Finito: A Faster, Permutable Incremental Gradient Method for Big Data Problems

Recent advances in optimization theory have shown that smooth strongly convex finite sums can be minimized faster than by treating them as a black box "batch" problem. In this work we introduce a new method in this class with a theoretical convergence rate four times faster than existing methods, for sums with sufficiently many terms. This method is also amendable to a sampling without replacement scheme that in practice gives further speed-ups. We give empirical results showing state of the art performance

Guarding International Borders Against HIV: A Comparative Study in Futility

Back in 1985, when knowledge of HIV began to spread, governments reacted by passing immigration laws to restrict the entry of HIV positive individuals. These laws required such individuals to either declare their HIV status or undergo mandatory HIV testing to secure entry. As justification for these initiatives, many countries claimed to be preserving the public health and their domestic economy. The United States, China, and Russia are three countries that have had, or still have, some form of HIV immigration restrictions. Initially, it may seem logical that preventing HIV positive individuals from entering a country will cut down on the spread of HIV and save the economy from health care costs. Nevertheless, an analysis of the HIV travel restrictions of these three countries will show that the public health and economic reasoning behind such laws is flawed because HIV is not spread by casual contact and because economic goals can be accomplished with less restrictive means. Moreover, this article will further reveal that HIV travel restrictions contribute to several health concerns and create issues with confidentially and stigmatization. In the end, a comparative analysis of these three countries, with specific attention paid to their successes and failures, reveals that the best system is one that works on both an international and domestic level. On the international level, border *90 testing must be voluntary, confidential, and informed. It should also utilize pre and post test counseling, and not be used to restrict entry. On the domestic level, individual countries need to educate the public and create programs to address high-risk groups responsible for the rapid spread of HIV. In doing so, society will find not only that it is more effectively protecting itself from the spread of HIV, but also that it is protecting the HIV community from the stigma and discrimination that contributed to the rapid spread of HIV in the first place

PERVASIVE TECHNOLOGY TO REDUCE ROAD RAGE: A STUDY ON THE EFFECTS OF METABOLIC CHANGES IN INDIVIDUALS WHILE DRIVING

poster abstractSince 1990, there have been 250,000 fatalities from car accidents in the United States (Warp, 2006). According to the United States Department of Transportation (nhtsa.dot.com), two-thirds of those fatalities are from acci-dents caused by road rage. That means 166,666 people died due to driver’s inability to control their anger on the road. Road rage is a serious issue that should be addressed. Often times, people don’t even realize they are becom-ing dangerously agitated until it is too late. The purpose of this study is to measure a drivers’ reaction to diverse stimuli in a simulated environment in order to examine how raising the awareness of the symptoms described might allow the driver to modify his/her behavior before engaging in disas-trous consequences. The stimuli used in testing for this study would include an array of graphics, videos and sounds. This study uses an Arduino board that connects to three bio-metric sensors which will track the users pulse, temperature and skin-conductivity. Whenever the human body is under mental stress, the parasympathetic activities of his/her heart decreases and the sympathetic activity increases (Rani, 2002). In other words, their pulse increases dramatically. Other signs of agitation include, but are not limited to: conductivity of skin increases and the tensing of muscles which causes the temperature of their extremities (fingers, hands and feet) to drop signifi-cantly. Upon IRB approval, this research will be conducted with fifty partici-pants. The data extracted from testing will be analyzed and finding’s report-ed

Structure and Function of a Mycobacterial NHEJ DNA Repair Polymerase

Non homologous end-joining (NHEJ)-mediated repair of DNA double-strand breaks in prokaryotes requires Ku and a specific multidomain DNA ligase (LigD). We present crystal structures of the primase/polymerisation domain (PolDom) of Mycobacterium tuberculosis LigD, alone and complexed with nucleotides. The PolDom structure combines the general fold of the archaeo-eukaryotic primase (AEP) superfamily with additional loops and domains that together form a deep cleft on the surface, likely used for DNA binding. Enzymatic analysis indicates that the PolDom of LigD, even in the absence of accessory domains and Ku proteins, has the potential to recognise DNA end-joining intermediates. Strikingly, one of the main signals for the specific and efficient binding of PolDom to DNA is the presence of a 5'-phosphate group, located at the single/double-stranded junction at both gapped and 3'-protruding DNA molecules. Although structurally unrelated, Pol lambda and Pol mu, the two eukaryotic DNA polymerases involved in NHEJ, are endowed with a similar capacity to bind a 5'-phosphate group. Other properties that are beneficial for NHEJ, such as the ability to generate template distortions and realignments of the primer, displayed by Pol lambda and Pol mu, are shared by the PolDom of bacterial LigD. In addition, PolDom can perform non-mutagenic translesion synthesis on termini containing modified bases. Significantly, ribonucleotide insertion appears to be a recurrent theme associated with NHEJ, maximised in this case by the deployment of a dedicated primase, although its in vivo relevance is unknown

Investigation of Exomic Variants Associated with Overall Survival in Ovarian Cancer

BACKGROUND: While numerous susceptibility loci for epithelial ovarian cancer (EOC) have been identified, few associations have been reported with overall survival. In the absence of common prognostic genetic markers, we hypothesize that rare coding variants may be associated with overall EOC survival and assessed their contribution in two exome-based genotyping projects of the Ovarian Cancer Association Consortium (OCAC). METHODS: The primary patient set (Set 1) included 14 independent EOC studies (4,293 patients) and 227,892 variants, and a secondary patient set (Set 2) included six additional EOC studies (1,744 patients) and 114,620 variants. Because power to detect rare variants individually is reduced, gene-level tests were conducted. Sets were analyzed separately at individual variants and by gene, and then combined with meta-analyses (73,203 variants and 13,163 genes overlapped). RESULTS: No individual variant reached genome-wide statistical significance. A SNP previously implicated to be associated with EOC risk and, to a lesser extent, survival, rs8170, showed the strongest evidence of association with survival and similar effect size estimates across sets (Pmeta = 1.1E-6, HRSet1 = 1.17, HRSet2 = 1.14). Rare variants in ATG2B, an autophagy gene important for apoptosis, were significantly associated with survival after multiple testing correction (Pmeta = 1.1E-6; Pcorrected = 0.01). CONCLUSIONS: Common variant rs8170 and rare variants in ATG2B may be associated with EOC overall survival, although further study is needed. IMPACT: This study represents the first exome-wide association study of EOC survival to include rare variant analyses, and suggests that complementary single variant and gene-level analyses in large studies are needed to identify rare variants that warrant follow-up study

Assessment of Multifactor Gene-Environment Interactions and Ovarian Cancer Risk: Candidate Genes, Obesity and Hormone-Related Risk Factors

BACKGROUND: Many epithelial ovarian cancer (EOC) risk factors relate to hormone exposure and elevated estrogen levels are associated with obesity in postmenopausal women. Therefore, we hypothesized that gene-environment interactions related to hormone-related risk factors could differ between obese and non-obese women. METHODS: We considered interactions between 11,441 SNPs within 80 candidate genes related to hormone biosynthesis and metabolism and insulin-like growth factors with six hormone-related factors (oral contraceptive use, parity, endometriosis, tubal ligation, hormone replacement therapy, and estrogen use) and assessed whether these interactions differed between obese and non-obese women. Interactions were assessed using logistic regression models and data from 14 case-control studies (6,247 cases; 10,379 controls). Histotype-specific analyses were also completed. RESULTS: SNPs in the following candidate genes showed notable interaction: IGF1R (rs41497346, estrogen plus progesterone hormone therapy, histology = all, P = 4.9 × 10(-6)) and ESR1 (rs12661437, endometriosis, histology = all, P = 1.5 × 10(-5)). The most notable obesity-gene-hormone risk factor interaction was within INSR (rs113759408, parity, histology = endometrioid, P = 8.8 × 10(-6)). CONCLUSIONS: We have demonstrated the feasibility of assessing multifactor interactions in large genetic epidemiology studies. Follow-up studies are necessary to assess the robustness of our findings for ESR1, CYP11A1, IGF1R, CYP11B1, INSR, and IGFBP2 Future work is needed to develop powerful statistical methods able to detect these complex interactions. IMPACT: Assessment of multifactor interaction is feasible, and, here, suggests that the relationship between genetic variants within candidate genes and hormone-related risk factors may vary EOC susceptibility

Heuristic Modeling for TRMM Lifetime Predictions

Analysis time for computing the expected mission lifetimes of proposed frequently maneuvering, tightly altitude constrained, Earth orbiting spacecraft have been significantly reduced by means of a heuristic modeling method implemented in a commercial-off-the-shelf spreadsheet product (QuattroPro) running on a personal computer (PC). The method uses a look-up table to estimate the maneuver frequency per month as a function of the spacecraft ballistic coefficient and the solar flux index, then computes the associated fuel use by a simple engine model. Maneuver frequency data points are produced by means of a single 1-month run of traditional mission analysis software for each of the 12 to 25 data points required for the table. As the data point computations are required only a mission design start-up and on the occasion of significant mission redesigns, the dependence on time consuming traditional modeling methods is dramatically reduced. Results to date have agreed with traditional methods to within 1 to 1.5 percent. The spreadsheet approach is applicable to a wide variety of Earth orbiting spacecraft with tight altitude constraints. It will be particularly useful to such missions as the Tropical Rainfall Measurement Mission scheduled for launch in 1997, whose mission lifetime calculations are heavily dependent on frequently revised solar flux predictions

Life satisfaction among a clinical eating disorder population

Background The primary objective was to understand life satisfaction (LS) of patients with eating disorders (EDs) in relation to eating pathology severity, personal/familial ED history, and key demographic and anthropometric variables. Methods Participants (N = 60) completed the Satisfaction with Life Scale (SWLS), the Eating Pathology Severity Index (EPSI), and demographic questionnaires. Bivariate associations via correlations and multiple linear regression models were used to explore these relationships. Results The SWLS mean score was 3.7 out of 7, suggesting it is below the population-based norm. LS was positively statistically significantly associated with private insurance, past ED, EPSI muscle building, EPSI restricted eating, and EPSI negative attitudes. When included in multiple linear regression, the model explained 33% of the variability of LS [F (7, 56) = 3.4, p = 0.0054, R2 = 0.33]. EPSI muscle building remained the strongest predictor (β = 0.13, p = 0.04). Conclusions Based on the data, individuals who have/have had EDs scored lower on the SWLS than the general population. Individuals scoring within this range typically experience significant issues in several areas of life or a substantial issue in one area