Verifying the fully “Laplacianised” posterior Naïve Bayesian approach and more

Mussa and Glen would like to thank Unilever for financial support, whereas Mussa and Mitchell thank the BBSRC for funding this research through grant BB/I00596X/1. Mitchell thanks the Scottish Universities Life Sciences Alliance (SULSA) for financial support.Background In a recent paper, Mussa, Mitchell and Glen (MMG) have mathematically demonstrated that the “Laplacian Corrected Modified Naïve Bayes” (LCMNB) algorithm can be viewed as a variant of the so-called Standard Naïve Bayes (SNB) scheme, whereby the role played by absence of compound features in classifying/assigning the compound to its appropriate class is ignored. MMG have also proffered guidelines regarding the conditions under which this omission may hold. Utilising three data sets, the present paper examines the validity of these guidelines in practice. The paper also extends MMG’s work and introduces a new version of the SNB classifier: “Tapered Naïve Bayes” (TNB). TNB does not discard the role of absence of a feature out of hand, nor does it fully consider its role. Hence, TNB encapsulates both SNB and LCMNB. Results LCMNB, SNB and TNB performed differently on classifying 4,658, 5,031 and 1,149 ligands (all chosen from the ChEMBL Database) distributed over 31 enzymes, 23 membrane receptors, and one ion-channel, four transporters and one transcription factor as their target proteins. When the number of features utilised was equal to or smaller than the “optimal” number of features for a given data set, SNB classifiers systematically gave better classification results than those yielded by LCMNB classifiers. The opposite was true when the number of features employed was markedly larger than the “optimal” number of features for this data set. Nonetheless, these LCMNB performances were worse than the classification performance achieved by SNB when the “optimal” number of features for the data set was utilised. TNB classifiers systematically outperformed both SNB and LCMNB classifiers. Conclusions The classification results obtained in this study concur with the mathematical based guidelines given in MMG’s paper—that is, ignoring the role of absence of a feature out of hand does not necessarily improve classification performance of the SNB approach; if anything, it could make the performance of the SNB method worse. The results obtained also lend support to the rationale, on which the TNB algorithm rests: handled judiciously, taking into account absence of features can enhance (not impair) the discriminatory classification power of the SNB approach.Publisher PDFPeer reviewe

Plasmodium falciparum isolate with histidine-rich protein 2 gene deletion from Nyala City, Western Sudan.

In remote areas of malaria-endemic countries, rapid diagnostic tests (RDTs) have dramatically improved parasitological confirmation of suspected malaria cases, especially when skilled microscopists are not available. This study was designed to determine the frequency of Plasmodium falciparum isolates with histidine-rich protein 2 (pfhrp2) gene deletion as one of the possible factors contributing to the failure of PfHRP2-based RDTs in detecting malaria. A total of 300 blood samples were collected from several health centres in Nyala City, Western Sudan. The performance of PfHRP2-based RDTs in relation to microscopy was examined and the PCR-confirmed samples were investigated for the presence of pfhrp2 gene. A total of 113 out of 300 patients were P. falciparum positive by microscopy. Among them, 93.81% (106 out of 113) were positives by the PfHRP2 RDTs. Seven isolates were identified as false negative on the basis of the RDTs results. Only one isolate (0.9%; 1/113) potentially has pfhrp2 gene deletion. The sensitivity and specificity of PfHRP2-based RDTs were 93.81% and 100%, respectively. The results provide insights into the pfhrp2 gene deletion amongst P. falciparum population from Sudan. However, further studies with a large and systematic collection from different geographical settings across the country are needed

Prevalence of high blood pressure and associated factors among adolescents and young people in Tanzania and Uganda.

We conducted a cross-sectional study among school/college students in Tanzania and Uganda to determine the prevalence of high blood pressure (BP) and associated factors. Participants were classified to have high BP if they had pre-hypertension or hypertension. Interviews were done using the WHO STEPS instrument. Using data from both countries (n = 1596), the overall prevalence of high BP was 40% (95% CI: 37-42). The prevalence of pre-hypertension was 29% (95% CI: 26-31) and that of hypertension was 11% (95% CI: 10-13). High BP was independently associated with obesity (aOR = 6.7, 95% CI: 2.2-20.0), male sex (aOR = 3.2, 95% CI: 2.4-4.4), and among males aged above 20 years (aOR = 5.5, 95% CI: 2.9-10.5). Consumption of fruits/vegetables was associated with decreased odds for high BP (aOR = 0.7, 95% CI: 0.50-0.98). The increasing burden of pre-hypertension across age groups could explain the early onset of hypertension and cardiovascular diseases (CVDs) among young African adults. There is a need for longitudinal studies to explore the drivers of pre-hypertension in East African adolescents

Smallholder Farmers’ Practices and Understanding of Climate Change and Climate Smart Agriculture in the Southern Highlands of Tanzania

Adverse effects of climate change and variability remain to be a major threat to smallholder farmers and rural livelihoods. It posed a challenge of developing innovative technologies to improve rural livelihoods, environmental conservation and ensuring adoption of such technologies. Climate-smart agriculture (CSA) is used as a mitigation and adaptation option to reduce the negative impacts of climate change and improve agricultural productivity. To achieve the desired objectives, CSA requires a complete package of practices that increase productivity and income, build resilience and reduce green gas emission.  However, adoption is largely dependent on farmers’ understanding, preferences and their capacity and willingness to practice. The study explores smallholder farmers’ understanding of climate change impacts and their proclivity on climate smart agricultural practices. In engaging with smallholder farmers, a range of methods was used, including focus group discussions (FGD), key informant interviews (KI), household questionnaire survey and field observations. Results indicate that less than half (26%) of smallholder farmers interviewed have low knowledge on climate change in the study area, however, they are adapting and coping with the impacts of climate change. The low knowledge, coupled with the low ability to effectively adapt to the impacts of climate change, might have contributed to reduced agricultural yields.  Developing appropriate and feasible climate smart and resilient agriculture practices, is a pre-requisite towards improving food security and income to smallholder farmers. The study suggests the need to consider appropriate and sustainable local-based technologies to increase production. The local-based knowledge and technologies are cost effective, easy to adopt and can be easily out-scaled to other communities within the region. We conclude that the availability of improved local-basedtechnologies alone is not a sufficient condition to bring about the change and transformation among smallholder farmers. Effective institutions and sustained policy support play a significant role in the adoption of CSA practices. There is an urgent need for scientists and users to co-produce the climate information and CSA practices so as to ensure action-oriented recommendations. Therefore, establishing an enabling local environment, including by supporting strong and innovative rural institutions, to increase the uptake of good practices are indispensable. Keywords: Climate change, climate smart agriculture, Southern Highland, smallholder farmers and perceptio

Endovascular-first approach is not associated with worse amputation-free survival in appropriately selected patients with critical limb ischemia

ObjectiveEndovascular interventions for critical limb ischemia are associated with inferior limb salvage (LS) rates in most randomized trials and large series. This study examined the long-term outcomes of selective use of endovascular-first (endo-first) and open-first strategies in 302 patients from March 2007 to December 2010.MethodsEndo-first was selected if (1) the patient had short (5-cm to 7-cm occlusions or stenoses in crural vessels); (2) the disease in the superficial femoral artery was limited to TransAtlantic Inter-Society Consensus II A, B, or C; and (3) no impending limb loss. Endo-first was performed in 187 (62%), open-first in 105 (35%), and 10 (3%) had hybrid procedures.ResultsThe endo-first group was older, with more diabetes and tissue loss. Bypass was used more to infrapopliteal targets (70% vs 50%, P = .031). The 5-year mortality was similar (open, 48%; endo, 42%; P = .107). Secondary procedures (endo or open) were more common after open-first (open, 71 of 105 [68%] vs endo, 102 of 187 [55%]; P = .029). Compared with open-first, the 5-year LS rate for endo-first was 85% vs 83% (P = .586), and amputation-free survival (AFS) was 45% vs 50% (P = .785). Predictors of death were age >75 years (hazard ratio [HR], 3.3; 95% confidence interval [CI], 1.7-6.6; P = .0007), end-stage renal disease (ESRD) (HR, 3.4; 95% CI, 2.1-5.6; P < .0001), and prior stroke (HR, 1.6; 95% CI, 1.03-2.3; P = .036). Predictors of limb loss were ESRD (HR, 2.5; 95% CI, 1.2-5.4; P = .015) and below-the-knee intervention (P = .041). Predictors of worse AFS were older age (HR, 2.03; 95% CI, 1.13-3.7; P = .018), ESRD (HR, 3.2; 95% CI, 2.1-5.11; P < .0001), prior stroke (P = .0054), and gangrene (P = .024).ConclusionsAt 5 years, endo-first and open-first revascularization strategies had equivalent LS rates and AFS in patients with critical limb ischemia when properly selected. A patient-centered approach with close surveillance improves long-term outcomes for both open and endo approaches

Upper Body-Based Power Wheelchair Control Interface for Individuals with Tetraplegia

Many power wheelchair control interfaces are not sufficient for individuals with severely limited upper limb mobility. The majority of controllers that do not rely on coordinated arm and hand movements provide users a limited vocabulary of commands and often do not take advantage of the user's residual motion. We developed a body-machine interface (BMI) that leverages the flexibility and customizability of redundant control by using high dimensional changes in shoulder kinematics to generate proportional control commands for a power wheelchair. In this study, three individuals with cervical spinal cord injuries were able to control a power wheelchair safely and accurately using only small shoulder movements. With the BMI, participants were able to achieve their desired trajectories and, after five sessions driving, were able to achieve smoothness that was similar to the smoothness with their current joystick. All participants were twice as slow using the BMI however improved with practice. Importantly, users were able to generalize training controlling a computer to driving a power wheelchair, and employed similar strategies when controlling both devices. Overall, this work suggests that the BMI can be an effective wheelchair control interface for individuals with high-level spinal cord injuries who have limited arm and hand control

Measurement of Aerosols at the Pierre Auger Observatory

The air fluorescence detectors (FDs) of the Pierre Auger Observatory are vital for the determination of the air shower energy scale. To compensate for variations in atmospheric conditions that affect the energy measurement, the Observatory operates an array of monitoring instruments to record hourly atmospheric conditions across the detector site, an area exceeding 3,000 square km. This paper presents results from four instruments used to characterize the aerosol component of the atmosphere: the Central Laser Facility (CLF), which provides the FDs with calibrated laser shots; the scanning backscatter lidars, which operate at three FD sites; the Aerosol Phase Function monitors (APFs), which measure the aerosol scattering cross section at two FD locations; and the Horizontal Attenuation Monitor (HAM), which measures the wavelength dependence of aerosol attenuation.Comment: Contribution to the 30th International Cosmic Ray Conference, Merida Mexico, July 2007; 4 pages, 4 figure