CATGNN: Cost-Efficient and Scalable Distributed Training for Graph Neural Networks

Graph neural networks have been shown successful in recent years. While different GNN architectures and training systems have been developed, GNN training on large-scale real-world graphs still remains challenging. Existing distributed systems load the entire graph in memory for graph partitioning, requiring a huge memory space to process large graphs and thus hindering GNN training on such large graphs using commodity workstations. In this paper, we propose CATGNN, a cost-efficient and scalable distributed GNN training system which focuses on scaling GNN training to billion-scale or larger graphs under limited computational resources. Among other features, it takes a stream of edges as input, instead of loading the entire graph in memory, for partitioning. We also propose a novel streaming partitioning algorithm named SPRING for distributed GNN training. We verify the correctness and effectiveness of CATGNN with SPRING on 16 open datasets. In particular, we demonstrate that CATGNN can handle the largest publicly available dataset with limited memory, which would have been infeasible without increasing the memory space. SPRING also outperforms state-of-the-art partitioning algorithms significantly, with a 50% reduction in replication factor on average

Centrifuge shaking table tests on effect of vertical drain systems for liquefied soil

It was observed that liquefaction induced by earthquake causes series damages to buildings and threatens the people and their properties. From the past studies, a number of countermeasures were proposed to reduce the build-up of excess pore water pressure and to enhance the stiffness of the soil during earthquake. The vertical drain systems are well known methods and used as remediation against earthquake-induced soil liquefaction for many years. The purpose of the study is to investigate the effect of different vertical drain systems for the liquefiable soil by centrifuge modeling technique. The seismic behavior of liquefiable soil was performed firstly. The free field soil models were then prepared with alternatively arranged drain-belts and gravel-pile drains to investigate the effect of different vertical drain systems on the liquefiable soil. Several arrays of accelerometers, the pore water pressure transducers and displacement transducers were placed to monitor the shear wave propagation, the excitation and dissipation of pore water pressure. Displacement transducers were placed to measure the ground surface settlement. From the test results, it was observed that the vertical drain systems reduce the settlement and excess pore water pressure significantly. In the future, the vertical systems will be applied around the structure and the test results would give engineers suggestions to deal with the arrangements of drain-belts and gravel drains to reduce the damage during and after the earthquake

Broken Ergodicity in Ideal, Homogeneous, Incompressible Turbulence

We discuss the statistical mechanics of numerical models of ideal homogeneous, incompressible turbulence and their relevance for dissipative fluids and magnetofluids. These numerical models are based on Fourier series and the relevant statistical theory predicts that Fourier coefficients of fluid velocity and magnetic fields (if present) are zero-mean random variables. However, numerical simulations clearly show that certain coefficients have a non-zero mean value that can be very large compared to the associated standard deviation. We explain this phenomena in terms of broken ergodicity', which is defined to occur when dynamical behavior does not match ensemble predictions on very long time-scales. We review the theoretical basis of broken ergodicity, apply it to 2-D and 3-D fluid and magnetohydrodynamic simulations of homogeneous turbulence, and show new results from simulations using GPU (graphical processing unit) computers

Household Income and Vegetable Consumption among White, Chinese, Korean and Vietnamese Americans

Objectives: This study aims to examine racial/ethnic differences in vegetable consumption between White and three major groups of Asian Americans. We hypothesize that racial/ethnic differences in frequency of vegetable consumption is significantly related to respondents’ household income. Methods: We used the 2009 California Health Survey Interview (CHIS) data set that has a total sample of 47,167 respondents aged 18 and over. The selected sample used in this study consisted of four racial and ethnic groups included Whites (31,582), Chinese (1,014), Korean (909), and Vietnamese (1,411). We used Ordinary Least Square regression and adjusted for complex survey sampling designs in all analyses. Interaction effect is visually presented. Results: Chinese and White respondents reported a greater frequency of weekly vegetable consumption than Korean and Vietnamese respondents. The significant interaction effect of race/ethnicity and household income revealed that White respondents with an annual household income from $150,000 and over consumed vegetables more frequently than White respondents with an annual household income under$150,000. However, among three selected Asian groups, respondents with an annual household income from $150,000 and over consumed vegetables less frequently than those with an annual household income under$150,000. Other demographic variables including sex, age, marital status, education, BMI also had significant associations with frequency of vegetable consumption. Conclusion: Culture and economic wealth might play an important role in vegetable consumption. Knowledge regarding racial/ethnic differences in vegetable consumption are important for community-based health education and intervention programs for Asian Americans

Spatiotemporal analysis of historical records (2001-2012) on dengue fever in Vietnam and development of a statistical model for forecasting risk

Background: Dengue fever is the most widespread infectious disease of humans transmitted by Aedes mosquitoes. It is the leading cause of hospitalization and death in children in the Southeast Asia and western Pacific regions. We analyzed surveillance records from health centers in Vietnam collected between 2001–2012 to determine seasonal trends, develop risk maps and an incidence forecasting model. Methods: The data were analyzed using a hierarchical spatial Bayesian model that approximates its posterior parameter distributions using the integrated Laplace approximation algorithm (INLA). Meteorological, altitude and land cover (LC) data were used as predictors. The data were grouped by province (n = 63) and month (n = 144) and divided into training (2001–2009) and validation (2010–2012) sets. Thirteen meteorological variables, 7 land cover data and altitude were considered as predictors. Only significant predictors were kept in the final multivariable model. Eleven dummy variables representing month were also fitted to account for seasonal effects. Spatial and temporal effects were accounted for using Besag-York-Mollie (BYM) and autoregressive (1) models. Their levels of significance were analyzed using deviance information criterion (DIC). The model was validated based on the Theil’s coefficient which compared predicted and observed incidence estimated using the validation data. Dengue incidence predictions for 2010–2012 were also used to generate risk maps. Results: The mean monthly dengue incidence during the period was 6.94 cases (SD 14.49) per 100,000 people. Analyses on the temporal trends of the disease showed regular seasonal epidemics that were interrupted every 3 years (specifically in July 2004, July 2007 and September 2010) by major fluctuations in incidence. Monthly mean minimum temperature, rainfall, area under urban settlement/build-up areas and altitude were significant in the final model. Minimum temperature and rainfall had non-linear effects and lagging them by two months provided a better fitting model compared to using unlagged variables. Forecasts for the validation period closely mirrored the observed data and accurately captured the troughs and peaks of dengue incidence trajectories. A favorable Theil’s coefficient of inequality of 0.22 was generated. Conclusions: The study identified temperature, rainfall, altitude and area under urban settlement as being significant predictors of dengue incidence. The statistical model fitted the data well based on Theil’s coefficient of inequality, and risk maps generated from its predictions identified most of the high-risk provinces throughout the country

Coordination of frontline defense mechanisms under severe oxidative stress

Inference of an environmental and gene regulatory influence network (EGRINOS) by integrating transcriptional responses to H2O2 and paraquat (PQ) has revealed a multi-tiered oxidative stress (OS)-management program to transcriptionally coordinate three peroxidase/catalase enzymes, two superoxide dismutases, production of rhodopsins, carotenoids and gas vesicles, metal trafficking, and various other aspects of metabolism.ChIP-chip, microarray, and survival assays have validated important architectural aspects of this network, identified novel defense mechanisms (including two evolutionarily distant peroxidase enxymes), and showed that general transcription factors of the transcription factor B family have an important function in coordinating the OS response (OSR) despite their inability to directly sense ROS.A comparison of transcriptional responses to sub-lethal doses of H2O2 and PQ with predictions of these responses made by an EGRIN model generated earlier from responses to other environmental factors has confirmed that a significant fraction of the OSR is made up of a generalized component that is also observed in response to other stressors.Analysis of active regulons within environment and gene regulatory influence network for OS (EGRINOS) across diverse environmental conditions has identified the specialized component of oxidative stress response (OSR) that is triggered by sub-lethal OS, but not by other stressors, including sub-inhibitory levels of redox-active metals, extreme changes in oxygen tension, and a sub-lethal dose of γ rays

Magnitude and patterns of severe Plasmodium vivax monoinfection in Vietnam: a 4-year single-center retrospective study

IntroductionInfection with Plasmodium vivax is a recognized cause of severe malaria including deaths. The exact burden and patterns of severe P. vivax monoinfections is however still not well quantified, especially in P. vivax endemic regions. We examined the magnitude and patterns of severe malaria caused by monoinfections of P. vivax and associated predictors among patients admitted to a tertiary care center for malaria in Vietnam.MethodsA retrospective cohort study was conducted based on the patients’ medical records at the Hospital for Tropical Diseases from January 2015 to December 2018. Extracted information included demographic, epidemiologic, clinical, laboratory and treatment characteristics.ResultsMonoinfections with P. vivax were found in 153 (34.5, 95% CI 30.3–39.1%) patients of whom, uncomplicated and severe malaria were documented in 89.5% (137/153, 95% CI 83.7–93.5%) and 10.5% (16/153, 95% CI 6.5–16.3%), respectively. Patterns of severe malaria included jaundice (8 cases), hypoglycemia (3 cases), shock (2 cases), anemia (2 cases), and cerebral malaria (1 case). Among 153 patients, 73 (47.7%) had classic malaria paroxysm, 57 (37.3%) had >7 days of illness at the time of admission, and 40 (26.1%) were referred from other hospitals. A misdiagnosis as having other diseases from malaria cases coming from other hospitals was up to 32.5% (13/40). Being admitted to hospital after day 7th of illness (AOR = 6.33, 95% CI 1.14–35.30, p = 0.035) was a predictor of severe malaria. Severe malaria was statistically associated with longer hospital length of stay (p = 0.035). Early and late treatment failures and recrudescence were not recorded. All patients recovered completely.DiscussionThis study confirms the emergence of severe vivax malaria in Vietnam which is associated with delayed hospital admission and increased hospital length of stay. Clinical manifestations of P. vivax infection can be misdiagnosed which results in delayed treatment. To meet the goal of malaria elimination by 2030, it is crucial that the non-tertiary hospitals have the capacity to quickly and correctly diagnose malaria and then provide treatment for malaria including P. vivax infections. More robust studies need to be conducted to fully elucidate the magnitude of severe P. vivax in Vietnam

The human touch: Using a webcam to autonomously monitor compliance during visual field assessments

Purpose: To explore the feasibility of using various easy-to-obtain biomarkers to monitor non-compliance (measurement error) during visual field assessments. Methods: Forty-two healthy adults (42 eyes) and seven glaucoma patients (14 eyes) underwent two same-day visual field assessments. An ordinary webcam was used to compute seven potential biomarkers of task compliance, based primarily on eye gaze, head pose, and facial expression. We quantified the association between each biomarker and measurement error, as defined by (1) test–retest differences in overall test scores (mean sensitivity), and (2) failures to respond to visible stimuli on individual trials (stimuli −3 dB or more brighter than threshold). Results: In healthy eyes, three of the seven biomarkers were significantly associated with overall (test–retest) measurement error (P = 0.003–0.007), and at least two others exhibited possible trends (P = 0.052–0.060). The weighted linear sum of all seven biomarkers was associated with overall measurement error, in both healthy eyes (r = 0.51, P < 0.001) and patients (r = 0.65, P < 0.001). Five biomarkers were each associated with failures to respond to visible stimuli on individual trials (all P < 0.001). Conclusions: Inexpensive, autonomous measures of task compliance are associated with measurement error in visual field assessments, in terms of both the overall reliability of a test and failures to respond on particular trials (“lapses”). This could be helpful for identifying low-quality assessments and for improving assessment techniques (e.g., by discounting suspect responses or by automatically triggering comfort breaks or encouragement). Translational Relevance: This study explores a potential way of improving the reliability of visual field assessments, a crucial but notoriously unreliable clinical measure

Prevalence of transcription promoters within archaeal operons and coding sequences

Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ∼64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein–DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3′ ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes—events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements

Ubiquitin Ligase RNF146 Regulates Tankyrase and Axin to Promote Wnt Signaling

Canonical Wnt signaling is controlled intracellularly by the level of β-catenin protein, which is dependent on Axin scaffolding of a complex that phosphorylates β-catenin to target it for ubiquitylation and proteasomal degradation. This function of Axin is counteracted through relocalization of Axin protein to the Wnt receptor complex to allow for ligand-activated Wnt signaling. AXIN1 and AXIN2 protein levels are regulated by tankyrase-mediated poly(ADP-ribosyl)ation (PARsylation), which destabilizes Axin and promotes signaling. Mechanistically, how tankyrase limits Axin protein accumulation, and how tankyrase levels and activity are regulated for this function, are currently under investigation. By RNAi screening, we identified the RNF146 RING-type ubiquitin E3 ligase as a positive regulator of Wnt signaling that operates with tankyrase to maintain low steady-state levels of Axin proteins. RNF146 also destabilizes tankyrases TNKS1 and TNKS2 proteins and, in a reciprocal relationship, tankyrase activity reduces RNF146 protein levels. We show that RNF146, tankyrase, and Axin form a protein complex, and that RNF146 mediates ubiquitylation of all three proteins to target them for proteasomal degradation. RNF146 is a cytoplasmic protein that also prevents tankyrase protein aggregation at a centrosomal location. Tankyrase auto-PARsylation and PARsylation of Axin is known to lead to proteasome-mediated degradation of these proteins, and we demonstrate that, through ubiquitylation, RNF146 mediates this process to regulate Wnt signaling