bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Immune Multi-Omics and Machine Learning to Improve Prognosis, Immune Landscape, and Sensitivity to First- and Second-Line Treatments for Head and Neck Squamous Cell Carcinoma
Authors: Yin Ji , Xu Lin , Wang Shange , Zhang Linshuai , Zhang Yujie , Zhai Zhenwei , Zeng Pengfei , Jiang Tao 
Published: July 2024

Abstract

Background: In recent years, immune checkpoint inhibitors (ICIs) has emerged as a fundamental component of the standard treatment regimen for patients with head and neck squamous cell carcinoma (HNSCC). However, accurately predicting the treatment effectiveness of ICIs for patients at the same TNM stage remains a challenge.
Methods: In this study, we first combined over ten types of omics data and clustering algorithms, successfully identifying two distinct cancer subtypes (CSs) (CS1 and CS2). Subsequently, immune-regulated genes (IRGs) and machine learning algorithms were utilized to construct a consensus machine learning-driven prediction immunotherapy signature (CMPIS). Further, the prognostic model was validated and compared across multiple datasets, including clinical characteristics, external datasets, and previously published models. Ultimately, the response of different CMPIS patients to immunotherapy, targeted therapy, radiotherapy and chemotherapy was also explored.
Results: First, Two distinct molecular subtypes were successfully identified by integrating immunomics data with machine learning techniques, and it was discovered that the CS1 subtype tended to be classified as "cold tumors" or "immunosuppressive tumors", whereas the CS2 subtype was more likely to represent "hot tumors" or "immune-activated tumors". Second, 303 different algorithms were employed to construct prognostic models and the average C-index value for each model was calculated across various cohorts. Ultimately, the StepCox [forward] + Ridge algorithm, which had the highest average C-index value of 0.666, was selected and this algorithm was used to construct the CMPIS predictive model comprising 16 key genes. Third, this predictive model was compared with patients' clinical features, such as age, gender, TNM stage, and grade stage. The findings indicated that this prognostic model exhibited the best performance in terms of C-index and AUC values. Additionally, it was compared with previously published models and it was found that the C-index of CMPIS ranked in the top 5 among 94 models across the TCGA, GSE27020, GSE41613, GSE42743, GSE65858, and META datasets. Lastly, the study revealed that patients with lower CMPIS were more sensitive to immunotherapy and chemotherapy, while those with higher CMPIS were more responsive to radiation therapy and EGFR-targeted treatments.
Conclusion: In summary, our study identified two CSs (CS1 and CS2) of HNSCC using multi-omics data and predicted patient prognosis and treatment response by constructing the CMPIS model with IRGs and 300 machine learning algorithms, which underscores the importance of immunotherapy biomarkers in providing more targeted, precise, and personalized immunotherapy plans for HNSCC patients, significantly contributing to the optimization of clinical treatment outcomes.
End of Weight Stigma: A Proposal for a Multilevel Classification of its Components for Intervention Purposes
Authors: de Souza Gabriela Cristina Arces , Laus Maria Fernanda , Penaforte Fernanda Rodrigues de Oliveira , Santos Lucas Brandão dos , Japur Camila Cremonezi 
Published: July 2024

Abstract

Background Weight stigma is a complex construct formed by various components. This study aimed to compile these components and classify them into the multilevel intervention levels of stigma (structural, interpersonal, and intrapersonal).Methods A non-systematic literature review was conducted to identify the most commonly used definitions of weight stigma components. Subsequently, a proposal was made to classify these components into different intervention levels as proposed (Structural, Interpersonal, Intrapersonal). The components were categorized based on their definitions and specificities at each level. A panel of experts evaluated the proposal, and the degree of agreement was assessed using Fleiss' Kappa coefficient (₭). Values of ₭ between 0.40 and 0.60 indicated moderate agreement; between 0.61 and 0.75, good agreement; and above 0.75, excellent agreement.Results Ten terms were identified and classified in the different levels of stigma, except “Weight stigma” and “Weight bias”. At the structural level were included "fatphobia" and "weight-based stereotypes"; at the interpersonal level, "weight discrimination" and "explicit weight bias"; and at the intrapersonal level, "implicit weight bias", "lipophobia," "fat stigma", and "internalized weight bias". Agreement among the experts' responses for the structural and interpersonal levels was 100% (₭ = 1.0). For the components allocated at the intrapersonal level, there were some disagreements in the classification of the “Fat stigma” component (₭ = 0.4), and “Lipophobia” and “Implicit weight bias” were considered inappropriate by one specialist (₭ = 0.6).Conclusion The proposed classification of weight stigma components across multi-level interventions is novel and deemed appropriate by the experts. In future studies, this classification can help assess associations between weight stigma components across inter- and intra-levels and guide interventions across different levels for more effective outcomes in combating weight stigma.
Genome sequence and comparative analysis of Mycobacterium tuberculosis resourced from Pakistan and global lineage strains insights into the virulence and drug resistance
Authors: Arif Saba , Shafiq Aatiqa , Javed Rafia , Hasan Ahmed , Hussain Annam , Alonazi Wadi B , Ibrahim Muhammad , Shen Jian 
Published: July 2024

Abstract

The current study unveiled the drug susceptibility profiling of randomly selected 102 out of 1,323 archives samples of Mycobacterium tuberculosis collected between 2020 to 2022 from the south Punjab province of Pakistan followed by genome sequence, In silico comparative analysis of genome, virulence, and drug resistance genes and analysis of molecular basis of niche adaptation. Out of 102 isolates, 15 (~ 12%) were culture-negative, 71 (69%) were culture-positive, and 16 (~ 15%) were contaminated. The 65 isolates were resistant to at least one drug, while the remaining six were sensitive to all drugs. The genome of M. tuberculosis strain MNPK1 has a size of 4.33 Mbp with greater than 95% similarity to strain H37RV, MNPK, and SWLPK. It encodes 4,321 coding genes including virulent, drug-resistant, PPE/PE, and HSPs associated genes. Molecular structure analysis of GroEL, grpE, and dnaK indicates the most conserved nature except minor differences in loop regions compared to H37Rv confirming evolutionary conservation of HSPs in M. tuberculosis strain MNPK1 and its lineages with reference strain H37Rv. Moreover, differential gene expression of HSPs-associated genes has revealed a significantly higher expression level under host-simulated conditions and sputum compared to growth conditions in 7H9 media revealing the role of HSPs in virulence and niche adaption. Overall, the study unveiled M. tuberculosis strain MNPK1 encodes virulent and MDR features, especially in relation to the Beijing genotype strain H37Rv, SWLPK, and strain MNPK and vital addition in ongoing research focused on therapy and diagnosis of M. tuberculosis not only locally but globally.
Lipoprotein Apheresis: An Established Therapeutic Modality for Homozygous Familial Hypercholesterolemia Patients Refractory to PCSK9 Inhibitors: A Case Report and Literature Review
Authors: guan mingjing , wang hao , wang fang , Liang Shichu , Ling Li , Wang Bo , Zhang Ling 
Published: July 2024

Abstract

Homozygous familial hypercholesterolemia (HoFH), is a rare genetic disorder characterized by dual mutations in the low-density lipoprotein receptor (LDLR) gene, leading to dysfunctional or absent LDLRs, often accompanied by severe premature Atherosclerotic Cardiovascular Disease (ASCVD) and exhibiting refractoriness to aggressive pharmacological interventions. Double filtration plasmapheresis (DFPP), a form of lipoprotein apheresis (LA), has been effectively utilized as an adjunctive treatment modality to reduce serum LDL-C levels in refractory cases of HoFH. Here, we report a case of a 36-year-old female with HoFH who developed xanthomas on her limbs and waist at age 7. Despite maximum-tolerated doses of statins from age 32, combined with ezetimibe and evolocumab, her LDL-C levels remained critically elevated at 12-14 mmol/L. Her genetic testing confirmed a homozygous LDLR mutation. At 35 years old, she experienced exertional chest pain, and percutaneous coronary intervention revealed severe calcific left main stenosis, necessitating stent implantation. Subsequently, she initiated once every 1-2 months DFPP. Pre-DFPP, her LDL-C and total cholesterol (TC) levels were 13.82±3.28 and 15.45±0.78 mmol/L, respectively. Post-DFPP, her LDL-C and TC levels significantly decreased to 2.43±0.33 mmol/L (81.76±4.11% reduction) and 3.59±0.41 mmol/L (76.76±2.75% reduction), respectively. Lipoprotein (a) and triglycerides also decreased by 89.10±1.39% and 42.29±15.68%, respectively. Two years later, there was no progression of coronary artery disease, and her symptoms and xanthomas regressed significantly. Collectively, DFPP effectively reduces LDL-C levels in refractory cases of HoFH and contributes to delaying ASCVD progression, representing an efficacious adjunctive therapeutic modality.
Community health worker knowledge and perceptions of neonatal jaundice in Kumasi, Ghana
Authors: Wolski Ann , Moyer Cheryl A. , Amoah Rexford , Otoo Benjamin , Kaselitz Elizabeth , Bakari Ashura 
Published: July 2024

Abstract

Background: This study sought to understand community health workers’ (CHW) knowledge and perceptions of community beliefs surrounding neonatal jaundice (NNJ), a treatable but potentially fatal condition prevalent in sub-Saharan Africa.
Methods: In this cross-sectional qualitative study, CHWs in Kumasi, Ghana, completed in-depth interviews with trained research assistants using a semi-structured interview guide. Interviews were audiotaped, transcribed verbatim, and analyzed using grounded theory methodology.
Results: Knowledge of NNJ varied widely among the 23 respondents: 74% knew NNJ could cause death, 57% knew how to screen for NNJ. 35% of CHWs favored home treatment (sunlight therapy or watchful waiting). Three main themes emerged: CHWs perceived that caregivers prefer home treatment, equating hospital care with death; sunlight and herbs are the most common home treatments; and caregivers attribute NNJ to supernatural causes, delaying jaundice diagnosis.
Interpretation: Incomplete understanding of NNJ among trained CHWs and local communities will require improved education among both groups to improve outcomes.
Nature inspired Meta-heuristic optimization integrated with ensemble machine learning for PM2.5 modeling: a potential approach for sustainable eco-friendly health risk management
Authors: Usman Abdullahi G. , Mati Sagiru , Naganna Sujay Raghavendra , Usman Jamilu , Jibril Mahmud Muhammad , Bafaqeer Abdullah , Rahman Syed Masiur , Abba Sani I. 
Published: July 2024

Abstract

Particulate Matter 2.5 (PM 2.5) is a major air pollutant that can deeply penetrate the respiratory system and enter the bloodstream when inhaled. Therefore, it is significant to monitor and model PM 2.5, which is also considered as a key indicator of overall air quality. The current study employs the use of both Nature inspired Meta-heuristic optimization algorithms and Ensemble Machine learning (ML) techniques for the prediction of PM 2.5 using Sulfur dioxide (SO2), Nitrogen Dioxide (NO2), Respiratory suspended particulate matter (RSPM). Prior to dwelling into the modelling step, various pre-analysis techniques were conducted for data clean up and to understand the behaviour of the data. The quantitative performance results obtained from the Metaheuristic algorithms indicates that ANN-PSO outperformed all the other techniques including; SVR-BO, ENN-GA and LR. Furthermore, the quantitative outcomes indicate that ANN-PSO has the ability of improving the performance of the other techniques up to 80.4% and 73.2% in the calibration and validation phases respectively. More also, recent visualizations such as Fan plot and Bump chart were used in ranking the performance results obtained in PM 2.5 prediction. Moreover, Neural network ensemble (NNE) technique equally showed superior potentials over Simple average (SA) ensemble technique. To conclude, the quantitative and visualized performances of both the Metaheuristic algorithms and the ensemble paradigms indicates their importance in modelling and mitigation of PM 2.5 pollution, which requires concerted efforts at the local, and international levels to mitigate its effects and improve air quality on a global scale.
Advancing virulence factor prediction using protein language models
Authors: Liu Yitong , Cao Xin , Li Jiani , Li Tao , Li Juanjuan , Ma Xiang , Chi Xue , Tang Yanqiong , Liu Zhu , Li Hong 
Published: July 2024

Abstract

Background
Bacterial infections have emerged as the second leading cause of death globally, with their virulence factors (VFs) playing a critical role. Accurate prediction of VFs serves not only to elucidate the mechanisms of bacterial pathogenicity, but also offers new avenues for treating bacterial diseases. Machine learning (ML) stands out as a powerful tool for swiftly and precisely identifying VFs. However, a persistent challenge with existing ML methods is the use of outdated embedding techniques and a lack of differentiation between VFs of Gram-positive and Gram-negative bacteria.
Results
In this study, we introduced pLM4VF, a predictive framework that utilized ESM protein language models to extract VF characteristics of G+ and G- bacteriaseparately, and further integrated the models using the stacking strategy. The top-performing ensemble models, constructed using ESM pLMs, for both types of bacteria collectively constituted pLM4VF. Extensive benchmarking experiments on the independent test demonstrated that pLM4VF outperformed state-of-the-art methods. Biological validations through cytotoxicity and acute toxicity assays further corroborated the reliability of pLM4VF. An online tool (http://139.9.105.117:8081/) has been developed that enables inexperienced researchers on ML to obtain VFs of various bacteria at the whole-genome scale.
Conclusion
We believe that pLM4VF will offer substantial support in uncovering pathogenic mechanisms, developing novel antibacterial treatments and vaccines, thereby aiding in the prevention and management of bacterial diseases.
Clinical characteristics and nomogram model for predicting the risk of recurrence of complicated urinary tract infection in pediatric patients
Authors: Jiang Jing , Chen Xiu-Ying , Guo Hui 
Published: July 2024

Abstract

Complicated urinary tract infection (cUTI) has higher incidences of antibiotic resistance, recurrence, chronicity, and progression. However, there has been no prediction model for cUTI recurrence in pediatric patients for targeted interventions. This study aimed to establish a nomogram to p`redict the risk of cUTI recurrence for better prevention and treatment of cUTI in pediatric patients. The nomogram was developed based on a retrospective cohort that included 421 pediatric patients with cUTI at West China Second University Hospital from January 2020 to August 2023. The patients were randomly divided into a training set and a validation set in a 3:1 ratio. Logistic regression analysis was used to identify risk factors and construct the nomogram for predicting the risk of cUTI recurrence, followed by validation and performance analysis. Of the 421 children with cUTI, the recurrence rate of cUTI was 68.4% (288 cases) during an average follow-up duration of 22.9 months. The nomogram comprised female gender, history of urinary tract surgery, Escherichia coli in urine culture, renal dysfunction, and vesicoureteral reflux as predictors of cUTI recurrence in pediatric patients. The model showed favorable performance with a C-index of 0.735 in the training dataset and a C-index of 0.750 in the validation dataset. The clinical decision curves revealed that the nomogram was clinically useful. The first reliable nomogram was constructed for predicting the risk of cUTI recurrence in pediatric patients, which would be beneficial for clinicians to identify children with high risks of cUTI recurrence for targeted interventions.
Sense of Coherence Promotes Acceptance of Others Among University Students Studying Abroad: A Retrospective Cohort Study
Authors: Takeuchi Jiro , Sakagami Rei , Sakagami Yu 
Published: July 2024

Abstract

Background
Sense of Coherence (SOC) is a concept used to overcome difficult situations. This study aims to investigate whether SOC promotes acceptance of the self and others among university students by studying abroad, addressing the gap in understanding the psychological impacts of studying abroad.
Methods
This single-center, retrospective cohort study included university students who studied abroad between 2017 and 2019. Data on gender, age, destination, study abroad experience, the 13-item seven-point SOC Japanese version (SOC-13), Berger's scales, and the 60-item version of the General Health Questionnaire Japanese version (GHQ-60) were collected via self-administered questionnaires. A linear regression model estimated the β coefficient and 95% confidence interval (CI). We submitted Berger's Acceptance-of-Others after studying abroad as a dependent variable, SOC-13 before studying abroad as an independent variable, and age, gender, experience of studying abroad, destination, Berger's Acceptance-of-Others before studying abroad, Berger’s Self-acceptance score before studying abroad, and GHQ-60 before studying abroad as independent variables to adjust for confounders in the analysis model.
Results
Of 1039 students, 330 (31.8%) submitted pre-departure questionnaires; 168 (50.9%) were male, median age was 21.3 years, and 260 (80.0%) were undergraduates. Of the 156 (15.0%) who completed both pre- and post-study abroad questionnaires, the mean Berger's Acceptance-of-Others score significantly decreased by 5.2 points (p = 0.02), and the SOC-13 score decreased by 0.8 points (p < 0.001). Cronbach's alpha remained above 0.80 for all scales. Between the complete questionnaire group and an incomplete group, the complete questionnaire group had a higher SOC-13 score (P = 0.01) but did not have a higher Berger’s Acceptance-of-Others Scale score (P = 0.997). An increasing SOC-13 score was associated with an increasing Berger's scale Acceptance-of-Others score after studying abroad (β coef. 0.34; 95%CI, 0.04–0.65, P = 0.03). No significant interactions were found between the variables.
Conclusions
SOC promotes acceptance among university students studying abroad.
Clinical Usefulness of Patient-Reported-Outcome-Measurement Information System in Pediatric Crohn’s Disease: A Cross-Sectional Study
Authors: Azevedo Sara , Oliveira Maria Miguel , Nogueira Paulo , Lopes Ana Isabel 
Published: July 2024

Abstract

Objectives: This study evaluates the clinical utility of the Patient-Reported Outcomes Measurement Information System (PROMIS®) by comparing it with objective clinical data and validated health-related quality of life (HRQOL) measures in pediatric Crohn’s disease (CD) patients.
Study Design: Cross-sectional study. Pediatric CD patients (aged 8-17 years) were enrolled prospectively over eight months from an outpatient pediatric gastroenterology center. We assessed the associations between PROMIS® Pediatric short-form measures, demographic and disease-related data, global clinical assessments, and HRQOL measures. A sub-analysis according to PCDAI score (remission versus active disease) was also conducted.
Results: 31 patients included (mean age: 15.3; 58% female) with a mean disease duration of 2.7 years; 80.6% were in remission or with mild disease. PROMIS® scores showed significant correlations with several factors: age negatively correlated with PROMIS® Global Health (r=-0.399; p=0.026) and Life Satisfaction (r=-0.359; p=0.047); gender was associated with PROMIS® Cognitive Function (t=2.20; p=0.038), favoring males; and school level inversely influenced PROMIS® Peer Relationships (F=3.90; p=0.003). Clinical assessments also revealed significant correlations: hemoglobin with PROMIS® Global Health (r=0.356; p=0.049) and Pain Interference (r=-0.360; p=0.046); ferritin with PROMIS® Meaning and Purpose (r=0.435; p=0.016) and Cognitive Function (r=0.450; p=0.011). Disease activity assessments correlated significantly with multiple PROMIS® measures, with better scores in remission patients. Treatment changes, particularly corticosteroids, negatively impacted PROMIS® Anxiety and Life Satisfaction scores. IMPACT-III scores correlated positively with PROMIS® Global Health, Meaning and Purpose, Life Satisfaction, peer relationships and negatively with Depression, Anxiety, Pain interference, and Fatigue. Group analysis indicated better PROMIS® scores and HRQOL scores in remission, as compared to active disease.
Conclusion: Consistent with recent evidence, PROMIS® scores reliably reflect disease activity and HRQOL. The meaningful associations with clinical assessment and treatment efficacy, reinforce the clinical relevance and utility of PROs in the patient-centered management of pediatric IBD and highlight the importance of self-reporting as a gold standard tool for assessing health status.
Changes in hedonic hunger and problematic eating behaviors in adults undergoing Roux-en-Y gastric bypass
Authors: YILMAZ Can Selim , INCE Zeynep Ayca , AYDEMIR Ayse Yagmur , CALISKAN Hilal 
Published: July 2024

Abstract

Background
Following RYGB, patients experience changes in hedonic hunger (the drive to eat food for pleasure in the absence of physiological hunger) and eating behaviors. The aim of this study was to determine changes in hedonic hunger and problematic eating behaviors (PEBs) in adults undergoing Roux-en-Y gastric bypass (RYGB).
Methods
This study was conducted between January 2024 and April 2024 with 70 adults undergoing RYGB who met the conditions for participation in the study. Hedonic hunger was assessed with the Power of Food Scale (PFS) and PEBs with the Eating Disorders Examination Questionnaire (EDE-Q), a week before and 12 week after surgery by the researcher through face-to-face. The PFS consists of 3 subscales [food available (FA), food present (FP) and food tasted (FT)] and the EDE-Q consists of 4 subscales [restraint (R), eating concern (EC), shape concern (SC) and weight concern (WC)]. Increasing scores for both PFS and EDE-Q represent increased hedonic hunger and severity of PEBs, respectively. SPSS 25.0 package program was applied to evaluate the data.
Results
A total of 70 participants completed the study (70% females; BMI: 37.4 ± 4.5 kg/m2; age: 32.4 ± 7.9 years). Average weight loss was 18.6 ± 5.3 kg (17.6%). Significantly reductions were observed in total (change in mean score ± SD = 1.16 ± 0.30; p < 0.001) and all subscales score of PFS [− 1,16 ± 0.45; p < 0.001 (FA subscale), − 1.36 ± 0.33; p < 0.001 (FP subscale) and − 0.81 ± 0.15; p < 0.01 (FT subscale)] at 12 weeks after surgery compared to baseline. Similarly significantly reductions were observed in EDE-Q scores in total (− 1.05 ± 0.37; p < 0.05) and subscales [− 1.22 ± 0.51; p < 0.05 (EC subscale),−1.97 ± 0.27; p < 0.001 (SC subscale) and − 1.34 ± 0.18; p < 0.001 (WC subscale)] except for the 'R' subscale (+ 0.31 ± 0.51; p < 0.001). Weight loss were non-significantly positively related to reduction in EDE-Q total and all subscale scores.
Conclusions
Hedonic hunger and severity of problematic eating behaviors reduced in the early postoperative period (12 week) of RYGB compare to pre-op. Although the relationship was not significantly, weight loss increased as problematic eating behaviors decreased.