Distribution of immunodeficiency fact files with XML – from Web to WAP

BACKGROUND: Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. METHODS: Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. RESULTS: IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at . A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. CONCLUSION: The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at

IDR knowledge base for primary immunodeficiencies

Background The ImmunoDeficiency Resource (IDR) is a knowledge base for the integration of the clinical, biochemical, genetic, genomic, proteomic, structural, and computational data of primary immunodeficiencies. The need for the IDR arises from the lack of structured and systematic information about primary immunodeficiencies on the Internet, and from the lack of a common platform which enables doctors, researchers, students, nurses and patients to find out validated information about these diseases. Description The IDR knowledge base, first released in 1999, has grown substantially. It contains information for 158 diseases, both from a clinical as well as molecular point of view. The database and the user interface have been reformatted. This new IDR release has a richer and more complete breadth, depth and scope. The service provides the most complete and up-to-date dataset. The IDR has been integrated with several internal and external databases and services. The contents of the IDR are validated and selected for different types of users (doctors, nurses, researchers and students, as well as patients and their families). The search engine has been improved and allows either a detailed or a broad search from a simple user interface. Conclusion The IDR is the first knowledge base specifically designed to capture in a systematic and validated way both clinical and molecular information for primary immunodeficiencies. The service is freely available at http://bioinf.uta.fi/idr and is regularly updated. The IDR facilitates primary immunodeficiencies informatics and helps to parameterise in silico modelling of these diseases. The IDR is useful also as an advanced education tool for medical students, and physicians.BioMed Central Open acces

Primary Immunodeficiency Information Knowledge Services

Tutkijat pystyvät tuottamaan uusilla menetelmillä suuria tietomääriä (esim. teksti- ja multimedialähteistä), mikä on haaste tutkijayhteisölle. Bioinformatiikan avulla voidaan madaltaa kynnystä tiedon hyödyntämiseen kehittämällä algoritmeja, työkaluja ja menetelmiä lisääntyvien tietomäärien käsittelyyn. Tämä tutkimushankkeen tärkeimpänä antina tuodaan käytettäväksi uusia ja parannettuja biolääketieteellisen informatiikan menetelmiä primaarien immuunipuutosten (PID) alalla. Potilailla, joilla on näitä tauteja, esiintyy tavallista useammin infektioita, mutta myös autoimmuunioireita ja kasvaimia. Monet näistä taudeista ovat erittäin harvinaisia ja kuolemaan johtavia, ja usein ne diagnosoidaan väärin tai myöhässä. Ohjelmistojen kehitys primaaristen immuunipuutosten alalla on erittäin haastava tehtävä. Tässä tutkimuksessa kehitettiin kaksi tietokantaa ja uusi PID:ien luokittelu. Tässä kuvattavissa tutkimuksissa käytetään poikkitieteellistä lähestymistapaa, joka perustuu tietokanta- ja tiedonlouhintamenetelmiin, tekoälyyn, koneoppimiseen ja tietoihin, joita on yhdistetty eri aloilta, kuten molekyylibiologiasta, perinnöllisyystieteestä, immunologiasta ja bioinformatiikasta. PID:ien laajaa alaa tutkittiin proteiinien, perinnöllisyyden ja kliinisen tilan tasolla sekä perustuen eri PID:ien analyyseihin. Kehitimme kaksi tietokantaa, ImmunoDeficiency Resources (IDR) ja IDdiagnostics. IDR on kattava PID:ien tietämyskanta, johon kuuluu työkaluja kliinisiä, biokemiallisia ja laskennallisia analyysejä varten, perinnöllisyyden ja proteiinirakenteiden analyysejä varten, sekä myös linkkejä muiden ylläpitämiin aiheeseen liittyviin tietoihin. IDdiagnostics on luettelo laboratorioista, jotka tekevät PID:ien perinnöllisyystestejä ja kliinisiä testejä. PID:ien bioinformatiikkatutkimuksen käsitekartta suunniteltiin monentyyppisille käyttäjille. Mallia voidaan käyttää erityyppisille perinnöllisille taudeille. Useasta PID:ien luokittelu- ja ryvästysmenetelmästä on kehitetty uusi luokittelu yhteentoista ryhmään, joka tuo esille aiemmin tuntemattomia PID:ien piirteitä ja samankaltaisuuksia. Nämä menetelmät tähtäävät PID:ien luokittelun automatisointiin, mikä olisi erittäin hyödyllistä PID:ien tutkimukselle ja kliiniselle yhteisölle. Luokittelun vertailu toisistaan riippumattomiin piirteisiin, kuten tautien vakavuuteen ja hoitoon, proteiinien toiminnalliseen luokitteluun ja vuorovaikutusverkostojen haavoittuvuteen viittaa vahvaan tilastolliseen tukeen. Menetelmää voidaan soveltaa mihin tahansa tautiryhmään.New technologies allow researchers to produce large amounts of data (e.g. from textual and multimedia sources), which represents a challenge for the scientific community. Bioinformatics fills the gaps by creating algorithms, tools and methods to process the increasing quantity of information. The main contribution of this research project was to introduce new and improved biomedical informatics methods in the field of primary immunodeficiency diseases (PIDs). Patients with these diseases have an increased rate of infections but also autoimmune and malignant manifestations. Many of these diseases are very rare with a fatal end and often they are misdiagnosed or have a delayed diagnosis. Developing software systems within the domain of primary immunodeficiencies is a highly challenging task. In this study two databases were created and a new classification for PIDs was developed. The studies described here use an interdisciplinary approach, based on database and datamining technologies, artificial intelligence, machine learning and combined data from different disciplines such as molecular biology, genetics, immunology, bioinformatics. The wide ranging domain of PIDs was investigated at the protein, genetic, and clinical level and, based on the analyses of different PIDs. Two databases, ImmunoDeficiency Resources (IDR) and IDdiagnostics were developed. IDR is a comprehensive knowledge base for PIDs, which includes tools for clinical, biochemical, genetic, structural and computational analyses as well as links to related information maintained by others. IDdiagnostics is a directory of laboratories performing genetic and clinical tests for PIDs. A concept map for the bioinformatics study of PIDs was designed for different types of users. The model can be used for different types of hereditary diseases. Several computational methods for the classification and clustering of PIDs have been developed a novel classification of 11 groups, which revealed previously unknown features and relationships of PIDs. These methods aim at automating the classification of PIDs and therefore would be very useful for the PID research and clinical community. Comparison of the classification to independent features such as severity and therapy of the diseases, functional classification of proteins, and network vulnerability, indicated a strong statistical support. The method can be applied to any group of diseases

Development of a cellphone based monitoring and management-support system for anti-retroviral therapy

Includes bibliographical references (leaves 129-135).HIV/Aids has had a major impact on global society since its discovery in 1981.Over the last two decades, HIV treatment research has resulted in the developmentof antiretroviral (ARV) drug therapy and treatment. However, there are many challenges to ARV Therapy (ART) and these challenges are further extended in the resource limited developing world, where the majority of infections occur. Therefore, ART is regarded as not only a medical challenge, but a logistical, monitoring and management challenge that requires the development and implementation of supporting systems. The Cell-Life system is a prototype engineering concept that uses locally available ICTs (Information and Communication Technologies), such as GSM (Global System for Mobile) and Internet connectivity to provide monitoring and management support for ART. This dissertation is an investigation and development of the system in order to create an effective solution for public health sector clinics.The investigation process is based upon a user-centred HCI (Human Computer Interface) model and it is carried out on five components of the system: cellphonemenu applications, SMS data submission and database integration, web applications, servers and user guide and training. This research has resulted in a progressive advancement and transformation of the prototype concept through the development, testing and pilot site implementation of an updated suite of components with valuable findings from usability testing. This study confirms that locally available ICTs can be developed to empower the resource limited clinic level public health sector to overcome some of the challenges of ART. This essentially contributes to bridging the “digital divide” and providing support in the developing context

The design of an intervention programme to address the prevalence of obesity and physical fitness of adolescents attending high school

Background: South Africa has the highest prevalence rate (8.3%) of childhood obesity in sub-Saharan Africa. Obesity is a complex condition to control as it has environmental, as well as genetic factors that influence its prevalence. Childhood obesity, a rising problem worldwide and within South Africa, has been negatively linked with both physical fitness and physical activity. PA and school-based nutrition intervention programmes have been shown to have positive effects on diet and PA behaviours in children. However, there is minimal literature reporting on the effectiveness of school-based interventions in a South African setting. The aim of this study was to determine the prevalence of obesity, levels of physical fitness and physical activity in adolescents attending school in an urban setting. Together with the literature, an intervention programme was designed addressing key outcome measures identified from the sample. Methodology: The study was conducted in two phases. Ten schools were randomly selected from the school education district in KwaZulu-Natal Department of Education (KZNDoE) for phase one. A total of 400 eligible students were identified by the respective school teachers and parental consent was obtained, with assent obtained from the participants. A sample of 278 (girls n = 150, boys n = 128) participants with a mean age of 15yrs 1 month (CI 95% 12,1 – 17.1 and SD 1.14), was measured for height, weight, hip circumference, waist circumference and physical fitness (standing broad jump, sit-ups in 30s, hand grip strength, sit-and-reach and 20m shuttle run). BMI and WHR were calculated using anthropometric measurements. Physical activity (PA) was self-reported using the Physical Activity Questionnaire for Adolescents (PAQ-A) and the International Study of Childhood Obesity, Lifestyle and the Environment (ISCOLE) demographic form were completed by the participants' guardians/parents. Phase two involved the design of a PA intervention programme using evidence-based outcome measures from previous studies and problem areas identified in this study. Results: The mean BMI z-score was 0.30 (CI 95% 0.12 to 0.49) with boys displaying a mean of 0.19 (CI 95% -0.89 to 0.46) and girls 0.39 (CI 95% 0.15 to 0.65). There was a 16.2% prevalence of overweight (1 < BMI-z score ≤ 2), 13.3% prevalence of obesity (2 < BMI-z score ≤ 3) and 2.9% prevalence of morbid obesity (3 < BMI-z score ≤ 4). Mean WHR for the sample was 0.82 (CI 95% 0.81 – 0.83). Low levels of PA were reported by 45% (girls n = 83, boys n = 42) of the sample and 53.6% (girls n = 66, boys n = 83) reported moderate levels of PA. Girls in the sample had a higher mean sit-and-reach (t = 4.68, p < 0.05) and hand grip strength (t = 5.49, p < 0.05) than the normative values. Boys in the sample had higher mean (t = 13.2, p < 0.05) sit-and-reach than normative values. Multiple regression models were applied and BMI was found to be an inverse predictor for sit-ups ß = -0.07 (p < 0.05, CI 95% -1.0 to -0.03) and broad jump ß = -0.01 (p < 0.05, CI 95% -0.01 to -0.005). BMI was also a direct predictor for hand grip strength ß = -0.07 (p < 0.05, CI 95% 0.05 to 0.09). Discussion: The 16.2% prevalence of obesity was higher than the reported 8.5% in another South African study on adolescent scholars and the national reported level of 5.5%. The waist-hip ratio (WHR) was lower than the national reference level of 0.84 and higher compared to values obtained from adolescents in Europe (comparisons were made to age and gender specific normative values obtained in Europe, as there are no national reference physical fitness values for adolescents). Girls displayed lower values in three of the five physical tests (standing broad jump, sit-ups and 20m shuttle run), while boys displayed lower values for four (standing broad jump, hand grip strength, sit-ups and 20m shuttle run) of the five physical fitness tests. PA is indirectly correlated with BMI, and with BMI being a predictor for physical fitness, the promotion of PA amongst adolescents is imperative and urgent to curb the growing prevalence of obesity. Using evidence from previous research an intervention programme was designed to address the problems areas identified. These were high prevalence of obesity and overweight, low PA levels, poor cardiovascular function , low muscular power and poor muscular endurance across the sample. Boys also exhibited low levels of muscular strength than the normal population mean. PA programmes must be 60 minutes of duration implemented at least three times per week over 12 weeks minimum in order to have a reduction in BMI. Programmes should incorporate aerobic and anaerobic training as concurrent training has shown best results for decreasing BMI. The aerobic component of the programme must include a high intensity interval training (HIIT) as this has positive benefits on cardiovascular markers. The anaerobic component must include free weights as this showed better improvements than using resisted exercise devices in body composition, increases in upper and lower limb muscle strength in boys and improved lower limb muscle power especially in girls. Programmes should be implemented in schools with trained instructors and incorporate the family as a combination of these showed favourable compliance and overall better outcome measures. PA programmes that have a circuit formation and that incorporate a fun element has also shown to have better outcome measures and compliance. Conclusion: Physical activity levels are on the decline and obesity prevalence is on a rapid upward trajectory amongst South African adolescents. These trends could be ominous for the next workforce generation as these have been linked to numerous non-communicable diseases where the already constrained health system is placed under added pressure. PA programmes should be incorporated into schools' curricula as this may be a viable way to implement successful interventions to address obesity, physical fitness and physical activity

Designing an architecture for secure sharing of personal health records : a case of developing countries

Includes bibliographical references.While there has been an increase in the design and development of Personal Health Record (PHR) systems in the developed world, little has been done to explore the utility of these systems in the developing world. Despite the usual problems of poor infrastructure, PHR systems designed for the developing world need to conform to users with different models of security and literacy than those designed for developed world. This study investigated a PHR system distributed across mobile devices with a security model and an interface that supports the usage and concerns of low literacy users in developing countries. The main question addressed in this study is: “Can personal health records be stored securely and usefully on mobile phones?” In this study, mobile phones were integrated into the PHR architecture that we/I designed because the literature reveals that the majority of the population in developing countries possess mobile phones. Additionally, mobile phones are very flexible and cost efficient devices that offer adequate storage and computing capabilities to users for typically communication operations. However, it is also worth noting that, mobile phones generally do not provide sufficient security mechanisms to protect the user data from unauthorized access

Clinical foundations and information architecture for the implementation of a federated health record service

Clinical care increasingly requires healthcare professionals to access patient record information that may be distributed across multiple sites, held in a variety of paper and electronic formats, and represented as mixtures of narrative, structured, coded and multi-media entries. A longitudinal person-centred electronic health record (EHR) is a much-anticipated solution to this problem, but its realisation is proving to be a long and complex journey. This Thesis explores the history and evolution of clinical information systems, and establishes a set of clinical and ethico-legal requirements for a generic EHR server. A federation approach (FHR) to harmonising distributed heterogeneous electronic clinical databases is advocated as the basis for meeting these requirements. A set of information models and middleware services, needed to implement a Federated Health Record server, are then described, thereby supporting access by clinical applications to a distributed set of feeder systems holding patient record information. The overall information architecture thus defined provides a generic means of combining such feeder system data to create a virtual electronic health record. Active collaboration in a wide range of clinical contexts, across the whole of Europe, has been central to the evolution of the approach taken. A federated health record server based on this architecture has been implemented by the author and colleagues and deployed in a live clinical environment in the Department of Cardiovascular Medicine at the Whittington Hospital in North London. This implementation experience has fed back into the conceptual development of the approach and has provided "proof-of-concept" verification of its completeness and practical utility. This research has benefited from collaboration with a wide range of healthcare sites, informatics organisations and industry across Europe though several EU Health Telematics projects: GEHR, Synapses, EHCR-SupA, SynEx, Medicate and 6WINIT. The information models published here have been placed in the public domain and have substantially contributed to two generations of CEN health informatics standards, including CEN TC/251 ENV 13606

Telemedicine

Telemedicine is a rapidly evolving field as new technologies are implemented for example for the development of wireless sensors, quality data transmission. Using the Internet applications such as counseling, clinical consultation support and home care monitoring and management are more and more realized, which improves access to high level medical care in underserved areas. The 23 chapters of this book present manifold examples of telemedicine treating both theoretical and practical foundations and application scenarios

Developing and evaluating comprehensive multiplex peptide array for serological diagnostic and surveillance of infectious disease in Zimbabwe.

Doctoral Degree. University of KwaZulu-Natal, Durban.Introduction: Peptides that mimic B-cell linear epitopes may be used as biomarkers for the diagnosis and surveillance of diseases. Peptide microarray technology provide rapid and high-throughput immunoassay platforms, for the simultaneous of identification of B-cell linear epitopes. In this framework, a peptide microarray was designed for the integrated surveillance of infectious diseases endemic in Zimbabwe. The peptide microarray was evaluated against peptides derived from Ascaris lumbricoides, Necator americanus, Shistosoma haematobium, Schistosoma mansoni, Trichuris trichiura, Bacillus anthracis, Mycobacterium leprae, Wuchereria bancrofti, Rabies lyssavirus, Chlamydia trachomatis, Trypanosoma brucei and severe acute respiratory syndrome coronavirus (SARS-CoV-2). Methods: Published peptides were retrieved from the Tackling Infection to Benefit Africa infectious diseases epitope microarray. Novel peptides were predicted using ABCpred. The peptide microarrays were printed in a laser based approach. IgG and IgM reactivity against the derived peptides were evaluated using peptide microarray immunoassays. Positive response was defined as fluorescence intensity ≥ 500 relative fluorescence units. Immunodominant peptides were identified using heat maps and bar graphs reflecting the obtained fluorescence signal intensities. Receiver Operating Characteristic (ROC) analysis and Mann-Whitney-U test were performed to determine the diagnostic validity of the peptides. Results: Species-specific responses with at least one peptide derived from each NTD pathogen were observed. The reactive peptides included; for S. haematobium, XP_035588858.1-206-220 and XP_035588858.1-206-220 immunodominant for IgG and IgM respectively, for S.mansoni, P20287.1-58-72 immunodominant for both antibodies and for T. trichuria, CDW52482.1-326-340 immunodominant for IgG and CDW57769.1-2017-2031 and CDW57769.1-1518-1532 immunodominant for IgM. For SARS-CoV-2 derived peptides, 4 (QTH34388.1- 1-14, QRU89900.1-41-54, QTN64908.1-136-149 and QLL35955.1-22-35) showed reactivity against IgG. Four peptides (QRU89900.1-41-54, QSM17284.1-76-89, QTN64908.1-136-149 and QPK73947.1-8-21) also showed reactivity against IgM. The SARS-CoV-2 reactive peptide were derived from the membrane glycoprotein and nucleocapsid protein. Conclusion: Species-specific sero-reactivity was indicative of exposure to the different NTDs parasites antigens. Multiplex peptide microarrays are a valuable tool for integrated NTDs surveillance and for screening parasites exposure in endemic areas. In silico peptide prediction and peptide microarray technology may provide a powerful platform for the discovery of SARS-CoV-2 B-cell epitopes. Nhanganyaya: Peptides akafanana nema B-cell linear epitopes akakosha nekuti anogona kushandiswa kuongorora kuti munhu anechirwere here nekurakidza kutenderera kwezvirwere munharaunda . Peptide microarray inotibatsira kutsvaka ma B-cell linear epitopes nekukasika panguva imwe. Nekuda kweizvozvo, peptide microarray yakagadzirirwa kuti tiongorore zvirwere zvinotapukira munyika yeZimbabwe. Iyo peptide microarray yakaongororwa mashoja emuviri anorwisa zvirwere zvinosanganisira chirwere cheelephantiasis, bhiraziya, chirwere chemakonye emudumbu (intestinal worms), chirwere chemaziso chetrachoma, chirwere chemapere mbudzi, chirwere cherabis chirwere che COVID-19 nechirwere cheanthrax. Maitiro: Mamwe mapeptides akawanikwa kubva ku Tackling Infection to Benefit Africa infectious diseases epitope microarray. Mapeptides matsva akawandikwa pachishandiswa chirongwa cheABCpred. Ma peptide microarray akagadzirwa ku Germany nemhando ye laser printer tekinoroji. Masoja emumiviri anoti IgG ne IgM ezvirwere zvambotaurwa akarongororwa tichishandisa peptide microarray tekinoroji. Zvakabuda muwongororo: Takaona kuti vanhu vemuZimbabwe vane masoja emuviri anokwanisa kurwisa mapeptides anowanikwa pahosha dzinokonzeresa zvirwere zvinosanganisira chirwere cheelephantiasis, bhiraziya, chirwere chemakonye emudumbu (intestinal worms), chirwere chemaziso chetrachoma, chirwere chemapere mbudzi, chirwere cherabis chirwere che COVID-19 nechirwere cheanthrax. Takaona zvakare kuti peptide microarray tekinoroji inokwanisa kushandiswa kuongorora zvirwere zvakawanda panguva imwe

A resource-based view of the firm : integrating the role of IT as a strategic resource - an empirical study of South African personal financial services (Assurance) firms, 1999-2003

Includes bibliographical references (p. 502-531).This research explores an "inside the black box" view on how IT enables sustainable competitive advantage. Most researchers have investigated IT competitive competencies that make up a firm's strategic framework to understand competitive advantage. However, Resource-Based Theory (RBT) probes into the inner workings of a firm, suggesting that a firm's IT assets and resources are the basis of a firm's "rare" core competencies to compete successfully. Using RBT and research in the economics, strategy, and IT literatures, an initial "Framework of Sustainability" was created, against which the case studies were conducted. This framework was used as foundation to develop semi-structured questionnaires in which 45, 90 minute (on average) interviews were conducted with managers in the four firms. Both internal and external documents about the firms and the industry were used as sources of corroborating evidence. In addition, a "bottoms up" view was obtained with evidence gathered from a short questionnaire and focus groups discussions held with 178 staff employees in the four firms