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

An extra-heating mechanism in Doppler-cooling experiments

In this paper we experimentally and theoretically investigate laser cooling of Strontium 88 atoms in one dimensional optical molasses. In our case, since the optical cooling dipole transition involves a $J_g=0$ groundstate, no Sisyphus-type mechanisms can occur. We are thus able to test quantitatively the predictions of the Doppler-cooling theory. We have found, in agreement with other similar experiments, that the measured temperatures are systematically larger than the theoretical predictions. We quantitatively interpret this discrepancy by taking into consideration the extra-heating mechanism induced by transverse spatial intensity fluctuations of the optical molasses. Experimental data are in good agreement with Monte-Carlo simulations of our theoretical model. We thus confirm the important role played by intensity fluctuations in the dynamics of cooling and for the steady-state regime

Non-Chlamydial Bacterial Infection and Progression of Conjunctival Scarring in Trachoma.

Purpose: The purpose of this study was to assess whether non-chlamydial bacterial infection is associated with progression of trachomatous scarring in adults. Methods: This was a cohort study involving 800 participants in northern Tanzania who underwent clinical examination, photography, and conjunctival swab collection for microbiology over a 24-month period. Samples for microbiology were inoculated onto blood and chocolate agar, and Chlamydia trachomatis was detected by PCR. Progression was determined by comparison of baseline to 24-month photographs. Results: C. trachomatis was detected in only four participants at baseline. At 24 months, 617 participants (77.1%) were followed up. Of those seen at 24 months, 452 could be reliably assessed. Definite scarring progression (progressors) was seen in 345 (55.9%); there was no progression (nonprogressors) in 107 (17.3%). Using combined baseline and 12-month microbiology results, progressors had significantly higher levels of commensal and pathogenic bacterial organisms detected compared with nonprogressors. After adjusting for age, baseline scarring, and ethnicity, there was weak evidence (P = 0.07) that the bacteria category was associated with scarring progression (commensal organisms only: odds ratio [OR] = 1.61; 95% confidence interval [CI]: 0.90 to 2.89; pathogenic organisms either with or without commensal: OR = 2.39; 95% CI: 1.10 to 5.16). Conclusion: The findings were consistent with the possibility that trachomatous scarring in adults is associated with the presence of non-chlamydial bacterial organisms, particularly pathogenic organisms. C. trachomatis was detected very infrequently and may not be an important factor in the pathogenesis of scarring progression in adults. This has implications for trachoma control programs, which largely concentrate on reducing C. trachomatis levels and transmission

The Stoics and the practical: a Roman reply to Aristotle

Scholarship stands divided on the question of what one must know in order to act ethically according to the central tenets of Stoicism. Prevailing opinion holds that one must attain universal knowledge of the nature of reality, or at a minimum, knowledge of one\u27s end (telos/finis) in life, but I argue that in Stoic thought, especially as described by Cicero, neither kind of knowledge is necessary for the achievement of human virtue or excellence (aretê/virtus). I begin by sketching the dominant ethical philosophies in relation to which Stoicism emerges, those of Plato and Aristotle. I offer an extensive discussion of Aristotle\u27s critique of Platonism, showing how it paves the way for Stoicism by assigning a greater role to pre-reflective impulses than to theoretical reason, while assigning to impulses the blame for vice and to reason the responsibility for ruling over them. I then proceed to Cicero\u27s De Academica, arguing that the very conflict between our reason and our impulses is avoidable in Stoicism precisely because it arises only in individuals who have allowed their reason to overstep its own limits, with the result that, deviating from the course of action their impulses would otherwise lead them to follow, they turn aside from their own end in life. Thereafter, I show with reference to Cicero\u27s De Divinatione and De Finibus, that the Stoics redefined technical expertise (technê/ars) in order to deny that having expertise in ethical matters implied knowing one’s end in life. Finally, I conclude that the Stoicism of the Tusculan Disputations places no emphasis upon gaining advance knowledge of one’s end in life or deducing from it the means by which it may be reached; instead, it places emphasis upon freeing oneself from the external causes of internal conflict which lead one astray: socially inculcated beliefs. Aside from doing greater justice to ancient texts, this interpretation allows ancient Stoicism to contribute to contemporary ethical debates in the manner Michel Foucault’s work suggests. In particular, the Stoics provide a model for living ethically and resisting social coercion even when no appeal to universal truths can be made

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

Absorbable versus silk sutures for surgical treatment of trachomatous trichiasis in Ethiopia: a randomised controlled trial.

BACKGROUND: Trachoma causes blindness through an anatomical abnormality called trichiasis (lashes touching the eye). Trichiasis can recur after corrective surgery. We tested the hypothesis that using absorbable sutures instead of silk sutures might reduce the risk of recurrent disease among patients with major trichiasis in a randomised trial. METHODS AND FINDINGS: 1,300 individuals with major trichiasis from rural villages in the Amhara Region of Ethiopia were recruited and assigned (1:1) by computer-generated randomisation sequence to receive trichiasis surgery using either an absorbable suture (polyglactin-910) or silk sutures (removed at 7-10 days) in an otherwise identical surgical technique. Participants were examined every 6 months for 2 years by clinicians masked to allocation. The primary outcome measure was recurrent trichiasis (≥one lash touching the eye) at 1 year. There was no difference in prevalence of recurrent trichiasis at 1 year (114 [18.2%] in the absorbable suture group versus 120 [19.7%] in the silk suture group; odds ratio = 0.90, 95% CI 0.68-1.20). The two groups also did not differ in terms of corneal opacification, visual acuity, conjunctival inflammation, and surgical complications. CONCLUSIONS: There was no evidence that use of absorbable polyglactin-910 sutures was associated with a lower prevalence of trichiasis recurrence at 1 year postsurgery than silk sutures. However, from a programmatic perspective, polyglactin-910 offers the major advantage that patients do not have to be seen soon after surgery for suture removal. The postoperative review after surgery using absorbable polyglactin-910 sutures can be delayed for 3-6 months, which might allow us to better determine whether a patient needs additional surgery. TRIAL REGISTRATION: ClinicalTrials.gov NCT00522860

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

Apes, lice and prehistory

Although most epidemic human infectious diseases are caused by recently introduced pathogens, cospeciation of parasite and host is commonplace for endemic infections. Occasional host infidelity, however, provides the endemic parasite with an opportunity to survive the potential extinction of its host. Such infidelity may account for the survival of certain types of human lice, and it is currently exemplified by viruses such as HIV

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

Implementation of break time for employee nursing mothers at the University of Louisville : a case study.

This dissertation is a mixed methods look at the barriers to successful implementation of the Break Time for Nursing Mothers provisions of the Affordable Care Act (ACA) at an upper southern-midwestern university. As public health and medical officials push the desire for an increase in breastfeeding initiation and duration, many mothers must overcome barriers within the employment arena. Previous work has failed to look at how the university setting presents unique challenges with a diverse workforce, varied jobs, and differing space availability. In other settings, barriers have been identified; the goal of this dissertation was to identify what the specific barriers were within a university setting. A mixed methods approach was used interviewing both nursing employees as well as members of the university’s lactation task force; in addition to this, a survey of employees who had utilized the Break Time provisions since 2010 was conducted. The outcomes confirmed that the barriers included space, time, and information, but included lack of social support as an additional barrier. Recommendations are made to the university to help alleviate these barriers to full implementation of the Break Time for Nursing Mothers