Clustering Acoustic Segments Using Multi-Stage Agglomerative Hierarchical Clustering

Agglomerative hierarchical clustering becomes infeasible when applied to large datasets due to its O(N ²) storage requirements. We present a multi-stage agglomerative hierarchical clustering (MAHC) approach aimed at large datasets of speech segments. The algorithm is based on an iterative divide-and-conquer strategy. The data is first split into independent subsets, each of which is clustered separately. Thus reduces the storage required for sequential implementations, and allows concurrent computation on parallel computing hardware. The resultant clusters are merged and subsequently re-divided into subsets, which are passed to the following iteration. We show that MAHC can match and even surpass the performance of the exact implementation when applied to datasets of speech segments.     

Influences of geochemical factors and substrate availability on Gram-positive and Gram-negative bacterial distribution and bio-processes in ageing municipal landfills

International Microbiology - Bacteria are primary agents of organic substrate metabolisation and elemental cycling in landfills. Two major bacterial groups, namely, Gram-positive (GP) and...     

Nevirapine- Versus Lopinavir/Ritonavir-Based Initial Therapy for HIV-1 Infection among Women in Africa: A Randomized Trial

Background

Nevirapine (NVP) is widely used in antiretroviral treatment (ART) of HIV-1 globally. The primary objective of the AA5208/OCTANE trial was to compare the efficacy of NVP-based versus lopinavir/ritonavir (LPV/r)-based initial ART.

Methods and Findings

In seven African countries (Botswana, Kenya, Malawi, South Africa, Uganda, Zambia, and Zimbabwe), 500 antiretroviral-naïve HIV-infected women with CD4<200 cells/mm³ were enrolled into a two-arm randomized trial to initiate open-label ART with tenofovir (TDF)/emtricitabine (FTC) once/day plus either NVP (n = 249) or LPV/r (n = 251) twice/day, and followed for ≥48 weeks. The primary endpoint was time from randomization to death or confirmed virologic failure ([VF]) (plasma HIV RNA<1 log₁₀ below baseline 12 weeks after treatment initiation, or ≥400 copies/ml at or after 24 weeks), with comparison between treatments based on hazard ratios (HRs) in intention-to-treat analysis. Equivalence of randomized treatments was defined as finding the 95% CI for HR for virological failure or death in the range 0.5 to 2.0. Baseline characteristics were (median): age = 34 years, CD4 = 121 cells/mm³, HIV RNA = 5.2 log₁₀copies/ml. Median follow-up = 118 weeks; 29 (6%) women were lost to follow-up. 42 women (37 VFs, five deaths; 17%) in the NVP and 50 (43 VFs, seven deaths; 20%) in the LPV/r arm reached the primary endpoint (HR 0.85, 95% CI 0.56–1.29). During initial assigned treatment, 14% and 16% of women receiving NVP and LPV/r experienced grade 3/4 signs/symptoms and 26% and 22% experienced grade 3/4 laboratory abnormalities. However, 35 (14%) women discontinued NVP because of adverse events, most in the first 8 weeks, versus none for LPV/r (p<0.001). VF, death, or permanent treatment discontinuation occurred in 80 (32%) of NVP and 54 (22%) of LPV/r arms (HR = 1.7, 95% CI 1.2–2.4), with the difference primarily due to more treatment discontinuation in the NVP arm. 13 (45%) of 29 women tested in the NVP versus six (15%) of 40 in the LPV/r arm had any drug resistance mutation at time of VF.

Conclusions

Initial ART with NVP+TDF/FTC demonstrated equivalent virologic efficacy but higher rates of treatment discontinuation and new drug resistance compared with LPV/r+TDF/FTC in antiretroviral-naïve women with CD4<200 cells/mm³.

Trial registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00089505","term_id":"NCT00089505"}}NCT00089505 Please see later in the article for the Editors'' Summary     

The Effect of a Maturing Antiretroviral Program on Early Mortality for Patients with Advanced Immune-Suppression in Soweto,South Africa

Objective

We hypothesize that time to initiate care and maturity of a treatment program impact on outcome of severely immuno-compromised patients with higher risk of mortality.

Design

We conducted a retrospective cohort analysis at the Perinatal HIV Research Unit Adult ART clinic, Soweto, South Africa.

Methods

Eligibility criteria for this analysis were: attendance for minimum one visit between August 2004 and August 2010, age >18 years, CD4 count < 50 cells/mm³ and ART-naïve at screening. We followed participants up to one year after ART initiation. We defined years 2004-2007 and 2008-2010 as the early and late eras respectively. Chi-square test and survival analysis methods were used for mortality comparisons between eras.

Results

Of 2357 patients eligible for antiretroviral treatment, 395 (17%) had CD4 counts < 50 cells/mm³ and ART-naïve at screening. Overall 261 (66%) were women. Patients had similar median age (35 vs. 33.5 years, p=0.08), time to HAART initiation (7 days, p=0.18) and baseline CD4 count (20 vs. 23 cells/mm³, p=0.5) between eras. Overall 63 (16%) patients died in their first year of treatment (2 per 100 person-months) and the main cause of death was tuberculosis (n=23, 37%). The proportion of deaths (52/262 vs. 11/133, p=0.003) and time to death from enrolment (logrank p=0.04) were significantly different between eras.

Conclusion

Mortality decreased as the ART program matured in Soweto while time to initiation of treatment remained similar in both eras. Because ART guidelines were consistent during both eras, it is possible that with time, management of patients improved as expertise was gained.     

Biological degradation and solubilisation of coal

This review focuses on ligninolytic fungi, soil bacteria, plants and root exudates in the degradation and solubilisation of low grade and waste coal and the interaction between these mutualistic biocatalysts. Coal represents a considerable portion of the total global fossil fuel reserve and continued demand for, and supply of this resource generates vast quantities of spoil and low grade waste. Large scale bioremediation technologies for the beneficiation of waste coal have unfortunately not yet been realised despite the many discoveries of microorganisms capable of lignite, lignin, and humic acid breakdown. Even so, solubilisation and depolymerization of low grade coal appears to involve either ligninolytic enzyme action or the production of alkaline substances or both. While the precise mechanism of coal biosolubilisation is unclear, a model for the phyto-biodegradation of low rank coal by mutualistic interaction between ligninolytic microorganisms and higher plants is proposed. Based on accumulated evidence this model suggests that solubilisation and degradation of lignite and waste coals commences upon plant root exudate and ligninolytic microorganism interaction, which is mutualistic, and includes soil bacteria and both mycorrhizal and non-mycorrhizal fungi. It is envisaged that this model and its further elaboration will aid in the development of functional technologies for commercial bioremediation of coal mine spoils, contribute to soil formation, and the overall biogeochemistry of organic carbon in the global ecosystem.