Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures

In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a “null model” of pairwise independence. In simulation studies, as well as for a real data analysis, we show that our approach provides a useful tool for the exploratory nonparametric Bayesian analysis of large multivariate data sets

Studies on the Effects of Media on Growth and Nutritional Composition of Pleurotus Tuber-regium (Fries) Singer Mushroom

The effects of different solutions and media on growth and nutrient composition of Pleurotus tuber-regium were investigated. The different solutions used are glucose, fructose, sucrose and Knop\'s solutions. The media used are cassava agar, cocoyam agar, corn agar, potato agar and yam agar. Glucose solution produced the highest growth in stipe height (9.50 ± 0.91cm), stipe diameter (4.46 ± 0.59cm) and pileus diameter (9.50 ± 0.59 cm). Knop\'s solution induced the least stipe diameter (7.20 ± 0.59cm) while sucrose produced the least stipe diameter (3.90±0.54cm) and pileus diameter (7.50 ± 0.95cm). Analyses of nutrient composition (%) showed that fructose solution induced the highest protein (13.6±0.99%) and fibre (15.6±0.36%) contents. The highest oil (15.0±0.17%) content was induced by glucose solution but it also induced the least protein (3.06 ± 0.09%) content. The best diametric mycelial extension (1.64cm±0.087), wet (1.105± 0.054g) and dry (0.768±0.008g) weights were observed on cocoyam agar. The least diametric mycelial extensions of 1.26± 0.087 and 1.33 ± 0.087cm were produced on corn agar and potato agar, respectively. Corn agar gave the least wet (0.845 ± 0.084g) and dry (0.74 ± 0.008g) weights. Keywords: Pleurotus tuber-regium, Growth, Nutritional composition, Sclerotium, MushroomBio-Research Vol. 6 (2) 2008: pp. 355-35

In situ non-invasive Raman spectroscopic characterisation of succinic acid polymorphism during segmented flow crystallisation

The kinetically regulated automated input crystalliser for Raman spectroscopy (KRAIC-R) combines highly controlled crystallisation environments, via tri segmented flow, with non-invasive confocal Raman spectroscopy. Taking advantage of the highly reproducible crystallisation environment within a segmented flow crystalliser and the non-invasive nature of confocal spectroscopy, we are able to shine light on the nucleation and growth of Raman active polymorphic materials without inducing unrepresentative crystallisation events through our analysis technique. Using the KRAIC-R we have probed the nucleation and subsequent growth of succinic acid. Succinic acid typically crystallises as β-SA from solution-based crystallisation although some examples of a small proportion of α-SA have been reported in the β-SA product. Here we show that α-SA and β-SA nucleate concomitantly but undergo Ostwald ripening to a predominantly β-SA product

Prediction of salt balances in irrigated soils along the lower Vaal River, South Africa

In arid and semi-arid regions irrigation tends to degrade soil and water quality through salt accumulation with devastating effects on some crops. This is, according to irrigators, also the case along the lower Vaal River in South Africa. Properly calibrated and tested salinity models could assist the agricultural community in improving salinity management under irrigation.This paper reports on, firstly, salt balances of soils in this region being irrigated for different time periods, and secondly, salt content changes that can be expected as a consequence of future irrigation. Two empirical models, viz. a general and specific salt-balance model were used together with existing water- and soil-quality data to generate such information. The soils selected for this study had been irrigated for periods of between 17 to 53 years. Over these periods addition of salts as a result of farming practices varied between 79 and 280 t·ha-1, with irrigation water being the major contributor. Between 78% to 87% of the salts added to the soils had been leached from the root zone Despite these large amounts of salts that have been removed, certain irrigation practices have promoted the build-up of salts in some of the soils. The freely drained sandy soils irrigated by centre pivot are of particular interest. Poor management of this system can reduce crop yields. On account of inadequate leaching salts are building up to levels that impair the potential evapotranspiration level of maize. Predictions also show that irrigation should rather be withdrawn from soils with poor internal drainage properties, such as the Arcadia soil at Spitskop. In contrast, flood irrigation on certain duplex soils, such as the Valsrivier at Vaalharts, with relatively good internal drainage properties, can improve their quality.Keywords: drained soils, root zone, soil quality, undrained soils, water qualit

Outbreak of West Nile virus causing severe neurological involvement in children, Nuba Mountains, Sudan, 2002.

An atypical outbreak of West Nile virus (WNV) occurred in Ngorban County, South Kordophan, Sudan, from May to August 2002. We investigated the epidemic and conducted a case-control study in the village of Limon. Blood samples were obtained for cases and controls. Patients with obvious sequelae underwent cerebrospinal fluid (CSF) sampling as well. We used enzyme-linked immunosorbent assay (ELISA) and neutralization tests for laboratory diagnosis and identified 31 cases with encephalitis, four of whom died. Median age was 36 months. Bivariate analysis did not reveal any significant association with the risk factors investigated. Laboratory analysis confirmed presence of IgM antibodies caused by WNV in eight of 13 cases, indicative of recent viral infection. The unique aspects of the WNW outbreak in Sudan, i.e. disease occurrence solely among children and the clinical domination of encephalitis, involving severe neurological sequelae, demonstrate the continuing evolution of WNV virulence. The spread of such a virus to other countries or continents cannot be excluded

Controlling passively-quenched single photon detectors by bright light

Single photon detectors based on passively-quenched avalanche photodiodes can be temporarily blinded by relatively bright light, of intensity less than a nanowatt. I describe a bright-light regime suitable for attacking a quantum key distribution system containing such detectors. In this regime, all single photon detectors in the receiver Bob are uniformly blinded by continuous illumination coming from the eavesdropper Eve. When Eve needs a certain detector in Bob to produce a click, she modifies polarization (or other parameter used to encode quantum states) of the light she sends to Bob such that the target detector stops receiving light while the other detector(s) continue to be illuminated. The target detector regains single photon sensitivity and, when Eve modifies the polarization again, produces a single click. Thus, Eve has full control of Bob and can do a successful intercept-resend attack. To check the feasibility of the attack, 3 different models of passively-quenched detectors have been tested. In the experiment, I have simulated the intensity diagrams the detectors would receive in a real quantum key distribution system under attack. Control parameters and side effects are considered. It appears that the attack could be practically possible.Comment: Experimental results from a third detector model added. Minor corrections and edits made. 11 pages, 10 figure

Type IIn supernovae at z ~ 2 from archival data

Supernovae have been confirmed to redshift z ~ 1.7 for type Ia (thermonuclear detonation of a white dwarf) and to z ~ 0.7 for type II (collapse of the core of the star). The subclass type IIn supernovae are luminous core-collapse explosions of massive stars and, unlike other types, are very bright in the ultraviolet, which should enable them to be found optically at redshifts z ~ 2 and higher. In addition, the interaction of the ejecta with circumstellar material creates strong, long-lived emission lines that allow spectroscopic confirmation of many events of this type at z ~ 2 for 3 - 5 years after explosion. Here we report three spectroscopically confirmed type IIn supernovae, at redshifts z = 0.808, 2.013 and 2.357, detected in archival data using a method designed to exploit these properties at z ~ 2. Type IIn supernovae directly probe the formation of massive stars at high redshift. The number found to date is consistent with the expectations of a locally measured stellar initial mass function, but not with an evolving initial mass function proposed to explain independent observations at low and high redshift.Comment: 8 pages, 2 figures, includes supplementary informatio

Development and Validation of a Composite Programmatic Assessment Tool for HIV Therapy

Background We developed and validated a new and simple metric, the Programmatic Compliance Score (PCS), based on the IAS-USA antiretroviral therapy management guidelines for HIV-infected adults, as a predictor of all-cause mortality, at a program-wide level. We hypothesized that non-compliance would be associated with the highest probability of mortality. Methods and Findings 3543 antiretroviral-naive HIV-infected patients aged ≥19 years who initiated antiretroviral therapy between January 1, 2000 and August 31, 2009 in British Columbia (BC), Canada, were followed until August 31, 2010. The PCS is composed by six non-performance indicators based on the IAS-USA guidelines: (1) having <3 CD4 count tests in the first year after starting antiretroviral therapy; (2) having <3 plasma viral load tests in the first year after starting antiretroviral therapy; (3) not having drug resistance testing done prior to starting antiretroviral therapy; (4) starting on a non-recommended antiretroviral therapy regimen; (5) starting therapy with CD4 <200 cells/mm3; and (6) not achieving viral suppression within 6 months since antiretroviral therapy initiation. The sum of these six indicators was used to develop the PCS score - higher score indicates poorer performance. The main outcome was all-cause mortality. Each PCS component was independently associated with mortality. In the mortality analysis, the odds ratio (OR) for PCS ≥4 versus 0 was 22.37 (95% CI 10.46–47.84). Conclusions PCS was strongly associated with all-cause mortality. These results lend independent validation to the IAS-USA treatment guidelines for HIV-infected adults. Further efforts are warranted to enhance the PCS as a means to further improve clinical outcomes. These should be specifically evaluated and targeted at healthcare providers and patients

Activation of the viral sensor oligoadenylate synthetase 2 (Oas2) prevents pregnancy-driven mammary cancer metastases.

BACKGROUND: The interferon response can influence the primary and metastatic activity of breast cancers and can interact with checkpoint immunotherapy to modulate its effects. Using N-ethyl-N-nitrosourea mutagenesis, we found a mouse with an activating mutation in oligoadenylate synthetase 2 (Oas2), a sensor of viral double stranded RNA, that resulted in an interferon response and prevented lactation in otherwise healthy mice. METHODS: To determine if sole activation of Oas2 could alter the course of mammary cancer, we combined the Oas2 mutation with the MMTV-PyMT oncogene model of breast cancer and examined disease progression and the effects of checkpoint immunotherapy using Kaplan-Meier survival analysis with immunohistochemistry and flow cytometry. RESULTS: Oas2 mutation prevented pregnancy from increasing metastases to lung. Checkpoint immunotherapy with antibodies against programmed death-ligand 1 was more effective when the Oas2 mutation was present. CONCLUSIONS: These data establish OAS2 as a therapeutic target for agents designed to reduce metastases and increase the effectiveness of checkpoint immunotherapy