Massively parallel approximate Gaussian process regression

We explore how the big-three computing paradigms -- symmetric multi-processor (SMC), graphical processing units (GPUs), and cluster computing -- can together be brought to bare on large-data Gaussian processes (GP) regression problems via a careful implementation of a newly developed local approximation scheme. Our methodological contribution focuses primarily on GPU computation, as this requires the most care and also provides the largest performance boost. However, in our empirical work we study the relative merits of all three paradigms to determine how best to combine them. The paper concludes with two case studies. One is a real data fluid-dynamics computer experiment which benefits from the local nature of our approximation; the second is a synthetic data example designed to find the largest design for which (accurate) GP emulation can performed on a commensurate predictive set under an hour.Comment: 24 pages, 6 figures, 1 tabl

A Quantitative Meta-Analysis of Functional Imaging Studies of Social Rejection

Early neuroimaging studies using Cyberball suggested that social rejection activated the pain matrix, as identified in studies of physical pain. However, these early studies were characterized by small sample sizes. Our statistical multi-level kernel density analysis (MKDA) of Cyberball neuroimaging studies with 244 participants fails to support the claim that social rejection operates on the same pain matrix as nociceptive stimuli, questioning whether social pain is more figurative or literal. We also performed an MKDA of the neuroimaging studies of reliving a romantic rejection to test whether the pain matrix was activated if the rejection were more meaningful. Results again failed to support the notion that rejection activates the neural matrix identified in studies of physical pain. Reliving an unwanted rejection by a romantic partner was significantly characterized by activation within and beyond the “Cyberball” brain network, suggesting that the neural correlates of social pain are more complex than previously thought

A Brief Educational Intervention Enhances Basic Cancer Literacy among Kentucky Middle and High School Students

Kentucky experiences the highest overall cancer incidence and mortality rates in the USA with the greatest burden in the eastern, Appalachian region of the state. Cancer disparities in Kentucky are driven in part by poor health behaviors, poverty, lack of health care access, low education levels, and low health literacy. Individuals with inadequate health literacy are less likely to participate in preventive measures such as obtaining screenings and making healthy lifestyle choices, thus increasing their chances of developing and dying from cancer. By increasing cancer literacy among youth and adults, it may be possible to decrease cancer disparities across Kentucky. This study aimed to establish connections with middle and high schools in Kentucky that would facilitate pilot implementation of a brief cancer education intervention and assessment of cancer health literacy among these student populations. A baseline pretest cancer literacy survey consisting of 10 items was given to 349 participants, followed by the delivery of a cancer education presentation. Immediately following the presentation, participants were given a posttest with identical items to the pretest. Participants were primarily Caucasian (89.4%), female (68.7%), and in 10th through 12th grade (80.5%). Significant (p \u3c 0.0001) increases in both average and median percent of correctly marked items were observed between the pretest and posttest (average, pretest = 56% versus posttest = 85%; median, pretest = 60% versus posttest = 90%). The scores for all individual items increased after the brief intervention. The results demonstrated a significant increase in cancer literacy levels immediately after the pilot educational intervention. We suggest that it may be possible to improve cancer literacy rates in Kentucky by integrating cancer education into middle and high school science and/or health education curricula. This could ultimately drive changes in behaviors that may help lower cancer incidence and mortality rates. Plans for future interventional studies measuring long-term cancer knowledge retention and resultant behavioral changes among middle and high school students as well as the feasibility of integrating cancer education into middle and high school curricula are also discussed

Potent and Broad Neutralization of HIV-1 by a Llama Antibody Elicited by Immunization

Llamas (Lama glama) naturally produce heavy chain–only antibodies (Abs) in addition to conventional Abs. The variable regions (VHH) in these heavy chain–only Abs demonstrate comparable affinity and specificity for antigens to conventional immunoglobulins despite their much smaller size. To date, immunizations in humans and animal models have yielded only Abs with limited ability to neutralize HIV-1. In this study, a VHH phagemid library generated from a llama that was multiply immunized with recombinant trimeric HIV-1 envelope proteins (Envs) was screened directly for HIV-1 neutralization. One VHH, L8CJ3 (J3), neutralized 96 of 100 tested HIV-1 strains, encompassing subtypes A, B, C, D, BC, AE, AG, AC, ACD, CD, and G. J3 also potently neutralized chimeric simian-HIV strains with HIV subtypes B and C Env. The sequence of J3 is highly divergent from previous anti–HIV-1 VHH and its own germline sequence. J3 achieves broad and potent neutralization of HIV-1 via interaction with the CD4-binding site of HIV-1 Env. This study may represent a new benchmark for immunogens to be included in B cell–based vaccines and supports the development of VHH as anti–HIV-1 microbicides

A gp41 MPER-specific llama VHH requires a hydrophobic CDR3 for neutralization but not for antigen recognition

The membrane proximal external region (MPER) of the HIV-1 glycoprotein gp41 is targeted by the broadly neutralizing antibodies 2F5 and 4E10. To date, no immunization regimen in animals or humans has produced HIV-1 neutralizing MPER-specific antibodies. We immunized llamas with gp41-MPER proteoliposomes and selected a MPER-specific single chain antibody (VHH), 2H10, whose epitope overlaps with that of mAb 2F5. Bi-2H10, a bivalent form of 2H10, which displayed an approximately 20-fold increased affinity compared to the monovalent 2H10, neutralized various sensitive and resistant HIV-1 strains, as well as SHIV strains in TZM-bl cells. X-ray and NMR analyses combined with mutagenesis and modeling revealed that 2H10 recognizes its gp41 epitope in a helical conformation. Notably, tryptophan 100 at the tip of the long CDR3 is not required for gp41 interaction but essential for neutralization. Thus bi-2H10 is an anti-MPER antibody generated by immunization that requires hydrophobic CDR3 determinants in addition to epitope recognition for neutralization similar to the mode of neutralization employed by mAbs 2F5 and 4E10

Searching for psychosis: INTREPID (1): systems for detecting untreated and first-episode cases of psychosis in diverse settings.

PURPOSE: Our understanding of psychotic disorders is largely based on studies conducted in North America, Europe and Australasia. Few methodologically robust and comparable studies have been carried out in other settings. INTREPID is a programme of research on psychoses in India, Nigeria, and Trinidad. As a platform for INTREPID, we sought to establish comprehensive systems for detecting representative samples of cases of psychosis by mapping and seeking to engage all professional and folk (traditional) providers and potential key informants in defined catchment areas. METHOD: We used a combination of official sources, local knowledge of principal investigators, and snowballing techniques. RESULTS: The structure of the mental health systems in each catchment area was similar, but the content (i.e., type, extent, and nature) differed. Tunapuna-Piarco (Trinidad), for example, has the most comprehensive and accessible professional services. By contrast, Ibadan (Nigeria) has the most extensive folk (traditional) sector. We identified and engaged in our detection system-(a) all professional mental health services in each site (in- and outpatient services-Chengalpet, 6; Ibadan, 3; Trinidad, 5); (b) a wide range of folk providers (Chengalpet, 3 major healing sites; Ibadan, 19 healers; Trinidad: 12 healers); and c) a number of key informants, depending on need (Chengalpet, 361; Ibadan, 54; Trinidad, 1). CONCLUSIONS: Marked differences in mental health systems in each catchment area illustrate the necessity of developing tailored systems for the detection of representative samples of cases with untreated and first-episode psychosis as a basis for robust, comparative epidemiological studies

Looking for pulsations in HgMn stars through CoRoT lightcurves

HgMn Chemically Peculiar stars are among the quietest stars of the main-sequence. However, according to theoretical predictions, these stars could have pulsations related to the very strong overabundances of iron peak elements, which are produced by atomic diffusion in upper layers. Such pulsations have never been detected from ground based observations. Our aim is to search for signatures of pulsations in HgMn stars using the high quality lightcurves provided by the CoRoT satellite. We identified three faint stars (V>12), from VLT-GIRAFFE multiobject spectrograph survey in a field which was planned for observation by CoRoT. They present the typical characteristics of HgMn stars. They were observed by the CoRoT satellite during the long run (131 days) which started from the 24th of October 2007, with the exoplanets CCD's (Additional Programme). In the present work, we present the analysis of the ground based spectra of these three stars and the analysis of the corresponding CoRoT lightcurves. Two of these three HgMn candidates show low amplitude (less than 1.6 mmag) periodic variations (4.3 and 2.53 days respectively, with harmonics) which are compatible with periods predicted by theoretical models.Comment: Accepted paper in A&A (7 May 2009

A cautionary tale of virus and disease

The recent identification of the gammaretrovirus XMRV and a second gammaretrovirus of a different subtype in chronic fatigue syndrome has aroused much interest, not least among sufferers. However, it remains highly controversial whether the detection of these viruses represents true infection or laboratory artifacts