BARNARDS
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33565 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A retrospective analysis of Staphylococci species causing neonatal sepsis in low- and middle- income countries
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Project description:Colorectal cancer is among the most common types of cancer worldwide. Population-based screening programs for breast, cervical, and colorectal cancer have been introduced as part of cancer control in many high-income countries. Population-based cancer screening programs do not exist in most low- and middle-income countries. There are some studies that report the awareness of colorectal cancer in Turkey.
| 2310980 | ecrin-mdr-crc
Project description:Maternal and neonatal rectal carriage of beta-lactamases from low- and middle-income countries: prevalence, risk factors and genomes (part of the BARNARDS study).
| PRJEB39293 | ENA
Project description:<p>Acute febrile illnesses are still a major cause of mortality and morbidity globally, particularly in low to middle income countries. The aim of this study was to determine any possible metabolic commonalities of patients infected with disparate pathogens that cause fever. Three liquid chromatography-mass spectrometry (LC-MS) datasets investigating the metabolic effects of malaria, leishmaniasis and Zika virus infection were used. The retention time (RT) drift between the datasets was determined using landmarks obtained from the internal standards generally used in the quality control of the LC-MS experiments. Fitted Gaussian Process models (GPs) were used to perform a high level correction of the RT drift between the experiments, which was followed by standard peakset alignment between the samples with corrected RTs of the three LC-MS datasets. Statistical analysis, annotation and pathway analysis of the integrated peaksets were subsequently performed. Metabolic dysregulation patterns common across the datasets were identified, with kynurenine pathway being the most affected pathway between all three fever-associated datasets.</p>
2023-07-17 | MTBLS4895 | MetaboLights
Project description:Cervical cancer ranks as the first in cancer mortality among women of low-middle income countries, where 80% of the 570,000 cases and 311,000 worldwide deaths estimated for 2018 occurred (Ferlay et al. 2018 ). Persistent infections with high-risk HPV (hrHPV) genotypes can lead to high-grade cervical intraepithelial (CIN) grade 2 (CIN2) or higher, (CIN2+), if untreated, a high percentage of these lesions may progress to cancer. Despite its high sensitivity, the hrHPV test has low specificity to detect CIN2+ lesions given that a high percentage of women (80 %) infected with hrHPV genotypes will resolve the infection spontaneously. microRNAs (miRNAs) are small non-coding RNAs and their differential expression patterns seen to be associated with cervical intraepithelial lesions. Our work aimed to identify miRNAs differentially expressed in CIN2+ respect with <CIN1 and to evaluate their potential use as biomarkers to distinguish low- from high-grade lesions within hrHPV positive women. For our discovery set we used small RNA sequencing (miRNA-seq) to compare the miRNA expression patterns in 20 Formalin-Fixed Paraffin-Embedded (FFPE) tissues from hrHPV-positive women from Medellin, Colombia presenting low- (n=10) and high-grade lesions (n=10). Top five miRNAs presenting high fold change and low coefficient of variation were used validated by RT-PCR in our validation set composed 210 age-matched independent hrHPV-positive FFPE tissues, and an in-silico approach was used to understand the function of the differentially expressed miRNAs in the context of HPV infection.
2023-05-07 | GSE167858 | GEO
Project description:Despite successful combination antiretroviral therapy (cART), persistent low-grade immune activation together with inflammation and toxic antiretroviral drugs can lead to long-lasting metabolic flexibility and adaptation in people living with HIV (PLWH). Our study investigated alterations in the plasma metabolic profiles by comparing PLWH on long-term cART(>5years) and matched HIV-negative controls (HC) in two cohorts from low- and middle-income countries (LMIC), Cameroon and India, respectively to understand the system-level dysregulation in HIV-infection. Using untargeted and targeted LC-MS/MS-based metabolic profiling and applying advanced system biology methods, an altered amino acid metabolism, more specifically to glutaminolysis in PLWH than HC were reported. A significantly lower level of neurosteroids were observed in both cohorts and could potentiate neurological impairments in PLWH. Further, modulation of cellular glutaminolysis promoted increased cell death and latency reversal in pre-monocytic HIV-1 latent cell model U1, which may be essential for the clearance of the inducible reservoir in HIV-integrated cells.
2021-11-24 | PXD028531 | Pride
Project description:Enterotoxigeneic Escherichia coli (ETEC) is a leading cause of diarrhoeal infections in young children living in endemic regions in low and middle-income countries and adults travelling to these destinations. CFA/I fimbriae have been identified as the predominant colonisation factor associated with human ETEC infections. Here we used used Transposon-directed insertion-site sequencing (TraDIS) and transcriptomic analysis to identify the essential genome of the prototypical CFA/I expressing ETEC strain H10407 and uncover the survival mechanisms that enhance persistence of ETEC isolates in water and within mammalian hosts. RNA transcription profiles of H10407 were identified under different in vitro growth conditions including aerobic growth in neutral LB media (pH7); aerobic growth in acidic media (pH5); aerobic growth in alkaline media (pH9); anaerobic growth in neutral LB media (pH7); and survival in fresh water. Research work including RNA preparation and bioinformatics and statistical analyses were conducted at the Wellcome Trust Sanger Institute (WTSI) and the Westmead Institute for Medical Research (WIMR), the University of Sydney. The sequencing data was generated in the Bioscience Core Laboratory at King Abdullah University of Science and Technology (KAUST).
2021-04-21 | E-MTAB-9364 | biostudies-arrayexpress
Project description:Breastfeeding provides defense against infectious disease during early life. The mechanisms underlying this protection are complex but likely include the vast array of immune cells and components, such as immunoglobulins, in milk. Simply characterizing the concentrations of these bioactives, however, provides only limited information regarding their potential relationships with disease risk in the recipient infant. Rather, understanding pathogen and antigen specificity profiles of milk-borne immunoglobulins might lead to a more complete understanding of how maternal immunity impacts infant health and wellbeing. Milk produced by women living in 11 geographically dispersed populations was applied to a protein microarray containing antigens from 16 pathogens, including diarrheagenic E. coli, Shigella spp., Salmonella enterica serovar Typhi, Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis and other pathogens of global health concern, and specific IgA and IgG binding was measured. Our analysis identified novel disease-specific antigen responses and suggests that some IgA and IgG responses vary substantially within and among populations. Patterns of antibody reactivity analyzed by principal component analysis and differential reactivity analysis were associated with either lower-to-middle-income countries (LMICs) or high-income countries (HICs). Antibody levels were generally higher in LMICs than HICs, particularly for Shigella and diarrheagenic E. coli antigens, although sets of S. aureus, S. pneumoniae, and some M. tuberculosis antigens were more reactive in HICs. Differential responses were typically specific to canonical immunodominant antigens, but a set of nondifferential but highly reactive antibodies were specific to antigens possibly universally recognized by antibodies in human milk. This approach provides a promising means to understand how breastfeeding and human milk protect (or do not protect) infants from environmentally relevant pathogens. Furthermore, this approach might lead to interventions to boost population-specific immunity in at-risk breastfeeding mothers and their infants.
2020-12-28 | GSE163902 | GEO
Project description:Breastfeeding provides defense against infectious disease during early life. The mechanisms underlying this protection are complex but likely include the vast array of immune cells and components, such as immunoglobulins, in milk. Simply characterizing the concentrations of these bioactives, however, provides only limited information regarding their potential relationships with disease risk in the recipient infant. Rather, understanding pathogen and antigen specificity profiles of milk-borne immunoglobulins might lead to a more complete understanding of how maternal immunity impacts infant health and wellbeing. Milk produced by women living in 11 geographically dispersed populations was applied to a protein microarray containing antigens from 16 pathogens, including diarrheagenic E. coli, Shigella spp., Salmonella enterica serovar Typhi, Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis and other pathogens of global health concern, and specific IgA and IgG binding was measured. Our analysis identified novel disease-specific antigen responses and suggests that some IgA and IgG responses vary substantially within and among populations. Patterns of antibody reactivity analyzed by principal component analysis and differential reactivity analysis were associated with either lower-to-middle-income countries (LMICs) or high-income countries (HICs). Antibody levels were generally higher in LMICs than HICs, particularly for Shigella and diarrheagenic E. coli antigens, although sets of S. aureus, S. pneumoniae, and some M. tuberculosis antigens were more reactive in HICs. Differential responses were typically specific to canonical immunodominant antigens, but a set of nondifferential but highly reactive antibodies were specific to antigens possibly universally recognized by antibodies in human milk. This approach provides a promising means to understand how breastfeeding and human milk protect (or do not protect) infants from environmentally relevant pathogens. Furthermore, this approach might lead to interventions to boost population-specific immunity in at-risk breastfeeding mothers and their infants.
2020-12-28 | GSE163901 | GEO