The goal of this study was to adapt a recently proposed linear large-scale support vector machine to large-scale binary cheminformatics classification problems and to assess its performance on ...various benchmarks using virtual screening performance measures. We extended the large-scale linear support vector machine library LIBLINEAR with state-of-the-art virtual high-throughput screening metrics to train classifiers on whole large and unbalanced data sets. The formulation of this linear support machine has an excellent performance if applied to high-dimensional sparse feature vectors. An additional advantage is the average linear complexity in the number of non-zero features of a prediction. Nevertheless, the approach assumes that a problem is linearly separable. Therefore, we conducted an extensive benchmarking to evaluate the performance on large-scale problems up to a size of 175000 samples. To examine the virtual screening performance, we determined the chemotype clusters using Feature Trees and integrated this information to compute weighted AUC-based performance measures and a leave-cluster-out cross-validation. We also considered the BEDROC score, a metric that was suggested to tackle the early enrichment problem. The performance on each problem was evaluated by a nested cross-validation and a nested leave-cluster-out cross-validation. We compared LIBLINEAR against a Naïve Bayes classifier, a random decision forest classifier, and a maximum similarity ranking approach. These reference approaches were outperformed in a direct comparison by LIBLINEAR. A comparison to literature results showed that the LIBLINEAR performance is competitive but without achieving results as good as the top-ranked nonlinear machines on these benchmarks. However, considering the overall convincing performance and computation time of the large-scale support vector machine, the approach provides an excellent alternative to established large-scale classification approaches.
Based on detailed structural mapping, geophysical information and structural consideration, we generated a 3D structural model of a segment of the Vredefort Dome. This model provides insight into the ...mechanism of mass transfer during central uplift formation of large impact structures. The model consists of geometrically and kinematically linked km-scale radial and concentric faults that affected the overturned limb of the rim syncline to the Vredefort Dome. The faults accomplished constrictional (centripetal) rock flow followed by radial spreading of uplifted and gravitationally unstable rocks in the crater centre. More specifically, concentric faults formed likely as normal faults during transient crater rim collapse, steepened and were transformed to reverse faults during central rock uplift and finally, were overturned during gravitational collapse of the central uplift. Radial faults, by contrast, formed at a later stage of convergent rock flow towards the crater centre and retained largely their orientation during central uplift formation. Displacement on individual faults is up to 2 km. Cumulative displacement, notably on concentric faults, can account for the large displacement magnitudes predicted by numerical models.
Blood-stream infection (BSI) is one of the principle determinants of the morbidity and mortality associated with advanced HIV infection, especially in sub-Saharan Africa. Over the last 10 years, ...there has been rapid roll-out of anti-retroviral therapy (ART) and cotrimoxazole prophylactic therapy (CPT) in many high HIV prevalence African countries.
A prospective cohort of adults with suspected BSI presenting to Queen's Hospital, Malawi was recruited between 2009 and 2010 to describe causes of and outcomes from BSI. Comparison was made with a cohort pre-dating ART roll-out to investigate whether and how ART and CPT have affected BSI. Malawian census and Ministry of Health ART data were used to estimate minimum incidence of BSI in Blantyre district.
2,007 patients were recruited, 90% were HIV infected. Since 1997/8, culture-confirmed BSI has fallen from 16% of suspected cases to 10% (p<0.001) and case fatality rate from confirmed BSI has fallen from 40% to 14% (p<0.001). Minimum incidence of BSI was estimated at 0.03/1000 years in HIV uninfected vs. 2.16/1000 years in HIV infected adults. Compared to HIV seronegative patients, the estimated incidence rate-ratio for BSI was 80 (95% CI:46-139) in HIV-infected/untreated adults, 568 (95% CI:302-1069) during the first 3 months of ART and 30 (95% CI:16-59) after 3 months of ART.
Following ART roll-out, the incidence of BSI has fallen and clinical outcomes have improved markedly. Nonetheless, BSI incidence remains high in the first 3 months of ART despite CPT. Further interventions to reduce BSI-associated mortality in the first 3 months of ART require urgent evaluation.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary Background Chronic obstructive pulmonary disease (COPD) is characterized by an enhanced and persistent innate and acquired immune response to tobacco smoking. Myeloid-derived suppressor cells ...(MDSCs) modulate T-cell responses by down-modulating the T cell receptor ζ chain (TCR ζ) through the catabolism of l -arginine. The effects of smoking on MDSCs and their potential participation in COPD immunopathogenesis have not been explored so far. Methods To investigate it, we compared the level of circulating Lineage-/HLA-DR-/CD33+/CD11b+ MDSCs, the serum concentration of arginase I (ARG I) and the expression of peripheral T-cell receptor ζ chain (TCR ζ) in never smokers, smokers with normal spirometry and COPD patients. Flow cytometry was used to quantify circulating MDSCs and TCR ζ expression. Serum ARG I levels were determined by ELISA. Results The main findings of this study were that: (1) current smoking upregulates and activates circulating MDSCs both in smoker controls and COPD patients; and, (2) at variance with the smokers with normal spirometry, in patients with COPD this effect persists after quitting smoking and is accompanied by a significant and specific down-regulation of the TCR ζ chain expression in circulating T lymphocytes. Conclusion Smoking modulates circulating MDSCs. Their regulation appears altered in patients with COPD.
Summary Despite the enormous progress made in scaling up antiretroviral therapy (ART) in sub-Saharan Africa, many challenges remain, not least of which are the identification and management of ...patients who have failed first-line therapy. Less than 3% of patients are receiving second-line treatment at present, whereas 15–25% of patients have detectable viral loads 12 months or more into treatment, of whom a substantial proportion might have virological failure. We discuss the reasons why virological ART failure is likely to be under-diagnosed in the routine health system, and address the current difficulties with standard recommended second-line ART regimens. The development of new diagnostic tools for ART failure, in particular a point-of-care HIV viral-load test, combined with simple and inexpensive second-line therapy, such as boosted protease-inhibitor monotherapy, could revolutionise the management of ART failure in resource-limited settings.
The presence and the transformations of organic fractions within biofilms are not usually included in biofilm models, mainly owing to the lack of knowledge of the important processes, the ...stoichiometry and the kinetics. A conceptual biofilm model taking into account microbial physiology with regard to production of extracellular polymers and their transformation within the biofilm is suggested. The suggested components in the biofilm are the cell biomass and the various extracellular polymeric substances (EPS), such as polysaccharides, protein, humic substances and nucleic acids. In addition, environmental factors that influence the microbial exopolymer production and composition are taken into account. The suggested conceptual model can be helpful in structuring the design and evaluation of biofilm experiments focusing on biofilm structure and properties.
Routine ART programme statistics generally only provide information about individuals who start treatment. We aimed to investigate the outcome of those who are eligible but do not start ART in the ...Malawi programme, factors associated with this dropout, and reasons for not starting treatment, in a prospective cohort study.
Individuals having a first screening visit at the ART clinic at Karonga District Hospital, northern Malawi, between September 2005 and July 2006 were interviewed. Study follow-up to identify treatment outcomes was conducted at the clinic and in the community. Logistic regression models were used to identify factors associated with dropout before ART initiation among participants identified as clinically eligible for ART.
88 participants eligible for ART at their first screening visit (out of 633, 13.9%) defaulted before starting ART. Participants with less education, difficulties in dressing, a more delayed ART initiation appointment, and mid-upper arm circumference (MUAC) < 22 cm were significantly less likely to have visited the clinic subsequently. Thirty-five (58%) of the 60 participants who defaulted and were tracked at home had died, 21 before their ART initiation appointment.
MUAC and reported difficulties in dressing may provide useful screening indicators to identify sicker ART-eligible individuals at high risk of dropping out of the programme who might benefit from being brought back quickly or admitted to hospital for observation. Individuals with less education may need adapted health information at screening. Deaths of ART-eligible individuals occurring prior to ART initiation are not included in routine programme statistics. Considering all those who are eligible for ART as a denominator for programme indicators would help to highlight this vulnerable group, in order to identify new opportunities for further improving ART programmes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Although the World Health Organization (WHO) provides information on the number of TB patients categorised as "other", there is limited information on treatment regimens or treatment outcomes for ..."other". Such information is important, as inappropriate treatment can lead to patients remaining infectious and becoming a potential source of drug resistance. Therefore, using a cohort of TB patients from a large registration centre in Lilongwe, Malawi, our study determined the proportion of all TB re-treatment patients who were registered as "other", and described their characteristics and treatment outcomes.
This retrospective observational study used routine program data to determine the proportion of all TB re-treatment patients who were registered as "other" and describe their characteristics and treatment outcomes between January 2006 and December 2008.
1,384 (12%) of 11,663 TB cases were registered as re-treatment cases. Of these, 898 (65%) were categorised as "other": 707 (79%) had sputum smear-negative pulmonary TB and 191 (21%) had extra pulmonary TB. Compared to the smear-positive relapse, re-treatment after default (RAD) and failure cases, smear-negative "other" cases were older than 34 years and less likely to have their HIV status ascertained. Among those with known HIV status, "other" TB cases were more likely to be HIV positive. Of TB patients categorised as "other", 462 (51%) were managed on the first-line regimen with a treatment success rate of 63%.
A large proportion of re-treatment patients were categorised as "other". Many of these patients were HIV-infected and over half were treated with a first-line regimen, contrary to national guidelines. Treatment success was low. More attention to recording, diagnosis and management of these patients is warranted as incorrect treatment regimen and poor outcomes could lead to the development of drug resistant forms of TB.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Pellagra is caused by niacin (vitamin B3) deficiency and manifested by a distinctive dermatitis. Isoniazid is critical for treating tuberculosis globally and is a component of most regimens to ...prevent tuberculosis. Isoniazid may contribute to pellagra by disrupting intracellular niacin synthesis. In 2017, Malawian clinicians recognized a high incidence of pellagra-like rashes after scale-up of isoniazid preventive treatment (IPT) to people living with HIV (PLHIV). This increase in pellagra incidence among PLHIV coincided with a seasonal period of sustained food insecurity in the region, which obscured epidemiological interpretations. Although isoniazid has been implicated as a secondary cause of pellagra for decades, no hypothesis-driven epidemiological study has assessed this relationship in a population exposed to isoniazid. We developed this case-control protocol to assess the association between large-scale isoniazid distribution and pellagra in Malawi.
We measure the relative odds of having pellagra among isoniazid-exposed people compared to those without exposure while controlling for other pellagra risk factors. Secondary aims include measuring time from isoniazid initiation to onset of dermatitis, comparing niacin metabolites 1-methylnicotinamide (1-MN), and l-methyl-2-pyridone-5-carboxamide (2-PYR) in urine as a proxy for total body niacin status among subpopulations, and describing clinical outcomes after 30-days multi-B vitamin (containing 300 mg nicotinamide daily) therapy and isoniazid cessation (if exposed). We aim to enroll 197 participants with pellagra and 788 age- and sex-matched controls (1:4 ratio) presenting at three dermatology clinics. Four randomly selected community clinics within 3-25 km of designated dermatology clinics will refer persons with pellagra-like symptoms to one of the study enrollment sites for diagnosis. Trained study dermatologists will conduct a detailed exposure questionnaire and perform anthropometric measurements. A subset of enrollees will provide a casual urine specimen for niacin metabolites quantification and/or point-of-care isoniazid detection to confirm whether participants recently ingested isoniazid. We will use conditional logistic regression, matching age and sex, to estimate odds ratios for the primary study aim.
The results of this study will inform the programmatic scale-up of isoniazid-containing regimens to prevent tuberculosis.
Background
The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than ...2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds.
Results
Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics.
Conclusions
Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible.
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