bluuebunny/crossref_metadata_2025_split huggingface dataset:
Child and adolescent mental health services in Uganda
Authors: Iversen Silje Akselberg , Nalugya Joyce , Babirye Juliet N. , Engebretsen Ingunn Marie Stadskleiv , Skokauskas Norbert 
Published: August 2021

AbstractIntroductionWorldwide, one in five children and adolescents suffer from mental health disorders, while facing limited opportunities for treatment and recovery. Growing up, they face multiple challenges that might contribute to the development of mental disorders. Uganda is a developing country with a history of prolonged civil and regional wars associated with child soldiers, large numbers of refugees and internally displaced people due to natural disasters and unrests, and a large infectious disease burden mainly due to acute respiratory tract infections, malaria and HIV/AIDS.ObjectiveThis paper aims to examine the current status of child and adolescent mental health services in Uganda.MethodologyA scoping review approach was used to select studies on child and adolescent mental health services (CAMHS) in Uganda. A search of MEDLINE, Wiley and PubMed databases was conducted using eligibility criteria. The papers were summarized in tables and then synthesized using the Frameworks for monitoring health systems performance designed by the World Health Organisation (WHO). This was done according to the Preferred Reporting Items for Systematic Review and M-Analyses Extension for Scoping Review (PRISMA-ScR) guidelines.ResultsTwelve studies were identified; five of them used qualitative methods and focused mostly on the current limitations and strengths of CAMHS in Uganda, while six quantitative studies investigated the effects of new interventions. One study used a mixed-methods approach. In summary, the papers outlined a need for collaboration with the primary health sector and traditional healers to ensure additional human resources, as well as the need to focus on groups such as orphans, HIV/AIDS-affected youth, former child soldiers and refugees.ConclusionRelatively few studies have been conducted on CAMHS in Uganda, and most of those that exist are part of larger studies involving multiple countries. CAMHS in Uganda require improvement and needs to focus especially on vulnerable groups such as orphans, HIV/AIDS-affected youth and former child soldiers.
Exclusive breastfeeding lowers the odds of childhood diarrhea and other medical conditions: evidence from the 2016 Ethiopian demographic and health survey
Authors: Mulatu Tesfahun , Yimer Nigus Bililign , Alemnew Birhan , Linger Melese , Liben Misgan Legesse 
Published: August 2021

AbstractBackgroundLack of exclusive breastfeeding during the first 6 months of infant life contributes to childhood morbidity and mortality. This study aimed to investigate the association of exclusive breastfeeding and childhood illnesses in Ethiopia.MethodsA secondary data analysis was conducted using data from the 2016 Ethiopian Demographic and Health Survey (EDHS). Descriptive and multivariable logistic regression analyses were carried out.ResultsA total of 1034 mother-infant pairs were included in the analysis. The overall magnitude of exclusive breastfeeding among infants aged under 6 months was 87.6% (95% CI: 84.3–90.3%). Compared to infants who were non-exclusively breastfed, the odds of having an illness with fever in the last 2 weeks among infants who were exclusively breastfed decreased by 66% (AOR: 0.34; 95% CI: 0.16, 0.75). Similarly, exclusively breastfed infants had lower odds of having an illness with a cough (AOR: 0.38; CI: 0.20, 0.72) and having diarrhea (AOR: 0.33; CI: 0.13, 0.83) compared to non-exclusively breastfed infants.ConclusionExclusive breastfeeding lowers the odds of an illness with fever, illness with cough and diarrhea. The findings of this study implicate the need for promotion of exclusive breastfeeding in the country.
Diagnostic chest X-rays and breast cancer risk among women with a hereditary predisposition to breast cancer unexplained by a BRCA1 or BRCA2 mutation
Authors: Ribeiro Guerra Maximiliano , Coignard Juliette , Eon-Marchais Séverine , Dondon Marie-Gabrielle , Le Gal Dorothée , Beauvallet Juana , Mebirouk Noura , Belotti Muriel , Caron Olivier , Gauthier-Villars Marion , Coupier Isabelle , Buecher Bruno , Lortholary Alain , Fricker Jean-Pierre , Gesta Paul , Noguès Catherine , Faivre Laurence , Berthet Pascaline , Luporsi Elisabeth , Delnatte Capucine , Bonadona Valérie , Maugard Christine M. , Pujol Pascal , Lasset Christine , Longy Michel , Bignon Yves-Jean , Adenis-Lavignasse Claude , Venat-Bouvet Laurence , Dreyfus Hélène , Gladieff Laurence , Mortemousque Isabelle , Audebert-Bellanger Séverine , Soubrier Florent , Giraud Sophie , Lejeune-Dumoulin Sophie , Limacher Jean-Marc , Chiesa Jean , Fajac Anne , Floquet Anne , Eisinger François , Tinat Julie , Fert-Ferrer Sandra , Colas Chrystelle , Frebourg Thierry , Damiola Francesca , Barjhoux Laure , Cavaciuti Eve , Mazoyer Sylvie , Tardivon Anne , Lesueur Fabienne , Stoppa-Lyonnet Dominique , Andrieu Nadine 
Published: August 2021

Abstract
Background
Diagnostic ionizing radiation is a risk factor for breast cancer (BC). BC risk increases with increased dose to the chest and decreases with increased age at exposure, with possible effect modification related to familial or genetic predisposition. While chest X-rays increase the BC risk of BRCA1/2 mutation carriers compared to non-carriers, little is known for women with a hereditary predisposition to BC but who tested negative for a BRCA1 or BRCA2 (BRCA1/2) mutation.

Methods
We evaluated the effect of chest X-rays from diagnostic medical procedures in a dataset composed of 1552 BC cases identified through French family cancer clinics and 1363 unrelated controls. Participants reported their history of X-ray exposures in a detailed questionnaire and were tested for 113 DNA repair genes. Logistic regression and multinomial logistic regression models were used to assess the association with BC.

Results
Chest X-ray exposure doubled BC risk. A 3% increased BC risk per additional exposure was observed. Being 20 years old or younger at first exposure or being exposed before first full-term pregnancy did not seem to modify this risk. Birth after 1960 or carrying a rare likely deleterious coding variant in a DNA repair gene other than BRCA1/2 modified the effect of chest X-ray exposure.

Conclusion
Ever/never chest X-ray exposure increases BC risk 2-fold regardless of age at first exposure and, by up to 5-fold when carrying 3 or more rare variants in a DNA repair gene.
Further studies are needed to evaluate other DNA repair genes or variants to identify those which could modify radiation sensitivity. Identification of subpopulations that are more or less susceptible to ionizing radiation is important and potentially clinically relevant.
Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Authors: Karousis Evangelos D. , Gypas Foivos , Zavolan Mihaela , Mühlemann Oliver 
Published: August 2021

AbstractBackgroundNonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains a challenge.ResultsTo identify and analyze endogenous targets of NMD, we apply cDNA Nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Our approach detects full-length NMD substrates that are highly unstable and increase in levels or even only appear when NMD is inhibited. Among the many new NMD-targeted isoforms that our analysis identifies, most derive from alternative exon usage. The isoform-aware analysis reveals many genes with significant changes in splicing but no significant changes in overall expression levels upon NMD knockdown. NMD-sensitive mRNAs have more exons in the 3΄UTR and, for those mRNAs with a termination codon in the last exon, the length of the 3΄UTR per se does not correlate with NMD sensitivity. Analysis of splicing signals reveals isoforms where NMD has been co-opted in the regulation of gene expression, though the main function of NMD seems to be ridding the transcriptome of isoforms resulting from spurious splicing events.ConclusionsLong-read sequencing enables the identification of many novel NMD-sensitive mRNAs and reveals both known and unexpected features concerning their biogenesis and their biological role. Our data provide a highly valuable resource of human NMD transcript targets for future genomic and transcriptomic applications.
Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences
Authors: Chiu Readman , Rajan-Babu Indhu-Shree , Friedman Jan M. , Birol Inanc 
Published: August 2021

AbstractTandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we present Straglr, a robust software tool for both targeted genotyping and novel expansion detection from long-read alignments. We benchmark Straglr using various simulations, targeted genotyping data of cell lines carrying expansions of known diseases, and whole genome sequencing data with chromosome-scale assembly. Our results suggest that Straglr may be useful for investigating disease-associated TR expansions using long-read sequencing.
Refractory catatonia in old age: a case report
Authors: Bean Emma , Findlay Callum , Gee Claire , Amin Jay 
Published: August 2021

Abstract
Background
Catatonia is a clinical syndrome characterized by psychomotor disruption, which often goes undiagnosed. Most reports have focused on interventions and outcomes for catatonia in younger people and those with schizophrenia. The clinical characteristics and course of catatonia in old age are poorly understood. We present a report of an older person whose catatonia was refractory to extensive treatment, and we identify important implications for the management of catatonia in old age.

Case presentation
We describe a 73-year-old white man with longstanding autistic spectrum disorder who presented with symptoms of depression. Following a period of diagnostic uncertainty and failure to improve with antidepressant medication, a lorazepam challenge yielded an abrupt improvement in presentation. The patient was treated extensively with lorazepam, zolpidem, and electroconvulsive therapy during his 16-month hospital admission, but his catatonia ultimately proved refractory to treatment.

Conclusions
Catatonia should be considered promptly as a differential diagnosis in older people presenting with atypical features of functional mental illness. Although partial improvement of catatonic features was achieved using benzodiazepines and electroconvulsive therapy, these were not sustained in our patient. We identified comorbid autistic spectrum disorder, prolonged duration of catatonia, and sensitivity to benzodiazepines as important factors in prognostication in old age.
DOA estimation based on sum–difference coarray with virtual array interpolation concept
Authors: Ding Yarong , Ren Shiwei , Wang Weijiang , Xue Chengbo 
Published: August 2021

AbstractThe sum–difference coarray is the union of difference coarray and the sum coarray, which is capable to obtain a higher number of degrees of freedom (DOF) than the difference coarray. However, this method fails to use all information provided by the coprime array because of the existence of holes. In this paper, we introduce the virtual array interpolation into the sum–difference coarray domain. After interpolating the virtual array, we estimate the DOA by reconstructing the covariance matrix to resolve an atomic norm minimization problem in a gridless way. The proposed method is gridless and can effectively utilize the DOF of a larger virtual array. Numerical simulation results verify the effectiveness and the superior performance of the proposed algorithm.
Powering jobs: the employment footprint of clean cooking solutions in Kenya
Authors: Lee Chih-Jung , Shirley Rebekah , Otieno Maureen , Nyambura Hope 
Published: August 2021

AbstractBackgroundThe delivery of clean cooking access to the 1.2 billion people who cook with charcoal, kerosene, and firewood may have a strong localized employment impact. With the challenge of a rapidly expanding youth population and growing job scarcity in sub-Saharan Africa, understanding the impact of clean cooking on employment as well as the skills gap is timely. However, there is little definitive data on clean cooking jobs. Recognizing this data gap, we sought to conduct a study focused specifically on employment from the clean cooking sectors in Kenya, covering liquefied petroleum gas (LPG), bioethanol, biogas, and electric cooking solutions. This study provides an initial baseline and early estimate of the clean cooking sector's direct formal and informal employment based on one year of company survey data, expert interviews, available literature, and local focus group discussion.ResultsIn Kenya, the clean cooking sector is estimated to provide about 19,000 direct, formal jobs and potentially 15,000 to 35,000 direct, informal jobs in 2019. While the clean cooking sector provided many jobs, the level of compensation and retention is low. In the LPG and electric cooking sector, sales and distribution are the biggest part of the workforce, while for bioethanol and biogas, manufacturing and assembling is dominant. The majority of the clean cooking sector's direct, formal workforce is reported to be skilled. Management, finance and legal, and product development and research are the most difficult skills to recruit for. Women’s participation is lower than 30% in the clean cooking sectors studied, and managerial positions have higher women’s participation than non-managerial ones.ConclusionThis research exercise establishes a baseline for understanding the employment impact of the clean cooking sectors. However, a massive data gap persists. Our study shows that while clean cooking sectors, especially LPG, are already providing tens of thousands of jobs, further studies are critically needed to map the employment impact of delivering universal clean cooking access.
Inflammatory metabolic profile of South African patients with prostate cancer
Authors: Cacciatore Stefano , Wium Martha , Licari Cristina , Ajayi-Smith Aderonke , Masieri Lorenzo , Anderson Chanelle , Salukazana Azola Samkele , Kaestner Lisa , Carini Marco , Carbone Giuseppina M. , Catapano Carlo V. , Loda Massimo , Libermann Towia A. , Zerbini Luiz F. 
Published: August 2021

Abstract
Background
Men with African ancestry are more likely to develop aggressive prostate cancer (PCa) and to die from this disease. The study of PCa in the South African population represents an opportunity for biomedical research due to the high prevalence of aggressive PCa. While inflammation is known to play a significant role in PCa progression, its association with tumor stage in populations of African descent has not been explored in detail. Identification of new metabolic biomarkers of inflammation may improve diagnosis of patients with aggressive PCa.

Methods
Plasma samples were profiled from 41 South African men with PCa using nuclear magnetic resonance (NMR) spectroscopy. A total of 41 features, including metabolites, lipid classes, total protein, and the inflammatory NMR markers, GlycA, and GlycB, were quantified from each NMR spectrum. The Bruker’s B.I.-LISA protocols were used to characterize 114 parameters related to the lipoproteins. The unsupervised KODAMA method was used to stratify the patients of our cohort based on their metabolic profile.

Results
We found that the plasma of patients with very high risk, aggressive PCa and high level of C-reactive protein have a peculiar metabolic phenotype (metabotype) characterized by extremely high levels of GlycA and GlycB. The inflammatory processes linked to the higher level of GlycA and GlycB are characterized by a deep change of the plasma metabolome that may be used to improve the stratification of patients with PCa. We also identified a not previously known relationship between high values of VLDL and low level of GlycB in a different metabotype of patients characterized by lower-risk PCa.

Conclusions
For the first time, a portrait of the metabolic changes in African men with PCa has been delineated indicating a strong association between inflammation and metabolic profiles. Our findings indicate how the metabolic profile could be used to identify those patients with high level of inflammation, characterized by aggressive PCa and short life expectancy. Integrating a metabolomic analysis as a tool for patient stratification could be important for opening the door to the development of new therapies. Further investigations are needed to understand the prevalence of an inflammatory metabotype in patients with aggressive PCa.
Adaptation to family-based treatment for Medicaid-insured youth with anorexia nervosa in publicly-funded settings: Protocol for a mixed methods implementation scale-out pilot study
Authors: Accurso Erin C. , Mu Karen J. , Landsverk John , Guydish Joseph 
Published: August 2021

Abstract
Background
Family-based treatment (FBT) for anorexia nervosa is an evidence-based treatment, but its effectiveness is untested among socioeconomically disadvantaged and racially diverse youth. Adapting FBT may facilitate “scale-out” for Medicaid-insured youth served in publicly-funded settings and potentially improve outcomes for more diverse populations.

Methods
This mixed methods effectiveness-implementation Hybrid Type 3 pilot study protocol included a planning period in collaboration with the San Francisco Department of Public Health, culminating in a two-day in-person FBT training for 25 therapists in the county, followed by the opportunity to engage in one year of weekly supervision. The training incorporated FBT adaptations intended to improve fit for low-income families within community-based settings. Treatment appropriateness and acceptability will be measured immediately post-training. Following the training, cases referred for FBT will only be assigned to the trained clinicians who voluntarily opted into long-term group supervision. Clinicians treating at least one FBT case during the supervision period will report on implementation, adaptations, and patient weight gain. Finally, semi-structured interviews with clinician participants will be conducted, focused on implementation challenges and facilitators, local treatment adaptations, and overall satisfaction with FBT.

Discussion
Learning about clinician adaptations will advance knowledge about treatment of eating disorders in publicly-funded community clinics, which serve a racially/ethnically and socioeconomically diverse group of youth. This project is designed to accelerate FBT implementation in publicly-funded mental health systems, and inform service improvements for underserved youth with eating disorders.
Characteristics of powerful learning environments in VET transition program for at-risk students: qualitative insights from teachers and support specialists implementing the program
Authors: Roos Liana , Trasberg Karmen , Kõiv Kristi , Säre Egle 
Published: August 2021

AbstractAt-risk students like those with special educational needs, learning difficulties, or pupils at risk of exclusion frequently struggle in transition from basic to secondary vocational education and training, often due to poor personal, learning and social skills. Therefore, several countries implement transition programs like the choice of profession training (CoPT) in Estonia to support youngsters’ readiness to continue their studies. This study aimed to identify how the characteristics of powerful learning environments in vocational education (PoLEVE) appear in CoPT in VET teachers and support specialists’ experiences. The deductive thematic analysis of 16 semistructured interviews illuminated the development of learning-, life-, cooperation- and self-determinations skills through adaptive teaching and learning support in a safe and positive learning community. Nevertheless, the results also call for empowering at-risk students to cope independently, supporting their construction of vocational knowledge through reflective dialogue and intellectually challenging problem-solving.
Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia
Authors: Natarajan Karthick , Eisfeldt Jesper , Hammond Maria , Laffita-Mesa José Miguel , Patra Kalicharan , Khoshnood Behzad , Öijerstedt Linn , Graff Caroline 
Published: August 2021

AbstractWe identified an autosomal dominant progranulin mutation carrier without symptoms of dementia in her lifetime (Reduced Penetrance Mutation Carrier, RedPenMC). This resistance to develop expected pathology presents a unique opportunity to interrogate neurodegenerative mechanisms. We performed multimodal single-nuclei analyses of post-mortem frontal cortex from RedPenMC, including transcriptomics and global levels of chromatin marks. RedPenMC had an increased ratio of GRN-expressing microglia, higher levels of activating histone mark H3k4me3 in microglia and lower levels of the repressive chromatin marks H3k9me1 and H3k9me3 in the frontal cortex than her affected mutation carrier son and evidence of higher protein levels of progranulin in both plasma and brain homogenates. Although the study is limited to one case, the results support that restoring brain progranulin levels may be sufficient to escape neurodegeneration and FTD. In addition to previously identified modifier genes, it is possible that epigenetic marks may contribute to the increased progranulin expression in cases of reduced penetrance. These findings may stimulate similar follow-up studies and new therapeutic approaches.
Advances in single-cell sequencing: insights from organ transplantation
Authors: Wang Ying , Wang Jian-Ye , Schnieke Angelika , Fischer Konrad 
Published: August 2021

AbstractSingle-cell RNA sequencing (scRNA-seq) is a comprehensive technical tool to analyze intracellular and intercellular interaction data by whole transcriptional profile analysis. Here, we describe the application in biomedical research, focusing on the immune system during organ transplantation and rejection. Unlike conventional transcriptome analysis, this method provides a full map of multiple cell populations in one specific tissue and presents a dynamic and transient unbiased method to explore the progression of allograft dysfunction, starting from the stress response to final graft failure. This promising sequencing technology remarkably improves individualized organ rejection treatment by identifying decisive cellular subgroups and cell-specific interactions.