bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing the quality and scope of paediatric primary care in South Africa: Evaluating contextual impacts of the introduction of the Practical Approach to Care Kit for children (PACK Child)
Authors: Murdoch Jamie , Curran Robyn , Cornick Ruth , Picken Sandy , Bachmann Max , Bateman Eric , Simelane Makhosazana Lungile , Fairall Lara 
Published: February 2020

Abstract
Background: Despite significant reductions in mortality, preventable and treatable conditions remain leading causes of death and illness in children in South Africa. The PACK Child intervention, comprising clinical decision support tool (guide), training strategy and health systems strengthening components, was developed to expand on WHO’s Integrated Management of Childhood Illness programme, extending care of children under 5 years to those aged 0-13 years, those with chronic conditions needing regular follow-up, integration of curative and preventive measures and routine care of the well child. In 2017-2018, PACK Child was piloted in 10 primary healthcare facilities in the Western Cape Province. Here we report findings from an investigation into the contextual features of South African primary care that shaped how clinicians delivered the PACK Child intervention within clinical consultations.
Methods: Process evaluation using linguistic ethnographic methodology which provides analytical tools for investigating human behaviour, and the shifting meaning of talk and text within context. Methods included semi-structured interviews, focus groups, ethnographic observation, audio-recorded consultations and documentary analysis. Analysis focused on how mapped contextual features structured clinician-caregiver interactions.
Results: Primary healthcare facilities demonstrated an institutionalised orientation to minimising risk upheld by provincial documentation, providing curative episodic care to children presenting with acute symptoms, and preventive care including immunisations, feeding and growth monitoring, all in children 5 years or younger. Children with chronic illnesses such as asthma rarely receive routine care. These contextual features constrained the ability of clinicians to use the PACK Child guide to facilitate diagnosis of long-term conditions, elicit and manage psychosocial issues, and navigate use of the guide alongside provincial documentation.
Conclusion: Our findings provide evidence that PACK Child is catalysing a transition to an approach that strikes a balance between assessing and minimising risk on the day of acute presentation and a larger remit of care for children over time. However, optimising success of the intervention requires reviewing priorities for paediatric care which will facilitate enhanced skills, knowledge and deployment of clinical staff to better address acute illnesses and long-term health conditions of children of all ages, as well as complex psychosocial issues surrounding the child.
One-step RT-qPCR assay for ZIKV RNA detection in Aedes aegypti samples: A protocol to study infection &amp; gene expression during ZIKV infection
Authors: Araujo Ricardo Vieira , Feitosa-Suntheimer Fabiana , Gold Alexander S. , Londono-Renteria Berlin , Colpitts Tonya Michelle 
Published: February 2020

Abstract
Background : Zika virus (ZIKV) is transmitted to humans during the bite of an infected mosquito. In a scenario of globalization and climate change, the frequency of outbreaks has and will increase in areas with competent vectors, revealing a need for continuous improvement of ZIKV detection tools in vector populations. A simple, rapid and sensitive assay for viral detection is qRT-PCR, yet oligos optimized for ZIKV detection in mammalian cells and samples have repeatedly shown high background when used on mosquito RNA. In this work we present a one-step qRT-PCR protocol that allows for the detection of ZIKV in mosquitoes and for the evaluation of gene expression from the same mosquito sample and RNA. This assay is a less expensive qRT-PCR approach than that most frequently used in the literature and has a much lower background, allowing for confident detection. Methods : Our new oligo design to detect ZIKV RNA included in silico analysis of both viral and mosquito ( Ae. aegypti and Ae. albopictus )genomes, targeting sequences conserved between Asian and African ZIKV lineages, but not matching Aedes genomes. This assay will allow researchers to avoid nonspecific amplification in insect samples due to viral integration into the mosquito genome, a phenomenon known to happen in wild and colonized populations of mosquitoes. Standard curves constructed with in vitro transcribed ZIKV RNA were used to optimize the sensitivity, efficiency and reproducibility of the assay. Results: Finally, the assay was used with success to detect both ZIKV RNA in infected mosquitoes and to detect expression of the Defensin A gene, an antimicrobial peptide (AMP) involved in Aedes aegypti immune response to virus infection. Conclusions : The experimental approach to detect ZIKV RNA in Aedes aegypti presented here has demonstrated to be specific, sensitive and reliable, and additionally it allows for the analysis of mosquito gene expression during ZIKV infection.
Five Novel PRNP Gene Polymorphisms and Their Potential Effect on Scrapie Susceptibility in Three Native Ethiopian Sheep Breeds
Authors: Teferedegn Eden Yitna , Yaman Yalcin , Un Cemal 
Published: February 2020

Abstract
Background Classical scrapie susceptibility in sheep has been linked to three polymorphisms at codon 136, 154, and 171 in the prion protein gene ( PRNP) whereas atypical scrapie susceptibility is related to polymorphisms at position 141. Many other variants over the length of the PRNP have been reported. Some of the variants may play crucial roles in fighting against the emergence of a new form of scrapie disease. Scrapie surveillance, scrapie associated genotyping and PRNP characterization studies have been conducted across the globe. However, such in-depth studies have never addressed the African continent’s sheep breeds. Therefore, genotyping native Ethiopian sheep breed’s PRNP gene has socioeconomic and scientific merits. This study aimed to identify PRNP variants in three native Ethiopian sheep breeds and their potential effect on scrapie susceptibility. Results Five novel variants were identified in the PRNP gene of three native Ethiopian sheep breeds. Four non-synonymous heterozygous substitutions i.e. H99Q (CAC-->CAA), H99L (CAC-->CTA), A116E (GCA-->GAA), A116T (GCA-->ACA) and one synonymous N103N (AAC-->AAT) were detected. In addition to the novel variants, polymorphisms at codon 126,127,138,142,146,231 and 237 were also identified. The haplotype ARR was observed in Menz and Afar breeds at frequencies of 0.02 and 0.05 respectively. Neither ARR/ARR nor VRQ/VRQ genotypes were identified in the population under study. Conclusion Two of the novel variants at codon 99 and 103 that are placed closer to the proteinase K cleavage site and the variant at codon 116 in the palindrome region along with variants at codon 127 in glycine repeat domain may influence the conformational flexibility of prion protein. The rarity of ARR haplotype and the abundance of 141L variant demonstrated that the present study population was less resistant to classical scrapie and less predisposed to genotype associated atypical scrapie. This study provides a valuable dataset that can be potentially integrated into selective breeding strategies during interbreeding, crossbreeding and help to take precautionary measures against scrapie. Keywords: Ethiopian sheep; Novel Variations; Polymorphism; Prion gene; Scrapie Susceptibility
A Randomized Controlled 24-week Trial to Evaluate the Efficacy and Safety of Bi Qi Capsule for the Treatment of Knee Osteoarthritis
Authors: Xia Xuan , Wang Huanrui , Liu Zehao , Cai Xiao , Chen Xianghong , Lv Yuan , Chen Xiumin , Huang Qingchun , Huang Runyue 
Published: February 2020

Abstract
Objective: To evaluate the efficacy and tolerability of Bi Qi capsule in knee osteoarthritis. Patients and methods: An open-label, 24-week, parallel randomized controlled trial conducted between October 2016 to October 2018. Patients with knee osteoarthritis were randomly assigned 1:1 to receive Bi Qi capsule (1.2g, twice a day) and Calcitriol capsule (0.25ug, once a day). Western Ontario and McMaster Universities Osteoarthritis (WOMAC) was the primary outcome, including pain, stiffness, and function subscale scores. Secondary outcome measures were visual analogue scale (VAS) score for the patients assessment of pain, bone mineral density (BMD), patient’s assessment of function using the Health Assessment Questionnaire (HAQ). Safety was assessed by recording adverse events (AEs). Results: 100 patients were included in the study. 15(15%) patients discontinued the study because of lack of efficacy, adverse events and loss of follow up. At the end of the treatment ,the decrease in WOMAC total score was -8.7(4.9) and -5.4(5.6) and improvement of WOMAC function was -4.88(3.6) and -2.70(3.86) in the Bi Qi group and the controlled group, respectively (p＜0.01). The improvement in BMD of left femoral neck was 0.05(0.2) and -0.01(0.04) , improvement in T score of left femoral neck was 0.15(0.5) and -0.05(0.3) in the Bi Qi group and the controlled group, respectively (p＜0.01). No significant difference was observed between treatment groups for changes in WOMAC pain, WOMAC stiffness, VAS, BMD of lumbar spine, T score of lumber spine and HAQ over 24 weeks. Two adverse events were reported in Bi Qi group: facial edema (n=1), nausea (n=1) and one adverse events was reported in controlled group: lip swelling (n=1). All these adverse events were mild and could be alleviated after withdrawing treatment. Conclusion: It can be concluded that Bi Qi capsule was found to be effective and safe in reducing WOMAC total score, improving WOMAC function and BMD in individuals suffering from KOA.
Epidemiological analysis of Porcine Viral Diarrhea Pathogens in Local Area
Authors: Shi Ying , Li Benqiang , Tao Jie , Cheng Jinghua , liu Huili 
Published: February 2020

Abstract
Background Porcine viral diarrhea can cause great damage to the pig industry and high mortality to piglets. Furthermore, multiple pathogen infections and synergistic infections commonly existed in clinic. This has resulted in great difficulties in determining the main pathogenic factors, which would delay the prevention and control of diseases. Methods A total of 518 porcine stool specimens were collected from 9 pig herds in Shanghai, China from 2015 to 2017 and used for pathogen detection. A Luminex xTAG multiplex detection method was developed for the detection of 11 viral diarrhea pathogens, which allows for the simultaneous qualitative and quantitative detection of viral diarrhea pathogens in clinical samples. Results The minimum detection rate of the Luminex xTAG multiplex detection method was at least 10 times higher than the traditional PCR method. As a result, 209 (40.3%) were positive for porcine kobuvirus (PKoV), 138 (26.6%) for porcine astrovirus (PAstV), 91 (17.6%) for porcine epidemic diarrhea virus (PEDV), 78 (15.1%) for porcine sapelovirus (PSV), 68 (13.1%) for porcine sapovirus (PoSaV), 27 (5.2%) for porcine teschovirus (PTV), 25 (4.8%) for porcine deltacoronavirus (PDCoV), 17 (3.3%) for porcine rotavirus (PoRV), 16 (3.1%) for transmissible gastroenteritis virus (TGEV), 10 (1.9%) for porcine torovirus (PToV), and 9 (1.7%) for bovine viral diarrhea virus (BVDV), respectively. Furthermore, multiple infection rate of diarrhea sample was 17.57% for dual-infection, 11.58%for triple-infection, 4.63% for quadruple-infection, 0.77% for quintuple-infection, 0.58% for sextuple-infection and septuple-infection, respectively. Infection pattern of the viral diarrheal pathogens was changing, and different farm had the various diarrhea infection patterns, which proved the great importance of epidemiological surveillance and the guidance effect to clinical production. PoSaV, PoRV, PAstV, PToV and PEDV were indicated as the predominant viruses of clinical samples collected in 2017 by the quantitative analysis. Conclusions Here we provide a Luminex xTAG multiple detection method for viral diarrhea pathogen infection in clinical,which was more sensitive and specific than general multiplex PCR method. Furthermore, the surveillance confirmed the complicated infection status in China, which demonstrated the need for continuous surveillance and provided data for the prevention and control of viral diarrhea.
An ATP-free packaging of T4 DNA
Authors: Hara Seiko , Koike Isao 
Published: February 2020

Abstract

Packaging of viral DNA into a capsid with the liquid crystalline density is a crucial step of the viral reproduction. The DNA packaging with the ATP fueled molecular motor is an established packaging system of viral DNA. However, the velocity and the efficiency are not well match with the in vivo processes. On the other hand, DNA compacts with the conformational change by multivalent cations exclusively of the valences higher than three. The conformational change of DNA was not considered as the vehicle of DNA packaging of viruses. Here, T4 DNA, ejected from a capsid in the ambient concentration of phosphate corresponding to the intra-cell concentration, is packaged into the capsid when the ambient concentration of phosphate decreases to the extra-cell concentration in the coexistence with divalent cations, Ca2+ and Mg2+. The compaction and packaging process coincide with the conformational change of DNA. Divalent cations can compact T4 DNA when the counter anion is phosphate. The DNA-packaged and re-generated virions showed equivalent infective ability with the original populations. The conformational changes of DNA between compact forms and coil forms were differentiated by the fluorescent microscopy. Identification between packaged- or unpackaged-DNA was confirmed by enzymatically. The infectious ability of the re-generated virions was confirmed by pfu. The concentration of ATP in the packaging process was measured by luminometric method. The packaging is proceeded in pM or lower concentration of ATP. This is a new packaging process of viral DNA practically free from ATP into which conformational change of DNA is incorporated. The conventional and new packaging processes may cooperate to accomplish the DNA packaging process of T4. The results may provide new interpretations of the life cycle of T4.
Infrared and Visible Image Fusion Based on Nonlinear Enhancement and NSST Decomposition
Authors: XING Xiaoxue , LIU Cheng , LUO Cong , XU Tingfa 
Published: February 2020

Abstract
In Multi-scale Geometric Analysis (MGA)-based fusion methods for infrared and visible images, adopting the same representation for the two types of the images will result in the non-obvious thermal radiation target in the fused image, which can hardly be distinguished from the background. To solve the problem, a novel fusion algorithm based on nonlinear enhancement and Non-Subsampled Shearlet Transform (NSST) decomposition is proposed. Firstly, NSST is used to decompose the two source images into low- and high-frequency sub-bands. Then, the wavelet transform(WT) is used to decompose high-frequency sub-bands into obtain approximate sub-bands and directional detail sub-bands. The “average” fusion rule is performed for fusion for approximate sub-bands. And the “max-absolute” fusion rule is performed for fusion for directional detail sub-bands. The inverse WT is used to reconstruct the high-frequency sub-bands. To highlight the thermal radiation target, we construct a non-linear transform function to determine the fusion weight of low-frequency sub-bands, and whose parameters can be further adjusted to meet different fusion requirements. Finally, the inverse NSST is used to reconstruct the fused image. The experimental results show that the proposed method can simultaneously enhance the thermal target in infrared images and preserve the texture details in visible images, and which is competitive with or even superior to the state-of-the-art fusion methods in terms of both visual and quantitative evaluations.
An Easy-to-use Clinical Nomogram for Predicting the Prognosis of Patients with Hepatocellular Carcinoma Concomitantly Suffer from Severe Fibrosis or Cirrhosis: A Population-based Analysis.
Authors: Hanyue Wang , Shiye Ruan , Yiping Zou , Liang Jin , Haosheng Jin , Chaofeng Hu 
Published: February 2020

Abstract
Background Patients with hepatocellular carcinoma (HCC) concomitantly suffer from liver cirrhosis may have worse prognosis. Based on Surveillance, Epidemiology, and End Results (SEER) database, we evaluated the overall survival (OS) and cancer-specific survival (CSS) of these patients. Methods A total of 2,369 patients were selected from the SEER database. They were classified into F0 (n=691) and F1 (n=1,678) groups by different Ishak fibrosis score. Propensity score matching (PSM) and Kaplan-Meier method were performed to evaluate the OS and CSS. The F1 group were randomized into training sub-set (n = 1,176, 70%) and validation sub-set (n = 502, 30%) for further construction and validation of nomogram . Results After matched, there were statistically significant worse outcome for F1 group patients compared with F0 group (n=587, OS: P<0.001, CSS: P<0.001). Six independent predictors for both OS and CSS were identified to construct the nomograms by COX regression analyses. The nomogram performed well concerning its ability of discrimination and calibration and its net benefits compared with the conventional staging system. Conclusions Patients with HCC concomitantly suffer from severe fibrosis or cirrhosis has a significant worse survival compared with none or moderate fibrosis patients. The validated nomograms provided useful prediction of survival.
Possible therapeutic effects of berberine on bone damage in high-fat diet-induced obese rats
Authors: Wang Yan , Chen Fulian , Wang Hongwei , Wang Yan , Zhang Mengqi , Huan Zhikun , Li Jiaxuan , Shao Shanshan , Yu Chunxiao , Xu Jin 
Published: February 2020

Abstract
Background Obesity has a negative impact on bone health; thus far, no specific pharmacotherapy has been approved. Berberine has shown improvements in osteoporosis in some animal models. However, it remains unknown whether berberine ameliorates obesity-induced bone damage. This study aims to evaluate the effect of berberine on bone damage in high-fat diet (HFD)-induced obese rats. Methods Male Sprague-Dawley rats were randomly assigned to a normal control diet (ND) group or HFD group. After the HFD induced obesity, the models were successfully established. Then, these rats were randomly divided into the HFD + berberine (HB) group or HFD group and were intraperitoneally administered berberine or an equivalent volume of DMSO, respectively, once a day for another 10 weeks. Micro-CT and three-point bending tests were conducted to evaluate bone microstructure and biomechanics. Serum was collected for the detection of P1NP, CTX-1, calcium (Ca) and phosphorus (P), tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β). HE staining was performed to observe the number of trabecular and bone marrow adipocytes. Results HFD-induced obese rats displayed decreased biomechanical properties, such as maximum load, maximum fracture load, ultimate tensile strength, stiffness, and energy absorption, compared with the ND rats (p<0.05). However, berberine attenuated bone damage, including maximum load, maximum fracture load, and stiffness, in the HB group compared with the HFD group (p<0.05). Trabecular bone markers were decreased in the HFD group compared with the ND group (p<0.05). All parameters were improved, as shown by micro-CT and HE staining, in the HB group compared to the HFD group. Cortical bone markers were not significantly different among all groups. Moreover, CTX-1, TNF-α, IL-1β and the number of adipocytes in bone marrow were significantly increased in HFD-induced obese rats. After treatment with berberine, TNF-α, IL-1β and the number of adipocytes in bone marrow were significantly decreased, and P1NP levels were higher in the HB group than in the HFD group. Conclusions Berberine might be a potential therapeutic agent for treating bone damage in HFD-induced obese rats by inhibiting inflammatory factors, reducing bone marrow adiposity and improving bone formation.
DeepSeqPanII: an interpretable recurrent neural network model with attention mechanism for peptide-HLA class II binding prediction
Authors: LIU ZHONGHAO , Jin Jing , Cui Yuxin , Xiong Zheng , Nasiri Alireza , Zhao Yong , Hu Jianjun 
Published: February 2020

Abstract
Background: Human leukocyte antigen (HLA) complex molecules play an essential role in immune interactions by presenting peptides on the cell surface to T cells. With significant progress in deep learning, a series of neural network based models have been proposed and demonstrated with their good performances for peptide-HLA class I binding prediction. However, there still lack effective binding prediction models for HLA class II protein binding with peptides due to its inherent challenges. In this work, we present a novel sequence-based pan-specific neural network structure, DeepSeaPanII, for peptide-HLA class II binding prediction. Compared with existing pan-specific models, our model is an end-to-end neural network model without the need for pre- or post-processing on input samples. Results: The leave-one-allele-out cross validation and benchmark evaluation results show that our proposed network model achieved state-of-the-art performance in HLA-II peptide binding. Besides state-of-the-art performance in binding affinity prediction, DeepSeqPanII can also extract biological insight on the binding mechanism over the peptide and HLA sequences by its attention mechanism based binding core prediction capability. Conclusions: In this work, we present a novel neural network structure for peptide-HLA class II binding prediction. It has state-of-the-art performance and could display insightful information it learned benefiting from attention module we carefully designed. Without requiring additional data, this structure could be applied to other related sequence problems. The source code and trained models are freely available at https://github.com/pcpLiu/DeepSeqPanII.
Propionic acid induces dendritic spine loss by MAPK/ERK signaling and dysregulation of autophagic flux
Authors: Choi Hyosun , Mun Ji Young 
Published: February 2020

Abstract
Propionic acid (PPA) is a short-chain fatty acid that is an important mediator of cellular metabolism. It is also a by-product of human gut enterobacteria and a common food preservative. A recent study found that rats administered with PPA showed autistic-like behaviors like restricted interest, impaired social behavior, and impaired reversal in a T-maze task. This study aimed to identify a link between PPA and autism phenotypes facilitated by signaling mechanisms in hippocampal neurons. Findings indicated autism-like pathogenesis associated with reduced dendritic spines in PPA-treated hippocampal neurons. To uncover the mechanisms underlying this loss, we evaluated autophagic flux, a functional readout of autophagy, using relevant biomedical markers. Results indicated that autophagic flux is impaired in PPA-treated hippocampal neurons. At a molecular level, the mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway was activated and autophagic activity was impaired. We also observed that a MAPK inhibitor rescued dendritic spine loss in PPA-treated hippocampal neurons. Taken together, these results suggest a previously unknown link between PPA and autophagy in spine formation regulation in hippocampal neurons via MAPK/ERK signaling. Our results indicate that MAPK/ERK signaling participates in autism pathogenesis by autophagy disruption affecting dendritic spine density. This study may help to elucidate other mechanisms underlying autism and provide a potential strategy for treating ASD-associated pathology.