bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of different types of migration on symptoms of anxiety or depression and experience of violence among people who use or inject drugs in Kachin State, Myanmar
Authors: Kyaw Khine Wut Yee , Platt Lucy , Bijl Murdo , Rathod Sujit D. , Naing Aung Yu , Roberts Bayard 
Published: April 2023

Abstract
Background
Evidence on the social determinants of mental health conditions and violence among people who inject or use drugs (PWUD) is limited, particularly in conflict-affected countries. We estimated the prevalence of symptoms of anxiety or depression and experience of emotional or physical violence among PWUD in Kachin State in Myanmar and examined their association with structural determinants, focusing on types of past migration (migration for any reason, economic or forced displacement).

Materials
A cross-sectional survey was conducted among PWUD attending a harm reduction centre between July and November 2021 in Kachin State, Myanmar. We used logistic regression models to measure associations between past migration, economic migration and forced displacement on two outcomes (1) symptoms of anxiety or depression (Patient Health Questionnaire-4) and (2) physical or emotional violence (last 12 months), adjusted for key confounders.

Results
A total of 406, predominantly male (96.8%), PWUD were recruited. The median age (IQR) was 30 (25, 37) years, most injected drugs (81.5%) and more commonly opioid substances such as heroin or opium (85%). Symptoms of anxiety or depression (PHQ4 ≥ 6) were high (32.8%) as was physical or emotional violence in the last 12 months (61.8%). Almost one-third (28.3%) had not lived in Waingmaw for their whole life (migration for any reason), 77.9% had left home for work at some point (economic migration) and 19.5% had been forced to leave home due to war or armed conflict (forced displacement). A third were in unstable housing in the last 3 months (30.1%) and reported going hungry in the last 12 months (27.7%). Only forced displacement was associated with symptoms of anxiety or depression [adjusted odds ratio, aOR 2.33 (95% confidence interval, CI 1.32–4.11)] and recent experience of violence [aOR 2.18 (95% CI 1.15–4.15)].

Conclusion
Findings highlight the importance of mental health services integrated into existing harm reduction services to address high levels of anxiety or depression among PWUD, particularly among those who have been displaced through armed conflict or war. Findings reinforce the need to address broader social determinants, in the form of food poverty, unstable housing and stigma, in order to reduce mental health and violence.
Natural killer cytotoxicity in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): a multi-site clinical assessment of ME/CFS (MCAM) sub-study
Authors: Querec Troy D. , Lin Jin-Mann S. , Chen Yang , Helton Britany , Kogelnik Andreas M. , Klimas Nancy G. , Peterson Daniel L. , Bateman Lucinda , Lapp Charles , Podell Richard N. , Natelson Benjamin H. , Unger Elizabeth R. ,   the MCAM Study Group, Unger Elizabeth , Lin Jin-Mann Sally , Cornelius Monica , Dimulescu Irina , Fall Elizabeth , Khin Maung , Rajeevan Mangalathu , Bland Jennifer , Jeys Patricia , Parkinson Veronica , Springs Wendy , Klimas Nancy , Balbin Elizabeth , Cournoyer Jeffry , Fernandez Melissa , Parnell Shuntae , Leaks-Gutierrez Precious , Natelson Benjamin , Blate Michelle , Lange Gudrun , Khan Sarah , Vu Diana , Kogelnik Andreas , Danver Joan , Kaufman David , Pa Macy , Phan Catt , Taleghani Sophia , Podell Richard N , Fitzpatrick Trisha , Licata Beverly , Peterson Daniel , Lascu Elena , Gottschalk Gunnar , Maynard Marco , Smith Janet 
Published: April 2023

Abstract
Background
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multisystem illness characterized by substantial reduction in function accompanied by profound unexplained fatigue not significantly relieved by rest, post-exertional malaise, and other symptoms. Reduced natural killer (NK) cell count and cytotoxicity has been investigated as a biomarker for ME/CFS, but few clinical laboratories offer the test and multi-site verification studies have not been conducted.

Methods
We determined NK cell counts and cytotoxicity in 174 (65%) ME/CFS, 86 (32%) healthy control (HC) and 10 (3.7%) participants with other fatigue associated conditions (ill control [IC]) from the Multi-Site Clinical Assessment of ME/CFS (MCAM) study using an assay validated for samples shipped overnight instead of testing on day of venipuncture.

Results
We found a large variation in percent cytotoxicity [mean and (IQR) for ME/CFS and HC respectively, 34.1% (IQR 22.4–44.3%) and 33.6% (IQR 22.9–43.7%)] and no statistically significant differences between patients with ME/CFS and HC (p-value = 0.79). Analysis stratified on illness domain measured with standardized questionnaires did not identify an association of NK cytotoxicity with domain scores. Among all participants, NK cytotoxicity was not associated with survey results of physical and mental well-being, or health factors such as history of infection, obesity, smoking, and co-morbid conditions.

Conclusion
These results indicate this assay is not ready for clinical implementation and studies are needed to further explore immune parameters that may be involved in the pathophysiology of ME/CFS.
Phase separation in cancer at a glance
Authors: Xie Qingqing , Cheng Jiejuan , Mei Wuxuan , Yang Dexing , Zhang Pengfei , Zeng Changchun 
Published: April 2023

AbstractEukaryotic cells are segmented into multiple compartments or organelles within the cell that regulate distinct chemical and biological processes. Membrane-less organelles are membrane-less microscopic cellular compartments that contain protein and RNA molecules that perform a wide range of functions. Liquid–liquid phase separation (LLPS) can reveal how membrane-less organelles develop via dynamic biomolecule assembly. LLPS either segregates undesirable molecules from cells or aggregates desired ones in cells. Aberrant LLPS results in the production of abnormal biomolecular condensates (BMCs), which can cause cancer. Here, we explore the intricate mechanisms behind the formation of BMCs and its biophysical properties. Additionally, we discuss recent discoveries related to biological LLPS in tumorigenesis, including aberrant signaling and transduction, stress granule formation, evading growth arrest, and genomic instability. We also discuss the therapeutic implications of LLPS in cancer. Understanding the concept and mechanism of LLPS and its role in tumorigenesis is crucial for antitumor therapeutic strategies.
Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales
Authors: Beale Sarah , Hoskins Susan , Byrne Thomas , Fong Wing Lam Erica , Fragaszy Ellen , Geismar Cyril , Kovar Jana , Navaratnam Annalan M. D. , Nguyen Vincent , Patel Parth , Yavlinsky Alexei , Johnson Anne M. , Van Tongeren Martie , Aldridge Robert W. , Hayward Andrew ,   the Virus Watch Collaborative, Michie Susan , Hardelid Pia , Wijlaars Linda , Nastouli Eleni , Spyer Moira , Killingley Ben , Cox Ingemar , McKendry Rachel A , Cheng Tao , Liu Yunzhe , Gibbs Jo , Gilson Richard , Rodger Alison 
Published: April 2023

Abstract
Background
Workers across different occupations vary in their risk of SARS-CoV-2 infection, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase.

Methods
Data from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR).

Results
Increased risk was seen in nurses (aRR = 1.44, 1.25–1.65; AF = 30%, 20–39%), doctors (aRR = 1.33, 1.08–1.65; AF = 25%, 7–39%), carers (1.45, 1.19–1.76; AF = 31%, 16–43%), primary school teachers (aRR = 1.67, 1.42- 1.96; AF = 40%, 30–49%), secondary school teachers (aRR = 1.48, 1.26–1.72; AF = 32%, 21–42%), and teaching support occupations (aRR = 1.42, 1.23–1.64; AF = 29%, 18–39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020—May 2021) and attenuated later (June—October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves.

Conclusions
Occupational differences in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.
HER2 exon 20 insertion mutations and myelosuppression in lung adenocarcinoma patient: a case report and response to trastuzumab deruxtecan
Authors: Wang Bin , Song Yang , Yang Xin , Chen Chuan 
Published: April 2023

Abstract
Background
Human epidermal growth factor receptor 2 (HER2) mutations occur in 2% of lung cancers.

Case presentation
In this report, we presented a case of an Asian female who was diagnosed with lung adenocarcinoma. NGS results indicated HER2 exon 20 insertion mutation and PET/CT results showed multiple metastases in lower lobes of both lungs. Thereafter, she was treated with chemotherapy alone, combination of chemotherapy and targeted therapy and immunotherapy. Due to progressive disease, she was then received DS-8201. Imaging data indicated partial response to DS-8201 and tumor marker values decreased significantly, suggesting good efficacy. Nevertheless, DS-8201 was discontinued because of the development of myelosuppression (grade 3). Finally, she died at home due to platelet deficiency, white blood cell (grade 4), granulocytopenia, intracranial hemorrhage and gastrointestinal hemorrhage.

Conclusions
This was an important case since it exerted effective response to DS-8201. Meanwhile, myelosuppression is also found in the patient, which requires attention to pulmonary symptoms and careful monitoring.
Prognostic marker C3AR1 is associated with ovarian cancer cell proliferation and immunosuppression in the tumor microenvironment
Authors: Huang Jinfa , Zhou Lei , Deng Kaixian 
Published: April 2023

Abstract
Background
C3AR1 was reported in driving tumor immunity in multiple cancers. However, its roles in ovarian cancer remain unclear. This study aims to determine role of C3AR1 in prognosis and regulating tumor infiltrating immune cells of ovarian cancer (OC).

Materials and methods
The expression, prognosis and clinical data related to C3AR1 were collected from public databases such as The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA) and Clinical Proteomics Tumor Analysis Alliance (CPTAC), and further analyze their relationship with immune infiltration. Immunohistochemistry verified the expression of C3AR1 in ovarian cancer and control tissues. C3AR1 was forced expressed in SKOV3 cells by plasmid transfection, and verified by qRT-PCR and Western blot. Cell proliferation were evaluated by EdU assay.

Results
Bioinformatics analysis (TCGA, CPTAC) and immunohistochemical staining of clinical samples confirmed higher C3AR1 expression in ovarian cancer than that in normal tissues. High C3AR1 expression predicted adverse clinical outcomes. KEGG and GO analysis showed that the biological processes of C3AR1 in ovarian cancer are mainly involved in T cell activation, cytokine and chemokine activation. C3AR1 expression was positively correlated with chemokines and their receptors in the tumor microenvironment, such as CCR1(R = 0.83), IL10RA (R = 0.92), and INFG (R = 0.74). In addition, increased C3AR1 expression predicted more infiltration of tumor-associated macrophages, dendritic cell and CD8 + T cell. Some important m6A regulators, such as IGF2BP2, ALKBH5, IGFBP3 and METL14, are significantly positively or negatively correlated with C3AR1. Finally, overexpression of C3AR1 significantly increased proliferation of SKOV3 cells.

Conclusion
In summary, our study suggested that C3AR1 is associated with the prognosis and immune cell infiltration of ovarian cancer, and is a promising immunotherapeutic target.
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
Authors: Mohamed Mourdas , Sabot François , Varoqui Marion , Mugat Bruno , Audouin Katell , Pélisson Alain , Fiston-Lavier Anna-Sophie , Chambeyron Séverine 
Published: April 2023

AbstractTransposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using high- or low-quality genome assemblies, TrEMOLO can detect most TE insertions and deletions and estimate their allele frequency in populations. Benchmarking with simulated data revealed that TrEMOLO outperforms other state-of-the-art computational tools. TE detection and frequency estimation by TrEMOLO were validated using simulated and experimental datasets. Therefore, TrEMOLO is a comprehensive and suitable tool to accurately study TE dynamics. TrEMOLO is available under GNU GPL3.0 at https://github.com/DrosophilaGenomeEvolution/TrEMOLO.
A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer
Authors: Mayoh Chelsea , Gifford Andrew J. , Terry Rachael , Lau Loretta M. S. , Wong Marie , Rao Padmashree , Shai-Hee Tyler , Saletta Federica , Khuong-Quang Dong-Anh , Qin Vicky , Mateos Marion K. , Meyran Deborah , Miller Katherine E. , Yuksel Aysen , Mould Emily V. A. , Bowen-James Rachel , Govender Dinisha , Senapati Akanksha , Zhukova Nataliya , Omer Natacha , Dholaria Hetal , Alvaro Frank , Tapp Heather , Diamond Yonatan , Pozza Luciano Dalla , Moore Andrew S. , Nicholls Wayne , Gottardo Nicholas G. , McCowage Geoffrey , Hansford Jordan R. , Khaw Seong-Lin , Wood Paul J. , Catchpoole Daniel , Cottrell Catherine E. , Mardis Elaine R. , Marshall Glenn M. , Tyrrell Vanessa , Haber Michelle , Ziegler David S. , Vittorio Orazio , Trapani Joseph A. , Cowley Mark J. , Neeson Paul J. , Ekert Paul G. 
Published: April 2023

AbstractBackgroundMolecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers.MethodsWe combined immunohistochemistry (IHC) with RNA sequencing and whole-genome sequencing across a diverse spectrum of high-risk paediatric cancers to develop an alternative, expression-based signature associated with CD8+T-cell infiltration of the TIME. Furthermore, we explored transcriptional features of immune archetypes and T-cell receptor sequencing diversity, assessed the relationship between CD8+and CD4+abundance by IHC and deconvolution predictions and assessed the common adult biomarkers such as neoantigen load and TMB.ResultsA novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), was identified. Using this signature, we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. In addition, we showed that PD-L1 protein expression is poorly correlated with PD-L1 RNA expression and TMB and neoantigen load are not predictive of T-cell infiltration in paediatrics. Furthermore, deconvolution algorithms are only weakly correlated with IHC measurements of T-cells.ConclusionsOur data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.
Crotonylation of GAPDH regulates human embryonic stem cell endodermal lineage differentiation and metabolic switch
Authors: Zhang Jingran , Shi Guang , Pang Junjie , Zhu Xing , Feng Qingcai , Na Jie , Ma Wenbin , Liu Dan , Songyang Zhou 
Published: April 2023

AbstractBackgroundPost-translational modifications of proteins are crucial to the regulation of their activity and function. As a newly discovered acylation modification, crotonylation of non-histone proteins remains largely unexplored, particularly in human embryonic stem cells (hESCs).MethodsWe investigated the role of crotonylation in hESC differentiation by introduce crotonate into the culture medium of GFP tagged LTR7 primed H9 cell and extended pluripotent stem cell lines. RNA-seq assay was used to determine the hESC transcriptional features. Through morphological changes, qPCR of pluripotent and germ layer-specific gene markers and flow cytometry analysis, we determined that the induced crotonylation resulted in hESC differentiating into the endodermal lineage. We performed targeted metabolomic analysis and seahorse metabolic measurement to investigate the metabolism features after crotonate induction. Then high-resolution tandem mass spectrometry (LC–MS/MS) revealed the target proteins in hESCs. In addition, the role of crotonylated glycolytic enzymes (GAPDH and ENOA) was evaluated by in vitro crotonylation and enzymatic activity assays. Finally, we used knocked-down hESCs by shRNA, wild GAPDH and GAPDH mutants to explore potential role of GAPDH crotonylation in regulating human embryonic stem cell differentiation and metabolic switch.ResultWe found that induced crotonylation in hESCs resulted in hESCs of different pluripotency states differentiating into the endodermal lineage. Increased protein crotonylation in hESCs was accompanied by transcriptomic shifts and decreased glycolysis. Large-scale crotonylation profiling of non-histone proteins revealed that metabolic enzymes were major targets of inducible crotonylation in hESCs. We further discovered GAPDH as a key glycolytic enzyme regulated by crotonylation during endodermal differentiation from hESCs.ConclusionsCrotonylation of GAPDH decreased its enzymatic activity thereby leading to reduced glycolysis during endodermal differentiation from hESCs.
Human cerebral organoids: the ethical stance of scientists
Authors: Lavazza Andrea , Chinaia Alice Andrea 
Published: April 2023

Abstract
Background
Human cerebral organoids (HCOs) offer unprecedented opportunities to study the human brain in vitro, but they also raise important ethical concerns. Here we report the first systematic analysis of scientists’ stance within the ethical debate.

Method
Twenty-one in-depth semi-structured interviews were analyzed through a constant comparative method to highlight how the ethical concerns filter in the laboratory.

Results
The results suggest that the potential emergence of consciousness is not yet seen with concern. However, there are some features of HCO research that need to be better accounted for. Communication to the public, the use of terms such as “mini-brains”, and informed consent appear to be the most pressing concerns of the scientific community. Nonetheless, respondents generally showed a positive attitude toward the ethical discussion, recognizing its value and the necessity of constant ethical scrutiny over scientific advancements.

Conclusions
This research paves the way for a better-informed dialogue between scientists and ethicists, highlighting the issues to be addressed whenever scholars of different backgrounds and interests meet.
Albumin-to-fibrinogen ratio is an independent predictor of corticosteroid response and prognosis in patients with IgA nephropathy
Authors: Zhang Yu , Man Liping 
Published: April 2023

Abstract
Background
The objective of this study was to investigate whether the albumin-to-fibrinogen ratio (AFR) can predict corticosteroid response and prognosis prediction among IgA nephropathy (IgAN) patients.

Methods
Eligible participants with diagnosed IgAN who were scheduled to receive corticosteroid therapy for persistent proteinuria were recruited. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the predictive value of AFR or estimated glomerular filtration rate (eGFR) for corticosteroid response in IgAN patients. Risk factors for corticosteroid response and prognosis were validated using univariate and multivariate Cox proportional analyses.

Results
AFR and eGFR were both effective predictors of corticosteroid response in IgAN patients, with area under the curve (AUC) values of 0.686 and 0.643, respectively (P < 0.001 and P = 0.002). Baseline AFR level at biopsy was an independent risk factor for remission after corticosteroid therapy (HR: 2.38, 95% CI 1.32–4.07, P = 0.015), 50% decline in eGFR (HR: 0.78, 95% CI 0.69–0.89, P = 0.025), kidney failure (HR: 2.46, 95%CI 1.16–3.71, P = 0.016), and a composite event (HR: 2.13, 95%CI 1.28–3.34, P = 0.009) in IgAN patients.

Conclusions
AFR level at biopsy was a potential predictor of corticosteroid response and prognosis among IgAN patients.
Differential pathways to disordered eating for immigrant and native adolescents in Taiwan
Authors: Chen Duan-Rung , Lin Li-Yin , Levin Brianna 
Published: April 2023

Abstract
Background
Few studies have investigated disparities in disordered eating between new immigrant and native adolescents in Taiwan. This study examines the differential pathways to disordered eating in these two populations.

Methods
This cross-sectional study analyzed data collected from March to June 2019. In total, 729 adolescents aged between 13 and 16 years recruited from 37 classes in 3 middle schools in New Taipei City were included in the final analysis. Standardized assessment tools measured disordered eating (EAT-26) and psychological distress (BSRS-5). Generalized structural equation modeling was used to conduct the path analysis.

Results
The prevalence of disordered eating was significantly higher in immigrant adolescents than in their native counterparts. Multipath models indicated that weight-teasing driven by overweight and obese status and weight overestimation could lead to disordered eating through psychological distress; however, the pathways differed for the two groups studied. Family weigh-teasing indirectly leads to disordered eating through psychological distress for native adolescents; by contrast, for immigrant adolescents, friend weigh-teasing indirectly leads to disordered eating through psychological distress. Additionally, weight overestimation directly leads to disordered eating and indirectly through psychological distress to disordered eating for immigrant adolescents.

Conclusion
This study offers a plausible explanation of the differences in the paths to disordered eating between immigrant and native adolescents in Taiwan, which was not reported previously. The study urges the need for school-based prevention programs to improve immigrant students’ mental health.