bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Phone Messaging improves Tuberculosis Treatment Success? A Systematic review and Meta-analysis
Authors: Gashu Kassahun Dessie , Gelaye Kassahun Alemu , Mekonnen Zeleke Abebaw , Lester Richard , Tilahun Binyam 
Published: September 2019

Abstract
Background: Compliance to anti-TB treatment is crucial in achieving cure and avoiding the emer­gence of drug resistance. Electronic health (eHealth) interventions are included in the strategy to end the global Tuberculosis (TB) epidemic by 2035. Evidences showed that mobile messaging systems could improve patient adherence to clinic appointment for diagnosis and treatment. This review aimed to assess the effect of mobile-phone messaging on anti-TB treatment success. Methods: All randomized controlled trial (RCT) and quasi-experimental studies done prior to August 26, 2019 were included in the review. Studies were retrieved from PubMed, EMBASE, Cochrane and ScienceDirect databases. In addition, gray literatures and non-indexed articles were searched on Google and Google scholar. Searching strategies was based on PICO criteria and using Medical Subject Headings (MeSH), Boolean search operators, truncation symbols to robust the searching scheme. Articles were independently screened and appraised by two authors. PRISMA flow diagrams were used to summarize article selection process, see Additional file 1. Results: A total of 1237 articles were identified, with 14 meeting the eligibility criteria for qualitative synthesis. Nine studies with a total of 6030 TB patients (2893 in intervention and 3137 in control groups) were included in meta-analysis. The pooled effect of mobile-phone messaging revealed a small increase in treatment success compared to standard of care (RR 1.04, 95% CI 1.02 to 1.06), with low heterogeneity (I 2 =25%, p<0.0001). In the review, performance, detection and attrition biases were reported as major risk of biases. Conclusions: Mobile-phone messaging showed a modest effect in improving anti-TB treatment success; however, the quality of evidence was low. Further controlled studies are needed to increase the evidence-base on the role of mHealth interventions to improve TB care. Protocol registration number: CRD420170744339 http://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42017074439 Key Words: Mobile phone, Treatment success, Text messaging, Tuberculosis
Machine learning reveals Mycobacterium tuberculosis genotypes and anatomic disease site impacts drug resistance and disease transmission among patients with proven extra-pulmonary tuberculosis
Authors: Sibandze Busizwe , Magazi Beki Themba , Malinga Lesibana Anthony , Maningi Nontuthuko Excellent , Shey Bong Akee , Pasipanodya Jotam G , Mbelle Nontombi N 
Published: September 2019

Abstract
Background Genotypic characterization of Mycobacteria tuberculosis ( Mtb ) isolates in pulmonary tuberculosis is well documented; however, there is dearth of information on extrapulmonary tuberculosis (EPTB). Here, we investigate Mtb drug resistance and transmission patterns in EPTB patients diagnosed and treated in the Tshwane metropolitan, South Africa. Methods Consecutive Mtb culture-positive non-pulmonary isolates underwent mycobacterial genotyping and were assigned to phylogenetic lineages and transmission clusters based on spoligotypes. The Genotype MTBDR plus assay was used for isoniazid and rifampin susceptibility testing. Ensembles of machine learning (ML) algorithms were used to identify clinically meaningful patterns in data. We computed odds ratio (OR), attributable risk (AR) and their corresponding 95% confidence intervals (CI). Based on ML outputs, we examined factors associated with EPTB sites, drug resistance and clustering for the period between July 1 st , 2014 and January 31 st , 2015. Results A total of 75 isolates were identified during study period: we excluded 5 (7%) Mycobacterium bovis isolates. The overall proven EPTB incidence of 4.43 (95% CI: 3.72-5.23) per 100,000 population per year is lower than prior reports. However, the frequency distribution across most frequently encountered EPTB disease sites, including pleura, peritoneum, meninges and skin, were consistent with those reports. The largest cluster comprised of 25 (36%) Mtb strains belonged to East Asian lineage. East Asian lineage was significantly more likely to occur within a chain of EPTB transmission when compared to Euro-American and East-African Indian lineages: OR= 10.11 (95% CI: 1.56-116). Lymphadenitis, meningitis and skin TB, were significantly more likely to be associated with drug resistance: OR=12.69 (95% CI: 1.82-141.60) and AR = 0.25 (95% CI: 0.06-0.43) when compared with other EPTB sites, which suggests that poor rifampin penetration might be a contributing factor. Conclusions Majority of Mtb strains circulating in the city of Tshwane metropolis belongs to East Asian, Euro-American and East-African Indian lineages, and each of these are likely to be clustered, suggesting on-going EPTB disease transmission. On the other hand, 25% of the drug resistance is attributable to sanctuary EPTB sites notorious for poor rifampin penetration, suggesting role for poor drug dosing.
Socio-Demographic, Economic and Clinical predictors of HAART Adherence Competence for HIV Positive adults at Felege Hiwot Teaching and Specialized Hospital, North West Ethiopia
Authors: Tegegne Awoke Seyoum 
Published: September 2019

Abstract
Background : Currently, around 36.7 million people in the world are living with HIV. Among these, 52% are living in sub-Saharan African. Antiretroviral therapy (ART) has played an important role in improving the prognosis and quality of life of HIV/AIDS patients, and in reducing the rate of disease progression and death. Several previous researches on factors affecting HAART adherence competence had controversies. As far as the author’s knowledge concerned, no research had been conducted on longitudinal HAART adherence competence in the study area. The main objective of this study was to identify Socio-demographic and Clinical factors associated with HAART adherence competence in successive visits among adult HIV patients after commencement of HAART. Methods : A retrospective cohort study on 792 HAART attendants was conducted to analyze the current study for HIV positive adults who had a minimum of two clinical visits. Secondary data were employed to examine Socio-demographic, economic, individual and clinical factors affecting the variable of interest overtime among HAART users. The Structural Equation modeling (SEM) was applied to identify predictors of HAART adherence competence over time. Results : In this longitudinal study, factors affecting long-term HAART adherence competence in successive visits had been identified. Socio-demographic factors (like Marital status, level of disclosure of the disease, residence area, education, economic factors (owner ship of cell phone, household income), individual factors (age, sex, weight) and clinical factors (CD4 cell count, WHO stages), directly associated with retention of HAART medication care. On the other hand, HAART medication care was significantly and independently associated with the longitudinal HAART adherence competence. Conclusion : The HAART adherence competence in successive visits increased with the number of follow-up visits, but the rate of increase was different for different groups such as male & female, urban & rural, and disclosing & hiding the disease to family members. An integrated health related education should be given for poor adherent patients like rural residents, males, patients living without partners, patients with no cell phone and aged patients.
HIV screening in men and women in Senegal: coverage and associated factors analysis of the 2017 demographic and health survey
Authors: Lakhe Ndeye Aissatou , Mbaye Khardiata Diallo , Sylla Khadime , Ndour Cheikh Tidiane 
Published: September 2019

Abstract
Introduction Despite the adoption of the provider-initiated HIV testing strategy, the rate of HIV testing is still very low in sub-Saharan Africa. The aim of this study was to assess the factors associated with HIV testing among in sexually active women and men in Senegal. Knowledge of HIV status is the gateway to antiretroviral treatment.Methods A secondary analysis of the 2017 Senegal Demographic and Health Survey (DHS) was performed, using data on sexually active women age 15-49 and men age 15-59. The outcome variable was the proportion of women and men who reported ever being tested for HIV in the last 12 months before the survey. Descriptive, bivariate, and multivariable logistic regression analyses were performed to identify the socio-demographic, HIV-knowledge, media exposure, and behavioral factors associated with HIV testing in Senegal.Results The study found that 62% of women and 27% of men were tested for HIV at the last 12 months. In multivariate analysis, among men the factors independently associated with being tested for HIV were: older age group (50-54); a high level of education; being in the richest household wealth quintile; being married; knowing about the efficacy of HART during pregnancy; and owning a mobile phone. Among women factors independently associated with HIV testing were: older age group (30-34); a high level of education; being in the richest household wealth quintile; being married; knowing about the efficacy of HART during pregnancy; having any STI in last 12 months; fearing stigma; owning a mobile phone; and having any number of ANC visits, versus none.Conclusion Although HIV remains a public health threat, 73% of men and 38% women in Senegal were not tested for HIV in the last 12 months. Low prevalence of HIV testing makes it difficult to interrupt the transmission chain within the community and to reach the UNAIDS goal for 2020 of “90-90-90”. Innovative community-based strategies are needed to address barriers and improve access to HIV testing, particularly for men and for the youngest and poorest populations, and to narrow the disparities in awareness of HIV status in Senegal.
The Safe Start Trial: A Cluster Randomized Controlled Trial for the Effect of an Infant Hygiene Intervention on Enteric Infections and Diarrhoea in Low-Income Informal Settlements of Kisumu, Kenya
Authors: Mumma Jane Awiti Odhiambo , Simiyu Sheillah , Aseyo Evalyne , Anderson John , Allen Elizabeth , Dreibelbis Robert , Baker Kelly K. , Cumming Oliver 
Published: September 2019

Abstract
Background Symptomatic and asymptomatic enteric infections in early childhood are associated with negative effects on childhood growth and development, especially in low and middle-income countries, and food may be an important transmission route. Although basic food hygiene practices might reduce exposure to faecal pathogens and resulting infections, there have been few rigorous interventions studies to assess this, and no studies in poor urban settings where risks are plausibly very high. The aim of this study is to evaluate the impact of a novel infant food hygiene intervention on infant enteric infections and diarrhoea in peri-urban settlements of Kisumu, Kenya. Methods This is a cluster randomized control trial with 50 clusters, representing the catchment areas of community health volunteers (CHVs), randomly assigned to intervention or control, and a total of 750 infants recruited on a rolling basis at 22 weeks of age and then followed for 15 weeks. The intervention targeted four caregiver behaviours related to food hygiene: 1) hand washing with soap before infant food preparation and feeding; 2) bringing all food to the boil before feeding, including when reserving; 3) storing all food in sealed containers; and, 4) using specific utensils for feeding which are kept separate and clean. The primary outcome of interest is the prevalence of one or more of 23 pre-specified enteric infections, determined using quantitative real-time polymerase chain reaction for enteric pathogen gene targets. Infant food samples were collected at 33 weeks, and faecal indicator bacteria (Enterococcus) isolated and enumerated to assess the impact of the intervention on food contamination. Discussion To our knowledge this is the first randomized controlled trial to assess the effect of an infant food hygiene intervention on enteric infections in a high burden, poor urban setting. Our trial responds to growing evidence that food may be a key pathway for early childhood enteric infection and disease and that basic food hygiene behaviours may be able to mitigate these risks. The study seeks to provide new evidence as to whether a locally appropriate infant food hygiene intervention delivered through the local health extension system can improve the health of young children.
Transcriptome analysis reveals the roles of stem nodes in cadmium transport to rice grain
Authors: Liu Ailing , Zhou Zhibo , Yi Yake , Chen Guanghui 
Published: September 2019

Abstract
Background: Node is the central organ of xylem to phloem transfer of nutrients and ions in plants. Cadmium (Cd)-induced crop pollution threatens food safety. Breeding cultivar with low Cd accumulation is a chance to resolve this universal problem. This study was performed to identify tissue specific genes involved in Cd accumulation in different rice stem nodes. Panicle node and the first node under panicle (node I) were sampled in two rice cultivars: Xiangwanxian No. 12 with low Cd accumulation and Yuzhenxiang with high Cd accumulation in the grains. RNA-seq analysis was performed to identify differentially expressed genes (DEGs) and microRNAs. Results: Xiangwanxian No. 12 had lower Cd concentration in panicle node, node I and grain compared with Yuzhenxiang , and node Ⅰ had the highest Cd concentration in the two cultivars. RNA seq analysis identified 4,535 differentially expressed genes and 70 miRNAs between the two cultivars. Most genes ( OsIRT1 , OsNramp5, OsVIT2 , OsNRT1.5A, and OsABCC1 ) related to the “transporter activity” blocked the transport of Cd up to panicle and accumulation in grains of low Cd-accumulative cultivar. Among the genes related to “response to stimulus”, we identified OsHSP70 and OsHSFA2d/B2c in “X”, but not in “y”, were all down-regulated by Cd stimulus. The up-regulation of miRNAs ( osa-miR528 and osa-miR408 ) played a potent role in lowering Cd accumulation via down regulation of genes, such as bZIP , ERF , MYB , SnRK1 and HSPs in Xiangwanxian No. 12 cultivar. Conclusions: Both panicle node and node I of Xiangwanxian No. 12 played a key role in blocking the upward transportation of Cd, while node I played a critical role in Yuzhenxiang . Distinct expression patterns of various transporter genes such as OsNRT1.5A, OsNramp5, OsIRT1, OsVIT2 and OsABCC1 resulted in differential Cd accumulation in different nodes. Likewise, distinct expression patterns of these transporter genes are likely responsible for the low Cd accumulation in Xiangwanxian No. 12 cultivar . MiRNAs drove multiple transcription factors, such as OsbZIPs, OsERFs, OsMYBs , to play a role in stress response, which contribute to the response to Cd stress in rice.
Genome-wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis
Authors: Hale Cecelia E. , Jordan Mark A. , Iriarte Gloria , Storer Andrew J. , Nalam Vamsi J. , Marshall Jordan 
Published: September 2019

Abstract
Background Ash ( Fraxinus spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest, Agrilus planipennis (Coleoptera: Buprestidae; emerald ash borer), having both negative impacts on forest ecosystems and economic interests. The majority of trees succumb to attack by A. planipennis , but some trees have been found to be tolerant to infestation despite years of exposure. Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to A. planipennis attack, in order to identify SNP patterns related to tolerance and health declines.Results A de novo reference genome was assembled and single nucleotide polymorphisms (SNPs) were called using SAMtools. After filtering criteria were implemented, a set of 17,807 SNPs were generated. Principle component analysis (PCA) of SNPs aligned individual trees into clusters related to geography, however, five tolerant trees clustered together despite geographic diversity. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are candidates for selection on host tolerance.Conclusions Identifying genetic markers associated with host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand A. planipennis infestation. This study was successful in using RAD-sequencing in order to identify SNPs that are potential candidates to identify tolerance to A. planipennis . This was a first step toward uncovering the genetic basis for host tolerance to A. planipennis . Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of A. planipennis attack.
Identification of porcine RUNX1 as an LPS-dependent gene expression regulator in PBMCs by Super deepSAGE sequencing of multiple tissues
Authors: Huang Tinghua , Yang Min , Dong Kaihui , Xu Mingjiang , Liu Jinhui , Chen Zhi , Zhu Shijia , Chen Wang , Yin Jun , Jin Kai , Deng Yu , Guan Zhou , Huang Xiali , Yang Jun , Han Rongxun , Yao Min 
Published: September 2019

Abstract
Background: Gene expression regulators identified in transcriptome profiling experiment may be selected as targets for genetic manipulations in farm animals. Results: In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 normal tissues collected from 32 animals using Super deepSAGE technology. Excellent sequencing depth has been achieved for each multiplexed library, and replicated samples from the same tissues cluster together, demonstrating the high quality of the Super deepSAGE data. Comparison with previous research indicated that our results not only have excellent reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis discovered ten groups of genes showing distinct expression patterns among those samples. Binding motif over representative analysis identified 41 regulators and finally, we demonstrate a potential application of this dataset to infectious and immune research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), and vav1 oncogene (VAV1), which belong to the T and B cell signaling pathways. Conclusions: the Super deepSAGE technology and tissue specific expression profiles are valuable resources for investigating the porcine gene expression regulations. The identified RUNX1 target genes belong to the T and B cell signaling pathways, making it a potential novel targets for the diagnostic and therapy of bacterial infections and other immune disorders.
Functional and population genetic features of copy number variations in two dairy cattle populations
Authors: Lee Young-Lim , Bosse Mirte , Mullaart Erik , Groenen Martien A. M. , Veerkamp Roel F. , Bouwman Aniek C. 
Published: September 2019

Abstract
Background Copy Number Variations (CNVs) are gain or loss of DNA segments that are known to play a role in shaping a wide range of phenotypes. In this study, we used two dairy cattle populations, Holstein Friesian and Jersey, to discover CNVs using the Illumina BovineHD Genotyping BeadChip aligned to the ARS-UCD1.2 assembly. The discovered CNVs were investigated for their functional impact and their population genetics features.

Results We discovered 14,272 autosomal CNVs, which were aggregated into 1,755 CNV regions (CNVR) from 451 animals. These CNVRs together cover 2.8% of the bovine autosomes. The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF < 0.01) are more likely to overlap with genes, than common CNVRs (0.05 ≤ MAF). The Population differentiation index (Fst) based on CNVRs revealed multiple highly diverged CNVRs between the two breeds. Some of these CNVRs overlapped with candidate genes such as MGAM and ADAMTS17 genes , which are related to starch digestion and stature, respectively. Lastly, linkage disequilibrium (LD) between CNVRs and BovineHD BeadChip SNPs was generally low, close to 0, although common deletions (MAF>0.05) showed slightly higher LD ( r 2 =~0.1 at 10kb distance) than the rest. Nevertheless, this LD is still lower than SNP-SNP LD ( r 2 =~0.5 at 10kb distance).

Conclusions Our analyses showed that CNVRs detected using BovineHD BeadChip arrays are likely to be functional. This finding indicates that CNVs can potentially disrupt the function of genes and thus might alter phenotypes. Also, the population differentiation index revealed two candidate genes, MGAM and ADAMTS17 , which hint at adaptive evolution between the two populations. Lastly, low CNVR-SNP LD implies that genetic variation from CNVs might not be fully captured in routine animal genetic evaluation, which relies solely on SNP markers.
Transcriptomic analysis reveals hub genes and subnetworks related to ROS metabolism in Hylocereus undatus through novel superoxide scavenger trypsin treatment during storage
Authors: Li Xin , Xueru Liu , Xinyue Pang , Yong Yin , Huichun Yu , Yunxia Yuan , Bairu Li 
Published: September 2019

Abstract
Background It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus .Results Trypsin significantly delayed the weight loss and decreased the levels of ROS and membrane lipid peroxidation. Transcriptome profiles of H. undatus treated with trypsin revealed the pathways and regulatory mechanisms of ROS genes that were up- or downregulated following trypsin treatment by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. The current results showed that through the regulation of the expression of hub redox enzymes, especially thioredoxin-related proteins, trypsin can maintain low levels of endogenous active oxygen species, reduce malondialdehyde content and delay fruit aging. In addition, the results of protein-protein interaction networks suggested that the downregulated NAD(P)H and lignin pathways might be the key regulatory mechanisms governed by trypsin.Conclusions Trypsin significantly prolonged the storage life of H. undatus through regulatory on the endogenous ROS metabolism. As a new biopreservative, trypsin is highly efficient, safe and economical. Therefore, trypsin possesses technical feasibility for the quality control of fruit storage.