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Concordance between bio-impedance analysis and clinical score in fluid-status assessment of maintenance haemodialysis patients: A single centre experience

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world Journal of Nephrology 2022年第4期11卷 127-138页

作者： Kamiti Muchiri Joshua K Kayima Elijah N Ogola Seth McLigeyo sally w ndung’u Samuel K Kabinga Clinical Medicine and Therapeutics University of NairobiNairobi+254Kenya Department of Clinical Medicine and Therapeutics University of NairobiNairobi+254Kenya Department of Public Health University of NairobiNairobi+254Kenya East African Kidney Institute University of NairobiNairobi+254Kenya

BACKGROuND The burden of chronic kidney disease(CKD)is rising rapidly *** overload(FO),an independent predictor of mortality in CKD,should be accurately assessed to guide estimation of the volume of fluid to be removed during haemodialysis(HD).Clinical score(CS)and bio-impedance analysis(BIA)have been utilized in assessment of FO and BIA has demonstrated reproducibility and accuracy in determination of fluid status in patients on *** is need to determine the performance of locally-developed CSs in fluid status assessment when evaluated against *** To assess the hydration status of patients on maintenance HD using BIA and a CS,as well as to evaluate the performance of that CS against BIA in fluid status *** This was a single-centre,hospital-based cross-sectional study which recruited adult patients with CKD who were on maintenance HD at Kenyatta National *** patients were aged 18 years and above and had been on maintenance HD for at least 3 *** with pacemakers,metallic implants,or bilateral limbs amputations were *** on the patients’clinical history,physical examination,and chest radiograph findings were *** was performed on each of the study participants using the Quantum®II bio-impedance analyser manufactured by RJL Systems together with the BC 4®*** evaluating the performance of the CS,BIA was considered as the gold standard test.A 2-by-2 table of the participants’fluid status at each of the CS values obtained compared to their paired BIA results was constructed(either++,+-,--or-+for FO using the CS and BIA,respectively).The results from this 2-by-2 table were used to compute the sensitivity and specificity of the CS at the various reference points and subsequently plot a receiver operating characteristic(ROC)curve that was used to determine the best cut-off *** above and below the best CS cut-off point as determined by the ROC were classified as being positive and negative for FO

关键词： Bio-impedance analysis Clinical score Chronic kidney disease Maintenance haemodialysis Fluid overload Concordance

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Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling

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Acta Pharmaceutica Sinica B 2017年第1期7卷 97-105页

作者： Harrison ndung'u Mwangi Peter wagacha Peterson Mathenge Fredrick Sijenyi Francis Mulaa Center for Biotechnology and Bioinformatics Chiromo CampusUniversity of Nairobi.HEP Bioinformatics Consultants Ltd. Department of Computing Informatics University of Nairobi DNA Software Inc. Department of Biochemistry Riverside DriveChiromo CampusUniversity of Nairobi

Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SwISS–MODEL were used to generate the 40 S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40 S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation(RMSD) value of 3.9 ? relative to the template's crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying thisapproach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.

关键词： Ribosome 40S subunit RNA structure Plasmodium falciparum 3D modeling De novo Homology

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Steady-State Analysis of the Distributed Queueing Algorithm in a Single-Channel M2M Network

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Journal of Computer and Communications 2020年第9期8卷 28-40页

作者： Romeo Nibitanga Elijah Mwangi Edward ndung’u Department of Electrical Engineering Pan African University Institute of Basic Sciences Technology and Innovation Nairobi Kenya Department of Electrical and Information Engineering University of Nairobi Nairobi Kenya Department of Telecommunication and Information Engineering Jomo Kenyatta University of Agriculture and Technology Juja Kenya

The Distributed Queuing (DQ) algorithm is predicted as one of the solutions to the issues currently found in IoT networks over the use of Aloha based algorithms. Since recently, the algorithm has been of interest to many IoT researchers as a replacement of those Aloha variants for channel access. However, previous works analyzed and evaluated the DQ algorithm without any consideration of the stability of its queues, assuming it is stable for any given number of nodes in the network. In this paper, we define the DQ stability condition in a single-channel M2M environment considering a traffic model of periodic and urgent frames from each node in the network. Besides, a steady-state evaluation of the algorithm’s performance metrics is also presented. In general, the DQ algorithm, when it is stable, was observed not to efficiently use the contention slots for the collision resolution. In a single-channel environment, the DQ algorithm is found to outperform the Aloha based algorithms only in an idle-to-saturation scenario.

关键词： Aloha Collision Resolution Distributed Queueing IoT Networks M2M Communications Stability Condition

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Hierarchical Penalized Mixed Model

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Open Journal of Statistics 2019年第6期9卷 657-663页

作者： A. w. ndung’u S. Mwalili L. Odongo Pan African university Nairobi Kenya Jomo Kenyatta university of Agriculture and Technology Nairobi Kenya Kenyatta university Nairobi Kenya

Penalized spline has been a popular method for estimating an unknown function in the non-parametric regression due to their use of low-rank spline bases, which make computations tractable. However its performance is poor when estimating functions that are rapidly varying in some regions and are smooth in other regions. This is contributed by the use of a global smoothing parameter that provides a constant amount of smoothing across the function. In order to make this spline spatially adaptive we have introduced hierarchical penalized splines which are obtained by modelling the global smoothing parameter as another spline.

关键词： Penalized Splines Mixed Model Smoothing Parameter

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Classification of Plant Endogenous States using Machine Learning-Derived Agricultural Indices

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Plant Phenomics 2023年第3期5卷 474-483页

作者： sally Shuxian Koh Kapil Dev Javier Jingheng Tan Valerie Xinhui Teo Shuyan Zhang Dinish u.S. Malini Olivo Daisuke urano Temasek Life Sciences Laboratory National University of SingaporeSingaporeSingapore Department of Biological Sciences National University of SingaporeSingaporeSingapore Translational Biophotonics Laboratory Institute of Bioengineering and BioimagingAgency for ScienceTechnology and Research(A*STAR)SingaporeSingapore Institute of Materials Research and Engineering(IMRE) Agency for ScienceTechnology and Research(A*STAR)SingaporeSingapore

Leaf color patterns vary depending on leaf age,pathogen infection,and environmental and nutritional stresses;thus,they are widely used to diagnose plant health statuses in agricultural *** visible-near infrared-shortwave infrared(VIS-NIR-SwIR)sensor measures the leaf color pattern from a wide spectral range with high spectral ***,spectral information has only been employed to understand general plant health statuses(e.g.,vegetation index)or phytopigment contents,rather than pinpointing defects of specific metabolic or signaling pathways in ***,we report feature engineering and machine learning methods that utilize VIS-NIR-SwIR leaf reflectance for robust plant health diagnostics,pinpointing physiological alterations associated with the stress hormone,abscisic acid(ABA).Leaf reflectance spectra of wild-type,ABA2-overexpression,and deficient plants were collected under watered and drought ***-and ABA-associated normalized reflectance indices(NRIs)were screened from all possible pairs of wavelength *** associated NRIs showed only a partial overlap with those related to ABA deficiency,but more NRIs were associated with drought due to additional spectral changes within the NIR wavelength *** support vector machine classifiers built with 20 NRIs predicted treatment or genotype groups with an accuracy greater than those with conventional vegetation *** selected NRIs were independent from leaf water content and chlorophyll content,2 well-characterized physiological changes under *** screening of NRIs,streamlined with the development of simple classifiers,serves as the most efficient means of detecting reflectance bands that are highly relevant to characteristics of interest.

关键词： drought reflectance indices

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A Bayesian Approach for Penalized Splines with Hierarchical Penalty

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Open Journal of Statistics 2022年第5期12卷 623-633页

作者： Anne wanjira ndung’u Samuel Musili Mwalili Leo Odongo Pan African university Nairobi Kenya Department of Mathematics Statistics and Actuarial Sciences JKUAT University Nairobi Kenya Department of Mathematics and Actuarial Sciences Kenyatta University Nairobi Kenya

Penalized spline has largely been applied in many research studies not limited to disease modeling and epidemiology. However, due to spatial heterogeneity of the data because different smoothing parameter leads to different amount of smoothing in different regions the penalized spline has not been exclusively appropriate to fit the data. The study assessed the properties of penalized spline hierarchical model;the hierarchy penalty improves the fit as well as the accuracy of inference. The simulation demonstrates the potential benefits of using the hierarchical penalty, which is obtained by modelling the global smoothing parameter as another spline. The results showed that mixed model with penalized hierarchical penalty had a better fit than the mixed model without hierarchy this was demonstrated by the rapid convergence of the model posterior parameters and the smallest DIC value of the model. Therefore hierarchical model with fifteen sub-knots provides a better fit of the data.

关键词： Penalized Splines Mixed Model Hierarchical Penalty

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Identification and Characterization of Hepatitis B Virus Immune Escape Mutants in Kenya

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American Journal of Molecular Biology 2023年第1期13卷 1-17页

作者： Rhoda Elizabeth King James Kimotho Rosaline Macharia Faith Njoki ndung’u Samson Muuo Nzou Robinson Mugasiali Irekwa Department of Molecular Biology and Biotechnology Institute for Basic Sciences Technology and Innovation Pan African University Nairobi Kenya Department of Innovation Technology and Transfer Kenya Medical Research Institute Nairobi Kenya Department of Biochemistry University of Nairobi Nairobi Kenya Department for Microbiology Research Kenya Medical Research Institute Nairobi Kenya

Hepatitis B Virus (HBV) infections affect about 400 million people globally and cause about 1.4 million deaths annually. The virus displays high levels of genetic variations/mutations, some of which are immune escape mutants. The prevalence of HBV infection in Kenya is high at about 8%. This study aimed at identifying and characterizing HBV immune escape mutants in Kenya. From 547 HBV sequences available in Kenya in NCBI, and HBVdb databases in July 2021, 120 full sequences were retrieved. The S gene sequences at position 1-225, which included the “a” determinant region of the gene were analyzed using various bioinformatics tools such as Bioedit software, and Emboss Cons. The clinical significance was flagged from the search of peer-reviewed journals. Forty-six HBV-positive blood donor samples were obtained from the Kenya National Blood Transfusion Services without personal identifiers, DNA extracted, and sequenced targeting positions 1 to 520 of S genes. Mutations were similarly identified from seventeen sequences after cleaning and analysis. Out of 120 sequences that were extracted from databases and analyzed, 79 different mutations were identified. Fifteen of them were of clinical importance with an occurrence frequency of at least 5% were obtained. The majority (64.6%, n = 51), with S207N and A194V being most dominant, could result in immune escape and reduced HBsAg detection signals while 24.1% (n = 19) could result in immune escape/reduced HBsAg detection signals and high probability of hepatocellular carcinoma. Most likely to occur on the amino acids Alanine, Lysine, Serine, Asparagine, and Valine in decreasing order. The most dominant genotype was found to be Genotype A (N = 10), while four sequences were Genotype D. In contrast to the in-silico studies, the sequences from HBV samples from blood donors did not demonstrate the presence of S207N and A194V mutations and all the genotypes were type A1. Only two (13.3%) samples showed the same mutations of sK122R

关键词： Hepatitis B Virus Mutations Hepatitis B Surface Antigen Gene Genotype

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Improved Detection of Sleeping Sickness Cases by LED Fluorescence Microscopy: Evidence from a Prospective Multi-Centric Study in the Democratic Republic of the Congo

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Microscopy Research 2015年第2期3卷 17-25页

作者： Patrick Mitashi Pascal Lutumba Crispin Lumbala Paul Bessell Sylvain Biéler Joseph Mathu ndung’u Tropical Medicine Department Faculty of Medicine University of Kinshasa Kinshasa Democratic Republic of the Congo Programme National de Lutte contre la Trypanosomiase Humaine Africaine (PNLTHA) Croisement de l’Avenue de la Libération et du Boulevard Triomphal 1 Kinshasa Democratic Republic of the Congo Foundation for Innovative New Diagnostics (FIND) Campus Biotech Chemin des Mines 9 Geneva Switzerland

Background: Confirmatory diagnosis of Trypanosoma brucei gambiense human African trypanosomiasis (HAT) is based on demonstration of parasites by microscopy. However, the sensitivity of routine microscopy methods is very low, and many cases are missed and left untreated. A clinical study was conducted in the Democratic Republic of the Congo to evaluate the accuracy of improved microscopy methods in diagnosis of HAT. These included examination by fluorescence microscopy (FM) of acridine orange (AO) stained smears of whole blood and smears made following a new procedure for concentrating trypanosomes by selective lysis of red blood cells (RBC). Methodology/Principal Findings: Venous blood was collected from 213 HAT cases, 101 HAT suspects and 95 controls and used to determine the accuracy of four microscopy methods: bright field microscopy of Giemsa-stained thick blood smears, FM of AO-stained thick blood smears, FM of AO-stained thick blood smears prepared after RBC lysis and concentration, and FM of AO-stained thin blood smears prepared after RBC lysis and concentration. The sensitivity of FM using thick blood smears stained with AO was 3 times higher than bright field microscopy using Giemsa-stained thick blood smears [19.7% (95% CI: 14.9% - 25.6%) versus 6.1% (95% CI: 3.6% - 10.2%)]. when the RBC lysis and concentration procedure was included, sensitivity of the test was further enhanced to 23.0% (95% CI: 17.9% - 29.1%) with thick blood smears and 34.3% (95% CI: 28.2% - 40.9%) with thin blood smears. Specificity of all four microscopy methods was 100% (95% CI: 96.1% - 100.0%). However, the miniature anion exchange chromatography technique (mAECT) and capillary tube centrifugation (CTC) method remained more sensitive. Conclusions: These new methods have practical advantages, including shorter staining time, ease of demonstration of parasites, and the possibility of archiving slides. They could, therefore, be alternative methods to improve case detection where concen

关键词： Human African Trypanosomiasis Trypanosome LED Fluorescence Microscopy Red Blood Cell Lysis Diagnosis

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Field Evaluation of LED Fluorescence Microscopy for Demonstration of <i>Trypanosoma brucei rhodesiense</i>in Patient Blood

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Microscopy Research 2019年第1期7卷 1-9页

作者： Enock Matovu Andrew Edielu James Ojom Ann Nanteza Charles Drago Kato Sylvain Biéler Joseph Mathu ndung’u College of Veterinary Medicine Animal Resources and Biosecurity Makerere University Kampala Uganda Lwala Hospital Soroti Uganda Foundation for Innovative New Diagnostics (FIND) Campus Biotech Chemin des Mines 9 Geneva Switzerland

Diagnosis of Trypanosoma brucei rhodesiense human African trypanosomiasis requires demonstration of parasites in body fluids by microscopy. The microscopy methods that are routinely used are difficult to deploy in resource-limited settings due to practical challenges, including lengthy and tedious procedures, and the need for specific equipment to centrifuge samples in glass capillary tubes. we report here on a study that was conducted in a rural region of eastern uganda to evaluate new methods that take advantage of a field-deployable LED fluorescence microscope. Examination of acridine orange-stained blood smears by LED fluorescence microscopy resulted in a diagnostic accuracy that was similar to that of routine methods, while the time needed to identify parasites was shortened significantly. These findings make these new microscopy methods attractive alternatives to procedures that are currently used for diagnosis of T. b. rhodesiense human African trypanosomiasis.

关键词： Human African Trypanosomiasis Rhodesiense LED Fluorescence Microscopy Red Blood Cell Lysis Diagnosis

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Effects of electron-and hole-current hysteresis on trap characterization in organo-inorganic halide perovskite

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Journal of Energy Chemistry 2023年第1期76卷 414-420,I0010页

作者： Fan wu sally Mabrouk Miaomiao Han Yanhua Tong Tiansheng Zhang Yuchen Zhang Raja Sekhar Bobba Quinn Qiao School of Science and Huzhou Key Lab of Materials for Energy Conversion and Storage Huzhou UniversityHuzhou 313000ZhejiangChina Mechanical and Aerospace Engineering Syracuse UniversitySyracuseNY13244United States

Charge trap density and carrier mobility of perovskite materials are the critical properties of perovskite solar *** space charge limited current(SCLC)method,which measures a dark current–voltage(I-V)curve of a single-carrier device has found extensive use for studying the trap density and charge carrier mobility in perovskite ***,it was found that the electron-and hole-current in organo-lead perovskite-based single-carrier device undergoes significant hysteresis under forward and reverse scanning due to the mobile *** addition,it was also observed that measuring history has a detrimental effect on hysteresis resulting in possible overestimation or underestimation of the extracted electrical values from the SCLC *** the forward/reverse scanning process,the mobile ionic defects enhance/shield the charge in the traps due to ionic charging/discharging,thereby increasing/reducing the interface barrier and net charge in the I-V scanning,which in turn affects the determination of transport properties of the *** results raise quite a few doubts over the direct application of classical SCLC measurements for the accurate characterization of intrinsic transport properties of the mixed ionicelectronic perovskite.

关键词： Organo-lead perovskite Ionic defects Space-charge-limited-current Trap density Mobility

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