Exact sampling from non-attractive distributions using summary states

Propp and Wilson's method of coupling from the past allows one to efficiently generate exact samples from attractive statistical distributions (e.g., the ferromagnetic Ising model). This method may be generalized to non-attractive distributions by the use of summary states, as first described by Huber. Using this method, we present exact samples from a frustrated antiferromagnetic triangular Ising model and the antiferromagnetic q=3 Potts model. We discuss the advantages and limitations of the method of summary states for practical sampling, paying particular attention to the slowing down of the algorithm at low temperature. In particular, we show that such a slowing down can occur in the absence of a physical phase transition.Comment: 5 pages, 6 EPS figures, REVTeX; additional information at http://wol.ra.phy.cam.ac.uk/mackay/exac

Generalization of the Bollob\'as-Riordan polynomial for tensor graphs

Tensor models are used nowadays for implementing a fundamental theory of quantum gravity. We define here a polynomial $\mathcal T$ encoding the supplementary topological information. This polynomial is a natural generalization of the Bollob\'as-Riordan polynomial (used to characterize matrix graphs) and is different of the Gur\uau polynomial, (R. Gur\uau, "Topological Graph Polynomials in Colored Group Field Theory", Annales Henri Poincare {\bf 11}, 565-584 (2010)) defined for a particular class of tensor graphs, the colorable ones. The polynomial $\mathcal T$ is defined for both colorable and non-colorable graphs and it is proved to satisfy the contraction/deletion relation. A non-trivial example of a non-colorable graphs is analyzed.Comment: 22 pages, 20 figure

High-Resolution Chandra X-Ray Imaging And Spectroscopy Of The Sigma Orionis Cluster

We present results of a 90 ks Chandra X-ray observation of the young sigma Orionis cluster ( age similar to 3 Myr) obtained with the HETGS. We use the high-resolution grating spectrum and moderate-resolution CCD spectrum of the massive central star sigma Ori AB (O9.5 V + B0.5 V) to test wind shock theories of X-ray emission and also analyze the high spatial resolution zero-order ACIS-S image of the central cluster region. Chandra detected 42 X-ray sources on the primary CCD (ACIS-S3). All but five have near-IR or optical counterparts and about one-fourth are variable. Notable high-mass stellar detections are sigma Ori AB, the magnetic B star sigma Ori E, and the B5 V binary HD 37525. Most of the other detections have properties consistent with lower mass K- or M-type stars. We present the first X-ray spectrum of the unusual infrared source IRS 1, located approximate to 3 \u27\u27 north of sigma Ori AB. Its X-ray properties and elongated mid-IR morphology suggest that it is an embedded low-mass T Tauri star whose disk/envelope is being photoevaporated by sigma Ori AB. We focus on the radiative wind shock interpretation of the soft luminous X-ray emission from sigma Ori AB, but also consider possible alternatives including magnetically confined wind shocks and colliding wind shocks. Its emission lines show no significant asymmetries or centroid shifts and are moderately broadened to HWHM approximate to 264 km s(-1), or one-fourth the terminal wind speed. Forbidden lines in He-like ions are formally undetected, implying strong UV suppression. The Mg XI triplet forms in the wind acceleration zone within one stellar radius above the surface. These X-ray properties are consistent in several respects with the predictions of radiative wind shock theory for an optically thin wind, but explaining the narrow line widths presents a challenge to the theory

A nipple shield delivery system for oral drug delivery to breastfeeding infants : Microbicide delivery to inactivate HIV

A new drug delivery method for infants is presented which incorporates an active pharmaceutical ingredient (API)-loaded insert into a nipple shield delivery system (NSDS). The API is released directly into milk during breastfeeding. This study investigates the feasibility of using the NSDS to deliver the microbicide sodium dodecyl sulfate (SDS), with the goal of preventing mother-to-child transmission (MTCT) of HIV during breastfeeding in low-resource settings, when there is no safer alternative for the infant but to breastfeed. SDS has been previously shown to effectively inactivate HIV in human milk. An apparatus was developed to simulate milk flow through and drug release from a NSDS. Using this apparatus milk was pulsed through a prototype device containing a non-woven fiber insert impregnated with SDS and the microbicide was rapidly released. The total SDS release from inserts ranged from 70 to 100% of the average 0.07 g load within 50 ml (the volume of a typical breastfeed). Human milk spiked with H9/HIVIIIB cells was also passed through the same set-up. Greater than 99% reduction of cell-associated HIV infectivity was achieved in the first 10 ml of milk. This proof of concept study demonstrates efficient drug delivery to breastfeeding infants is achievable using the NSDS

Therapeutic ultrasound as a potential male contraceptive: power, frequency and temperature required to deplete rat testes of meiotic cells and epididymides of sperm determined using a commercially available system

<p>Abstract</p> <p>Background</p> <p>Studies published in the 1970s by Mostafa S. Fahim and colleagues showed that a short treatment with ultrasound caused the depletion of germ cells and infertility. The goal of the current study was to determine if a commercially available therapeutic ultrasound generator and transducer could be used as the basis for a male contraceptive.</p> <p>Methods</p> <p>Sprague-Dawley rats were anesthetized and their testes were treated with 1 MHz or 3 MHz ultrasound while varying power, duration and temperature of treatment.</p> <p>Results</p> <p>We found that 3 MHz ultrasound delivered with 2.2 Watt per square cm power for fifteen minutes was necessary to deplete spermatocytes and spermatids from the testis and that this treatment significantly reduced epididymal sperm reserves. 3 MHz ultrasound treatment reduced total epididymal sperm count 10-fold lower than the wet-heat control and decreased motile sperm counts 1,000-fold lower than wet-heat alone. The current treatment regimen provided nominally more energy to the treatment chamber than Fahim's originally reported conditions of 1 MHz ultrasound delivered at 1 Watt per square cm for ten minutes. However, the true spatial average intensity, effective radiating area and power output of the transducers used by Fahim were not reported, making a direct comparison impossible. We found that germ cell depletion was most uniform and effective when we rotated the therapeutic transducer to mitigate non-uniformity of the beam field. The lowest sperm count was achieved when the coupling medium (3% saline) was held at 37 degrees C and two consecutive 15-minute treatments of 3 MHz ultrasound at 2.2 Watt per square cm were separated by 2 days.</p> <p>Conclusions</p> <p>The non-invasive nature of ultrasound and its efficacy in reducing sperm count make therapeutic ultrasound a promising candidate for a male contraceptive. However, further studies must be conducted to confirm its efficacy in providing a contraceptive effect, to test the result of repeated use, to verify that the contraceptive effect is reversible and to demonstrate that there are no detrimental, long-term effects from using ultrasound as a method of male contraception.</p

Bayesian hierarchical clustering for studying cancer gene expression data with unknown statistics

Clustering analysis is an important tool in studying gene expression data. The Bayesian hierarchical clustering (BHC) algorithm can automatically infer the number of clusters and uses Bayesian model selection to improve clustering quality. In this paper, we present an extension of the BHC algorithm. Our Gaussian BHC (GBHC) algorithm represents data as a mixture of Gaussian distributions. It uses normal-gamma distribution as a conjugate prior on the mean and precision of each of the Gaussian components. We tested GBHC over 11 cancer and 3 synthetic datasets. The results on cancer datasets show that in sample clustering, GBHC on average produces a clustering partition that is more concordant with the ground truth than those obtained from other commonly used algorithms. Furthermore, GBHC frequently infers the number of clusters that is often close to the ground truth. In gene clustering, GBHC also produces a clustering partition that is more biologically plausible than several other state-of-the-art methods. This suggests GBHC as an alternative tool for studying gene expression data. The implementation of GBHC is available at https://sites. google.com/site/gaussianbhc

Frequency and patterns of early recanalization after vasectomy

BACKGROUND: Our understanding of early post-vasectomy recanalization is limited to histopathological studies. The objective of this study was to estimate the frequency and to describe semen analysis patterns of early recanalization after vasectomy. METHODS: Charts displaying serial post-vasectomy semen analyses were created using the semen analysis results from 826 and 389 men participating in a randomized trial of fascial interposition (FI) and an observational study of cautery, respectively. In the FI trial, participants were randomly allocated to vas occlusion by ligation and excision with or without FI. In the cautery study, sites used their usual cautery occlusion technique, two with and two without FI. Presumed early recanalization was based on the assessment of individual semen analysis charts by three independent reviewers. Discrepancies were resolved by consensus. RESULTS: Presumed early recanalization was characterized by a very low sperm concentration within two weeks after vasectomy followed by return to large numbers of sperm over the next few weeks. The overall proportion of men with presumed early recanalization was 13% (95% CI 12%–15%). The risk was highest with ligation and excision without FI (25%) and lowest for thermal cautery with FI (0%). The highest proportion of presumed early recanalization was observed among men classified as vasectomy failures. CONCLUSION: Early recanalization, occurring within the first weeks after vasectomy, is more common than generally recognized. Its frequency depends on the occlusion technique performed

Thinking like a man? The cultures of science

Culture includes science and science includes culture, but conflicts between the two traditions persist, often seen as clashes between interpretation and knowledge. One way of highlighting this false polarity has been to explore the gendered symbolism of science. Feminism has contributed to science studies and the critical interrogation of knowledge, aware that practical knowledge and scientific understanding have never been synonymous. Persisting notions of an underlying unity to scientific endeavour have often impeded rather than fostered the useful application of knowledge. This has been particularly evident in the recent rise of molecular biology, with its delusory dream of the total conquest of disease. It is equally prominent in evolutionary psychology, with its renewed attempts to depict the fundamental basis of sex differences. Wars over science have continued to intensify over the last decade, even as our knowledge of the political, economic and ideological significance of science funding and research has become ever more apparent

Measurement of S-phase duration of adult stem cells in the flatworm Macrostomum lignano by double replication labelling and quantitative colocalization analysis

Platyhelminthes are highly attractive models for addressing fundamental aspects of stem cell biology in vivo. These organisms possess a unique stem cell system comprised of neoblasts that are the only proliferating cells during adulthood. We have investigated T-s (S-phase duration) of neoblasts during homoeostasis and regeneration in the flatworm, Macrostomum lignano. A double immunohistochemical technique was used, performing sequential pulses with the thymidine analogues CldU (chlorodeoxyuridine) and IdU (iododeoxyuridine), separated by variable chase times in the presence of colchicine. Owing to the localized nature of the fluorescent signals (cell nuclei) and variable levels of autofluorescence, standard intensity-based colocalization analyses could not be applied to accurately determine the colocalization. Therefore, an object-based colocalization approach was devised to score the relative number of double-positive cells. Using this approach, T-s (S-phase duration) in the main population of neoblasts was similar to 13 h. During early regeneration, no significant change in T-s was observed

Effectiveness of vasectomy using cautery

BACKGROUND: Little evidence supports the use of any one vas occlusion method. Data from a number of studies now suggest that there are differences in effectiveness among different occlusion methods. The main objectives of this study were to estimate the effectiveness of vasectomy by cautery and to describe the trends in sperm counts after cautery vasectomy. Other objectives were to estimate time and number of ejaculations to success and to determine the predictive value of success at 12 weeks for final status at 24 weeks. METHODS: A prospective, non-comparative observational study was conducted between November 2001 and June 2002 at 4 centers in Brazil, Canada, the UK, and the US. Four hundred men who chose vasectomy were enrolled and followed for 6 months. Sites used their usual cautery vasectomy technique. Earlier and more frequent than normal semen analyses (2, 5, 8, 12, 16, 20, and 24 weeks after vasectomy) were performed. Planned outcomes included effectiveness (early failure based on semen analysis), trends in sperm counts, time and number of ejaculations to success, predictive value of success at 12 weeks for the outcome at 24 weeks, and safety evaluation. RESULTS: A total of 364 (91%) participants completed follow-up. The overall failure rate based on semen analysis was 0.8% (95% confidence interval 0.2, 2.3). By 12 weeks 96.4% of participants showed azoospermia or severe oligozoospermia (< 100,000 sperm/mL). The predictive value of a single severely oligozoospermia sample at 12 weeks for vasectomy success at the end of the study was 99.7%. One serious unrelated adverse event and no pregnancies were reported. CONCLUSION: Cautery is a very effective method for occluding the vas. Failure based on semen analysis is rare. In settings where semen analysis is not practical, using 12 weeks as a guideline for when men can rely on their vasectomy should lessen the risk of failure compared to using a guideline of 20 ejaculations after vasectomy