Physical activity is a potential measure of physical resilience in older adults receiving hemodialysis

BackgroundPhysical resilience, or the ability to recover after a physical stressor, declines with aging. Efforts to preserve physical resilience in the older dialysis population are critically needed; however, validated, patient-centered measures that are sensitive to change are also needed. Our objective was to assess accelerometer-derived step count variability, or a measure of intra-individual variation in physical activity, as a potential measure of physical resilience among older adults receiving hemodialysis.MethodsCommunity-dwelling ambulatory older adults receiving in-center hemodialysis were prospectively enrolled. Participants wore wrist accelerometers during daytime hours on both dialysis and non-dialysis days up to 14 days, and the feasibility of accelerometer use was assessed from wear time. We used accelerometer data to compute step counts in 4-hour blocks and step count variability. Physical function was assessed with the Short Physical Performance Battery (SPPB which includes gait speed test), grip strength, activities of daily living (ADLs) instruments, and life space mobility. We assessed interval fatigue (subjective rating from 0 to 10) on dialysis and non-dialysis days and self-reported recovery time. We assessed the correlations of step count variability with measures of physical function and step count and interval fatigue.ResultsOf 37 enrolled participants, 29 had sufficient accelerometer data for analyses. Among the 29 participants, mean (SD) age was 70.6(4.8) years, and 55% (n=16) were male and 72% (n=21) were Black race. Participants were largely sedentary with median (Q1-Q3) self-reported total kilocalories per week of 200 (36–552). Step count variability was positively correlated with measures of physical function: SPPB (r=0.50, p<0.05), gait speed (r=0.59, p<0.05), handgrip strength (r=0.71, p<0.05), Instrumental ADLs (r=0.44, p<0.05) and life space mobility (r=0.54, p<0.05).There was a weak inverse correlation between post-dialysis step counts (4-hour blocks after a dialysis session) and post-dialysis interval fatigue [r=-0.19 (n=102, p=0.06).ConclusionsPhysical activity assessment via accelerometer is feasible for older adults receiving hemodialysis. Step count variability correlated with physical function, so it may be a novel measure of physical resilience. Further studies are needed to validate this measure

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu

Pathoadaptive conditional regulation of the type VI secretion system in Vibrio cholerae O1 strains

The most recently discovered secretion pathway in gram-negative bacteria, the type VI secretion system (T6SS), is present in many species and is considered important for the survival of non-O1 non-O139 Vibrio cholerae in aquatic environments. Until now, it was not known whether there is a functionally active T6SS in wild-type V. cholerae O1 strains, the cause of cholera disease in humans. Here, we demonstrate the presence of a functionally active T6SS in wild-type V. cholerae O1 strains, as evidenced by the secretion of the T6SS substrate Hcp, which required several gene products encoded within the putative vas gene cluster. Our analyses showed that the T6SS of wild-type V. cholerae O1 strain A1552 was functionally activated when the bacteria were grown under high-osmolarity conditions. The T6SS was also active when the bacteria were grown under low temperature (23°C), suggesting that the system may be important for the survival of the bacterium in the environment. A test of the interbacterial virulence of V. cholerae strain A1552 against an Escherichia coli K-12 strain showed that it was strongly enhanced under high osmolarity and that it depended on the hcp genes. Interestingly, we found that the newly recognized osmoregulatory protein OscR plays a role in the regulation of T6SS gene expression and secretion of Hcp from V. cholerae O1 strains