Comparative Analysis of the C4.5 and ID3 Decision Tree Algorithms for Disease Symptom Classification and Diagnosis

Most disease surveillance outfits and authrorities around the world battle with one key challenge – the useful and objective handling and processing of the huge sets of disease data being generated on a regular basis as their personnel exercise their disease surveillance mandate. Many theories have been put forth on how best this could be tackled. Among these, is the use of information technology and mathematical theories and concepts to alleviate the problem. One of the most solid and promising methods includes the use of artificial intelligence techniques to help break down and make good sense of the data sets. This research looks to compare the usage of the C4.5 and the ID3 decision tree theory concepts as means of tackling making the best of disease surveillance data. The C4.5 and ID3 algorithms provide a method of breaking down the data and generating (among other useful information) the entropies and information gains of some predefined variables from huge sets of disease outbreak data. Once the information gain scores for the variables are computed, they can be easily ranked to determine the variable to define the root node in the decision tree, as the rest of the variables follow through as leaf nodes. Notably, there will be two sets of entropies and information gains; one from the C4.5 algortihm and the other from the ID3 algorithm. Both decision trees shall have validation steps after each branch pass to determine whether it is time to stop growing it or not. This is one of the mechanisms employed here to avoid overfiting of the decision tree (especially for the ID3 algorithm)

Lessons learnt from the 2014 West Africa ebola viral disease (EVD) outbreak: economic, political and social impacts of disease outbreaks

In many disease outbreaks, their effects can invariably be measured in both direct and indirect terms; directly by observable, measurable outcomes and indirectly by looking for knock-on effects post the disease outbreak. Some of these angles and degrees of measure could matter more and provide a different yet more objective measure of a true disease outbreak’s impact. Such measures include the economic, social and political implications following a disease outbreak. This research looks to study and document the economic, social and political implications of the 2014 West African EVD outbreak that mainly ravaged Guinea, Liberia and Sierra Leone. Whilst the outbreak may have been theoretically localized around the three countries, other neighboring and far flung but somewhat affiliated nations also had their share of the outbreak’s implications. This research also looks to study and identify knock-on effects of the outbreak in the other countries (outside the three at the outbreak’s epicenter). The research looks to inform and boost the focus on early and targeted mitigation efforts if only to safeguard the interests of regional blocks and other nations that may be victims of negative downturns as a result of such disease outbreaks. The research hopes to inform and spur intraregional and inter-national discussions and engagements on how to best deal with such disease outbreak in a measurable and sustainable manner, with an aim to possibly safeguard their socio-economic and political interests

An in vitro evaluation of drugs used in the Kenyan ART program

The majority of anti-HIV drug susceptibility tests have been performed on subtype B HIV-1 strains, since these are the most prevalent in countries designing, testing, and manufacturing the current anti-HIV agents. The increasing global spread of HIV subtype highlights the need to determine the activity of anti-HIV drugs against subtypes of HIV other than subtype B. Furthermore an increasing number of individuals infected with many of the non subtype B virus strains now receive antiretroviral therapy because of rollout programs in developing countries as well as increasing migration to the developed world. The phenotypic susceptibility of two laboratory strains HIV-1JFRL and HIV-1IIIB (representing subtype B) and two clinical isolates HIV-104RTA and HIV-1025RTA (representing subtypes A and D respectively) was determined. The in vitro drug susceptibility testing of the isolates was carried out in C8166 cell line and in peripheral blood mononuclear cells (PBMCs). The study revealed that the drugs used in the Kenyan national ART program inhibited HIV-1 replication in-vitro as their inhibitory concentrations (IC50) compared well with the standard Inhibitory concentration values. The results also suggest a biochemical similarity of the reverse transcriptase (RT) and protease enzymes from these subtypes despite the divergence at the genetic level. The findings suggest that similar clinical benefits of antiviral therapy obtain in persons infected with other subtypes of HIV-1other than subtype B and that the generic drugs used in the national ART program in Kenya are as efficacious as branded drugs in inhibiting HIV replication in vitro despite the limited number of the viruses studied.Pan African Medical Journal 2016; 2

Trends of HIV infection among infants born to HIV infected mothers on PMCT antiretroviral treatment in western Kenya.

Background : More than 365,000 of unborn children are at risk of getting HIV infection in the developing world through "vertical" transmission. Although, ARVs are being used to reduce maternal HIV transmission, limited information exists indicating their impact on the trend of HIV prevalence among infants born to HIV infected mothers. Objective : To determine the trend of HIV infection among infants born to HIV infected mothers in relation to specific ARVs administered to pregnant women and lactating mothers of 18 months and below infants. Methodology : Dried blood spot samples in the following quantities per year thus, in 2010, n = 4,210, in 2011, n=4,093, in 2012, n=4,686, in 2013, n=3,080 were collected from infants aged ≤18 months whose mothers were HIV positive. The samples were analyzed using Cobas Polymerase Chain Reaction Assay in early infant diagnosis laboratory at the Center for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute (KEMRI). Results: Out of the total number of samples tested 2010, 409(9.7%) tested HIV positive. In 2011, 350(8.5%), in 2012, 368(7.9%) and in 2013, 221(7.2%) were HIV positive respectively. The trend of HIV in infants whose mothers had been put on various ARVs was as follows: AZT+3TC +EFV, in 2010, the number was 10.4%. In 2011, it moved to 9.1%, in 2012, to 6.3% and 2013, dropped to 6.0%. AZT+3TC+NVP, in 2010, the number was 7.1%, in 2011, moved to 6.1%, in 2012, falling to 4.7% and 2013 to3.9%. SdNVP, in 2010, the number was 10.3%. In 2011, moved to 7.4%, in 2012, dropping to 6.2% and in 2013, at 6.0%. Those mothers who had not been given any ARVs, their infants had HIV prevalence as follows: in 2010, the number was 11.2%. In 2011, it climbed to 12.6%, moving to 12.7% in 2012, and 12.9% in 2013. Conclusion: There was direct relationship between specific ARV administration and HIV infection among those infants. That was evident by the fact that, HIV appeared to decrease with sub-sequent years of provision of specific drugs. However, HAART (AZT+3TC+ EFV) seemed to provide greater impact in HIV prevention compared to other HAART (AZT+3TC+NVP) and SdNVP. The worst groups are those not on any ARVs. Single-dose Nevirapine commonly is used for prevention event-hough prior studies have shown exposure to it develop drug resistance, which can compromise the effective not only of itself, but also other non-nucleoside reverse transcriptase inhibitors (NNRTIs) Recommendation : There is need for all HIV positive pregnant women to be put on ARVs and monitored for ARVs uptake to reduce the transmission of HIV from mother to child. Key words: HIV, ARVs, Infants, &nbsp

Seroprevalence of chikungunya fever virus and O’nyong Nyong fever virus among febrile patients visiting selected hospitals in 2011-2012 Trans Nzoia County, Kenya

Background: Chikungunya virus (CHIKV) is an alphavirus in the Semliki Forest complex, and is most closely related to O’Nyong Nyong virus (ONNV). CHIKV and ONNV are mosquito-borne alphaviruses endemic in East Africa that cause acute febrile illness and arthralgia. The objectives of this study were to measure seroprevalence of CHIKV and ONNV in selected health facilities in Western Kenya and link it to demographics and other risk factors.Methods: The study design was cross sectional in selected health facilities. We tested for anti-CHIKV antibodies using In-house Indirect IgG Enzyme Linked Immunosorbent Assay (ELISA) and In-house IgM Capture ELISA and confirmed with Focus Reduction Neutralization Test (FRNT) for specific alphavirus neutralizing antibodies against CHIKV or ONNV. Mean, median and standard deviation were used to summarize the data. Comparisons of means and medians were done using Student’s t test. Prevalence rates were determined using descriptive statistics (e.g. proportions, rates).Results: From the 382 samples that were successfully collected, 114 (29.84%) had anti-CHIKV antibodies by the ELISA test. Of these, 27 (7.1%) had CHIKV-specific neutralizing antibodies and 5 (1.3%) had ONNV-specific neutralizing antibodies. Age was significantly associated with seropositivity (OR=1.03; P=0.015, 95% C.I 1.01-1.06). Males were less likely to be seropositive (OR=0.67; P=0.358, 95% C.I 0.27-1.52). Risk factors associated with seropositivity included collecting firewood (OR=2.73 95% 1.13- 6.41) and walls with holes and cracks (OR=0.23 95% C.I 0.04 -0.86).Conclusions: Both CHIKV and ONNV infections were confirmed in the participants’ more so in women and adults, demonstrating undocumented and ongoing transmission in Western Kenya. In 2011 and 2012 CHIKV and ONNV contributed 8.4% of fevers presented in the three selected health facilities in Western Kenya

Mother-To-Child HIV Transmission using Single, Dual and Triple ARV Prophylaxis Regimens and their Correlates in Western Kenya: Chart Review

Background: It is estimated that 2.1 million individuals worldwide became newly infected with HIV in 2013, and this included 240,000 children (<15 years).  Most of these children live in sub-Saharan Africa and were infected by their HIV-positive mothers during pregnancy, childbirth or breastfeeding. Objective: This study sought to ascertain the different PMTCT approaches or regimens that mothers and infants receive, their Mother-To-Child Transmission of HIV (MTCT) rates and associated correlates in Western Kenya. Methods: A retrospective cohort study using prospectively collected data in Ministry of Health HIV-Exposed Infant (HEI) register from 24 health facilities.  The study population was HIV-positive mothers enrolled from January 2012 to June 2013. The main outcomes were infant HIV status at 6 weeks, 9 to <18 months and 18-24 months. The correlates were maternal haemoglobin levels, WHO staging, CD4 counts, duration between enrolment and delivery, duration between enrolment and ART initiation, TB status, place of delivery, mode of delivery, and infant feeding options at 6 weeks, 9 to <18 months and 18-24 months. Proportions were analyzed using Chi-square tests while associations between MTCT correlates and outcomes were established using logistic regression. Results: 1,751 HIV mother-baby pairs were enrolled in the 24 health facilities: 78.1% received Highly Active Antiretroviral Therapy (HAART), 14.2% received Zidovudine (AZT), 1.7% received Single-dose Nevirapine (SdNVP), and 4.3% received no prophylaxis. MTCT rates were 5.5%, 7.4% and 5.6% at 6 weeks, 9 to <18 months and 18-24 months, respectively. MTCT rate at 18-24 months showed a significant difference (p<0.001) across PMTCT regimens. Women with CD4 cells between 350 to 500 cells/mm3 were about twice as likely to have HIV-negative babies compared to those with CD4 cells count <350cells/mm3. Women on TB treatment are less likely to have HIV-negative babies compared to those without TB. Exclusive breastfeeding at 6 weeks was associated with lower MTCT rates.  Feeding option at 6 weeks is a strong predictor of HIV status (p<0.001) as compared to babies on exclusive breastfeeding (EBF). Conclusion: Most of the mother-baby pairs received HAART. AZT depicted the lowest MTCT rate at 18-24 months.  Higher CD4 counts, no TB signs, and EBF at 6 weeks were associated with lower MTCT rates at 18-24 months Key words:  Antiretroviral prophylaxis, Mother-To-Child Transmission of HIV rates

The effect of participant nonresponse on HIV prevalence estimates in a population-based survey in two informal settlements in Nairobi city

BACKGROUND: Participant nonresponse in an HIV serosurvey can affect estimates of HIV prevalence. Nonresponse can arise from a participant's refusal to provide a blood sample or the failure to trace a sampled individual. In a serosurvey conducted by the African Population and Health Research Center and Kenya Medical Research Centre in the slums of Nairobi, 43% of sampled individuals did not provide a blood sample. This paper describes selective participation in the serosurvey and estimates bias in HIV prevalence figures. METHODS: The paper uses data derived from an HIV serosurvey nested in an on-going demographic surveillance system. Nonresponse was assessed using logistic regression and multiple imputation methods to impute missing data for HIV status using a set of common variables available for all sampled participants. RESULTS: Age, residence, high mobility, wealth, and ethnicity were independent predictors of a sampled individual not being contacted. Individuals aged 30-34 years, females, individuals from the Kikuyu and Kamba ethnicity, married participants, and residents of Viwandani were all less likely to accept HIV testing when contacted. Although men were less likely to be contacted, those found were more willing to be tested compared to females. The overall observed HIV prevalence was overestimated by 2%. The observed prevalence for male participants was underestimated by about 1% and that for females was overestimated by 3%. These differences were small and did not affect the overall estimate substantially as the observed estimates fell within the confidence limits of the corrected prevalence estimate. CONCLUSIONS: Nonresponse in the HIV serosurvey in the two informal settlements was high, however, the effect on overall prevalence estimate was minimal

Combating antibiotic resistance using guidelines and enhanced stewardship in Kenya: a protocol for an implementation science approach

Introduction: Antimicrobial resistance (AMR) is a growing problem globally especially in Sub-Saharan Africa including Kenya. Without any intervention, lower/middle-income countries (LMICs) will be most affected due to already higher AMR levels compared with higher income countries and due to the far higher burden of diseases in the LMICs. Studies have consistently shown that inappropriate use of antimicrobials is the major driver of AMR. To address this challenge, hospitals are now implementing antibiotic stewardship programmes (ASPs), which have been shown to achieve reduced antibiotic usage, to decrease the prevalence of resistance and lead to significant economic benefits. However, the implementation of the guideline is highly dependent on the settings in which they are rolled out. This study, employing an implementation science approach, aims to address the knowledge gap in this area and provide critical data as well as practical experiences when using antibiotic guidelines and stewardship programmes in the public health sector. This will provide evidence of ASP performance and potentially contribute to the county, national and regional policies on antibiotics use. Methods and analysis: The study will be conducted in three geographically diverse regions, each represented by two hospitals. A baseline study on antibiotic usage, resistance and de-escalation, duration of hospital stay, rates of readmission and costs will be carried out in the preimplementation phase. The intervention, that is, the use of antibiotic guidelines and ASPs will be instituted for 18 months using a stepwise implementation strategy that will facilitate learning and continuous improvement of stewardship activities and updating of guidelines to reflect the evolving antibiotic needs. Ethics and dissemination: Approvals to carry out the study have been obtained from the National Commission for Science, Technology and Innovation and the Mount Kenya University Ethics Review Committee. The approvals from the two institutions were used to obtain permission to conduct the study at each of the participating hospitals. Study findings will be presented to policy stakeholders and published in peer-reviewed scientific journals. It is anticipated that the findings will inform the appropriate antibiotic use guidelines within our local context

Evaluation of Clinical and Immunological Markers for predicting Virological Failure in a HIV/AIDS treatment cohort in Busia, Kenya

In resource-limited settings where viral load (VL) monitoring is scarce or unavailable, clinicians must use immunological and clinical criteria to define HIV virological treatment failure. This study examined the performance of World Health Organization (WHO) clinical and immunological failure criteria in predicting virological failure in HIV patients receiving antiretroviral therapy (ART)

Species-Specific Serological Detection for Schistosomiasis by Serine Protease Inhibitor (SERPIN) in Multiplex Assay

Background: Both Schistosoma mansoni and Schistosoma haematobium cause schistosomiasis in sub-Saharan Africa. We assessed the diagnostic value of selected Schistosoma antigens for the development of a multiplex serological immunoassay for sero-epidemiological surveillance. Methodology/Principal Findings: Diagnostic ability of recombinant antigens from S. mansoni and S. haematobium was assessed by Luminex multiplex immunoassay using plasma from school children in two areas of Kenya, endemic for different species of schistosomiasis. S. mansoni serine protease inhibitor (SERPIN) and Sm-RP26 showed significantly higher reactivity to patient plasma as compared to the control group. Sm-Filamin, Sm-GAPDH, Sm-GST, Sm-LAP1, Sm-LAP2, Sm-Sm31, Sm-Sm32 and Sm-Tropomyosin did not show difference in reactivity between S. mansoni infected and uninfected pupils. Sm-RP26 was cross-reactive to plasma from S. haematobium patients, whereas Sm-SERPIN was species-specific. Sh-SEPRIN was partially cross-reactive to S. mansoni infected patients. ROC analysis for Sm-RP26, Sm-SERPIN and Sh-SERPIN showed AUC values of 0.833, 0.888 and 0.947, respectively. Using Spearman’s rank correlation coefficient analysis, we also found significant positive correlation between the number of excreted eggs and median fluorescence intensity (MFI) from the multiplex immunoassays for Sm-SERPIN (ρ = 0.430, p-value = 0.003) and Sh-SERPIN (ρ = 0.433, p-value = 0.006). Conclusions/Significance: Sm-SERPIN is a promising species-specific diagnostic antigen. Sh-SEPRIN was partially cross-reactive to S. mansoni infected patients. SERPINs showed correlation with the number of excreted eggs. These indicate prospects for inclusion of SERPINs in the multiplex serological immunoassay system