bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two extraction-free reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2
Authors: Lai Meng Yee , Bukhari Fatma Diyana Mohd , Zulkefli Nur Zulaikha , Ismail Ilyiana , Mustapa Nur Izati , Soh Tuan Suhaila Tuan , Hassan Afifah Haji , Peariasamy Kalaiarasu M. , Lee Yee Leng , Suppiah Jeyanthi , Thayan Ravindran , Lau Yee Ling 
Published: November 2021

Abstract
Background
Current assays for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on time consuming, costly and laboratory based methods for virus isolation, purification and removing inhibitors. To address this limitation, we propose a simple method for testing RNA from nasopharyngeal swab samples that bypasses the RNA purification step.

Methods
In the current project, we have described two extraction-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of SARS-CoV-2 by using E gene and RdRp gene as the targets.

Results
Here, results showed that reverse transcription loop-mediated isothermal amplification assays with 88.4% sensitive (95% CI: 74.9–96.1%) and 67.4% sensitive (95% CI: 51.5–80.9%) for E gene and RdRp gene, respectively.

Conclusion
Without the need of RNA purification, our developed RT-LAMP assays for direct detection of SARS-CoV-2 from nasopharyngeal swab samples could be turned into alternatives to qRT-PCR for rapid screening.
Comprehensive analysis of lymph nodes metastasis associated genes in cervical cancer and its significance in treatment and prognosis
Authors: Yang Ping , Ruan Youqin , Yan Zhiling , Gao Yang , Yang Hongying , Wang Shaojia 
Published: November 2021

Abstract
Background
Cervical carcinoma is one of the most common malignant tumors of the female reproductive system. Lymph nodes metastasis, the most common metastasis, which can be detected even in small-size tumor patients, results in worse prognosis. Therefore, it is of great significance to explore novel lymph nodes metastasis associated biomarkers, which can predict the prognosis and provide a good reference for clinical decision making in cervical carcinoma patients. However, systematic and comprehensive studies related to the key molecules in lymph node metastasis in cervical carcinoma patients are still absent.

Methods
Transcriptome and clinical data of 307 cervical carcinoma patients were obtained from The Cancer Genome Atlas (TCGA). Then, survival of patients with and without lymph node metastasis was analyzed by Kaplan-Meier (K-M) curves. Differential expressed genes (DEGs) were detected between tumor and control samples using limma package and defined as lymph node metastasis related genes. Univariate and multivariate Cox regression analyses were carried out to screen robust prognostic gene signature. The risk score model and nomogram for predicting survival were constructed based on prognostic gene signature. The performance of the risk score model was evaluated by operating characteristic (ROC) curves. Based on risk score, patients were divided into low- and high- risk groups. DEGs, functional enrichment analysis and tumor microenvironment (immune infiltration and expressions of immune checkpoints) were detected in low- and high-risk groups.

Results
A total of 103 lymph node metastasis-associated genes were identified. Univariate and multivariate Cox regression analyses identified TEKT2, LPIN2, FABP4 and CXCL2 as prognostic gene signature. The risk score model was constructed and validated in cervical carcinoma patients. 345 DEGs identified between high- and low-risk groups were significantly enriched into immune-related biological processes. Furthermore, we found that the immune infiltration and expressions of immune checkpoints were significantly different between low- and high-risk groups.

Conclusion
Our study revealed that lymph node metastasis played an important role in the prognosis of cervical carcinoma patients. Furthermore, we established a risk score model based on lymph node metastasis related genes, which could accurately predict the survival of cervical carcinoma patients. Besides, our findings in tumor microenvironments of low- and high-risk groups improved our understanding of the relationship between lymph node metastasis related genes and cervical carcinoma.
The landscape of coding RNA editing events in pediatric cancer
Authors: Wen Ji , Rusch Michael , Brady Samuel W. , Shao Ying , Edmonson Michael N. , Shaw Timothy I. , Powers Brent B. , Tian Liqing , Easton John , Mullighan Charles G. , Gruber Tanja , Ellison David , Zhang Jinghui 
Published: November 2021

Abstract
Background
RNA editing leads to post-transcriptional variation in protein sequences and has important biological implications. We sought to elucidate the landscape of RNA editing events across pediatric cancers.

Methods
Using RNA-Seq data mapped by a pipeline designed to minimize mapping ambiguity, we investigated RNA editing in 711 pediatric cancers from the St. Jude/Washington University Pediatric Cancer Genome Project focusing on coding variants which can potentially increase protein sequence diversity. We combined de novo detection using paired tumor DNA-RNA data with analysis of known RNA editing sites.

Results
We identified 722 unique RNA editing sites in coding regions across pediatric cancers, 70% of which were nonsynonymous recoding variants. Nearly all editing sites represented the canonical A-to-I (n = 706) or C-to-U sites (n = 14). RNA editing was enriched in brain tumors compared to other cancers, including editing of glutamate receptors and ion channels involved in neurotransmitter signaling. RNA editing profiles of each pediatric cancer subtype resembled those of the corresponding normal tissue profiled by the Genotype-Tissue Expression (GTEx) project.

Conclusions
In this first comprehensive analysis of RNA editing events in pediatric cancer, we found that the RNA editing profile of each cancer subtype is similar to its normal tissue of origin. Tumor-specific RNA editing events were not identified indicating that successful immunotherapeutic targeting of RNA-edited peptides in pediatric cancer should rely on increased antigen presentation on tumor cells compared to normal but not on tumor-specific RNA editing per se.
A novel PDX modeling strategy and its application in metabolomics study for malignant pleural mesothelioma
Authors: Chen Zhongjian , Yang Chenxi , Guo Zhenying , Song Siyu , Gao Yun , Wang Ding , Mao Weimin , Liu Junping 
Published: November 2021

Abstract
Background
Malignant pleural mesothelioma (MPM) is a rare and aggressive carcinoma located in pleural cavity. Due to lack of effective diagnostic biomarkers and therapeutic targets in MPM, the prognosis is extremely poor. Because of difficulties in sample extraction, and the high rate of misdiagnosis, MPM is rarely studied. Therefore, novel modeling methodology is crucially needed to facilitate MPM research.

Methods
A novel patient-derived xenograft (PDX) modeling strategy was designed, which included preliminary screening of patients with pleural thickening using computerized tomography (CT) scan, further reviewing history of disease and imaging by a senior sonographer as well as histopathological analysis by a senior pathologist, and PDX model construction using ultrasound-guided pleural biopsy from MPM patients. Gas chromatography-mass spectrometry-based metabolomics was further utilized for investigating circulating metabolic features of the PDX models. Univariate and multivariate analysis, and pathway analysis were performed to explore the differential metabolites, enriched metabolism pathways and potential metabolic targets.

Results
After screening using our strategy, 5 out of 116 patients were confirmed to be MPM, and their specimens were used for modeling. Two PDX models were established successfully. Metabolomics analysis revealed significant metabolic shifts in PDX models, such as dysregulations in amino acid metabolism, TCA cycle and glycolysis, and nucleotide metabolism.

Conclusions
To sum up, we suggested a novel modeling strategy that may facilitate specimen availability for MM research, and by applying metabolomics in this model, several metabolic features were identified, whereas future studies with large sample size are needed.
Why parents agree or disagree for minimally invasive tissue sampling (MITS) to identify causes of death in under-five children and stillbirth in North India: a qualitative study
Authors: Das Manoja Kumar , Arora Narendra Kumar , Debata Pradeep , Chellani Harish , Rasaily Reeta , Gaikwad Harsha , Meena K. R. , Kaur Gurkirat , Malik Prikanksha , Joshi Shipra , Kumari Mahisha 
Published: November 2021

Abstract
Background
Information on exact causes of death and stillbirth are limited in low and middle income countries. Minimally invasive tissue sampling (MITS) is increasingly practiced in place of autopsy across several settings. A formative research documented the experiences of counselling and consenting for MITS in north India.

Methods
This exploratory qualitative study was conducted at a tertiary care hospital in Delhi. During the early implementation of MITS, observations of the counselling and consenting process (n = 13) for under-five child death and stillbirths were conducted. In-depth interviews with MITS team members (n = 3) were also conducted. Observation and interview data were transcribed and inductively analysed using thematic content analysis to identify emerging themes and codes.

Results
The MITS team participated in daily ward rounds for familiarisation with parents/families. Following death declaration the counselling was done in counselling corner of the ward or adjacent corridor. Mostly the counselling was targeted at the father and family members present, using verbal explanation and the consent document in local language. The key concerns raised by parents/family were possible disfigurement, time needed and possible benefits. Most of the parents consulted family members before consent. Among those who consented, desire for next pregnancy, previous pregnancy or neonatal loss and participation of treating senior doctor were the key factors. The negative experience of hospital care, poor comprehension and distance from residence were the factors for consent refusal. Lesser number of parents of deceased children consented for MITS compared to the neonates and stillbirths.

Conclusions
The initial experiences of obtaining consent for MITS were encouraging. Consent for MITS may be improved with active involvement of the treating doctors and nurses, better bereavement support, private counselling area along with improvement in quality of care and communication during hospitalisation. Special efforts and refinement in counselling are needed to improve consent for MITS in older children.
Association of intimate partner violence and other risk factors with HIV infection among married women in India: evidence from National Family Health Survey 2015–16
Authors: Shri Neha , Muhammad T. 
Published: November 2021

Abstract
Background
Human immunodeficiency virus (HIV) infection remains an important public health concern in many countries. It is fuelled by gender inequality and disparity, which has resulted in a fundamental violation of women’s human rights. This study aims to find out the association of intimate partner violence (IPV) and other risk factors with the prevalence of HIV infection among married women in India.

Methods
This study is based on data from the India National Family Health Survey (2015–16). Bivariate analysis has been performed to estimate the prevalence of HIV. Logistic regression analysis is conducted to find out the association between IPV, factors such as having alcoholic husband and lifetime partner, and HIV infection among currently married women.

Results
Married women who had faced physical, sexual, and emotional violence from their husbands/partners were almost twice more likely to have tested HIV positive compared to married women who did not face violence [OR: 2.14, CI: 1.08–4.50]. The odds of testing for HIV positive was significantly higher among the married women experiencing IPV and having alcoholic husband [OR: 4.48, CI: 1.87–10.70] than those who did not experience IPV and had non-alcoholic husband. The use of condom did not show any significant association with HIV infection. Again, having more than one lifetime partner had a positive association with HIV infection compared to those with one partner [OR: 2.45, CI: 1.21–4.16].

Conclusions
The study revealed that factors such as experiencing all types of IPV, having an alcoholic husband, increased number of lifetime partners, being sexually inactive, belonging to vulnerable social groups, and urban place of residence are important risk factors of HIV infection among married women in India. The results also suggest that gender-based violence and an alcoholic husband may represent a significant factor of HIV infection among married women and interventions should on focus such vulnerable populations.
Educational differences in diabetes and diabetes self-management behaviours in WHO SAGE countries
Authors: Lamb Karen E. , Crawford David , Thornton Lukar E. , Shariful Islam Sheikh M. , Maddison Ralph , Ball Kylie 
Published: November 2021

Abstract
Background
Diabetes mellitus represents a substantial global health challenge, with prevalence rising in low- and middle-income countries (LMICs). Although diabetes is known to follow a socioeconomic gradient, patterns in LMICs are unclear. This study examined associations between education and diabetes, and diabetes self-management behaviours, in six LMICs.

Methods
Cross-sectional data for 31,780 participants from China, Ghana, India, Mexico, Russia, and South Africa from the World Health Organization Study on Global AGEing and adult health (SAGE) study were used. Participants aged ≥50 years completed face-to-face interviews between 2007 and 2010. Participants self-reported diabetes diagnosis, physical activity, sedentary time, fruit and vegetable consumption, any special diet/program for diabetes, whether they were taking insulin for diabetes and number of years of education. Height, weight, waist, and hip circumference were measured. Country-specific survey-weighted log-binomial regression models were fitted to examine associations between the number of years of education and self-reported diabetes diagnosis (primary analysis). In secondary analyses, among those with a self-reported diabetes diagnosis, generalised linear regression models were fitted to examine associations between education and i) physical activity, ii) sedentary time, iii) fruit and vegetable consumption, iv) special diet for diabetes, v) taking insulin, vi) BMI, vii) waist circumference and viii) hip circumference.

Results
There was strong evidence of an association between years of education and diabetes diagnosis in Ghana (RR = 1.09, 95% CI: 1.06–1.13) and India (RR = 1.09, 95% CI: 1.07–1.12) only. In India, greater years of education was associated with higher leisure physical activity, fruit and vegetable intake, rates following a special diet or taking insulin, but also higher mean BMI, waist and hip circumference. Relationships between education and self-management behaviours were rarely seen in the other countries.

Conclusions
Associations between education and diabetes, and behavioural self-management (India only) was more evident in the two least developed (Ghana and India) of the WHO SAGE countries, indicating increasing diabetes diagnosis with greater numbers of years of education. The lack of gradients elsewhere may reflect shifting risk from higher to lower educated populations. While there was some suggestion that self-management behaviours were greater with increased education in India, this was not observed in the other countries.
The impact of behavioural risk factors on communicable diseases: a systematic review of reviews
Authors: Wood Sara , Harrison Sophie E. , Judd Natasha , Bellis Mark A. , Hughes Karen , Jones Andrew 
Published: November 2021

Abstract
Background
The coronavirus (COVID-19) pandemic has highlighted that individuals with behavioural risk factors commonly associated with non-communicable diseases (NCDs), such as smoking, harmful alcohol use, obesity, and physical inactivity, are more likely to experience severe symptoms from COVID-19. These risk factors have been shown to increase the risk of NCDs, but less is known about their broader influence on communicable diseases. Taking a wide focus on a range of common communicable diseases, this review aimed to synthesise research examining the impact of behavioural risk factors commonly associated with NCDs on risks of contracting, or having more severe outcomes from, communicable diseases.

Methods
Literature searches identified systematic reviews and meta-analyses that examined the association between behavioural risk factors (alcohol, smoking, illicit drug use, physical inactivity, obesity and poor diet) and the contraction/severity of common communicable diseases, including infection or associated pathogens. An a priori, prospectively registered protocol was followed (PROSPERO; registration number CRD42020223890).

Results
Fifty-three systematic reviews were included, of which 36 were also meta-analyses. Reviews focused on: tuberculosis, human immunodeficiency virus, hepatitis C virus, hepatitis B virus, invasive bacterial diseases, pneumonia, influenza, and COVID-19. Twenty-one reviews examined the association between behavioural risk factors and communicable disease contraction and 35 examined their association with communicable disease outcomes (three examined their association with both contraction and outcomes). Fifty out of 53 reviews (94%) concluded that at least one of the behavioural risk factors studied increased the risk of contracting or experiencing worse health outcomes from a communicable disease. Across all reviews, effect sizes, where calculated, ranged from 0.83 to 8.22.

Conclusions
Behavioural risk factors play a significant role in the risk of contracting and experiencing more severe outcomes from communicable diseases. Prevention of communicable diseases is likely to be most successful if it involves the prevention of behavioural risk factors commonly associated with NCDs. These findings are important for understanding risks associated with communicable disease, and timely, given the COVID-19 pandemic and the need for improvements in future pandemic preparedness. Addressing behavioural risk factors should be an important part of work to build resilience against any emerging and future epidemics and pandemics.
PAX7 gene polymorphism in muscular temporomandibular disorders as potentially related to muscle stem cells
Authors: Quinelato Valquiria , Bonato Letícia Ladeira , Vieira Alexandre Rezende , Granjeiro José Mauro , Menezes Karla , Borojevic Radovan , Casado Priscila Ladeira , Calasans-Maia Jose Albuquerque , Tesch Ricardo 
Published: November 2021

Abstract
Background
Temporomandibular disorders (TMD) are a group of painful and debilitating disorders, involving the masticatory muscles and/or the temporomandibular joint (TMJ). Chronic TMD pain can be associated with genetic changes in the key muscle development genes.

Objective
To evaluate the association between polymorphisms in the PAX7 (paired box 7) gene and masticatory myalgia in patients with temporomandibular disorders (TMD).

Materials and methods
This is a case-control study. Patients with TMD were divided into two groups: (a) presence of muscular TMD (n = 122) and (b) absence of muscular TMD (n = 49). Genomic DNA was obtained from saliva samples from all participants to allow for genotyping single nucleotide polymorphisms in PAX7 (rs766325 and rs6659735). Over-representation of alleles was tested using chi-square or Fisher’s exact tests. Values of p < 0.05 were considered to be statistically significant.

Results
Individuals without muscular TMD were less likely to have the PAX7 rs6659735 GG genotype (p = 0.03). No associations were found for PAX7 rs766325.

Conclusions
Alterations in PAX7 may influence muscular pathophysiology and individuals with TMD and the rs6659735 homozygous genotype (GG) are seemingly associated with muscular involvement of the disorder. No associations were found in the region rs766325.
Drug knowledge discovery via multi-task learning and pre-trained models
Authors: Li Dongfang , Xiong Ying , Hu Baotian , Tang Buzhou , Peng Weihua , Chen Qingcai 
Published: November 2021

AbstractBackgroundDrug repurposing is to find new indications of approved drugs, which is essential for investigating new uses for approved or investigational drug efficiency. The active gene annotation corpus (named AGAC) is annotated by human experts, which was developed to support knowledge discovery for drug repurposing. The AGAC track of the BioNLP Open Shared Tasks using this corpus is organized by EMNLP-BioNLP 2019, where the “Selective annotation” attribution makes AGAC track more challenging than other traditional sequence labeling tasks. In this work, we show our methods for trigger word detection (Task 1) and its thematic role identification (Task 2) in the AGAC track. As a step forward to drug repurposing research, our work can also be applied to large-scale automatic extraction of medical text knowledge.MethodsTo meet the challenges of the two tasks, we consider Task 1 as the medical name entity recognition (NER), which cultivates molecular phenomena related to gene mutation. And we regard Task 2 as a relation extraction task, which captures the thematic roles between entities. In this work, we exploit pre-trained biomedical language representation models (e.g., BioBERT) in the information extraction pipeline for mutation-disease knowledge collection from PubMed. Moreover, we design the fine-tuning framework by using a multi-task learning technique and extra features. We further investigate different approaches to consolidate and transfer the knowledge from varying sources and illustrate the performance of our model on the AGAC corpus. Our approach is based on fine-tuned BERT, BioBERT, NCBI BERT, and ClinicalBERT using multi-task learning. Further experiments show the effectiveness of knowledge transformation and the ensemble integration of models of two tasks. We conduct a performance comparison of various algorithms. We also do an ablation study on the development set of Task 1 to examine the effectiveness of each component of our method.ResultsCompared with competitor methods, our model obtained the highest Precision (0.63), Recall (0.56), and F-score value (0.60) in Task 1, which ranks first place. It outperformed the baseline method provided by the organizers by 0.10 in F-score. The model shared the same encoding layers for the named entity recognition and relation extraction parts. And we obtained a second high F-score (0.25) in Task 2 with a simple but effective framework.ConclusionsExperimental results on the benchmark annotation of genes with active mutation-centric function changes corpus show that integrating pre-trained biomedical language representation models (i.e., BERT, NCBI BERT, ClinicalBERT, BioBERT) into a pipe of information extraction methods with multi-task learning can improve the ability to collect mutation-disease knowledge from PubMed.