Gradual Program Analysis

Dataflow analysis and gradual typing are both well-studied methods to gain information about computer programs in a finite amount of time. The gradual program analysis project seeks to combine those two techniques in order to gain the benefits of both. This thesis explores the background information necessary to understand gradual program analysis, and then briefly discusses the research itself, with reference to publication of work done so far. The background topics include essential aspects of programming language theory, such as syntax, semantics, and static typing; dataflow analysis concepts, such as abstract interpretation, semilattices, and fixpoint computations; and gradual typing theory, such as the concept of an unknown type, liftings of predicates, and liftings of functions

A Brief Study of Open Source Graph Databases

With the proliferation of large irregular sparse relational datasets, new storage and analysis platforms have arisen to fill gaps in performance and capability left by conventional approaches built on traditional database technologies and query languages. Many of these platforms apply graph structures and analysis techniques to enable users to ingest, update, query and compute on the topological structure of these relationships represented as set(s) of edges between set(s) of vertices. To store and process Facebook-scale datasets, they must be able to support data sources with billions of edges, update rates of millions of updates per second, and complex analysis kernels. These platforms must provide intuitive interfaces that enable graph experts and novice programmers to write implementations of common graph algorithms. In this paper, we explore a variety of graph analysis and storage platforms. We compare their capabil- ities, interfaces, and performance by implementing and computing a set of real-world graph algorithms on synthetic graphs with up to 256 million edges. In the spirit of full disclosure, several authors are affiliated with the development of STINGER.Comment: WSSSPE13, 4 Pages, 18 Pages with Appendix, 25 figure

Stem cell mechanobiology

Stem cells are undifferentiated cells that are capable of proliferation, self-maintenance and differentiation towards specific cell phenotypes. These processes are controlled by a variety of cues including physicochemical factors associated with the specific mechanical environment in which the cells reside. The control of stem cell biology through mechanical factors remains poorly understood and is the focus of the developing field of mechanobiology. This review provides an insight into the current knowledge of the role of mechanical forces in the induction of differentiation of stem cells. While the details associated with individual studies are complex and typically associated with the stem cell type studied and model system adopted, certain key themes emerge. First, the differentiation process affects the mechanical properties of the cells and of specific subcellular components. Secondly, that stem cells are able to detect and respond to alterations in the stiffness of their surrounding microenvironment via induction of lineage-specific differentiation. Finally, the application of external mechanical forces to stem cells, transduced through a variety of mechanisms, can initiate and drive differentiation processes. The coalescence of these three key concepts permit the introduction of a new theory for the maintenance of stem cells and alternatively their differentiation via the concept of a stem cell 'mechano-niche', defined as a specific combination of cell mechanical properties, extracellular matrix stiffness and external mechanical cues conducive to the maintenance of the stem cell population.<br/

An exploratory study of the effects of the pH of synthetic urine on skin integrity in healthy participants.

BACKGROUND: Incontinence-associated dermatitis (IAD) develops from prolonged exposure of skin to urine and/or stool and represents a common complication in older adults, reducing the quality of life. Increased pH is an important etiologic factor of IAD; however, the relationship between urinary pH and skin barrier disruption remains unclear. OBJECTIVE: The aim of this study is to examine the effects of synthetic urine (s-urine) at various pHs on transepidermal water loss (TEWL), stratum corneum hydration (SCH), and skin surface pH. METHODS: S-urine solutions (pH 5.0–9.0) were applied to the volar forearms of 15 healthy participants for 2 h, with another site serving as the untreated control. Measurements of TEWL, SCH, and skin surface pH were obtained at baseline (BL) and after each challenge. Skin buffering capacity was also examined in 5 volunteers by recording skin pH at BL, after 2 h exposure and every 5 min for 40 min. RESULTS: TEWL and SCH were increased following exposure to s-urine compared to BL values. Although there was a tendency for pH to increase after exposure, further investigation showed that changes are only temporal as pH value is restored to BL within 5 mins. There were no significant differences between solutions. CONCLUSIONS: This study revealed that urine disrupts healthy skin integrity; however, its effects are not pH dependent. Transient changes were observed on the acid mantle of the skin due to its innate buffering capacity. Future studies need to examine the effects of urine combined with bacteria responsible for pH elevation in patients with urinary incontinence

RNA-Seq optimization with eQTL gold standards.

BackgroundRNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results sensitive to systematic sample stratification or, in more extreme cases, to outliers. Further, a method to assess normalization and adjustment measures imposed on the data is lacking.ResultsTo address these issues, we utilize previously published eQTLs as a novel gold standard at the center of a framework that integrates DNA genotypes and RNA-Seq data to optimize analysis and aid in the understanding of genetic variation and gene expression. After detecting sample contamination and sequencing outliers in RNA-Seq data, a set of previously published brain eQTLs was used to determine if sample outlier removal was appropriate. Improved replication of known eQTLs supported removal of these samples in downstream analyses. eQTL replication was further employed to assess normalization methods, covariate inclusion, and gene annotation. This method was validated in an independent RNA-Seq blood data set from the GTEx project and a tissue-appropriate set of eQTLs. eQTL replication in both data sets highlights the necessity of accounting for unknown covariates in RNA-Seq data analysis.ConclusionAs each RNA-Seq experiment is unique with its own experiment-specific limitations, we offer an easily-implementable method that uses the replication of known eQTLs to guide each step in one's data analysis pipeline. In the two data sets presented herein, we highlight not only the necessity of careful outlier detection but also the need to account for unknown covariates in RNA-Seq experiments

Monitoring contractile dermal lymphatic activity following uniaxial mechanical loading

It is proposed that direct mechanical loading can impair dermal lymphatic function, contributing to the causal pathway of pressure ulcers. The present study aims to investigate the effects of loading on human dermal lymphatic vessels. Ten participants were recruited with ages ranging from 24-61 years. Participants had intradermal indocyanine green injections administrated between left finger digits. Fluorescence was imaged for 5 minute sequences with an Infra-Red camera prior to lymph vessel loading, immediately after axial loading (60mmHg) and following a recovery period. Image processing was employed to defined transient lymph packets and compare lymph function between each test phase. The results revealed that between 1-8 transient events (median =4) occurred at baseline, with a median velocity of 8.1mm/sec (range 4.1-20.1mm/sec). Immediately post-loading, there was a significant (p&lt;0.05) reduction in velocity (median = 6.4, range 2.2-13.5mm/sec), although the number of transient lymph packages varied between participants. During the recovery period the number (range 1-7) and velocity (recovery median =9.6mm/sec) of transient packets were largely restored to basal values. The present study revealed that some individuals present with impaired dermal lymphatic function immediately after uniaxial mechanical loading. More research is needed to investigate the effects of pressure and shear on lymphatic vessel patency. <br/

Fast Association Tests for Genes with FAST

Gene-based tests of association can increase the power of a genome-wide association study by aggregating multiple independent effects across a gene or locus into a single stronger signal. Recent gene-based tests have distinct approaches to selecting which variants to aggregate within a locus, modeling the effects of linkage disequilibrium, representing fractional allele counts from imputation, and managing permutation tests for p-values. Implementing these tests in a single, efficient framework has great practical value. Fast ASsociation Tests (Fast) addresses this need by implementing leading gene-based association tests together with conventional SNP-based univariate tests and providing a consolidated, easily interpreted report. Fast scales readily to genome-wide SNP data with millions of SNPs and tens of thousands of individuals, provides implementations that are orders of magnitude faster than original literature reports, and provides a unified framework for performing several gene based association tests concurrently and efficiently on the same data. Availability: https://bitbucket.org/baderlab/fast/downloads/FAST.tar.gz, with documentation at https://bitbucket.org/baderlab/fast/wiki/Hom

Biomechanical signals and the C-type natriuretic peptide counteract catabolic activities induced by IL-1β in chondrocyte/agarose constructs

Introduction: The present study examined the effect of C-type natriuretic peptide (CNP) on the anabolic and catabolic activities in chondrocyte/agarose constructs subjected to dynamic compression. Methods: Constructs were cultured under free-swelling conditions or subjected to dynamic compression with low (0.1 to 100 pM) or high concentrations (1 to 1,000 nM) of CNP, interleukin-1? (IL-1?), and/or KT-5823 (inhibits cyclic GMP-dependent protein kinase II (PKGII)). Anabolic and catabolic activities were assessed as follows: nitric oxide (NO) and prostaglandin E2 (PGE2) release, and [3H]-thymidine and 35SO4 incorporation were quantified by using biochemical assays. Gene expression of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), aggrecan, and collagen type II were assessed with real-time quantitative PCR (qPCR). Two-way ANOVA and the post hoc Bonferroni-corrected t tests were used to examine data. Results: CNP reduced NO and PGE2 release and partially restored [3H]-thymidine and 35SO4 incorporation in constructs cultured with IL-1?. The response was dependent on the concentration of CNP, such that 100 pM increased [3H]-thymidine incorporation (P &lt; 0.001). This is in contrast to 35SO4 incorporation, which was enhanced with 100 or 1000 nM CNP in the presence and absence of IL-1? (P &lt; 0.001). Stimulation by both dynamic compression and CNP and/or the PKGII inhibitor further reduced NO and PGE2 release and restored [3H]-thymidine and 35SO4 incorporation. In the presence and absence of IL-1?, the magnitude of stimulation for [3H]-thymidine and 35SO4 incorporation by dynamic compression was dependent on the concentration of CNP and the response was inhibited with the PKGII inhibitor. In addition, stimulation by CNP and/or dynamic compression reduced IL-1?-induced iNOS and COX-2 expression and restored aggrecan and collagen type II expression. The catabolic response was not further influenced with the PKGII inhibitor in IL-1?-treated constructs. Conclusions: Treatment with CNP and dynamic compression increased anabolic activities and blocked catabolic effects induced by IL-1?. The anabolic response was PKGII mediated and raises important questions about the molecular mechanisms of CNP with mechanical signals in cartilage. Therapeutic agents like CNP could be administered in conjunction with controlled exercise therapy to slow the OA disease progression and to repair damaged cartilage. The findings from this research provide the potential for developing novel agents to slow the pathophysiologic mechanisms and to treat OA in the young and old. <br/