Accelerating Backward Aggregation in GCN Training with Execution Path Preparing on GPUs

The emerging Graph Convolutional Network (GCN) has now been widely used in many domains, and it is challenging to improve the efficiencies of applications by accelerating the GCN trainings. For the sparsity nature and exploding scales of input real-world graphs, state-of-the-art GCN training systems (e.g., GNNAdvisor) employ graph processing techniques to accelerate the message exchanging (i.e. aggregations) among the graph vertices. Nevertheless, these systems treat both the aggregation stages of forward and backward propagation phases as all-active graph processing procedures that indiscriminately conduct computation on all vertices of an input graph. In this paper, we first point out that in a GCN training problem with a given training set, the aggregation stages of its backward propagation phase (called as backward aggregations in this paper) can be converted to partially-active graph processing procedures, which conduct computation on only partial vertices of the input graph. By leveraging such a finding, we propose an execution path preparing method that collects and coalesces the data used during backward propagations of GCN training conducted on GPUs. The experimental results show that compared with GNNAdvisor, our approach improves the performance of the backward aggregation of GCN trainings on typical real-world graphs by 1.48x~5.65x. Moreover, the execution path preparing can be conducted either before the training (during preprocessing) or on-the-fly with the training. When used during preprocessing, our approach improves the overall GCN training by 1.05x~1.37x. And when used on-the-fly, our approach improves the overall GCN training by 1.03x~1.35x

Improvements on the optical properties of Ge-Sb-Se chalcogenide glasses with iodine incorporation

International audienceDecreasing glass network defects and improving optical transmittance are essential work for material researchers. We studied the function of halogen iodine (I) acting as a glass network modifier in Ge–Sb–Se–based chalcogenide glass system. A systematic series of Ge20Sb5Se75-xIx (x = 0, 5, 10, 15, 20 at%) infrared (IR) chalcohalide glasses were investigated to decrease the weak absorption tail (WAT) and improve the mid-IR transparency. The mechanisms of the halogen I affecting the physical, thermal, and optical properties of Se-based chalcogenide glasses were reported. The structural evolutions of these glasses were also revealed by Raman spectroscopy and camera imaging. The progressive substitution of I for Se increased the optical bandgap. The WAT and scatting loss significantly decreased corresponding to the progressive decrease in structural defects caused by dangling bands and structure defects in the original Ge20Sb5Se75 glass. The achieved maximum IR transparency of Ge–Sb–Se–I glasses can reach up to 80% with an effective transmission window between 0.94 μm to 17 μm, whereas the absorption coefficient decreased to 0.029 cm-1 at 10.16 μm. Thus, these materials are promising candidates for developing low-loss IR fibers

Fabrication and characterization of Ge–Sb–Se–I glasses and fibers

International audienceChalcogenide glasses of the Ge20Sb5Se75−x I x (x = 0, 5, 10, 15, 20 at.%) system were prepared. This study was performed to examine some Ge–Sb–Se–I glass physical and optical properties, the structural evolution of the glass network, and the optical properties of the infrared glass fibers based on our previous studies. The variation process of the glass physical properties, such as transition temperature, glass density, and refractive index, was investigated from the glass of Ge20Sb5Se75 to the Ge20Sb5Se75−x I x glass series. The structural evolutions of these glasses were examined by Raman spectroscopy. The Ge20Sb5Se55I20 composition was selected for the preparation of the IR fiber. The Ge20Sb5Se55I20 glass was purified through distillation, and the intensity of the impurity absorption peaks caused by Ge–O, H2O, and Se–H was reduced or eliminated in the purified glasses. Then, Ge20Sb5Se55I20 chalcogenide glass fiber for mid-infrared transmission was fabricated using high-purity materials. The transmission loss of the Ge20Sb5Se55I20 fiber was greatly reduced compared with that of the Ge20Sb5Se75 glass fiber. The lowest losses obtained were 3.5 dB/m at 3.3 μm for Ge20Sb5Se75I20 fiber, which was remarkably improved compared with 48 dB/m of the unpurified Ge20Sb5Se75 fiber

Promoting influenza prevention for elderly people in Hong Kong using health action process approach: Study protocol

Background: People 65 years or older are at greater risk of serious complications from the seasonal influenza compared with young. To promote elderly people's behavioral compliance toward influenza prevention, the aim of the current project is to develop, implement, and evaluate a theory-based low-administration-cost intervention building on a leading psychological theory, the Health Action Process Approach (HAPA). Methods: The target group is Hong Kong Chinese elderly people aged 65 or older who rarely or never adopt any preventive actions. This project will be conducted in three phases over 24 months. In phase 1, intervention program will be developed building on the HAPA theoretical framework which comprises both the initiation and maintenance of influenza prevention behaviors. In phase 2, intervention will be implemented and evaluated using a randomized controlled trial, including: (a) behavior initiation only, (b) behavior initiation + behavior maintenance, and (c) control group. Both the initiation and maintenance components will comprise weekly-delivered telephone-based individual intervention sessions in 3 months. In phase 3, outcome evaluation of behavioral and psychological variables and process evaluation will be conducted. The effectiveness of the intervention will be analyzed using a series of linear mixed models on each behavioral and psychological outcome variable. Structural equation modelling will be used to test the hypothesized theoretical sequence in the HAPA model. Discussion: The proposed project is expected to design theory-based intervention materials to promote the influenza prevention behaviors in Hong Kong elderly people and provide information on its effectiveness and the potential changing mechanism of behavior initiation and maintenance. Trial registration: This randomized controlled trial was funded by the Health and Medical Research Fund (HMRF), Food and Health Bureau of the Government of the Hong Kong Special Administrative Region (Ref: 16151222) and was registered on 13/10/2017 at CCRB Clinical Trials Registry of the Chinese University of Hong Kong, a Partner Registry of a WHO Primary Registry (Ref: CUHK-CCRB00567)

The Infection of Chicken Tracheal Epithelial Cells with a H6N1 Avian Influenza Virus

Sialic acids (SAs) linked to galactose (Gal) in α2,3- and α2,6-configurations are the receptors for avian and human influenza viruses, respectively. We demonstrate that chicken tracheal ciliated cells express α2,3-linked SA, while goblet cells mainly express α2,6-linked SA. In addition, the plant lectin MAL-II, but not MAA/MAL-I, is bound to the surface of goblet cells, suggesting that SA2,3-linked oligosaccharides with Galβ1–3GalNAc subterminal residues are specifically present on the goblet cells. Moreover, both α2,3- and α2,6-linked SAs are detected on single tracheal basal cells. At a low multiplicity of infection (MOI) avian influenza virus H6N1 is exclusively detected in the ciliated cells, suggesting that the ciliated cell is the major target cell of the H6N1 virus. At a MOI of 1, ciliated, goblet and basal cells are all permissive to the AIV infection. This result clearly elucidates the receptor distribution for the avian influenza virus among chicken tracheal epithelial cells and illustrates a primary cell model for evaluating the cell tropisms of respiratory viruses in poultry

Digital crowdsourced intervention to promote HIV testing among MSM in China: study protocol for a cluster randomized controlled trial.

BACKGROUND: Men who have sex with men (MSM) are an important HIV key population in China. However, HIV testing rates among MSM remain suboptimal. Digital crowdsourced media interventions may be a useful tool to reach this marginalized population. We define digital crowdsourced media as using social media, mobile phone applications, Internet, or other digital approaches to disseminate messages developed from crowdsourcing contests. The proposed cluster randomized controlled trial (RCT) study aims to assess the effectiveness of a digital crowdsourced intervention to increase HIV testing uptake and decrease risky sexual behaviors among Chinese MSM. METHODS: A two-arm, cluster-randomized controlled trial will be implemented in eleven cities (ten clusters) in Shandong Province, China. Targeted study participants will be 250 MSM per arm and 50 participants per cluster. MSM who are 18 years old or above, live in the study city, have not been tested for HIV in the past 3 months, are not living with HIV or have never been tested for HIV, and are willing to provide informed consent will be enrolled. Participants will be recruited through banner advertisements on Blued, the largest gay dating app in China, and in-person at community-based organizations (CBOs). The intervention includes a series of crowdsourced intervention materials (24 images and four short videos about HIV testing and safe sexual behaviors) and HIV self-test services provided by the study team. The intervention was developed through a series of participatory crowdsourcing contests before this study. The self-test kits will be sent to the participants in the intervention group at the 2nd and 3rd follow-ups. Participants will be followed up quarterly during the 12-month period. The primary outcome will be self-reported HIV testing uptake at 12 months. Secondary outcomes will include changes in condomless sex, self-test efficacy, social network engagement, HIV testing social norms, and testing stigma. DISCUSSION: Innovative approaches to HIV testing among marginalized population are urgently needed. Through this cluster randomized controlled trial, we will evaluate the effectiveness of a digital crowdsourced intervention, improving HIV testing uptake among MSM and providing a resource in related public health fields. TRIAL REGISTRATION: ChiCTR1900024350 . Registered on 6 July 2019

Functional Diversification of Paralogous Transcription Factors via Divergence in DNA Binding Site Motif and in Expression

BACKGROUND: Gene duplication is a major driver of evolutionary innovation as it allows for an organism to elaborate its existing biological functions via specialization or diversification of initially redundant gene paralogs. Gene function can diversify in several ways. Transcription factor gene paralogs in particular, can diversify either by changes in their tissue-specific expression pattern or by changes in the DNA binding site motif recognized by their protein product, which in turn alters their gene targets. The relationship between these two modes of functional diversification of transcription factor paralogs has not been previously investigated, and is essential for understanding adaptive evolution of transcription factor gene families. FINDINGS: Based on a large set of human paralogous transcription factor pairs, we show that when the DNA binding site motifs of transcription factor paralogs are similar, the expressions of the genes that encode the paralogs have diverged, so in general, at most one of the paralogs is highly expressed in a tissue. Moreover, paralogs with diverged DNA binding site motifs tend to be diverged in their function. Conversely, two paralogs that are highly expressed in a tissue tend to have dissimilar DNA binding site motifs. We have also found that in general, within a paralogous family, tissue-specific decrease in gene expression is more frequent than what is expected by chance. CONCLUSIONS: While previous investigations of paralogous gene diversification have only considered coding sequence divergence, by explicitly quantifying divergence in DNA binding site motif, our work presents a new paradigm for investigating functional diversification. Consistent with evolutionary expectation, our quantitative analysis suggests that paralogous transcription factors have survived extinction in part, either through diversification of their DNA binding site motifs or through alterations in their tissue-specific expression levels