The TexiSense « Smart Sock » - a device for a daily prevention of pressure ulcers in the diabetic foot

International audienceGoals.– The term « diabetic foot » refers to a set of foot pathologies essentially stemming from the neuropathy and arteriopathy of the lower limb associated with diabetes mellitus. Chronic ischemia weakens the healing potential and favors the development of wounds on a more vulnerable foot. Friction or repeated micro-traumas can lead to an ulceration (which in turn can end up in an amputation) that will remain unnoticed because of the somato-sensory deficiency. The current prevention techniques largely relying on visual inspection of the foot and enhancement of the foot/insole interface are not fully satisfying as the prevalence of plantar ulcers remains very high.Patients and methods.– A device for the prevention of plantar ulcers–called “Smart Sock” is described. It consists of:– a sock made of a 100% textile pressure sensing fabric developed by the TexiSense company;– a microcontroller running a biomechanical model of the soft tissues of the foot of the diabetic person;– a vibrating watch (and eventually a smartphone) used to warn the bearer if a pressure pattern threatens the soft tissues integrity.Results.– Internal overpressures within the soft tissues, especially nearby bony prominences are likely to develop into deep foot ulcerations. The biomechanical model gives an estimation of their magnitude based on the external pressures measured by the sock/sensor. This modeling relies on a faithful representation of the morphology of the diabetic subject. The device sends a vibro-tactile alert in case of occasional overpressure or excessive stress dose accumulated during daytime activities.Discussion.– The continuous use of the device, compatible with daytime activities of the diabetic person, helps compensate for the lack of attention in the prevention of pressure ulcer formation. The TexiSense “Smart Sock” can be designed so that when worn, pressure sensors fall onto sensitive anatomical areas such as the dorsal side of the toes or the posterior side of the heel, which makes it also possible to monitor regions located outside the sole of the foot

Blood ties: ABO is a trans-species polymorphism in primates

The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World Monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multi-allelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the ABO polymorphism is a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years, to date, the only such example in Hominoids and Old World Monkeys outside of the Major Histocompatibility Complex.Comment: 45 pages, 4 Figures, 4 Supplementary Figures, 5 Supplementary Table

Inference of population splits and mixtures from genome-wide allele frequency data

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.comComment: 28 pages, 6 figures in main text. Attached supplement is 22 pages, 15 figures. This is an updated version of the preprint available at http://precedings.nature.com/documents/6956/version/

Feasibility and acceptability of rapid HIV screening in a labour ward in Togo

Background: HIV screening in a labour ward is the last opportunity to initiate an antiretroviral prophylaxis among pregnant women living with HIV to prevent mother-to-child HIV transmission. Little is known about the feasibility and acceptability of HIV screening during labour in West Africa. Findings: A cross-sectional survey was conducted in the labour ward at the Tokoin Teaching Hospital in Lomé (Togo) between May and August 2010. Pregnant women admitted for labour were randomly selected to enter the study and were interviewed on the knowledge of their HIV status. Clinical and biological data were collected from the individual maternal health chart. HIV testing or re-testing was systematically proposed to all pregnant women. Among 1530 pregnant women admitted for labour, 508 (32.2%) were included in the study. Information on HIV screening was available in the charts of 359 women (71%). Overall, 467 women accepted HIV testing in the labour ward (92%). The HIV prevalence was 8.8% (95% confidence interval: 6.4 to 11.7%). Among the 41 women diagnosed as living with HIV during labour, 34% had not been tested for HIV during pregnancy and were missed opportunities. Antiretroviral prophylaxis had been initiated antenatally for 24 women living with HIV and 17 in the labour room. Conclusions: This study is the first to show in West Africa that HIV testing in a labour room is feasible and well accepted by pregnant women. HIV screening in labour rooms needs to be routinely implemented to reduce missed opportunities for intervention aimed at HIV care and prevention, especially PMTCT

Composite likelihood estimation of demographic parameters

which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: Most existing likelihood-based methods for fitting historical demographic models to DNA sequence polymorphism data to do not scale feasibly up to the level of whole-genome data sets. Computational economies can be achieved by incorporating two forms of pseudo-likelihood: composite and approximate likelihood methods. Composite likelihood enables scaling up to large data sets because it takes the product of marginal likelihoods as an estimator of the likelihood of the complete data set. This approach is especially useful when a large number of genomic regions constitutes the data set. Additionally, approximate likelihood methods can reduce the dimensionality of the data by summarizing the information in the original data by either a sufficient statistic, or a set of statistics. Both composite and approximate likelihood methods hold promise for analyzing large data sets or for use in situations where the underlying demographic model is complex and has many parameters. This paper considers a simple demographic model of allopatric divergence between two populations, in which one of the population is hypothesized to have experienced a founder event, or population bottleneck. A large resequencing data set from human populations is summarized by the joint frequency spectrum, which is a matrix of the genomic frequency spectrum of derived base frequencies in two populations. A Bayesia

BMJ Open

INTRODUCTION: Acute malnutrition (AM) is a continuum condition, arbitrarily divided into moderate and severe AM (SAM) categories, funded and managed in separate programmes under different protocols. Optimising acute MAlnutrition (OptiMA) treatment aims to simplify and optimise AM management by treating children with mid-upper arm circumference (MUAC) <125 mm or oedema with one product-ready-to-use therapeutic food-at a gradually tapered dose. Our main objective was to compare the OptiMA strategy with the standard nutritional protocol in children 6-59 months presenting with MUAC <125 mm or oedema without additional complications, as well as in children classified as uncomplicated SAM (ie, MUAC <115 mm or weight-for-height Z-score (WHZ) <-3 or with oedema). METHODS AND ANALYSIS: This study was a non-inferiority, individually randomised controlled clinical trial conducted at community level in the Democratic Republic of Congo. Children 6-59 months presenting with MUAC <125 mm or WHZ <-3 or with bipedal oedema and without medical complication were included after signed informed consent in outpatient health facilities. All participants were followed for 6 months. Success in both arms was defined at 6 months post inclusion as being alive, not acutely malnourished per the definition applied at inclusion and without an additional episode of AM throughout the 6-month observation period. Recovery among children with uncomplicated SAM was the main secondary outcome. For the primary objective, 890 participants were needed, and 480 children with SAM were needed for the main secondary objective. We will perform non-inferiority analyses in per-protocol and intention-to-treat basis for both outcomes. ETHICS AND DISSEMINATION: Ethics approvals were obtained from the National Health Ethics Committee of the Democratic Republic of Congo and from the Ethics Evaluation Committee of Inserm, the French National Institute for Health and Medical Research (Paris, France). We will submit results for publication to a peer-reviewed journal and disseminate findings in international and national conferences and meetings. TRIAL REGISTRATION NUMBER: NCT03751475. Registered 19 September 2018, https://clinicaltrials.gov/ct2/show/NCT03751475

Discovery of error-tolerant biclusters from noisy gene expression data

An important analysis performed on microarray gene-expression data is to discover biclusters, which denote groups of genes that are coherently expressed for a subset of conditions. Various biclustering algorithms have been proposed to find different types of biclusters from these real-valued gene-expression data sets. However, these algorithms suffer from several limitations such as inability to explicitly handle errors/noise in the data; difficulty in discovering small bicliusters due to their top-down approach; inability of some of the approaches to find overlapping biclusters, which is crucial as many genes participate in multiple biological processes. Association pattern mining also produce biclusters as their result and can naturally address some of these limitations. However, traditional association mining only finds exact biclusters, whic

Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10–20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions