Urine Specimens from Pregnant and Nonpregnant Women Inhibitory to Amplification of \u3cem\u3eChlamydia trachomatis\u3c/em\u3e Nucleic Acid by PCR, Ligase Chain Reaction, and Transcription-Mediated Amplification: Identification of Urinary Substances Associated with Inhibition and Removal of Inhibitory Activity

The presence of endogenous amplification inhibitors in urine may produce false-negative results for the detection of Chlamydia trachomatis nucleic acids by tests such as PCR, ligase chain reaction (LCR), and transcription-mediated amplification (TMA). Consecutive urine specimens from 101 pregnant women and 287 nonpregnant women submitted for urinalysis were processed for C. trachomatis detection. Aliquots were spiked with the equivalent of one C. trachomatis elementary body and were tested by three commercial assays: AMPLICOR CT/NG, Chlamydia LCX, and Chlamydia TMA. The prevalence of inhibitors resulting in complete inhibition of amplification was 4.9% for PCR, 2.6% for LCR, and 7.5% for TMA. In addition, all three assays were partially inhibited by additional urine specimens. Only PCR was more often inhibited by urine from pregnant women than by urine from nonpregnant women (9.9 versus 3.1%; P = 0.011). A complete urinalysis including dipstick and a microscopic examination was performed. Logistic regression analysis revealed that the following substances were associated with amplification inhibition: beta-human chorionic gonadotropin (odd ratio [OR], 3.3) and crystals (OR, 3.3) for PCR, nitrites for LCR (OR, 14.4), and hemoglobin (OR, 3.3), nitrites (OR, 3.3), and crystals (OR, 3.3) for TMA. Aliquots of each inhibitory urine specimen were stored at 4 and -70°C and a dilution of 1:10 (84% for PCR, 100% for LCR, and 92% for TMA). Five urine specimens (three for PCR and two for TMA) required phenol-chloroform extraction to remove inhibitors. The results indicate that the prevalence of nucleic acid amplification inhibitors in female urine is different for each technology, that this prevalence may be predicted by the presence of urinary factors, and that storage and dilution remove most of the inhibitors

Factors Associated with Diabetes Risk in South Texas College Students

International Journal of Exercise Science 7(2) : 110-118, 2014. South Texas has a high prevalence of diabetes and college students may be particularly at risk. While increased BMI, sedentary activity and depression have been associated with diabetes progression in the general population, it has not been established whether these factors contribute to increased diabetes risk in college students. The purpose of this study was to assess diabetes risk and determine whether depressive symptoms or physical activity patterns are associated with increased diabetes risk in college students. Sixty-nine college students were assessed for diabetes risk using the Finnish Diabetes Risk Score (FINDRISC) . Each participant completed the International Physical Activity Questionnaire (IPAQ) which included a sitting subscale, the Zung Self-Rated Depression Scale, and had anthropometric measures taken. Of the participants, 21.7% reported elevated risk (FINDRISC score 7-11), and 4.3% of participants had a moderate-to-high risk of developing diabetes (FINDRISC \u3e12). On average, the sample was overweight (BMI = 26.81±0.75 kg . m-2), and BMI was associated with diabetes risk (r = 0.626, p \u3c 0.001). While diabetes risk was not correlated with IPAQ total physical activity score (r = 0.019, p = 0.874), it was modestly correlated with time spent sitting (r = 0.295, p = 0.015). There was no association between self-reported depressive symptoms and diabetes risk (r =0.078, p = 0.525). Although diabetes risk was not associated with total activity and depressive symptoms, it was associated with time spent sitting and BMI. These results suggest that in this population, sitting less and reducing weight may help lower the risk of developing diabetes

rCUR: an R package for CUR matrix decomposition

BACKGROUND: Many methods for dimensionality reduction of large data sets such as those generated in microarray studies boil down to the Singular Value Decomposition (SVD). Although singular vectors associated with the largest singular values have strong optimality properties and can often be quite useful as a tool to summarize the data, they are linear combinations of up to all of the data points, and thus it is typically quite hard to interpret those vectors in terms of the application domain from which the data are drawn. Recently, an alternative dimensionality reduction paradigm, CUR matrix decompositions, has been proposed to address this problem and has been applied to genetic and internet data. CUR decompositions are low-rank matrix decompositions that are explicitly expressed in terms of a small number of actual columns and/or actual rows of the data matrix. Since they are constructed from actual data elements, CUR decompositions are interpretable by practitioners of the field from which the data are drawn. RESULTS: We present an implementation to perform CUR matrix decompositions, in the form of a freely available, open source R-package called rCUR. This package will help users to perform CUR-based analysis on large-scale data, such as those obtained from different high-throughput technologies, in an interactive and exploratory manner. We show two examples that illustrate how CUR-based techniques make it possible to reduce significantly the number of probes, while at the same time maintaining major trends in data and keeping the same classification accuracy. CONCLUSIONS: The package rCUR provides functions for the users to perform CUR-based matrix decompositions in the R environment. In gene expression studies, it gives an additional way of analysis of differential expression and discriminant gene selection based on the use of statistical leverage scores. These scores, which have been used historically in diagnostic regression analysis to identify outliers, can be used by rCUR to identify the most informative data points with respect to which to express the remaining data points

Effect of water-wall interaction potential on the properties of nanoconfined water

Much of the understanding of bulk liquids has progressed through study of the limiting case in which molecules interact via purely repulsive forces, such as a hard-core potential. In the same spirit, we report progress on the understanding of confined water by examining the behavior of water-like molecules interacting with planar walls via purely repulsive forces and compare our results with those obtained for Lennard-Jones (LJ) interactions between the molecules and the walls. Specifically, we perform molecular dynamics simulations of 512 water-like molecules which are confined between two smooth planar walls that are separated by 1.1 nm. At this separation, there are either two or three molecular layers of water, depending on density. We study two different forms of repulsive confinements, when the interaction potential between water-wall is (i) $1/r^9$ and (ii) WCA-like repulsive potential. We find that the thermodynamic, dynamic and structural properties of the liquid in purely repulsive confinements qualitatively match those for a system with a pure LJ attraction to the wall. In previous studies that include attractions, freezing into monolayer or trilayer ice was seen for this wall separation. Using the same separation as these previous studies, we find that the crystal state is not stable with $1/r^9$ repulsive walls but is stable with WCA-like repulsive confinement. However, by carefully adjusting the separation of the plates with $1/r^9$ repulsive interactions so that the effective space available to the molecules is the same as that for LJ confinement, we find that the same crystal phases are stable. This result emphasizes the importance of comparing systems only using the same effective confinement, which may differ from the geometric separation of the confining surfaces.Comment: 20 pages, 10 figure

Thermodynamics, Structure, and Dynamics of Water Confined between Hydrophobic Plates

We perform molecular dynamics simulations of 512 water-like molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic properties of water are shifted to lower temperatures relative to the bulk by $\approx 40$ K. The dynamics and structure of the confined water resemble bulk water at higher temperatures, consistent with the shift of thermodynamic anomalies to lower temperature. Due to this $T$ shift, our confined water simulations (down to $T = 220$ K) do not reach sufficiently low temperature to observe a liquid-liquid phase transition found for bulk water at $T\approx 215$ K using the TIP5P potential. We find that the different crystalline structures that can form for two different separations of the plates, 0.7 nm and 1.10 nm, have no counterparts in the bulk system, and discuss the relevance to experiments on confined water.Comment: 31 pages, 14 figure

Interplay Between Time-Temperature-Transformation and the Liquid-Liquid Phase Transition in Water

We study the TIP5P water model proposed by Mahoney and Jorgensen, which is closer to real water than previously-proposed classical pairwise additive potentials. We simulate the model in a wide range of deeply supercooled states and find (i) the existence of a non-monotonic ``nose-shaped'' temperature of maximum density line and a non-reentrant spinodal, (ii) the presence of a low temperature phase transition, (iii) the free evolution of bulk water to ice, and (iv) the time-temperature-transformation curves at different densities.Comment: RevTeX4, 4 pages, 4 eps figure

Broadband Spectral Analysis of PKS 0528+134: A Report on Six Years of EGRET Observations

The multiwavelength spectra of PKS 0528+134 during six years of observations by EGRET have been analyzed using synchrotron self-Compton (SSC) and external radiation Compton (ERC) models. We find that a two-component model, in which the target photons are produced externally to the gamma-ray emitting region, but also including an SSC component, is required to suitably reproduce the spectral energy distributions of the source. Our analysis indicates that there is a trend in the observed properties of PKS 0528+134, as the source goes from a gamma-ray low state to a flaring state. We observe that during the higher gamma-ray states, the bulk Lorentz factor of the jet increases and the ERC component dominates the high-energy emission. Our model calculations indicate the trend that the energies of the electrons giving rise to the synchrotron peak decreases, and the power-ratio of the gamma-ray and low energy spectral components increases, as the source goes from a low to a high gamma-ray state.Comment: 36 pages, 13 figures, final version accepted for publication in ApJ; includes minor modification