Psychological distress and depression in urbanising elderly black persons

The findings of a comparative community survey of the socioeconomic, cultural and psychiatric state of elderly black persons in a newly settled township (Khayelitsha - 170 persons) and a long established one (Langa - 195 persons) revealed marked differences. Symptoms of psychological distress, depression and limitation of daily activities were generally more marked in the former and strikingly so among women: 66% had symptoms warranting further investigation and 44% would have been treated for a depressive disorder if seen by a psychiatrist. Extreme poverty existed in both townships but the Khayelitsha subjects were less well educated, their accommodation was poorer, and fewer had old-age pensions. Elderly black women in newly settled townships have therefore been identified as having high priority for psychiatric and social services

Is prosodic production driven by lexical development ? Longitudinal evidence from babble and words

This study investigated the relation between lexical development and the production of prosodic prominence in disyllabic babble and words. Monthly recordings from nine typically developing Belgian-Dutch-speaking infants were analysed from the onset of babbling until a cumulative vocabulary of 200 words was reached. The differentiation between the two syllables of isolated disyllabic utterances was computed for f0, intensity and duration measurements. Results showed that the ambient trochaic pattern emerged in babble, but became enhanced in words. Words showed more prosodic differentiation in terms of f0 and intensity and a more even duration ratio. Age or vocabulary size did not predict the expansion of f0 or intensity in words, whereas vocabulary size was related to the production of more even-timed syllables. The findings are discussed in terms of lexicalist accounts of phonetic development and a potential phonetic highlighting function of first words

CoCoCoNet: conserved and comparative co-expression across a diverse set of species

Co-expression analysis has provided insight into gene function in organisms from Arabidopsis to zebrafish. Comparison across species has the potential to enrich these results, for example by prioritizing among candidate human disease genes based on their network properties or by finding alternative model systems where their co-expression is conserved. Here, we present CoCoCoNet as a tool for identifying conserved gene modules and comparing co-expression networks. CoCoCoNet is a resource for both data and methods, providing gold standard networks and sophisticated tools for on-the-fly comparative analyses across 14 species. We show how CoCoCoNet can be used in two use cases. In the first, we demonstrate deep conservation of a nucleolus gene module across very divergent organisms, and in the second, we show how the heterogeneity of autism mechanisms in humans can be broken down by functional groups and translated to model organisms. CoCoCoNet is free to use and available to all at https://milton.cshl.edu/CoCoCoNet, with data and R scripts available at ftp://milton.cshl.edu/data

Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction

The expansion of protein-ligand annotation databases has enabled large-scale networking of proteins by ligand similarity. These ligand-based protein networks, which implicitly predict the ability of neighboring proteins to bind related ligands, may complement biologically-oriented gene networks, which are used to predict functional or disease relevance. To quantify the degree to which such ligand-based protein associations might complement functional genomic associations, including sequence similarity, physical protein-protein interactions, co-expression, and disease gene annotations, we calculated a network based on the Similarity Ensemble Approach (SEA: sea.docking.org), where protein neighbors reflect the similarity of their ligands. We also measured the similarity with functional genomic networks over a common set of 1,131 genes, and found that the networks had only small overlaps, which were significant only due to the large scale of the data. Consistent with the view that the networks contain different information, combining them substantially improved Molecular Function prediction within GO (from AUROC~0.63-0.75 for the individual data modalities to AUROC~0.8 in the aggregate). We investigated the boost in guilt-by-association gene function prediction when the networks are combined and describe underlying properties that can be further exploited

GreenSTEM’s microbe technology is an efficient, effective, and affordable way to clean up fuel and chemical spills

Non-Peer ReviewedPetroleum hydrocarbons are used as fuel and for chemical synthesis. If spilled, fuels and chemicals poison our soil and water, causing local environmental disasters. Bioremediation uses organisms to clean up (remediate) pollutants. We have isolated and characterized microbe strains from contaminated sites, and use them to remediate contaminated sites elsewhere. We identify our strains using their DNA sequences and their appearance. Some microbes, called fungal endophytes, form symbioses, in other words metabolic partnerships between a plant and a fungus. These symbioses have been shown to stimulate plant growth and root formation, even on contaminated soil. Surprisingly, some of our other microbes can degrade hydrocarbons underground, without plants. GreenSTEM has powerful technology: we use native microbes to degrade hydrocarbons and chemicals as they grow on the contaminants as food. Based on our progress to date with fuels and other chemicals, we anticipate isolating new strains specific for other intractable toxins

Exploiting single-cell expression to characterize co-expression replicability

BACKGROUND: Co-expression networks have been a useful tool for functional genomics, providing important clues about the cellular and biochemical mechanisms that are active in normal and disease processes. However, co-expression analysis is often treated as a black box with results being hard to trace to their basis in the data. Here, we use both published and novel single-cell RNA sequencing (RNA-seq) data to understand fundamental drivers of gene-gene connectivity and replicability in co-expression networks. RESULTS: We perform the first major analysis of single-cell co-expression, sampling from 31 individual studies. Using neighbor voting in cross-validation, we find that single-cell network connectivity is less likely to overlap with known functions than co-expression derived from bulk data, with functional variation within cell types strongly resembling that also occurring across cell types. To identify features and analysis practices that contribute to this connectivity, we perform our own single-cell RNA-seq experiment of 126 cortical interneurons in an experimental design targeted to co-expression. By assessing network replicability, semantic similarity and overall functional connectivity, we identify technical factors influencing co-expression and suggest how they can be controlled for. Many of the technical effects we identify are expression-level dependent, making expression level itself highly predictive of network topology. We show this occurs generally through re-analysis of the BrainSpan RNA-seq data. CONCLUSIONS: Technical properties of single-cell RNA-seq data create confounds in co-expression networks which can be identified and explicitly controlled for in any supervised analysis. This is useful both in improving co-expression performance and in characterizing single-cell data in generally applicable terms, permitting cross-laboratory comparison within a common framework

Rotation-induced 3D vorticity in 4He superfluid films adsorbed on a porous glass

Detailed study of torsional oscillator experiments under steady rotation up to 6.28 rad/sec is reported for a 4He superfluid monolayer film formed in 1 micrometer-pore diameter porous glass. We found a new dissipation peak with the height being in proportion to the rotation speed, which is located to the lower temperature than the vortex pair unbinding peak observed in the static state. We propose that 3D coreless vortices ("pore vortices") appear under rotation to explain this new peak. That is, the new peak originates from dissipation close to the pore vortex lines, where large superfluid velocity shifts the vortex pair unbinding dissipation to lower temperature. This explanation is confirmed by observation of nonlinear effects at high oscillation amplitudes.Comment: 4pages, 5figure

Transverse NMR relaxation as a probe of mesoscopic structure

Transverse NMR relaxation in a macroscopic sample is shown to be extremely sensitive to the structure of mesoscopic magnetic susceptibility variations. Such a sensitivity is proposed as a novel kind of contrast in the NMR measurements. For suspensions of arbitrary shaped paramagnetic objects, the transverse relaxation is found in the case of a small dephasing effect of an individual object. Strong relaxation rate dependence on the objects' shape agrees with experiments on whole blood. Demonstrated structure sensitivity is a generic effect that arises in NMR relaxation in porous media, biological systems, as well as in kinetics of diffusion limited reactions.Comment: 4 pages, 3 figure