bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fusion transcript detection using spatial transcriptomics
Authors: Friedrich Stefanie , Sonnhammer Erik LL 
Published: April 2020

Abstract
Background Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high spatial resolution in tissue sections due to the lack of full-length transcripts with spatial information. New high-throughput technologies like spatial transcriptomics measure the transcriptome of tissue sections on almost single-cell level. While this technique does not allow for direct detection of fusion transcripts, we show that they can be inferred using the relative poly(A) tail abundance of the involved parental genes. Method We present a new method STfusion, which uses spatial transcriptomics to infer the presence and absence of poly(A) tails. A fusion transcript lacks a poly(A) tail for the 5´ gene and has an elevated number of poly(A) tails for the 3´ gene. Its expression level is defined by the upstream promoter of the 5´ gene. STfusion measures the difference between the observed and expected number of poly(A) tails with a novel C-score. Results We verified the STfusion ability to predict fusion transcripts on HeLa cells with known fusions. STfusion and C-score applied to clinical prostate cancer data revealed the spatial distribution of the cis-SAGe SLC45A3-ELK4 in 12 tissue sections with almost single-cell resolution. The cis-SAGe occurred in disease areas, e.g. inflamed, prostatic intraepithelial neoplastic, or cancerous areas, and occasionally in normal glands. Conclusions STfusion detects fusion transcripts in cancer cell line and clinical tissue data, and distinguishes chimeric transcripts from chimeras caused by trans-splicing events. With STfusion and the use of C-scores, fusion transcripts can be spatially localised in clinical tissue sections on almost single cell level.
Prognostic nutrition index as a predictor of coronary artery aneurysm in Kawasaki Disease
Authors: Tai I Hsin , Wu Pei-Lin , Guo Mindy Ming-Huey , Lee Jessica , Chu Chi-Hsiang , Hsieh Kai-Sheng , Kuo Ho-Chang 
Published: April 2020

Abstract
Background: Kawasaki Disease (KD) is considered a major acquired heart disease in children under the age of 5. Coronary artery aneurysm (CAA) can occur in serious cases despite extreme therapy efforts. Previous studies have reported low serum albumin level was associated with disease outcome, but no further investigation was addressed yet. Method: This retrospective (case-control) study randomly included children with KD who were admitted and underwent laboratory tests before undergoing IVIG treatment in this institution, the largest tertiary medical center in southern Taiwan from 2012-2016. Prognostic nutrition index (PNI), an albumin-based formula product, was evaluated as a predictor of CAA the first time. The progression of CAA was monitored using serial echocardiography for six months. We performed multivariable logistic regression analysis on the laboratory test and PNI with the disease outcome of the KD patients. Result: Of the 275 children, 149 had CAA, including transient dilatation, while the other 126 did not develop CAA during the 6-month follow-up period. A multivariate logistic regression model revealed that PNI, gender, IVIG non-responder, and platelet count are significant predictors of CAA with a 95% confidence interval estimator of 1.999, 3.058, 3.864 and1.004, respectively. Using PNI to predict CAA presence gave an area under the receiver-operating-characteristics (ROC) curve of 0.596. For a cutoff of 0.5 in the logistic regression model and the PNI cut-off point is taken as 55 together with IVIG non-responder, boy gender, and platelet count take into account, sensitivity and specificity were 65.7% and 70.4%. Conclusion: PNI could be a candidate of adjunctive predictor of coronary artery aneurysm in addition to IVIG non-responder. Together with low PNI, IVIG non-responder, male gender and platelet count will give high odds to predict coronary artery aneurysm within 6 months of illness.
Identification and analysis of CYP450 and UGT supergene family members from the transcriptome of Aralia elata (Miq.) Seem reveal candidate genes for triterpenoid saponin biosynthesis
Authors: Cheng Yao , Liu Hanbing , Tong Xuejiao , Liu Zaimin , Zhang Xin , Li Dalong , Jiang Xinmei , Yu Xihong 
Published: April 2020

Abstract
Background: Members of the cytochrome P450 (CYP450) and UDP-glycosyltransferase (UGT) gene superfamily have been shown to play essential roles in regulating secondary metabolite biosynthesis. However, the systematic identification of CYP450s and UGTs has not been reported in Aralia elata (Miq.) Seem, a highly valued medicinal plant. Results: In the present study, we conducted the RNA-sequencing (RNA-seq) analysis of the leaves, stems, and roots of A. elata, yielding 66,713 total unigenes. Following annotation and KEGG pathway analysis, we were able to identify 64 unigenes related to triterpenoid skeleton biosynthesis, 254 CYP450s and 122 UGTs, respectively. A total of 150 CYP450s and 92 UGTs encoding >300 amino acid proteins were utilized for phylogenetic and tissue-specific expression analyses. This allowed us to cluster 150 CYP450s into 9 clans and 40 families, and then these CYP450 proteins were further grouped into two primary branches: A-type (53%) and non-A-type (47%). A phylogenetic analysis of 92 UGTs and other plant UGTs led to clustering into 16 groups (A-P). We further assessed the expression patterns of these CYP450 and UGT genes across A. elata tissues, with 23 CYP450 and 16 UGT members being selected for qRT-PCR validation, respectively. From these data, we identified CYP716A295 and CYP716A296 as the candidate genes most likely to be associated with oleanolic acid synthesis, while CYP72A763 and CYP72A776 were identified as being the most likely to play roles in hederagenin biosynthesis. We also selected five unigenes as the best candidates for oleanolic acid 3-O-glucosyltransferase. Finally, we assessed the subcellular localization of three CYP450 proteins within Arabidopsis protoplasts, highlighting the fact that they localize to the endoplasmic reticulum.Conclusions: This study presents a systematic analysis of the CYP450 and UGT gene family in A. elata and provides a foundation for further functional characterization of these two multigene families.
Nano-copper Enhanced Flexible Device for Simultaneous Measurement of Human Respiratory and Electro-cardiac Activities
Authors: Wang Li , Zhang Feng , Lu Kechao , Abdulaziz Mohammed , Li Chao , Zhang Chongyu , Chen Jun , Li Yunlun 
Published: April 2020

Abstract
Background: Dysfunction of human respiratory and electro-cardiac activities could affect the ability of the heart to pump blood and the lungs to inhale oxygen. Thus, a device could simultaneously measure electro-cardiac signal and respiratory pressure could provide vital signs for predicting early warning of cardio-pulmonary function-related chronic diseases such as cardiovascular disease, and respiratory system disease. Results: In this study, a flexible device integrated with piezo-resistive sensing element and voltage-sensing element was developed to simultaneously measure human respiration and electro-cardiac signal (including respiratory pressure, respiration frequency, and respiration rhythm; electro-cardio frequency, electro-cardio amplitude, and electro-cardio rhythm). When applied to the measurement of respiratory pressure, the piezo-resistive performance of the device was enhanced by nano-copper modification, which detection limitation of pressure can reduce to 100 Pa and the sensitivity of pressure can achieve to 0.053 ± 0.00079 kPa-1. In addition, the signal-to-noise ratio during bio-electrical measurement was increased to 10.7 ± 1.4, five times better than that of the non-modified device. Conclusion: This paper presents a flexible device for the simultaneous detection of human respiration and cardiac electrical activity. To avoid interference between the two signals, the layout of the electrode and the strain sensor was optimized by FEA simulation analysis. To improve the piezo-resistive sensitivity and bio-electric capturing capability of the device, a feather-shaped nano-copper was modified onto the surface of carbon fiber. The operation simplicity, compact size, and portability of the device open up new possibilities for multi-parameter monitoring.
Subclinical Cardiovascular Risk Signs in Adults with Juvenile Idiopathic Arthritis in Sustained Remission
Authors: Aranda-Valera Inmaculada Concepcion , Rosa Iván Arias de la , Roldan-Molina Rosa , Abalos-Aguilera Maria del Carmen , Torres-Granados Carmen , Patiño-Trives Alejandra , Luque-Tevar Maria , Ibañez-Costa Alejandro , Guzman-Ruiz Rocio , Malagón Maria del Mar , Escudero-Contreras Alejandro , Lopez-Pedrera Chary , Collantes-Estevez Eduardo , Barbarroja Nuria 
Published: April 2020

Abstract
Background: Juvenile Idiopathic Arthritis (JIA) is one of the most common chronic diseases of childhood that often persists into adulthood and can result in significant long-term morbidity. As a long lasting chronic inflammatory disease, concern has been raised regarding the risk of premature development of cardiovascular disease (CVD) in JIA. This study aims to determine whether adults with JIA in clinical remission display clinical and subclinical signs of CVD risk: inflammatory mediators, adipokines, endothelial dysfunction and oxidative stress markers.Methods: This is a cross-sectional study including 25 patients diagnosed with JIA according to the International League of Associations for Rheumatology criteria (ILAR 2001) and 25 age- and sex-matched controls. Remission was determined by JADAS10<1 and according to Wallace criteria. The presence of traditional CVD risk factors was analyzed. An extensive clinical analysis including body mass index (BMI), lipid profile, homeostatic model assessment – insulin resistance (HOMA-IR) and arterial blood pressure was performed. Intima media thickness of the common carotid artery (CIMT) was measured as a marker of subclinical atherosclerosis. Several proinflammatory cytokines, molecules involved in the endothelial dysfunction, oxidative stress and adipokines were quantified on serum by ELISA and on peripheral blood mononuclear cells (PBMCs) by RT-PCR. In vitro studies were carried out in healthy PBMCs, adipocytes and endothelial cells which were treated with serum from JIA patients under sustained remission. Results: Mean duration of the disease was 13.47 ± 5.47 years. Mean age was 25.11 ± 7.21. Time in remission was 3.52 ± 3.33 years. Patients were in remission with no treatment (40%) and with treatments (60%). CVD risk factors and CIMT were similar in JIA patients and controls. However, cholesterol levels were significantly elevated in JIA patients. Levels of adipocytokines, oxidative stress and endothelial activation markers were elevated in serum and PBMCs from JIA patients. Serum of those JIA patients induced the activation of adipocytes, endothelial cells and healthy PBMCs.Conclusions: JIA adult patients in remission have subclinical signs of inflammation and CVD risk, showed by an increase in the levels of inflammatory cytokines, endothelial activation and oxidative stress markers and adipokines, molecules closely involved in the alteration of the vascular system.
The quality of clinical practice guidelines for preoperative care using the AGREE II instrument: a systematic review
Authors: Ciapponi Agustín , Elena Tapia-López , Sacha Virgilio , Bardach Ariel 
Published: April 2020

Abstract
Background: Our aim was to summarize and compare relevant recommendations from evidence-based CPGs (EB-CPGs). Methods: Systematic review of clinical practice guidelines. Data sources: PubMed, EMBase, Cochrane Library, LILACS, Tripdatabase and additional sources. In July 2017, we searched CPGs that were published in the last 10 years, without language restrictions, in electronic databases, and also searched specific CPG sources, reference lists and consulted experts. Pairs of independent reviewers selected EB-CPGs and rated their methodological quality using the AGREE-II instrument. We summarized recommendations, its supporting evidence and strength of recommendations according to the GRADE methodology.Results: We included 16 EB-CPGs out of 2262 references identified. Only nine of them had searches within the last five years and seven used GRADE. The median (percentile 25-75) AGREE-II scores for rigor of development was 49% (35-76%) and the domain ‘applicability’ obtained the worst score: 16% (9-31%). We summarized 31 risk stratification recommendations, 21.6% of which were supported by high/moderate quality of evidence (41% of them were strong recommendations), and 16 therapeutic/preventive recommendations, 59% of which were supported by high/moderate quality of evidence (75.7% strong). We found inconsistency in ratings of evidence level. ‘Guidelines’ applicability’ and ‘monitoring’ were the most deficient domains. Only half of the EB-CPGs were updated in the past five years. Conclusions: We present many strong recommendations that are ready to be considered for implementation as well as others to be interrupted, and we reveal opportunities to improve guidelines’ quality.
e-Health Interventions for Healthy Aging: A Systematic Review
Authors: Buyl Ronald , Beogo Idrissa , Fobelets Maaike , Deletroz Carole , Landuyt Philip Van , Dequanter Samantha , Gorus Ellen , Bourbonnais Anne , Giguère Anik , Lechasseur Kathleen , Gagnon Marie-Pierre 
Published: April 2020

Abstract
Background: Healthy aging (HA) is a contemporary challenge for population health worldwide. Electronic health (e-Health) interventions have the potential to support empowerment and education of adults aged 50 and over. Objectives: To summarize evidence on the effectiveness of e-Health interventions on HA and explore how specific e-Health interventions and their characteristics effectively impact HA.Methods: A systematic review was conducted based on the Cochrane Collaboration methods including any experimental study design published in French, Dutch, Spanish and English from 2000 to 2018. Results: Fourteen studies comparing various e-Health interventions to multiple components controls were included. The target population, type of interventions and outcomes measured were very heterogeneous across studies, thus a meta-analysis was not possible. However, effect estimates indicate that e-Health interventions could improve physical activity. Positive effects were also found for other healthy behaviors (e.g. healthy eating), psychological outcomes (e.g. memory) and clinical parameters (e.g. blood pressure). Given the low certainty of the evidence related to most outcomes, these results should be interpreted cautiously.Conclusions: This systematic review found limited evidence supporting the effectiveness of e-Health interventions, although the majority of studies show positive effects of these interventions for improving physical activity in older adults. Thus, better quality evidence is needed regarding the effects of eHealth on the physiological, psychological and social dimensions of HA.Systematic review registration: The review protocol was registered in PROSPERO (registration number: CRD42016033163).
Engineering of sugar transporters for improvement of xylose utilization during high-temperature alcoholic fermentation in Ogataea polymorpha yeast
Authors: Vasylyshyn Roksolana , Kurylenko Olena , Ruchala Justyna , Shevchuk Nadiya , Kuliesiene Neringa , Khroustalyova Galina , Rapoport Alexandr , Daugelavicius Rimantas , Dmytruk Kostyantyn , Sibirny Andriy 
Published: April 2020

Abstract
Background Xylose transport is one of the bottlenecks in the conversion of lignocellulosic biomass to ethanol. Xylose consumption by the wild-type strains of xylose-utilizing yeasts occurs once glucose is depleted resulting in a long fermentation process and overall slow and incomplete conversion of sugars liberated from lignocellulosic hydrolysates. Therefore, the engineering of endogenous transporters for the facilitation of glucose-xylose co-consumption is an important prerequisite for efficient ethanol production from lignocellulosic hydrolysates. Results In this study, several engineering approaches formerly used for the low-affinity glucose transporters in Saccharomyces cerevisiae , were successfully applied for earlier identified transporter Hxt1 in Ogataea polymorpha to improve xylose consumption (engineering involved asparagine substitution to alanine at position 358 and replacement of N-terminal lysine residues predicted to be the target of ubiquitination for arginine residues). Moreover, the modified versions of S. cerevisiae Hxt7 and Gal2 transporters also led to improved xylose fermentation when expressed in O. polymorpha . Conclusions The O. polymorpha strains with modified Hxt1 were characterized by simultaneous utilization of both glucose and xylose, in contrast to the wild-type and parental strain with elevated ethanol production from xylose. When the engineered Hxt1 transporter was introduced into constructed earlier advanced ethanol producer form xylose, the resulted strain showed further increase in ethanol accumulation during xylose fermentation. The overexpression of heterologous S. cerevisiae Gal2 had a less profound positive effects on sugars uptake rate, while overexpression of Hxt7 revealed the least impact on sugars consumption.
Prevalence, antimicrobial susceptibility pattern, and associated factors of Salmonella and Shigella among food handlers in Adigrat University student’s cafeteria, Northern Ethiopia, 2018
Authors: Legese Haftom , Kahsay Tsega , Gebrewahd Aderajew , Berhe Brhane , Fseha Berhane , Tadesse Senait , Gebremariam Guesh , Negash Hadush , Mardu Fitsum , Tesfay Kebede , Adhanom Gebre 
Published: April 2020

Abstract
Background: Food handlers play a significant role in the transmission of foodborne infection. Salmonella and Shigella are the most common foodborne pathogens and their infections are a major public health problem of the globe. Thus, this study was aimed to determine the prevalence, antimicrobial susceptibility patterns, and associated factors of Salmonella and Shigella among food handlers. Methodology: A cross-sectional study was conducted from March to August 2018 at Adigrat University student cafeteria, Northern Ethiopia. Data on socio-demographic and associated factors were collected using a structured questionnaire. Fresh stool samples were collected from 301 food handlers and transported to Adigrat University Microbiology Laboratory. Bacterial isolation and antimicrobial susceptibility test were performed using standard bacteriological methods. Data analysis was performed using SPSS version 22 and P < 0.05 with a corresponding 95% confidence interval was considered statistically significant. Results: A total of 301 food handlers were included in this study. The majority of study participants were females 265 (88.0 %). About 22 (7.3%) and 11 (3.7%) of food handlers were found to be positive for Salmonella and Shigella respectively. Hand washing after using a bathroom with water only, hand washing after using the bathroom, hand washing after touching dirty materials, hand washing before food handling and fingernails status were significant associated factors identified. None of the Salmonella and Shigella isolates was sensitive to ampicillin. On the other hand, low resistance was found for chloramphenicol, ceftriaxone, and ciprofloxacin. Conclusion: The present study revealed that the prevalence of Salmonella and Shigella among food handlers found to be 22 (7.3%) and 11 (3.7%) respectively. Such colonized food handlers can contaminate food, drinks and could serve as a source of infection to consumers via the food chain. This indicates that the need for strengthened infection control measures to prevent Salmonella and Shigella transmission in the students’ cafeteria.
“You talk about problems until you feel free”: South African adolescent girls' and young women’s narratives on the value of HIV prevention peer support clubs
Authors: Baron Deborah , Scorgie Fiona , Ramskin Lethabo , Khoza Nomhle , Schutzman Jennifer , Stangl Anne , Harvey Sheila , Delany-Moretlwe Sinead 
Published: April 2020

Abstract
Background: Daily oral pre-exposure prophylaxis (PrEP) can reduce HIV infection in adolescent girls and young women if used consistently during periods of risk. The EMPOWER study evaluated peer-based clubs incorporating an empowerment curriculum offered to adolescent girls and young women (16-24 years) in South Africa and Tanzania for adherence support. Methods: Using serial in-depth interviews (n=33), we assessed the benefits and challenges of club attendance among 13 EMPOWER participants in the Johannesburg site who were randomised to clubs. We used a summary matrix of coded data to support a narrative, case-based analysis. Four case studies are presented. Results: Club participants reported benefits such as increased self-esteem and self-efficacy, reduced isolation, and greater insight into gender-based violence and strategies to address it. Day-to-day PrEP adherence was not the only topic discussed in clubs; participants also appreciated the safe space for sharing problems (such as relationship conflict and PrEP stigma) and found interactive exercises helpful in improving partner communication.Conclusions: Findings support the use of peer-based clubs using a structured empowerment approach, which may offer valuable PrEP initiation support to adolescent girls and young women in settings with high HIV and gender-based violence prevalence.
Differential microRNAs expression profiles in liver from three different lifestyle modification mice models
Authors: Gong Huan , Zhang Ming , Han Yiwen , Zhang Ying , Pang Jing , Zhao Yanyang , Chen Beidong , Wu Wei , Qi Ruomei , Zhang Tiemei 
Published: April 2020

Abstract
Background MicroRNAs play an important role in many fundamental biological and pathological processes. Defining the microRNAs profile underlying the processes by beneficial and detrimental lifestyles, including caloric restriction(CR), exercise and high-fat diet(HF), is necessary for understanding both normal physiology and the pathogenesis of metabolic disease. We used the microarray to detect microRNAs expression in livers from CR, EX and HF mice models. After predicted potential target genes of differentially expressed microRNAs with four algorithms, we applied GO and KEGG to analyze the function of predicted microRNA targets. Results We describe the overall microRNAs expression pattern, and identified 84 differentially expressed microRNAs changed by one or two or even all the three lifestyle modifications. The common and different enriched categories of gene function and main biochemical and signal transduction pathways were presented. Conclusions We provided for the first time a comprehensive and thorough comparison of microRNAs expression profiles in liver among these lifestyle modifications.With this knowledge, our findings provide us with an overall vision of microRNAs in the molecular impact of lifestyle on health as well as useful clues for future and thorough research of the role of microRNAs.