CURE: Flexible Categorical Data Representation by Hierarchical Coupling Learning

© 1989-2012 IEEE. The representation of categorical data with hierarchical value coupling relationships (i.e., various value-to-value cluster interactions) is very critical yet challenging for capturing complex data characteristics in learning tasks. This paper proposes a novel and flexible coupled unsupervised categorical data representation (CURE) framework, which not only captures the hierarchical couplings but is also flexible enough to be instantiated for contrastive learning tasks. CURE first learns the value clusters of different granularities based on multiple value coupling functions and then learns the value representation from the couplings between the obtained value clusters. With two complementary value coupling functions, CURE is instantiated into two models: coupled data embedding (CDE) for clustering and coupled outlier scoring of high-dimensional data (COSH) for outlier detection. These show that CURE is flexible for value clustering and coupling learning between value clusters for different learning tasks. CDE embeds categorical data into a new space in which features are independent and semantics are rich. COSH represents data w.r.t. an outlying vector to capture complex outlying behaviors of objects in high-dimensional data. Substantial experiments show that CDE significantly outperforms three popular unsupervised encoding methods and three state-of-the-art similarity measures, and COSH performs significantly better than five state-of-the-art outlier detection methods on high-dimensional data. CDE and COSH are scalable and stable, linear to data size and quadratic to the number of features, and are insensitive to their parameters

Ultraviolet emission of silicon quantum tips

Silicon tips used as field emitters have dimensions that are within the quantum confinement regime. Therefore they can be considered as freestanding silicon tips. In this letter, a photoluminescence spectrum of a 100×100100×100 array of silicon tips was taken at 10 K. Narrow ultraviolet luminescence peaks were observed. Using the empirical pseudopotential homojunction model, it is demonstrated that these luminescence peaks come from energy levels arising from quantum confinement. By fitting the theoretical result to the experimental result, we conclude that the luminescence peaks come from Si quantum tips of about 20 Å in width and that they are covered by silicon dioxide. © 1999 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71101/2/APPLAB-74-3-386-1.pd

A PH Domain in ACAP1 Possesses Key Features of the BAR Domain in Promoting Membrane Curvature

SummaryThe BAR (Bin-Amphiphysin-Rvs) domain undergoes dimerization to produce a curved protein structure, which superimposes onto membrane through electrostatic interactions to sense and impart membrane curvature. In some cases, a BAR domain also possesses an amphipathic helix that inserts into the membrane to induce curvature. ACAP1 (Arfgap with Coil coil, Ankyrin repeat, and PH domain protein 1) contains a BAR domain. Here, we show that this BAR domain can neither bind membrane nor impart curvature, but instead requires a neighboring PH (Pleckstrin Homology) domain to achieve these functions. Specific residues within the PH domain are responsible for both membrane binding and curvature generation. The BAR domain adjacent to the PH domain instead interacts with the BAR domains of neighboring ACAP1 proteins to enable clustering at the membrane. Thus, we have uncovered the molecular basis for an unexpected and unconventional collaboration between PH and BAR domains in membrane bending

SNP rs1533428 at 2p16.3 as a marker for late-onset primary open-angle glaucoma

Purpose: To investigate the associations between gene variants in cholesterol 24S-hydroxylase (CYP46A1), LIM homeobox transcription factor 1-beta (LMX1B), plexin domain containing 2 (PLXDC2), toll-like receptor 4 (TLR4), transmembrane and tetratricopeptide repeat containing 2 (TMTC2), zona pellucida glycoprotein 4 (ZP4), chromosome 2p16.3, and primary open-angle glaucoma (POAG). Methods: We studied 462 POAG patients and 577 controls from three cohorts (Hong Kong, Shantou, and Beijing, China). Twelve single-nucleotide polymorphisms (SNPs) were genotyped in the Hong Kong cohort using TaqMan genotyping assay. Significant associations were validated in the Shantou and Beijing cohorts. Results: Association of POAG with TLR4 rs7037117, in a recessive model, was identified in the Hong Kong and Shantou cohorts (both southern Chinese, $p_{rec}$=0.0019) but not the Beijing cohort (northern Chinese). rs1533428 at chromosome 2p16.3 showed a consistent trend of age-specific association in all three cohorts. Genotypes TT + CT conferred a 2.16 fold of significantly increased risk to late-onset POAG ($p_{dom}$=0.00025), but no significant risk to POAG of younger ages of onset in the combined cohort. A joint effect was found between rs7037117 and rs1533428, with carriers of both higher-risk genotypes having a 4.53 fold of increased disease risk (p=0.00028). Conclusions: Our study reveals discrepant association patterns of 12 candidate SNPs in 7 genes/loci with POAG in Chinese, provides positive replications for POAG markers rs1533428 at 2p16.3 and TLR4 rs7037117, and suggests that rs1533428 is a putative risk variant for late-onset POAG. The identification of an age-specific association between rs1533428 and late-onset POAG highlights a new genotype-phenotype association in POAG. Further studies are warranted to confirm the age-specific association

The uptake of soluble and nanoparticulate imaging isotope in model liver tumours after intra-venous and intra-arterial administration

Delivery of chemotherapeutic drugs to tumours by reformulation as nanoparticles has often been proposed as a means of facilitating increased selective uptake, exploiting the increased permeability of the tumour vasculature. However realisation of this improvement in drug delivery in cancer patients has met with limited success. We have compared tumour uptake of soluble Tc99m-pertechnetate and a colloid of nanoparticles with a Tc99m core, using both intra-venous and intra-arterial routes of administration in a rabbit liver VX2 tumour model. The radiolabelled nanoparticles were tested both in untreated and cationised form. The results from this tumour model in an internal organ show a marked advantage in intra-arterial administration over the intra-venous route, even for the soluble isotope. Tumour accumulation of nanoparticles from arterial administration was augmented by cationisation of the nanoparticle surface with histone proteins, which consistently facilitated selective accumulation within microvessels at the periphery of tumours.Sources of support for this research: Sirtex Medical Ltd, Sydney Australia

Prevalence of low back pain and associated occupational factors among Chinese coal miners

<p>Abstract</p> <p>Background</p> <p>Very few studies have evaluated the association between occupational factors and low back pain (LBP) among miners. The epidemiological data on LBP in Chinese miners are limited. The aim of this study was to measure the prevalence of low back pain in Chinese coal miners and to investigate the role of occupational factors.</p> <p>Methods</p> <p>A cross-sectional survey was conducted to examine 1573 coal miners in northern China. The prevalence of LBP over a 12-month period was assessed using the Nordic Musculoskeletal Questionnaire. Odds ratios were calculated to examine the association between the prevalence of LBP over a 12-month period and occupational factors using logistic regression.</p> <p>Results</p> <p>Among the coal miners, 64.9% self-reported LBP in a 12-month period. Occupational factors associated with LBP were identified, including tasks with a high degree of repetitiveness (OR 1.3, 95%CI 1.0-1.6), tasks characterized by a high level of physical demand (OR 1.4, 95% CI 1.1-1.8), posture requiring extreme bending (OR 1.6, 95% CI 1.2-1.7) and insufficient recovery time (OR 1.4, 95% CI 1.0-1.8).</p> <p>Conclusion</p> <p>Low back pain is common among Chinese miners. There were strong associations with occupational factors.</p

PMeS: Prediction of Methylation Sites Based on Enhanced Feature Encoding Scheme

Protein methylation is predominantly found on lysine and arginine residues, and carries many important biological functions, including gene regulation and signal transduction. Given their important involvement in gene expression, protein methylation and their regulatory enzymes are implicated in a variety of human disease states such as cancer, coronary heart disease and neurodegenerative disorders. Thus, identification of methylation sites can be very helpful for the drug designs of various related diseases. In this study, we developed a method called PMeS to improve the prediction of protein methylation sites based on an enhanced feature encoding scheme and support vector machine. The enhanced feature encoding scheme was composed of the sparse property coding, normalized van der Waals volume, position weight amino acid composition and accessible surface area. The PMeS achieved a promising performance with a sensitivity of 92.45%, a specificity of 93.18%, an accuracy of 92.82% and a Matthew’s correlation coefficient of 85.69% for arginine as well as a sensitivity of 84.38%, a specificity of 93.94%, an accuracy of 89.16% and a Matthew’s correlation coefficient of 78.68% for lysine in 10-fold cross validation. Compared with other existing methods, the PMeS provides better predictive performance and greater robustness. It can be anticipated that the PMeS might be useful to guide future experiments needed to identify potential methylation sites in proteins of interest. The online service is available at http://bioinfo.ncu.edu.cn/inquiries_PMeS.aspx

Health-related quality of life in glioma patients in China

<p>Abstract</p> <p>Background</p> <p>Health-related quality of life (HRQOL) has been increasingly emphasized in cancer patients. There are no reports comparing baseline HRQOL of different subgroups of glioma patients prior to surgery.</p> <p>Methods</p> <p>HRQOL assessments by the standard Chinese version of the European Organization for Research and Treatment of Cancer Quality of Life Core Questionnaire 30 (EORTC QLQ-C30, version 3.0), the Mini-Mental State Examination and Karnofsky Performance Status were obtained from glioma patients prior to surgery.</p> <p>Results</p> <p>Ninety-two pathologically confirmed glioma patients were recruited. There were 84.8% patients with emotional impairment, 75% with social and cognitive impairment, 70.7% with physical impairment, and 50% with role impairment. Eighty-two percent of patients reported fatigue symptoms, 72.8% reported pain, 50% reported appetite loss, 39.1% reported insomnia, and 36.9% reported nausea/vomiting, whereas other symptoms (dyspnea, diarrhea, constipation) in the QLQ-C30 were reported by fewer than 30% of patients. Fatigue and pain symptoms and all "functioning" scales were strongly correlated with global health status/quality of life (QoL). Fatigue was strongly related to all functioning scales, pain, appetite loss, and global health status/QoL. No difference in baseline HRQOL prior to surgery was reported between females and males, among different lesion locations, or between normal- and abnormal-cognition subgroups of glioma patients. Age, KPS, WHO grade, and tumor recurrence significantly affected HRQOL in glioma patients.</p> <p>Conclusions</p> <p>These data provided the baseline HRQOL in glioma patients prior to surgery in China. Most pre-surgery glioma patients indicated emotional, social, cognitive, physical, and role impairment. Fatigue, pain, appetite loss, insomnia, and nausea/vomiting were common in these patients. The fatigue and pain symptoms and all types of functioning strongly affected global health status/QoL. Old age, worse performance status, WHO grade IV and tumor recurrence had deleterious effects on HRQOL.</p