Prevalence, clinical pattern and immediate outcomes of HIV-infected children admitted to Al Sabah Children’s Hospital, South Sudan

Introduction: HIV continues to be a major global health issue. There were approximately 2.1 million infected children aged <15 years in 2017 and most were in sub-Saharan Africa. South Sudan with its low prevention of mother to child transmission (PMTCT) coverage has a greater risk of high transmission rates of HIV from mothers to their children.Objective: To determine the prevalence of HIV infection, the clinical pattern, and the immediate outcomes of children admitted to Al Sabah Children’s Hospital.Method: This was a cross sectional descriptive study, with a longitudinal component for the immediate outcome. A total of 828 children were recruited: 424 aged <18 months and 424 aged ≥ 18 months. HIV rapid tests were done to confirm the HIV infection for children aged ≥18 months, while HIV DNA-PCR was done to confirm the HIV infection for children aged <18 months found to be HIV exposed.Results: Twenty four children tested HIV positive giving an overall HIV prevalence of 2.8% (95% CI 1.8 – 4.2). The clinical characteristics associated with HIV infection were: a history of cough (p=0.001), weight loss (p <0.001), oral thrush (p <0.001), lymphadenopathy (p=0.001), ear discharge (p <0.001), skin lesion (p <0.001), hepatomegaly (p <0.001), and splenomegaly (p <0.01). Factors associated with prolonged hospital stay were history of weight loss (OR=4.96, 95% CI 2.68-9.18), skin lesions (OR=3.60, 95% CI 1.36-9.56), and weight for height/length z score<-3SD (OR=8.67, 95% CI 4.70-15.99).Conclusion: The prevalence of HIV among this hospital based population of children aged less than 15 years was 2.8%. Children who presented with cough, weight loss, oral thrush, lymphadenopathy, ear discharge, skin lesion, hepatomegaly, and splenomegaly in this setting were likely to have HIV infection and should therefore raise suspicion for testing and early diagnosis.Keywords: HIV infection, clinical characteristics, children, hospital stay, South SudanSouth Sudan Medical Journal Vol 12 No 3 August 201

myKaryoView: A Light-Weight Client for Visualization of Genomic Data

The Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoView's ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com

Challenges of beta-deformation

A brief review of problems, arising in the study of the beta-deformation, also known as "refinement", which appears as a central difficult element in a number of related modern subjects: beta \neq 1 is responsible for deviation from free fermions in 2d conformal theories, from symmetric omega-backgrounds with epsilon_2 = - epsilon_1 in instanton sums in 4d SYM theories, from eigenvalue matrix models to beta-ensembles, from HOMFLY to super-polynomials in Chern-Simons theory, from quantum groups to elliptic and hyperbolic algebras etc. The main attention is paid to the context of AGT relation and its possible generalizations.Comment: 20 page

DNA sequence properties that predict susceptibility to epiallelic switching.

Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon-derived, methylated at all cytosines, which may or may not form epialleles. We provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness of the loci predispose their susceptibility to epiallelic switching. The importance and predictive power of these genetic features were confirmed by analyses of common epialleles in natural Arabidopsis accessions, epigenetic recombinant inbred lines (epiRILs) and also verified in rice.Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss‐of‐function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon‐derived, methylated at all cytosines, which may or may not form epialleles. We provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness of the loci predispose their susceptibility to epiallelic switching. The importance and predictive power of these genetic features were confirmed by analyses of common epialleles in natural Arabidopsis accessions, epigenetic recombinant inbred lines (epiRILs) and also verified in rice

Selective gating to vibrational modes through resonant X ray scattering

The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X ray scattering RIXS study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X ray excitation to different core excited potential energy surfaces PESs will act as spatial gates to selectively probe the particular ground state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra high resolution RIXS measurements for gas phase water with state of the art simulation

One dimensional cuts through multidimensional potential energy surfaces by tunable x rays

The concept of the potential energy surface PES and directional reaction coordinates is the backbone of our description of chemical reaction mechanisms. Although the eigenenergies of the nuclear Hamiltonian uniquely link a PES to its spectrum, this information is in general experimentally inaccessible in large polyatomic systems. This is due to near degenerate rovibrational levels across the parameter space of all degrees of freedom, which effectively forms a pseudospectrum given by the centers of gravity of groups of close lying vibrational levels. We show here that resonant inelastic x ray scattering RIXS constitutes an ideal probe for revealing one dimensional cuts through the ground state PES of molecular systems, even far away from the equilibrium geometry, where the independent mode picture is broken. We strictly link the center of gravity of close lying vibrational peaks in RIXS to a pseudospectrum which is shown to coincide with the eigenvalues of an effective one dimensional Hamiltonian along the propagation coordinate of the core excited wave packet. This concept, combined with directional and site selectivity of the core excited states, allows us to experimentally extract cuts through the ground state PES along three complementary directions for the showcase H2O molecul

The Glasgow Voice Memory Test: Assessing the ability to memorize and recognize unfamiliar voices

One thousand one hundred and twenty subjects as well as a developmental phonagnosic subject (KH) along with age-matched controls performed the Glasgow Voice Memory Test, which assesses the ability to encode and immediately recognize, through an old/new judgment, both unfamiliar voices (delivered as vowels, making language requirements minimal) and bell sounds. The inclusion of non-vocal stimuli allows the detection of significant dissociations between the two categories (vocal vs. non-vocal stimuli). The distributions of accuracy and sensitivity scores (d’) reflected a wide range of individual differences in voice recognition performance in the population. As expected, KH showed a dissociation between the recognition of voices and bell sounds, her performance being significantly poorer than matched controls for voices but not for bells. By providing normative data of a large sample and by testing a developmental phonagnosic subject, we demonstrated that the Glasgow Voice Memory Test, available online and accessible fromall over the world, can be a valid screening tool (~5 min) for a preliminary detection of potential cases of phonagnosia and of “super recognizers” for voices

A study of the water molecule using frequency control over nuclear dynamics in resonant X ray scattering

In this combined theoretical and experimental study we report a full analysis of the resonant inelastic X ray scattering RIXS spectra of H 2O, D 2O and HDO. We demonstrate that electronically elastic RIXS has an inherent capability to map the potential energy surface and to perform vibrational analysis of the electronic ground state in multimode systems. We show that the control and selection of vibrational excitation can be performed by tuning the X ray frequency across core excited molecular bands and that this is clearly reflected in the RIXS spectra. Using high level ab initio electronic structure and quantum nuclear wave packet calculations together with high resolution RIXS measurements, we discuss in detail the mode coupling, mode localization and anharmonicity in the studied system

Ultrafast dissociation features in RIXS spectra of the water molecule

In this combined theoretical and experimental study we report on an analysis of the resonant inelastic X ray scattering RIXS spectra of gas phase water via the lowest dissociative core excited state 1s amp; 8722;1O4a11 amp; 12297;. We focus on the spectral feature near the dissociation limit of the electronic ground state. We show that the narrow atomic like peak consists of the overlapping contribution from the RIXS channels back to the ground state and to the first valence excited state 1b amp; 8722;114a11 amp; 12297; of the molecule. The spectral feature has signatures of ultrafast dissociation UFD in the core excited state, as we show by means of ab initio calculations and time dependent nuclear wave packet simulations. We show that the electronically elastic RIXS channel gives substantial contribution to the atomic like resonance due to the strong bond length dependence of the magnitude and orientation of the transition dipole moment. By studying the RIXS for an excitation energy scan over the core excited state resonance, we can understand and single out the molecular and atomic like contributions in the decay to the lowest valence excited state. Our study is complemented by a theoretical discussion of RIXS in the case of isotopically substituted water HDO and D2O where the nuclear dynamics is significantly affected by the heavier fragments mas

The Fastest Flights in Nature: High-Speed Spore Discharge Mechanisms among Fungi

BACKGROUND: A variety of spore discharge processes have evolved among the fungi. Those with the longest ranges are powered by hydrostatic pressure and include "squirt guns" that are most common in the Ascomycota and Zygomycota. In these fungi, fluid-filled stalks that support single spores or spore-filled sporangia, or cells called asci that contain multiple spores, are pressurized by osmosis. Because spores are discharged at such high speeds, most of the information on launch processes from previous studies has been inferred from mathematical models and is subject to a number of errors. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have used ultra-high-speed video cameras running at maximum frame rates of 250,000 fps to analyze the entire launch process in four species of fungi that grow on the dung of herbivores. For the first time we have direct measurements of launch speeds and empirical estimates of acceleration in these fungi. Launch speeds ranged from 2 to 25 m s(-1) and corresponding accelerations of 20,000 to 180,000 g propelled spores over distances of up to 2.5 meters. In addition, quantitative spectroscopic methods were used to identify the organic and inorganic osmolytes responsible for generating the turgor pressures that drive spore discharge. CONCLUSIONS/SIGNIFICANCE: The new video data allowed us to test different models for the effect of viscous drag and identify errors in the previous approaches to modeling spore motion. The spectroscopic data show that high speed spore discharge mechanisms in fungi are powered by the same levels of turgor pressure that are characteristic of fungal hyphae and do not require any special mechanisms of osmolyte accumulation