bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two novel ECHS1 variants, affecting splicing and reducing enzyme activity, is associated with mitochondrial encephalopathy in infant: a case report
Authors: Wu Miaojuan , Gao Wenqi , Deng Zhifang , Liu Zhisheng , Ma Jiehui , Xiao Han , Xu Yu , Sun Dan 
Published: April 2020

Abstract
Background
Short-chain enoyl-CoA hydratase (ECHS1) is a multifunctional mitochondrial matrix enzyme involved in the second step of mitochondrial fatty acid β-oxidation. Mitochondrial diseases resulting from ECHS1 mutations are often characterised by encephalopathy, deafness, epilepsy, optic atrophy, cardiomyopathy, dystonia, and lactic acidosis. In this study, we report two novel heterogeneous variants, c.414 + 5G > A (in intron 3) and c.310C > G (in CDS), of ECHS1 in an infant with mitochondrial encephalopathy.

Case presentation
The two novel variants, c.414 + 5G > A (Chr10:135183403) in intron 3 and c.310C > G (Chr10:135183512) in CDS, were identified by next generation sequencing (NGS). A minigene assay was used to analyse the function of the c.414 + 5G > A variant. ECHS1 enzyme activity was measured by spectrophotometry in the patient-derived myoblasts. The 2-year old patient presented with mitochondrial encephalopathy since birth. Clinical features were encephalopathy, epilepsy, and hindered psychomotor and language development. Serum lactate and blood ammonia levels were elevated, and brain magnetic resonance imaging showed abnormal signals in the bilateral frontal, parietal, and occipital cortices and brainstem and basal ganglia. We found two novel heterogeneous variants in ECHS1 in this patient. Minigene assay revealed the c.414 + 5G > A variant as the cause of intronic cryptic splice site activation and 39 bp deletion in mature mRNA. In silico analysis predicted that c.310C > G might change glutamine (Q) to glutamic acid (E) in the 104th amino acid sequence (p.Q104E). To investigate the impact of these two variants on protein function, we constructed a 3D model of human ECHS1 and showed that the variants might alter the highly conserved region in close proximity to the active site, which might hinder, or even halt, enzymatic activity. The experimental assay showed that ECHS1 enzyme activity in the patient-derived myoblasts decreased compared to that in control.

Conclusions
Our findings are the first to report a mitochondrial encephalopathy infant carrying two novel ECHS1 variants, c.414 + 5G > A and c.310C > G, which might be deleterious variants, function as pathogenicity markers for mitochondrial encephalopathy, and facilitate disease diagnosis.
Supervisors’ intention to observe clinical task performance: an exploratory study using the theory of planned behaviour during postgraduate medical training
Authors: de Jonge Laury P. J. W. M. , Mesters Ilse , Govaerts Marjan J. B. , Timmerman Angelique A. , Muris Jean W. M. , Kramer Anneke W. M. , van der Vleuten Cees P. M. 
Published: April 2020

AbstractBackgroundDirect observation of clinical task performance plays a pivotal role in competency-based medical education. Although formal guidelines require supervisors to engage in direct observations, research demonstrates that trainees are infrequently observed. Supervisors may not only experience practical and socio-cultural barriers to direct observations in healthcare settings, they may also question usefulness or have low perceived self-efficacy in performing direct observations. A better understanding of how these multiple factors interact to influence supervisors’ intention to perform direct observations may help us to more effectively implement the aforementioned guidelines and increase the frequency of direct observations.MethodsWe conducted an exploratory quantitative study, using the Theory of Planned Behaviour (TPB) as our theoretical framework. In applying the TPB, we transfer a psychological theory to medical education to get insight in the influence of cognitive and emotional processes on intentions to use direct observations in workplace based learning and assessment. We developed an instrument to investigate supervisors intention to perform direct observations. The relationships between the TPB measures of our questionnaire were explored by computing bivariate correlations using Pearson’s R tests. Hierarchical regression analysis was performed in order to assess the impact of the respective TPB measures as predictors on the intention to perform direct observations.ResultsIn our study 82 GP supervisors completed our TPB questionnaire. We found that supervisors had a positive attitude towards direct observations. Our TPB model explained 45% of the variance in supervisors’ intentions to perform them. Normative beliefs and past behaviour were significant determinants of this intention.ConclusionOur study suggests that supervisors use their past experiences to form intentions to perform direct observations in a careful, thoughtful manner and, in doing so, also take the preferences of the learner and other stakeholders potentially engaged in direct observations into consideration. These findings have potential implications for research into work-based assessments and the development of training interventions to foster a shared mental model on the use of direct observations.
Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records
Authors: Chen Qingyu , Du Jingcheng , Kim Sun , Wilbur W. John , Lu Zhiyong 
Published: April 2020

AbstractBackgroundCapturing sentence semantics plays a vital role in a range of text mining applications. Despite continuous efforts on the development of related datasets and models in the general domain, both datasets and models are limited in biomedical and clinical domains. The BioCreative/OHNLP2018 organizers have made the first attempt to annotate 1068 sentence pairs from clinical notes and have called for a community effort to tackle the Semantic Textual Similarity (BioCreative/OHNLP STS) challenge.MethodsWe developed models using traditional machine learning and deep learning approaches. For the post challenge, we focused on two models: the Random Forest and the Encoder Network. We applied sentence embeddings pre-trained on PubMed abstracts and MIMIC-III clinical notes and updated the Random Forest and the Encoder Network accordingly.ResultsThe official results demonstrated our best submission was the ensemble of eight models. It achieved a Person correlation coefficient of 0.8328 – the highest performance among 13 submissions from 4 teams. For the post challenge, the performance of both Random Forest and the Encoder Network was improved; in particular, the correlation of the Encoder Network was improved by ~ 13%. During the challenge task, no end-to-end deep learning models had better performance than machine learning models that take manually-crafted features. In contrast, with the sentence embeddings pre-trained on biomedical corpora, the Encoder Network now achieves a correlation of ~ 0.84, which is higher than the original best model. The ensembled model taking the improved versions of the Random Forest and Encoder Network as inputs further increased performance to 0.8528.ConclusionsDeep learning models with sentence embeddings pre-trained on biomedical corpora achieve the highest performance on the test set. Through error analysis, we find that end-to-end deep learning models and traditional machine learning models with manually-crafted features complement each other by finding different types of sentences. We suggest a combination of these models can better find similar sentences in practice.
The PRECISE (PREgnancy Care Integrating translational Science, Everywhere) database: open-access data collection in maternal and newborn health
Authors:   The PRECISE Network, Magee Laura A. , Strang Amber , Li Larry , Tu Domena , Tumtaweetikul Warancha , Craik Rachel , Daniele Marina , Etyang Angela Koech , D’Alessandro Umberto , Ogochukwu Ofordile , Roca Anna , Sevene Esperança , Chin Paulo , Tchavana Corssino , Temmerman Marleen , von Dadelszen Peter 
Published: April 2020

AbstractIn less-resourced settings, adverse pregnancy outcome rates are unacceptably high. To effect improvement, we need accurate epidemiological data about rates of death and morbidity, as well as social determinants of health and processes of care, and from each country (or region) to contextualise strategies. The PRECISE database is a unique core infrastructure of a generic, unified data collection platform. It is built on previous work in data harmonisation, outcome and data field standardisation, open-access software (District Health Information System 2 and the Baobab Laboratory Information Management System), and clinical research networks. The database contains globally-recommended indicators included in Health Management Information System recording and reporting forms. It comprises key outcomes (maternal and perinatal death), life-saving interventions (Human Immunodeficiency Virus testing, blood pressure measurement, iron therapy, uterotonic use after delivery, postpartum maternal assessment within 48 h of birth, and newborn resuscitation, immediate skin-to-skin contact, and immediate drying), and an additional 17 core administrative variables for the mother and babies. In addition, the database has a suite of additional modules for ‘deep phenotyping’ based on established tools. These include social determinants of health (including socioeconomic status, nutrition and the environment), maternal co-morbidities, mental health, violence against women and health systems. The database has the potential to enable future high-quality epidemiological research integrated with clinical care and discovery bioscience.
PRECISE pregnancy cohort: challenges and strategies in setting up a biorepository in sub-Saharan Africa
Authors:   The PRECISE Network, Craik Rachel , Russell Donna , Tribe Rachel M. , Poston Lucilla , Omuse Geoffrey , Okiro Patricia , Chege David , Diatta Mathurin , Sesay Abdul Karim , Cuamba Inocencia , Carrilho Carla , Sevene Esperança , Flint-O’Kane Meriel , von Dadelszen Peter 
Published: April 2020

Abstract
Background and objective
PRECISE is a population-based, prospective pregnancy cohort study designed for deep phenotyping of pregnancies in women with placenta-related disorders, and in healthy controls. The PRECISE Network is recruiting ~ 10,000 pregnant women in three countries (The Gambia, Kenya, and Mozambique) representing sub-Saharan Africa. The principal aim is to improve our understanding of pre-eclampsia, fetal growth restriction and stillbirth. This involves the creation of a highly curated biorepository for state of the art discovery science and a rich database of antenatal variables and maternal and neonatal outcomes. Our overarching aim is to provide large sample numbers with adequate power to address key scientific questions. Here we describe our experience of establishing a biorepository in the PRECISE Network and review the issues and challenges surrounding set-up, management and scientific use.

Methods
The feasibility of collecting and processing each sample type was assessed in each setting and plans made for establishing the necessary infrastructure. Quality control (QC) protocols were established to ensure that biological samples are ‘fit-for-purpose'. The management structures required for standardised sample collection and processing were developed. This included the need for transport of samples between participating countries and to external academic/commercial institutions.

Results
Numerous practical challenges were encountered in setting up the infrastructure including facilities, staffing, training, cultural barriers, procurement, shipping and sample storage. Whilst delaying the project, these were overcome by establishing good communication with the sites, training workshops and constant engagement with the necessary commercial suppliers. A Project Executive Committee and Biology Working Group together defined the biospecimens required to answer the research questions paying particular attention to harmonisation of protocols with other cohorts so as to enable cross-biorepository collaboration. Governance structures implemented include a Data and Sample Committee to ensure biospecimens and data will be used according to consent, and prioritisation by scientific excellence. A coordinated sample and data transfer agreement will prevent delay in sample sharing.

Discussion
With adequate training and infrastructure, it is possible to establish high quality sample collections to facilitate research programmes such as the PRECISE Network in sub-Saharan Africa. These preparations are pre-requisites for effective execution of a biomarker-based approach to better understand the complexities of placental disease in these settings, and others.
Clinical course and outcome of 107 patients infected with the novel coronavirus, SARS-CoV-2, discharged from two hospitals in Wuhan, China
Authors: Wang Dawei , Yin Yimei , Hu Chang , Liu Xing , Zhang Xingguo , Zhou Shuliang , Jian Mingzhi , Xu Haibo , Prowle John , Hu Bo , Li Yirong , Peng Zhiyong 
Published: April 2020

Abstract
Background
In December 2019, coronavirus disease 2019 (COVID-19) outbreak was reported from Wuhan, China. Information on the clinical course and prognosis of COVID-19 was not thoroughly described. We described the clinical courses and prognosis in COVID-19 patients.

Methods
Retrospective case series of COVID-19 patients from Zhongnan Hospital of Wuhan University in Wuhan and Xishui Hospital, Hubei Province, China, up to February 10, 2020. Epidemiological, demographic, and clinical data were collected. The clinical course of survivors and non-survivors were compared. Risk factors for death were analyzed.

Results
A total of 107 discharged patients with COVID-19 were enrolled. The clinical course of COVID-19 presented as a tri-phasic pattern. Week 1 after illness onset was characterized by fever, cough, dyspnea, lymphopenia, and radiological multi-lobar pulmonary infiltrates. In severe cases, thrombocytopenia, acute kidney injury, acute myocardial injury, and adult respiratory distress syndrome were observed. During week 2, in mild cases, fever, cough, and systemic symptoms began to resolve and platelet count rose to normal range, but lymphopenia persisted. In severe cases, leukocytosis, neutrophilia, and deteriorating multi-organ dysfunction were dominant. By week 3, mild cases had clinically resolved except for lymphopenia. However, severe cases showed persistent lymphopenia, severe acute respiratory dyspnea syndrome, refractory shock, anuric acute kidney injury, coagulopathy, thrombocytopenia, and death. Older age and male sex were independent risk factors for poor outcome of the illness.

Conclusions
A period of 7–13 days after illness onset is the critical stage in the COVID-19 course. Age and male gender were independent risk factors for death of COVID-19.
Evaluation of the probiotic attributes of Bacillus strains isolated from traditional fermented African locust bean seeds (Parkia biglobosa), “daddawa”
Authors: Nwagu Tochukwu Nwamaka , Ugwuodo Chika Jude , Onwosi Chukwudi O. , Inyima Ogechukwu , Uchendu Oluoma Chizaram , Akpuru Chioma 
Published: April 2020

Abstract
Background
The involvement of probiotic cultures in food fermentation guarantees enhanced organoleptic properties and maximum consumer health benefits. In this study, isolated Bacillus cultures used in the fermentation of African locust bean seeds “Parkia biglobosa” into the food condiment “daddawa” were evaluated for probiotic attributes. Bacillus cereus strains BC1 and BC2 were tested for tolerance to acid, common salt (NaCl), and bile salt. Auto-aggregation and adhesion to epithelial cells, antibiotic sensitivity profile, hemolytic pattern, and antibacterial activity were also evaluated. To demonstrate further health benefit, spores of strain BC1 were investigated for anti-inflammatory potential employing the rat paw edema technique.

Results
Both Bacillus cereus strains showed antagonistic activity against pathogenic Escherichia coli and Staphylococcus aureus. BC1 was more acid-stress tolerant than BC2, maintaining 107.6% viability after 3 h incubation in MRS broth of pH 2.5. However, at 97.74% viability after incubation for 3 h, BC2 was more tolerant to 0.4 % bile salt. The Bacillus cereus strains were susceptible to all antibiotics tested with the exception of norfloxacin and thrived under high saline stress. Both strains were protease producers and non-hemolytic on sheep blood agar. The edema inhibition study revealed that spores of Bacillus cereus strain BC1 had anti-inflammation potential and produced no physiological toxicity on the animals.

Conclusion
These results indicate that the Bacillus cultures for “daddawa” production are good candidates for probiotics and have the potential for application in both animal and human formulations for increased health benefit to consumers.
Application of propidium monoazide coupled with quantitative PCR to evaluate cell viability of Bifidobacterium animalis subsp. lactis in a non-dairy probiotic beverage
Authors: Dias Carolinne Odebrecht , Scariot Mirella Crhistine , de Mello Castanho Amboni Renata Dias , Arisi Ana Carolina Maisonnave 
Published: April 2020

AbstractPurposeIn this study, a PMA-qPCR assay was developed for the enumeration ofBifidobacterium animalissubsp.lactisBB-12 viable cells in a non-dairy probiotic beverage.MethodsProbiotic viability was monitored in three formulations of probiotic passion fruit juice microencapsulated by spray drying, during 30 days of storage at 4 °C. Viable cells were quantified using qPCR and PMA-qPCR assays targetingtufgene and by plate counting method.ResultsThe limit of detection for all samples was 103genome copies, corresponding to 21.3 pg of DNA. Higher CFU values were obtained forB. lactisBB-12 enumeration by qPCR, when compared to those obtained by PMA-qPCR and plate count, for all probiotic juice microcapsules. Similar quantification values were obtained by PMA-qPCR and plate counting for all samples and remained above 8 log CFU/g during the storage period.ConclusionThese results demonstrated that the PMA-qPCR technique is a promising approach forB. lactisBB-12 viable cell enumeration in complex matrices such as passion fruit juice microcapsules. This PMA-qPCR assay allowed the achievement of reliable results faster than with the traditional plate counting method.
Perceptions of health providers towards the use of standardised trauma form in managing trauma patients: a qualitative study from Tanzania
Authors: Sawe Hendry R. , Sirili Nathanael , Weber Ellen , Coats Timothy J. , Reynolds Teri A. , Wallis Lee A. 
Published: April 2020

Abstract
Background
Trauma registries (TRs) are essential to informing the quality of trauma care within health systems. Lack of standardised trauma documentation is a major cause of inconsistent and poor availability of trauma data in most low- and middle-income countries (LMICs), hindering the development of TRs in these regions. We explored health providers’ perceptions on the use of a standardised trauma form to record trauma patient information in Tanzania.

Methods
An exploratory qualitative research using a semi-structured interview guide was carried out to purposefully selected key informants comprising of healthcare providers working in Emergency Units and surgical disciplines in five regional hospitals in Tanzania. Data were analysed using a thematic analysis approach to identify key themes surrounding potential implementation of the standardised trauma form.

Results
Thirty-three healthcare providers participated, the majority of whom had no experience in the use of standardised charting. Only five respondents had prior experience with trauma forms. Responses fell into three themes: perspectives on the concept of a standardised trauma form, potential benefits of a trauma form, and concerns regarding successful and sustainable implementation.

Conclusion
Findings of this study revealed wide healthcare provider acceptance of moving towards standardised clinical documentation for trauma patients. Successful implementation likely depends on the perceived benefits of using a trauma form as a tool to guide clinical management, standardise care and standardise data reporting; however, it will be important moving forward to factor concerns brought up in this study. Potential barriers to successful and sustainable implementation of the form, including the need for training and tailoring of form to match existing resources and knowledge of providers, must be considered.
Beneficial insect community of Moroccan citrus groves: assessment of their potential to enhance biocontrol services
Authors: Smaili Moulay Chrif , Boutaleb-Joutei Abdelmalek , Blenzar Abdelaali 
Published: April 2020

AbstractIn citrus groves, beneficial insects that reduce abundance of pests are considered a key component of integrated pest management strategies. The aim of this article was to assess the biodiversity of parasitoids and predators in citrus orchards in Moroccoto facilitate future investigations on their potential as biocontrol agents. Data of 105 citrus beneficial insects were gathered and summarized in a data matrix. Variables such nature, target pests, type, establishment, and efficacy were assessed. More than two-thirds of parasitoids and predators species identified in citrus groves of Morocco (105 species) are native (> 70%). Both groups represent only a small fraction of the introduced species. The mostly attack armored scale insects (Diaspididae) and aphids (Aphididae). The ladybeetleRodolia cardinalis(Mulsant) (Coleoptera: Coccinellidae) is the first beneficial species introduced in 1921 to the Moroccan citrus orchards to control the cottony cushion scaleIcerya purchasi(Maskell) (Hemiptera: Monophlebidae). Major introductions of these parasitoids and predators were carried out during the ninetieth to control the main citrus pests whereas they were accidentally introduced. These purposely introduced species are mainly Aphelinidae, Encyrtidae, Eulophidae, Coccinellidae, and Phytoseiidae. Whereas a high proportion of the introduced beneficial insects was established and no species have been reported to be harmful to this date. Considering only the introduced species used in classical biological control context, about 20 and 40% of them are considered as effective or partially effective, respectively.
INTERAÇÃO ENTRE TEXTO E LEITOR: UMA LEITURA DE “TCHAU”, DE LYGIA BOJUNGA / Interaction between text and reader: a reading of “Tchau”, by Lygia Bojunga
Authors: Macêdo Jhennefer Alves 
Published: April 2020

Ao realizarmos uma breve revisão no panorama histórico que abarca os estudos que elegem a literatura como corpus de investigação e análise, constata-se que nas novas roupagens teóricas, as quais foram iniciadas desde a década de 60, um novo elo foi formado: a leitura, a experiência estética e o leitor. A partir de então, entende-se que uma obra literária, antes vista como fechada e imutável, é aberta a possíveis interpretações do leitor, assim como está em constante processo de transformação. Ademais, interligada a essa concepção está a ideia de que os leitores não são meros receptores de textos literários acabados, ao contrário, os receptores são participantes ativos no processo da leitura e possuem relevante importância em relação à recepção e à permanência de uma obra no decorrer do tempo. Sabendo disso, o presente artigo objetiva evidenciar, por meio de um relato acerca de uma experiência, sendo essa desenvolvida em uma turma de 7º ano, do Ensino Fundamental II, de leitura com o conto “Tchau” (2008), de Lygia Bojunga, como aconteceu a recepção desse texto em sala de aula, bem como o efeito que este causou em seus leitores. Sendo assim, para fundamentarmos as discussões desenvolvidas no decorrer desse estudo, realizamos a leitura das obras de alguns autores, tais como Iser (1996), Solé (1998), Colomer (2017) e Girotto e Souza (2010).