Miracle-dz/UniFAR-FTUs huggingface dataset:
Implementation of prevention of mother-to-child transmission (PMTCT) in South Africa: outcomes from a population-based birth cohort study in Paarl, Western Cape

Objectives The coverage of prevention of mother-to-child transmission (PMTCT) services in South Africa is variable. Identifying gaps in the implementation of these services is necessary to isolate steps needed to further reduce paediatric infections and eliminate transmission. Setting Two primary care clinics in Paarl, South Africa. Participants 1225 pregnant women; inclusion criteria were 18 years or older, clinic attendance and remaining in area for at least 1 year. Methods Data were collected through the Drakenstein Child Health Study, a population-based birth cohort in a periurban area of the Western Cape, South Africa. A combination of clinic records, hospital records, national database searches and maternal self-report were collected during the study. Results Of the 1225 mothers enrolled in the cohort between 2012 and 2015, 260 (21%) were confirmed HIV infected antenatally and 1 mother tested positive in the postnatal period. Of those with documentation (n=250/260, 96%), the majority (99%) received antiretroviral prophylaxis or therapy (ART) before labour; however, there was a high rate of defaulting from ART noted during pregnancy (20%). All HIV-exposed infants with data received antiretroviral prophylaxis, 35% were exclusively breast fed until 6 weeks and 16% for 6 months. There were two cases of infant HIV infection (0.8%) who were initiated on ART but had complicated histories. Conclusion Despite the low transmission rate in this cohort, reaching elimination will require further work, and this study illustrates several areas to improve implementation of PMTCT services and reduce paediatric infections including retesting at-risk HIV-negative mothers through the duration of breast feeding, infant HIV testing at any admission in addition to routine testing and improved counselling to prevent defaulting from treatment. Better data surveillance systems are essential for determining the implementation of PMTCT guidelines.
ARTHROPLASTY IN HIV INFECTED PATIENTS – A 5 YEAR FOLLOW UP

The increased prevalence of HIV has increased awareness and concern for the diagnosis and treatment of patients requiring total joint arthroplasty. Collective experience with HIV and arthroplasty at any institution is small and limited. This study evaluates the clinical outcome of arthroplasty in HIV infected patients. Between July 2000 and August 2001, we treated 14 patients (4 female) and with uncemented total hip replacement. (Mean age of 42 years). Informed consent was obtained before HIV testing and counselling was provided for all patients. Patients were classified according to the WHO and CDC classification. All patients were operated on by a single surgeon using the Hardinge approach. 14 Patients were followed up with a mean follow up 62 months. The pre-lymphycyte subset analysis was TLC-2.24, CD4 425, CD8 873, CD4/CD8-0.52. All patients were fully ambulant. One patient sustained a periprosthetic fracture following a high energy car accident which was treated non operatively. Three patients have dropped their CD4 count to below 200 and are presently receiving antiretroviral treatment. There was no loosening, infection or dislocation. The literature on complications associated with arthroplasty in HIV infected patients is inconsistent. A few authors have reported a 40% incidence of infection with total joint replacement. In this series there were no infections, and the outcome of total joint arthroplasty depends on the nutritional status of the patient, the stage of the under lying disease, as well as previous surgery and co-morbidities. Orthopaedic Surgeons should be aware of the increasing prevalence of HIV infection, and that arthroplasty in these patients can be safely performed with minimum complications.
Virus–virus interactions impact the population dynamics of influenza and the common cold

Significance When multiple pathogens cocirculate this can lead to competitive or cooperative forms of pathogen–pathogen interactions. It is believed that such interactions occur among cold and flu viruses, perhaps through broad-acting immunity, resulting in interlinked epidemiological patterns of infection. However, to date, quantitative evidence has been limited. We analyzed a large collection of diagnostic reports collected over multiple years for 11 respiratory viruses. Our analyses provide strong statistical support for the existence of interactions among respiratory viruses. Using computer simulations, we found that very short-lived interferences may explain why common cold infections are less frequent during flu seasons. Improved understanding of how the epidemiology of viral infections is interlinked can help improve disease forecasting and evaluation of disease control interventions. The human respiratory tract hosts a diverse community of cocirculating viruses that are responsible for acute respiratory infections. This shared niche provides the opportunity for virus–virus interactions which have the potential to affect individual infection risks and in turn influence dynamics of infection at population scales. However, quantitative evidence for interactions has lacked suitable data and appropriate analytical tools. Here, we expose and quantify interactions among respiratory viruses using bespoke analyses of infection time series at the population scale and coinfections at the individual host scale. We analyzed diagnostic data from 44,230 cases of respiratory illness that were tested for 11 taxonomically broad groups of respiratory viruses over 9 y. Key to our analyses was accounting for alternative drivers of correlated infection frequency, such as age and seasonal dependencies in infection risk, allowing us to obtain strong support for the existence of negative interactions between influenza and noninfluenza viruses and positive interactions among noninfluenza viruses. In mathematical simulations that mimic 2-pathogen dynamics, we show that transient immune-mediated interference can cause a relatively ubiquitous common cold-like virus to diminish during peak activity of a seasonal virus, supporting the potential role of innate immunity in driving the asynchronous circulation of influenza A and rhinovirus. These findings have important implications for understanding the linked epidemiological dynamics of viral respiratory infections, an important step towards improved accuracy of disease forecasting models and evaluation of disease control interventions.
The Hot Spring Hypothesis for an Origin of Life

We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. “To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic. ” —Leslie Orgel
Enfermedad renal crónica determinada mediante la creatinina sérica Chronic kidney disease as measured by serum creatinine

chronic kidney disease is associated with an increased risk of end-stage renal disease, cardiovascular diseases and death; hence, it is necessary to make a diagnosis in the early phases of the disease. Many equations for estimating glomerular filtration rates are available for this purpose, and are based on serum creatinine concentration. Although creatinine is not the ideal analyte to gauge glomerular filtration rate, it will be used until there is extensive availability of other markers, such as cystatin C. On these grounds, clinical laboratories must offer results with high standards of quality control, and accordingly, they must measure serum creatinine with suitable methods, previously standardized by reference measurement procedures. The aim of this module is to assess early diagnosis of chronic kidney disease through serum creatinine quantification and glomerular filtration rate estimation.
Physical function and quality of life in adolescents with haemophilia (SO-FIT study)

Abstract Introduction Self-completed measures of physical function and quality of life are increasingly being used in clinical practice yet little is known about how these measures correlate with joint scores in boys with severe haemophilia. In addition, it is not known whether currently used measures of functional outcome correlate with quality of life measures, which measure of physical function is most accurate and whether these measures are acceptable to a well treated contemporary cohort of boys. Methods The Study Of physical Function In adolescenTs with haemophilia (SO-FIT) is a multicenter, randomized cross-over study designed to answer these questions, and to determine whether these self-reported measures are completed more fully and frequently if made available on mobile devices rather than with conventional pen and paper questionnaires. The study is being run by haemophilia nurse specialists and physiotherapists in UK haemophilia centres and will recruit 120 boys with severe haemophilia A or B, with or without inhibitors aged 8-16 years. Results The SO-FIT study is now underway, and is expected to complete by the end of 2014.
Biological control of Erwinia mallotivora, the causal agent of papaya dieback disease by indigenous seed-borne endophytic lactic acid bacteria consortium

Dieback disease caused by Erwinia mallotivora is a major threat to papaya plantation in Malaysia. The current study was conducted to evaluate the potential of endophytic lactic acid bacteria (LAB) isolated from papaya seeds for disease suppression of papaya dieback. Two hundred and thirty isolates were screened against E. mallotivora BT-MARDI, and the inhibitory activity of the isolates against the pathogen was ranging from 11.7–23.7 mm inhibition zones. The synergistic experiments revealed that combination of W. cibaria PPKSD19 and Lactococcus lactis subsp. lactis PPSSD39 increased antibacterial activity against the pathogen. The antibacterial activity was partially due to the production of bacteriocin-like inhibitory substances (BLIS). The nursery experiment confirmed that the application of bacterial consortium W. cibaria PPKSD19 and L. lactis subsp. lactis PPSSD39 significantly reduced disease severity to 19% and increased biocontrol efficacy to 69% of infected papaya plants after 18 days of treatment. This study showed that W. cibaria PPKSD19 and L. lactis subsp. lactis PPSSD39 are potential candidate as biocontrol agents against papaya dieback disease.
Transcriptional changes in the aphid species Myzus cerasi under different host and environmental conditions

Aphids feature complex life cycles, which in the case of many agriculturally important species involve primary and secondary host plant species. Whilst host alternation between primary and secondary host can occur in the field depending on host availability and the environment, aphid populations maintained as laboratory stocks generally are kept under conditions that allow asexual reproduction by parthenogenesis on secondary hosts. We used Myzus cerasi (black cherry aphid) to assess aphid transcriptional differences between populations collected from primary hosts in the field and those adapted to secondary hosts under controlled environment conditions. Transfer of M. cerasi collected from local cherry trees to reported secondary host species resulted in low survival rates. Moreover, aphids were unable to survive on the secondary host land cress, unless first adapted to another secondary host, cleavers. Transcriptome analyses of the different aphid populations (field collected and adapted) revealed extensive transcriptional plasticity to a change in environment, with predominantly genes involved in redox reactions differentially regulated. Most of the differentially expressed genes were duplicated and we found evidence for differential exon usage. Our data suggest that aphid adaptation to different environments may pose a major hurdle and leads to extensive gene expression changes.
Executive Summary: Identification, Evaluation, and Management of Children With Autism Spectrum Disorder

* Abbreviations: ASD — : autism spectrum disorder DSM-5 — : Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition Autism spectrum disorder (ASD) is a common neurodevelopmental disorder with reported prevalence in the United States of 1 in 59 children (approximately 1.7%). ASD significantly influences the lives of affected children and families because they may need extensive behavioral, educational, health, and other services. Primary care providers play a critical role in identifying, diagnosing, and managing ASD in children and providing support for their families. This document provides a summary of the clinical report “Identification, Evaluation, and Management of Children with Autism Spectrum Disorder,” published concurrently in the online version of Pediatrics . In the years since 2007, when the American Academy of Pediatrics published the clinical reports “Identification and Diagnosis of Children with Autism Spectrum Disorders” and “Management of Children with Autism Spectrum Disorders,” reported prevalence rates of children with ASD have increased, understanding of potential risk factors has expanded, awareness of co-occurring medical and behavioral conditions and genetic contribution to etiology has improved, and the body of research supporting evidence-based interventions has grown substantially. The updated document discusses evaluation and treatment as a continuum in 1 publication with a table of contents to help the reader identify topic areas within the report. ASD is more commonly diagnosed than in the past, and the significant health, educational, and social needs of individuals with ASD and their families constitute an area of critical need for resources, research, and professional education. Address correspondence to Susan L. Hyman, MD. E-mail: susan_hyman{at}RMC.Rochester. edu
Promoting Optimal Development: Identifying Infants and Young Children With Developmental Disorders Through Developmental Surveillance and Screening

Early identification and intervention for developmental disorders are critical to the well-being of children and are the responsibility of pediatric professionals as an integral function of the medical home. This report models a universal system of developmental surveillance and screening for the early identification of conditions that affect children’s early and long-term development and achievement, followed by ongoing care. These conditions include autism, deafness/hard-of-hearing, intellectual and motor disabilities, behavioral conditions, and those seen in other medical conditions. Developmental surveillance is supported at every health supervision visit, as is as the administration of standardized screening tests at the 9-, 18-, and 30-month visits. Developmental concerns elicited on surveillance at any visit should be followed by standardized developmental screening testing or direct referral to intervention and specialty medical care. Special attention to surveillance is recommended at the 4- to 5-year well-child visit, prior to entry into elementary education, with screening completed if there are any concerns. Developmental surveillance includes bidirectional communication with early childhood professionals in child care, preschools, Head Start, and other programs, including home visitation and parenting, particularly around developmental screening. The identification of problems should lead to developmental and medical evaluations, diagnosis, counseling, and treatment, in addition to early developmental intervention. Children with diagnosed developmental disorders are identified as having special health care needs, with initiation of chronic condition management in the pediatric medical home.
Arsenic and gallbladder cancer risk: Mendelian randomization analysis of European prospective data

Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany Department of Basic and Clinical Oncology, Medical Faculty, University of Chile, Santiago, Chile International Agency for Research on Cancer, World Health Organization, Lyon, France Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition PotsdamRehbruecke (DIfE), Nuthetal, Germany Institute of Nutritional Science, University of Potsdam, Potsdam, Germany Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany Unit of Nutrition and Cancer, Cancer Epidemiology Research Programme, Catalan Institute of Oncology (ICO), Barcelona, Spain Division of Epidemiology, Department of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia Lifelines, Groningen, Netherlands Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany Saarland Cancer Registry, Saarbrücken, Germany The Nord-Trøndelag Health (HUNT) Research Centre, Norwegian University of Science and Technology (NTNU), Trondheim, Norway K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology (NTNU), Trondheim, Norway Genomiikka ja Biomarkkerit, National Institute for Health and Welfare (THL), Helsinki, Finland Interfakultäres Institut für Genetik und Funktionelle Genomforschung, Universitätsmedizin Greifswald, Germany Research Unit of Molecular Epidemiology and Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
Pathological findings in central nervous system demyelination associated with infliximab

Background: Tumor necrosis factor alpha (TNF-alpha) inhibitors, such as infliximab, are commonly used to treat rheumatoid arthritis (RA) and other immune-mediated disorders. Objective: To determine whether infliximab-associated central nervous system (CNS) demyelination can be differentiated from multiple sclerosis (MS). Methods: We present a case of pathologically proven CNS demyelination in a patient treated with infliximab and describe clinical–radiographic–neuropathological findings. Putative mechanisms of TNF-alpha inhibitor-associated CNS demyelination are described. Results and conclusion: Infliximab treatment is associated with CNS inflammatory demyelinating activity, which is histopathologically indistinguishable from MS.
Comparing and Contrasting the Multiple Roles of Butenolide Plant Growth Regulators: Strigolactones and Karrikins in Plant Development and Adaptation to Abiotic Stresses

Strigolactones (SLs) and karrikins (KARs) are both butenolide molecules that play essential roles in plant growth and development. SLs are phytohormones, with SLs having known functions within the plant they are produced in, while KARs are found in smoke emitted from burning plant matter and affect seeds and seedlings in areas of wildfire. It has been suggested that SL and KAR signaling may share similar mechanisms. The α/β hydrolases DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2), which act as receptors of SL and KAR, respectively, both interact with the F-box protein MORE AXILLARY GROWTH 2 (MAX2) in order to target SUPPRESSOR OF MAX2 1 (SMAX1)-LIKE/D53 family members for degradation via the 26S proteasome. Recent reports suggest that SLs and/or KARs are also involved in regulating plant responses and adaptation to various abiotic stresses, particularly nutrient deficiency, drought, salinity, and chilling. There is also crosstalk with other hormone signaling pathways, including auxin, gibberellic acid (GA), abscisic acid (ABA), cytokinin (CK), and ethylene (ET), under normal and abiotic stress conditions. This review briefly covers the biosynthetic and signaling pathways of SLs and KARs, compares their functions in plant growth and development, and reviews the effects of any crosstalk between SLs or KARs and other plant hormones at various stages of plant development. We also focus on the distinct responses, adaptations, and regulatory mechanisms related to SLs and/or KARs in response to various abiotic stresses. The review closes with discussion on ways to gain additional insights into the SL and KAR pathways and the crosstalk between these related phytohormones.