Low-Rank Matrix Approximations with Flip-Flop Spectrum-Revealing QR Factorization

We present Flip-Flop Spectrum-Revealing QR (Flip-Flop SRQR) factorization, a significantly faster and more reliable variant of the QLP factorization of Stewart, for low-rank matrix approximations. Flip-Flop SRQR uses SRQR factorization to initialize a partial column pivoted QR factorization and then compute a partial LQ factorization. As observed by Stewart in his original QLP work, Flip-Flop SRQR tracks the exact singular values with "considerable fidelity". We develop singular value lower bounds and residual error upper bounds for Flip-Flop SRQR factorization. In situations where singular values of the input matrix decay relatively quickly, the low-rank approximation computed by SRQR is guaranteed to be as accurate as truncated SVD. We also perform a complexity analysis to show that for the same accuracy, Flip-Flop SRQR is faster than randomized subspace iteration for approximating the SVD, the standard method used in Matlab tensor toolbox. We also compare Flip-Flop SRQR with alternatives on two applications, tensor approximation and nuclear norm minimization, to demonstrate its efficiency and effectiveness

Predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using short polypeptide clusters

Background: Protein synthetic lethal genetic interactions are useful to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interactions remains unclear. Results: In this study we used the clusters of short polypeptide sequences, which are typically shorter than the classically defined protein domains, to characterize the functionalities of proteins. We developed a framework to identify significant short polypeptide clusters from yeast protein sequences, and then used these short polypeptide clusters as features to predict yeast synthetic lethal genetic interactions. The short polypeptide clusters based approach provides much higher coverage for predicting yeast synthetic lethal genetic interactions. Evaluation using experimental data sets showed that the short polypeptide clusters based approach is superior to the previous protein domain based one. Conclusion: We were able to achieve higher performance in yeast synthetic lethal genetic interactions prediction using short polypeptide clusters as features. Our study suggests that the short polypeptide cluster may help better understand the functionalities of proteins

Predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using short polypeptide clusters

Background: Protein synthetic lethal genetic interactions are useful to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interactions remains unclear. Results: In this study we used the clusters of short polypeptide sequences, which are typically shorter than the classically defined protein domains, to characterize the functionalities of proteins. We developed a framework to identify significant short polypeptide clusters from yeast protein sequences, and then used these short polypeptide clusters as features to predict yeast synthetic lethal genetic interactions. The short polypeptide clusters based approach provides much higher coverage for predicting yeast synthetic lethal genetic interactions. Evaluation using experimental data sets showed that the short polypeptide clusters based approach is superior to the previous protein domain based one. Conclusion: We were able to achieve higher performance in yeast synthetic lethal genetic interactions prediction using short polypeptide clusters as features. Our study suggests that the short polypeptide cluster may help better understand the functionalities of proteins

Prevalence of pulmonary tuberculosis in western China in 2010–11: a population-based, cross-sectional survey

Background Progress in tuberculosis control in China has been the slowest in western areas, which have the highest prevalence. We assessed the prevalence of pulmonary tuberculosis in the Xinjiang province, China, 10 years after introduction of a control programme based on directly observed treatment, short course. Methods In this population-based, cross-sectional survey, we used a multistage stratifi ed random cluster sample design to estimate the prevalence of smear-positive and bacteriologically confi rmed (either smear positive or culture positive, or both) pulmonary tuberculosis among adults (aged ≥15 years) in Xinjiang who had been resident in their household for the last 6 months. The screening strategy and diagnosis followed WHO guidelines. We estimated prevalence by combining inverse probability weighting and multiple imputation of missing data. We compared our prevalence survey estimates with the ones from the 2010 China national pulmonary tuberculosis survey and the ones from a provincial pulmonary survey done in Xinjiang in 2000. The new smear-positive pulmonary tuberculosis notifi cation rate in 2011 in Xinjiang was obtained to allow the calculation of patient diagnosis rate (PDR). Findings Between Sept 1, 2010, and July 31, 2011, 31 081 individuals were eligible, of whom 29 835 (96·0%) participated in the survey. We identifi ed 50 (0·2%) smear-positive and 101 (0·3%) bacteriologically confi rmed pulmonary tuberculosis cases. The weighted prevalence of smear-positive pulmonary tuberculosis was 170 (95% CI 103–233) per 100 000 people and of bacteriologically confi rmed pulmonary tuberculosis was 430 (249–611) per 100 000 people. Compared with 2000 Xinjiang survey estimates, the prevalence of smear-positive pulmonary tuberculosis has decreased by 26·4% (from 231 [95% CI 148–314] per 100 000 people), whereas the prevalence of bacteriologically confi rmed pulmonary tuberculosis has increased by 17·8% (from 365 [237–493] per 100 000 people). In each age group and sex, the pulmonary tuberculosis prevalence was higher in the 2010–11 Xinjiang survey than in the 2010 national survey. The PDR in 2011 was 0·34 (95% CI 0·25–0·44). Interpretation Despite progress in other parts of China, the prevalence of pulmonary tuberculosis in Xinjiang remains high. The very low PDR suggests poor access to diagnosis and care. Further studies are needed to understand the barriers to diagnosis and care of this population, and eff orts are urgently needed to enhance tuberculosis screening in this area

Dual-factor Synergistically Activated ESIPT-based Probe:Differential Fluorescence Signals to Simultaneously Detect α-Naphthyl Acetate and Acid α-Naphthyl Acetate Esterase

[Image: see text] α-Naphthyl acetate esterase (α-NAE) and acid α-naphthyl acetate esterase (ANAE), a class of special esterases, are important for lymphocyte typing and immunocompetence-monitoring. As such, the simultaneous detection of α-NAE and ANAE has become a target to effectively improve the accuracy in lymphocyte typing. Therefore, we developed a dual-factor synergistically activated ESIPT-based probe (HBT-NA) to detect α-NAE and ANAE sensitively, rapidly, and simultaneously in a differential manner. HBT-NA exhibits differential fluorescence signal outputs toward small changes of α-NAE and ANAE activities. HBT-NA displays a weak fluorescence signal at 392 nm over a pH range from 6.0 to 7.4. However, when it interacts with α-NAE (0–25 U) at pH = 7.4, the fluorescence intensity at 392 nm enhanced linearly within 60 s (F(392 nm)/F0(392 nm) = 0.042 C(α-NAE) + 1.1, R(2) = 0.99). Furthermore, HBT-NA emits ratiometric fluorescence signals (F(505 nm)/F(392 nm)) for ANAE (0–25 U) at pH = 6.0 within 2.0 min, exhibiting a good linear relationship (F(505 nm)/F(392 nm) = 0.83C(ANAE) – 1.75, R(2) = 0.99). The differential fluorescence signals can be used to simultaneously detect the activities of α-NAE and ANAE in solutions and complex living organisms. More importantly, based on the differential fluorescence signals toward α-NAE and ANAE, T lymphocytes and B lymphocytes could be successfully typed and differentiated among nontyped lymphocytes, facilitating the real-time evaluation of their immune functions using flow cytometry. Hence, HBT-NA could be used for the ultrasensitive detection of the enzyme activities of α-NAE and ANAE, the real-time precise typing of lymphocytes, and the monitoring of immunocompetence

Comparing the predictive value of quantitative magnetic resonance imaging parametric response mapping and conventional perfusion magnetic resonance imaging for clinical outcomes in patients with chronic ischemic stroke

Predicting clinical outcomes after stroke, using magnetic resonance imaging (MRI) measures, remains a challenge. The purpose of this study was to investigate the prediction of long-term clinical outcomes after ischemic stroke using parametric response mapping (PRM) based on perfusion MRI data. Multiparametric perfusion MRI datasets from 30 patients with chronic ischemic stroke were acquired at four-time points ranging from V2 (6  weeks) to V5 (7  months) after stroke onset. All perfusion MR parameters were analyzed using the classic whole-lesion approach and voxel-based PRM at each time point. The imaging biomarkers from each acquired MRI metric that was predictive of both neurological and functional outcomes were prospectively investigated. For predicting clinical outcomes at V5, it was identified that PRMTmax-, PRMrCBV-, and PRMrCBV+ at V3 were superior to the mean values of the corresponding maps at V3. We identified correlations between the clinical prognosis after stroke and MRI parameters, emphasizing the superiority of the PRM over the whole-lesion approach for predicting long-term clinical outcomes. This indicates that complementary information for the predictive assessment of clinical outcomes can be obtained using PRM analysis. Moreover, new insights into the heterogeneity of stroke lesions revealed by PRM can help optimize the accurate stratification of patients with stroke and guide rehabilitation

Palmitic acid suppresses apolipoprotein M gene expression via the pathway of PPARβ/δ in HepG2 cells.

It has been demonstrated that apolipoprotein M (APOM) is a vasculoprotective constituent of high density lipoprotein (HDL), which could be related to the anti-atherosclerotic property of HDL. Investigation of regulation of APOM expression is of important for further exploring its pathophysiological function in vivo. Our previous studies indicated that expression of APOM could be regulated by platelet activating factor (PAF), transforming growth factors (TGF), insulin-like growth factor (IGF), leptin, hyperglycemia and etc., in vivo and/or in vitro. In the present study, we demonstrated that palmitic acid could significantly inhibit APOM gene expression in HepG2 cells. Further study indicated neither PI-3 kinase (PI3K) inhibitor LY294002 nor protein kinase C (PKC) inhibitor GFX could abolish palmitic acid induced down-regulation of APOM expression. In contrast, the peroxisome proliferator-activated receptor beta/delta (PPARβ/δ) antagonist GSK3787 could totally reverse the palmitic acid-induced down-regulation of APOM expression, which clearly demonstrates that down-regulation of APOM expression induced by palmitic acid is mediated via the PPARβ/δ pathway