Potato tissue resistance to the growth of Phytophthora infestans (Mont.) de Bary

This thesis describes an investigation of aspects of race nonspecific resistance which determines the rate at which tuber tissue is colonized by Phytophthora infestans. It was mainly concerned to deterimine whether active resistance mechanisms are involved or whether resistance could be explained by passive factors only. Five clones with different levels of race non-specific resistanc were used. Hyphal growth rates in all clones and in all tissues tested were similar and thus growth rate can play no part in the differences in race non-specific resistance between these clones. The growth rates in all experiments at all temperatures used were linear indicating that resistance does not involve active factors accumulating in the tissue ahead of the lesion to concentrations high enough to affect hyphal growth. Thus resistance to hyphal growth would appear to depend upon passive factors only. The growth rate on different media was always faster than that in tuber tissue indicating that hyphal growth in vivo may be affected by inhibitory factors, but if so, these factors are equally active in all clones. The total time required for the penetration and initiation of hyphal growth at the inoculated surface and for the establishment of visible sporulating mycelium on the opposite surface (Growth phases I and III) differed between clones and thus is a factor in the differences in race non-specific resistance 'between the clones. The rate of initiation and spread of lesions in the tubers differed between clones. These rates, in all clones, were slower than those calculated for the initiation of hyphal growth and for hyphal growth itself, indicating that the hyphae are growing ahead of the fluorescent tissue surrounding the nectoric tissue. The tuber tissues of the different clones were colonized to an equal extent and thus there was no evidence to indicate that active factors might accumulate to different levels in the tissues behind the hyphal front in the different clones and thus affect the extent to which lateral branches developed to further colonize the tissues. Hyphae were distributed non-randomly in the medullary tissue in the tubers and stems of Craigs Alliance and in the tubers of Pentland Dell and Pentland Squire, indicating that this tissue is not uniformly susceptible to colonization, but that there are pockets of tissue more resistant than others. Four types of haustoria were found in tuber and stem tissue but only two types were found in leaf tissue and there was no obvious relation between haustorial type and resistance. Haustoria were distributed non-randomly between cells indicating that cells may differ in their resistance to penetration. There were also differences between clones in total number of haustoria produced which appeared to be correlated with resistance to growth phases I and III and to resistance to lesion growth. Thus factors affecting haustorial formation may be important in the differences in race non-specific resistance between the clones

Fabrication of ZnO/nanobentonite as a new efficient adsorbent for rapid elimination of xylenol orange dye

A novel ZnO-nanobentonite (ZnO/NB) nanocomposite was successfully prepared using hexadecyltrimethylammonium bromide (HDTMA) as a surfactant and used as an efficient adsorbent to remove the xylenol orange (XO) from aqueous solutions. The fabricated nanocomposite was fully characterized by FTIR, FESEM, XRD, EDX, and BET measurements. The ZnO33%/NB sample with a high SBET and low total pore volume compared with the nanobentonite clay, based on BET results, indicated an increase in SBET due to the incorporation of ZnO nanoparticles into the layer of nanobentonite. For achieving the optimum condition, the effect of ZnO33%/NB sorbent dosage, initial pH, reaction time, and primary dye concentration, on XO dye elimination was investigated. The result show that the 97% elimination of XO dye occurred at optimum condition (40 mgl/l of dye concentration, pH 2, 15 mg of ZnO33%/NB adsorbent at 30 minutes), and the adsorption capacity and residual XO after treatment at this conditions is 48.5 and 1.2 ppm, respectively. Langmuir models and Freundlich model were used to studying the adsorption isotherms of the elimination process and results authenticated that XO dye adsorption followed the Langmuir model. Also, the recycling experiments showed that ZnO33%/NB adsorbent had more stability and recoverability. High adsorption capacity, simple fabrication method, short reaction time, and supreme reusability of ZnO33%/NB nanocomposite make it an effective sorbent for the elimination of XO dye from wastewaters

Iris recognition method based on segmentation

The development of science and studies has led to the creation of many modern means and technologies that focused and directed their interests on enhancing security due to the increased need for high degrees of security and protection for individuals and societies. Hence identification using a person's vital characteristics is an important privacy topic for governments, businesses and individuals. A lot of biometric features such as fingerprint, facial measurements, acid, palm, gait, fingernails and iris have been studied and used among all the biometrics, in particular, the iris gets the attention because it has unique advantages as the iris pattern is unique and does not change over time, providing the required accuracy and stability in verification systems. This feature is impossible to modify without risk. When identifying with the iris of the eye, the discrimination system only needs to compare the data of the characteristics of the iris of the person to be tested to determine the individual's identity, so the iris is extracted only from the images taken. Determining correct iris segmentation methods is the most important stage in the verification system, including determining the limbic boundaries of the iris and pupil, whether there is an effect of eyelids and shadows, and not exaggerating centralization that reduces the effectiveness of the iris recognition system. There are many techniques for subtracting the iris from the captured image. This paper presents the architecture of biometric systems that use iris to distinguish people and a recent survey of iris segmentation methods used in recent research, discusses methods and algorithms used for this purpose, presents datasets and the accuracy of each method, and compares the performance of each method used in previous studie

Development of Bioinformatics Infrastructure for Genomics Research:

Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community

Development of Bioinformatics Infrastructure for Genomics Research in H3Africa

Background: Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet’s role has evolved in response to changing needs from the consortium and the African bioinformatics community. Objectives: H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Methods and Results: Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training. Conclusions: For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Effects of antibiotic resistance, drug target attainment, bacterial pathogenicity and virulence, and antibiotic access and affordability on outcomes in neonatal sepsis: an international microbiology and drug evaluation prospective substudy (BARNARDS)

Background Sepsis is a major contributor to neonatal mortality, particularly in low-income and middle-income countries (LMICs). WHO advocates ampicillin–gentamicin as first-line therapy for the management of neonatal sepsis. In the BARNARDS observational cohort study of neonatal sepsis and antimicrobial resistance in LMICs, common sepsis pathogens were characterised via whole genome sequencing (WGS) and antimicrobial resistance profiles. In this substudy of BARNARDS, we aimed to assess the use and efficacy of empirical antibiotic therapies commonly used in LMICs for neonatal sepsis. Methods In BARNARDS, consenting mother–neonates aged 0–60 days dyads were enrolled on delivery or neonatal presentation with suspected sepsis at 12 BARNARDS clinical sites in Bangladesh, Ethiopia, India, Pakistan, Nigeria, Rwanda, and South Africa. Stillborn babies were excluded from the study. Blood samples were collected from neonates presenting with clinical signs of sepsis, and WGS and minimum inhibitory concentrations for antibiotic treatment were determined for bacterial isolates from culture-confirmed sepsis. Neonatal outcome data were collected following enrolment until 60 days of life. Antibiotic usage and neonatal outcome data were assessed. Survival analyses were adjusted to take into account potential clinical confounding variables related to the birth and pathogen. Additionally, resistance profiles, pharmacokinetic–pharmacodynamic probability of target attainment, and frequency of resistance (ie, resistance defined by in-vitro growth of isolates when challenged by antibiotics) were assessed. Questionnaires on health structures and antibiotic costs evaluated accessibility and affordability. Findings Between Nov 12, 2015, and Feb 1, 2018, 36 285 neonates were enrolled into the main BARNARDS study, of whom 9874 had clinically diagnosed sepsis and 5749 had available antibiotic data. The four most commonly prescribed antibiotic combinations given to 4451 neonates (77·42%) of 5749 were ampicillin–gentamicin, ceftazidime–amikacin, piperacillin–tazobactam–amikacin, and amoxicillin clavulanate–amikacin. This dataset assessed 476 prescriptions for 442 neonates treated with one of these antibiotic combinations with WGS data (all BARNARDS countries were represented in this subset except India). Multiple pathogens were isolated, totalling 457 isolates. Reported mortality was lower for neonates treated with ceftazidime–amikacin than for neonates treated with ampicillin–gentamicin (hazard ratio [adjusted for clinical variables considered potential confounders to outcomes] 0·32, 95% CI 0·14–0·72; p=0·0060). Of 390 Gram-negative isolates, 379 (97·2%) were resistant to ampicillin and 274 (70·3%) were resistant to gentamicin. Susceptibility of Gram-negative isolates to at least one antibiotic in a treatment combination was noted in 111 (28·5%) to ampicillin–gentamicin; 286 (73·3%) to amoxicillin clavulanate–amikacin; 301 (77·2%) to ceftazidime–amikacin; and 312 (80·0%) to piperacillin–tazobactam–amikacin. A probability of target attainment of 80% or more was noted in 26 neonates (33·7% [SD 0·59]) of 78 with ampicillin–gentamicin; 15 (68·0% [3·84]) of 27 with amoxicillin clavulanate–amikacin; 93 (92·7% [0·24]) of 109 with ceftazidime–amikacin; and 70 (85·3% [0·47]) of 76 with piperacillin–tazobactam–amikacin. However, antibiotic and country effects could not be distinguished. Frequency of resistance was recorded most frequently with fosfomycin (in 78 isolates [68·4%] of 114), followed by colistin (55 isolates [57·3%] of 96), and gentamicin (62 isolates [53·0%] of 117). Sites in six of the seven countries (excluding South Africa) stated that the cost of antibiotics would influence treatment of neonatal sepsis