the richness and depth of the phenomenon under investigation. Quantitative data was gathered through structured surveys distributed among employees who had participated in training programs within private banks. Likert scales were employed to assess perceived improvements in skill levels and performance outcomes. Concurrently, qualitative data was obtained through in-depth interviews with key stakeholders, including human resource professionals and training facilitators, providing a more holistic understanding of the contextual factors influencing program efficacy. Preliminary analysis of the data suggests an overall positive perception among employees regarding the impact of training and skill development programs on their performance. Quantitative results reveal statistically significant improvements in self-reported skill levels and job performance. Qualitative findings enrich the understanding by uncovering the nuanced role of program design, support mechanisms, and organizational culture in shaping the outcomes of training initiatives. The ensuing discussion synthesizes the quantitative and qualitative findings, exploring the implications of the results for human resource management practices and organizational strategy within private banks. This section delves into potential areas for improvement in the design and implementation of training programs, offering actionable recommendations for private banks seeking to optimize the impact of these initiatives on employee performance. In doing so, this research contributes valuable insights to both academic research and the practical realm of human resource management and organizational development within the banking sector.
Modelling multi-stage energy optimization in the smart hub energy system with hybrid demand management and local supply by Electric Vehicles
Authors: jafari saeed , Najafi Mojtaba , Pirkolachahi Naghi Moaddabi , Shirazi Najmeh Cheraghi
Published: January 2024

The interdependence of energy with social sustainability, economic viability, and environmental impact has led energy operators to conduct thorough investigations into energy scheduling issues. These investigations have prompted the development of new strategies for energy generation, such as the utilization of energy carriers including electrical, gas, and thermal loads. This article presents a model for multi-stage energy optimization in a smart system like energy hub, with a focus on hybrid demand management at the consumer level. The proposed multi-stage energy optimization approach aims to address demand management in the upper stage, while also minimizing energy generation costs and emission pollution in the lower stage. The hybrid demand management is proposed considering two demand response programs like optimal shifting and interrupting of the thermal and electrical demands. The modeling of emission pollution and energy generation costs in the lower stage is done by multi-criteria optimization. As well, local supply strategy is implemented via electric vehicles (EVs) in lower stage by consumers to supply self-electrical demand. The proposed two-stage multi-criteria optimization by using GAMS software is solved. On the other hand, multi-criteria optimization is handled by a modified epsilon-constraint method and max-min fuzzy decision approach in the lower stage of optimization. To validate the mentioned approach, three scenarios are compared, and the results clearly illustrate the energy optimization for minimizing the energy costs and emissions achieved through the presented approach.
Representing Indonesia’s “Revolusi” years in film : a case study of the depiction of “The Long March of the Siliwangi Division” (1948)
Authors:   , Alkhajar Eka Nada Shofa
Published: January 2024

This study investigates a historical event that occurred during the Indonesian Revolution as depicted in Indonesian historical films and argues that these films not only attempt to depict the past but also use the past as a means of social commentary, teaching moral insight, and historical reinforcement. The historical films selected are The Long March (Darah dan Do’a) (1950) and Mereka Kembali (1972). Both films deal with the Long March event experienced by the troops of the Siliwangi Division in 1948. These troops were previously assigned to infiltrate Yogyakarta and its surrounding areas. They were instructed to march back to their original base in West Java as a part of the military strategies to confront the Dutch during the Indonesian Revolution, also known as the Indonesian War of Independence. This event became known as the Long March of the Siliwangi Division. This study examines not only the representation of the past or the texts of the films but also the production process, which includes the motivations of the filmmakers and the public reception when the films were screened for the public at the time—in 1950 and 1972, respectively. This approach provides a broader and richer dimension, valuable insights into the behind-the-scenes process of making the selected historical films, and essential information about the public reception of the films. From the production point of view, there are two main reasons for making these historical films: personal reason and social engagement. Further, the military also plays a vital role in these historical film productions. From the historical representation aspect, these two films depict the events of the Long March of the Siliwangi Division as a journey full of various obstacles and difficulties, such as harsh terrain, lack of food, battles against the Dutch, and internal disputes with fellow Indonesians: Darul Islam. From the reception aspect, the audience’s point of view, these films provide several representations that meet their expectations about the Long March of the Siliwangi Division. However, the audience disagrees with some of the other representations. Finally, the study revealed that historical films are potential vehicles for telling, interpreting, entertaining, legitimating and preserving the past. In addition, this study has a vital implication for reopening the tradition of Indonesian film studies and reigniting attention to old films.
Langzeitüberleben und und Mortalitätsprädiktoren nach perkutanem kathetergestütztem Aortenklappenersatz
Authors:   , Dietz Sara-Viktoria
Published: January 2024

Ziel dieser Studie war die Evaluation von Patienten, die eine transfemorale oder eine transapikale TAVI erhalten haben, in Bezug auf ihre Mortalitätsprädiktoren und ihre Langzeit-Mortalität. Methoden Untersucht wurden Patienten mit einer minimalen FU-Zeit von sechs Jahren, welche im Zeitraum von 2006 – 2014 eine TAVI im Herzkatheterlabor des Universitätsklinikums in Frankfurt erhalten haben. Das Patientenkollektiv wurde basierend auf dem Zugangsweg (transfemoral oder transapikal) analysiert. Ergebnisse Insgesamt wurden 679 Patienten in die Studie eingeschlossen. 408 Patienten (59,82 %) bekamen eine transfemorale TAVI und 271 Patienten (39,74 %) bekamen eine transapikale TAVI. Der durchschnittliche STS-Score betrug in der transfemoralen Gruppe 4,21 ± 2,4 % und in der transapikalen Gruppe 4,19 ± 2,7 %. Die Mortalität war nach 30 Tagen (15,8 % transapikal versus 8,2 % transfemoral, p = 0,00) sowie im Langzeit-FU (79,5 % transapikal versus 68,3 % transfemoral, p = 0,00) signifikant höher in der transapikalen Gruppe. Viele postinterventionelle Komplikationen waren häufiger in der transfemoralen Gruppe. Postinterventionelle Schrittmacherimplantationen (15,7 % versus 4,1 %, p = 0,00), große und kleine vaskuläre Komplikationen (5,1 % versus 1,1 %, p = 0,01) sowie große und kleine zerebrovaskuläre Insulte (31,8 % versus 9,1 %, p = 0,00) kamen in der transfemoralen Gruppe signifikant häufiger vor. Allerdings war der transfemorale Zugangsweg mit einer besseren Überlebensrate assoziiert (Log Rank Test p = 0,01 und HR 1,33 (1,04 – 1,71), p = 0,03). Patienten mit einem hohen STS-Score (HR 1,09 (1,03 – 1,15), p = 0,00), einem vorbestehenden Diabetes Mellitus (HR 0,75 (0,58 – 0,97), p = 0,03) sowie großen Gefäßkomplikationen (HR 0,60 (0,37 – 0,99), p = 0,04) korrelieren mit einem schlechteren Langzeit-Überleben. Zusammenfassung Für den kathetergestützten Aortenklappenersatz weisen beide Zugangswege spezifische Risiken auf, daher sollte die individuell beste Variante für jeden Patienten ausgewählt werden.
HOW PRODUCT DEVELOPMENT, ADVERTISING, AND SERVICE QUALITY INFLUENCE CUSTOMERS SAVING DECISION CASE STUDY ON STATED-OWNED BANKS IN JAKARTA
Authors: Novela Selly , Hanafie Steffi Mutia Irenda
Published: January 2024

The competition between Banks in Indonesia required the existence of a marketing strategy for appropriate banking products and services offered on the state-owned bank in Indonesia, including in Jakarta. This study aims to determine whether there is influence between variable Product Development, Advertising and Service Quality, to Saving Decision in State-Owned Bank in Jakarta. Methods of data collection using a survey distributed to 127 customers. The research method used quantitative descriptive analysis and method of data analysis used in this research is multiple regressions. The results of this study, shows that Product Development, Advertising and Service Quality has an influence on Customers Saving Decision at State-Owned Banks in Jakarta.
THE EFFECT OF SELF CONFIDENCE, QUALITY EDUCATION AND FAMILY ENVIRONMENT ON INDONESIAN YOUTH IN ENTREPRENEURSHIP
Authors: Novita Novita , Irawan Damar Aji , Suwitorahardjo Benyamin
Published: January 2024

The biggest challenge faced by students nowadays and in the future, is how to deal with the increasingly high competition in the world, the increasing number of undergraduate and limited job opportunities. In this kind of situations, the students had to find a creative way and change the approach of being a university graduate looking for a job, to become scholars who can create their own jobs, or even able to create jobs for others.The purpose of this study was to determine the youth interest on entrepreneurship in Indonesia. It seems that the youth are unaware to see that the job is increasingly difficult to find nowadays. So through this study, researchers wanted to find out what causes youth in Indonesia, reluctant to become an entrepreneur. While being an entrepreneur, the youth can open or create jobs for others and can reduce the level of unemployment in Indonesia.Self-confidence is an important factor in entrepreneurship. Family environment and quality education also participate in creating interest for youth in entrepreneurship. This research is using basic research method; where researchers will try to link the theories of the existing variables. Thus, researchers can conduct research by distributing questionnaires to the youth throughout Indonesia. This study aims to determine the cause of Indonesian youth lack of interest in entrepreneurship.