Models and tools for value systems analysis in collaborative environments

Dissertation to obtain the degree of Doctor in Electrical and Computer Engineering, specialization of Collaborative Networks

Determination of microalgae cellular composition after phycoremediation of swine wastewaters.

Phycoremediation of swine wastewaters has been widely reported as an attractive tertiary treatment system, that effectively removes the excessive nutrient loadswhilst offering a valuable source of feedstock biomass. Digestate from an upflow anaerobic sludge blanket (UASB, 6%v/v) and a nitrification reactor (NR; 50% v/v) were used as culturing media to microalgae. Experiments were carried out in lab scale photobioreactors (PBRs) using a consortia of Chlorella and Scenedesmus. Ammonia (44 to 90%) and phosphorus (77%) were efficiently removed from both effluents tested after 4 days. Microalgae biomass harvested from the UASB effluent showed 57, 34 and 1% of proteins, carbohydrates and lipids, respectively. Comparatively, the cellular composition of microalgae grown on NR effluent had lower protein (43%) but higher carbohydrate (42%) contents. Negligible difference in lipid fraction was observed independently of the effluents tested. The results suggest that the biomass harvested from phycoremediation of swine wastewaters can offer a valuable protein and carbohydrate feedstock for nutritional and biotechnological applications.

Quality control and conduct of genome-wide association meta-analyses.

Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete.

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.

Circulating levels of adiponectin, a hormone produced predominantly by adipocytes, are highly heritable and are inversely associated with type 2 diabetes mellitus (T2D) and other metabolic traits. We conducted a meta-analysis of genome-wide association studies in 39,883 individuals of European ancestry to identify genes associated with metabolic disease. We identified 8 novel loci associated with adiponectin levels and confirmed 2 previously reported loci (P = 4.5×10(-8)-1.2×10(-43)). Using a novel method to combine data across ethnicities (N = 4,232 African Americans, N = 1,776 Asians, and N = 29,347 Europeans), we identified two additional novel loci. Expression analyses of 436 human adipocyte samples revealed that mRNA levels of 18 genes at candidate regions were associated with adiponectin concentrations after accounting for multiple testing (p<3×10(-4)). We next developed a multi-SNP genotypic risk score to test the association of adiponectin decreasing risk alleles on metabolic traits and diseases using consortia-level meta-analytic data. This risk score was associated with increased risk of T2D (p = 4.3×10(-3), n = 22,044), increased triglycerides (p = 2.6×10(-14), n = 93,440), increased waist-to-hip ratio (p = 1.8×10(-5), n = 77,167), increased glucose two hours post oral glucose tolerance testing (p = 4.4×10(-3), n = 15,234), increased fasting insulin (p = 0.015, n = 48,238), but with lower in HDL-cholesterol concentrations (p = 4.5×10(-13), n = 96,748) and decreased BMI (p = 1.4×10(-4), n = 121,335). These findings identify novel genetic determinants of adiponectin levels, which, taken together, influence risk of T2D and markers of insulin resistance.

Genome-wide profiling of blood pressure in adults and children.

Hypertension is an important determinant of cardiovascular morbidity and mortality and has a substantial heritability, which is likely of polygenic origin. The aim of this study was to assess to what extent multiple common genetic variants contribute to blood pressure regulation in both adults and children and to assess overlap in variants between different age groups, using genome-wide profiling. Single nucleotide polymorphism sets were defined based on a meta-analysis of genome-wide association studies on systolic blood pressure and diastolic blood pressure performed by the Cohort for Heart and Aging Research in Genome Epidemiology (n=29 136), using different P value thresholds for selecting single nucleotide polymorphisms. Subsequently, genetic risk scores for systolic blood pressure and diastolic blood pressure were calculated in an independent adult population (n=2072) and a child population (n=1034). The explained variance of the genetic risk scores was evaluated using linear regression models, including sex, age, and body mass index. Genetic risk scores, including also many nongenome-wide significant single nucleotide polymorphisms, explained more of the variance than scores based only on very significant single nucleotide polymorphisms in adults and children. Genetic risk scores significantly explained ≤1.2% (P=9.6*10(-8)) of the variance in adult systolic blood pressure and 0.8% (P=0.004) in children. For diastolic blood pressure, the variance explained was similar in adults and children (1.7% [P=8.9*10(-10)] and 1.4% [P=3.3*10(-5)], respectively). These findings suggest the presence of many genetic loci with small effects on blood pressure regulation both in adults and children, indicating also a (partly) common polygenic regulation of blood pressure throughout different periods of life.

Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.

Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genome-wide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 × 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of ∼110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.

Access 2005 Edmonton

Court rapport de la conférence Access 2005 tenue à Edmonton, Canada. Résumé des idées et tendances principales exposées.

A portal for the Canadian Virtual Health Library / Bibliothèque virtuelle canadienne de la santé (CVHL/BVCS): Accomplishments and possibilities, scope and structure - a review of best practices

Introduction: Coordination through CVHL/BVCS gives Canadian health libraries access to information technology they could not offer individually, thereby enhancing the library services offered to Canadian health professionals. An example is the portal being developed. Portal best practices are of increasing interest (usability.gov; Wikipedia portals; JISC subject portal project; Stanford clinical portals) but conclusive research is not yet available. This paper will identify best practices for a portal bringing together knowledge for Canadian health professionals supported through a network of libraries. Description: The portal for Canadian health professionals will include capabilities such as: • Authentication • Question referral • Specialist “branch libraries” • Integration of commercial resources, web resources and health systems data • Cross-resource search engine • Infrastructure to enable links from EHR and decision support systems • Knowledge translation tools, such as highlighting of best evidence Best practices will be determined by studying the capabilities of existing portals, including consortia/networks and individual institutions, and through a literature review. Outcomes: Best practices in portals will be reviewed. The collaboratively developed Virtual Library, currently the heart of cvhl.ca, is a unique database collecting high quality, free web documents and sites relevant to Canadian health care. The evident strengths of the Virtual Library will be discussed in light of best practices. Discussion: Identification of best practices will support cost-benefit analysis of options and provide direction for CVHL/BVCS. Open discussion with stakeholders (libraries and professionals) informed by this review will lead to adoption of the best technical solutions supporting Canadian health libraries and their users.

Re-engineering and Re-defining University Libraries in the context of modern Information and Communication Technologies: a study with special reference to the University Libraries in Kerala

Information and communication technologies are the tools that underpin the emerging “Knowledge Society”. Exchange of information or knowledge between people and through networks of people has always taken place. But the ICT has radically changed the magnitude of this exchange, and thus factors such as timeliness of information and information dissemination patterns have become more important than ever.Since information and knowledge are so vital for the all round human development, libraries and institutions that manage these resources are indeed invaluable. So, the Library and Information Centres have a key role in the acquisition, processing, preservation and dissemination of information and knowledge. ln the modern context, library is providing service based on different types of documents such as manuscripts, printed, digital, etc. At the same time, acquisition, access, process, service etc. of these resources have become complicated now than ever before. The lCT made instrumental to extend libraries beyond the physical walls of a building and providing assistance in navigating and analyzing tremendous amounts of knowledge with a variety of digital tools. Thus, modern libraries are increasingly being re-defined as places to get unrestricted access to information in many formats and from many sources.The research was conducted in the university libraries in Kerala State, India. lt was identified that even though the information resources are flooding world over and several technologies have emerged to manage the situation for providing effective services to its clientele, most of the university libraries in Kerala were unable to exploit these technologies at maximum level. Though the libraries have automated many of their functions, wide gap prevails between the possible services and provided services. There are many good examples world over in the application of lCTs in libraries for the maximization of services and many such libraries have adopted the principles of reengineering and re-defining as a management strategy. Hence this study was targeted to look into how effectively adopted the modern lCTs in our libraries for maximizing the efficiency of operations and services and whether the principles of re-engineering and- redefining can be applied towards this.Data‘ was collected from library users, viz; student as well as faculty users; library ,professionals and university librarians, using structured questionnaires. This has been .supplemented by-observation of working of the libraries, discussions and interviews with the different types of users and staff, review of literature, etc. Personal observation of the organization set up, management practices, functions, facilities, resources, utilization of information resources and facilities by the users, etc. of the university libraries in Kerala have been made. Statistical techniques like percentage, mean, weighted mean, standard deviation, correlation, trend analysis, etc. have been used to analyse data.All the libraries could exploit only a very few possibilities of modern lCTs and hence they could not achieve effective Universal Bibliographic Control and desired efficiency and effectiveness in services. Because of this, the users as well as professionals are dissatisfied. Functional effectiveness in acquisition, access and process of information resources in various formats, development and maintenance of OPAC and WebOPAC, digital document delivery to remote users, Web based clearing of library counter services and resources, development of full-text databases, digital libraries and institutional repositories, consortia based operations for e-journals and databases, user education and information literacy, professional development with stress on lCTs, network administration and website maintenance, marketing of information, etc. are major areas need special attention to improve the situation. Finance, knowledge level on ICTs among library staff, professional dynamism and leadership, vision and support of the administrators and policy makers, prevailing educational set up and social environment in the state, etc. are some of the major hurdles in reaping the maximum possibilities of lCTs by the university libraries in Kerala. The principles of Business Process Re-engineering are found suitable to effectively apply to re-structure and redefine the operations and service system of the libraries. Most of the conventional departments or divisions prevailing in the university libraries were functioning as watertight compartments and their existing management system was more rigid to adopt the principles of change management. Hence, a thorough re-structuring of the divisions was indicated. Consortia based activities and pooling and sharing of information resources was advocated to meet the varied needs of the users in the main campuses and off campuses of the universities, affiliated colleges and remote stations. A uniform staff policy similar to that prevailing in CSIR, DRDO, ISRO, etc. has been proposed by the study not only in the university libraries in kerala but for the entire country.Restructuring of Lis education,integrated and Planned development of school,college,research and public library systems,etc.were also justified for reaping maximum benefits of the modern ICTs.

Development of nitrifying and photosynthetic sulfur bacteria based bioaugmentation systems for the bioremediation of ammonia and hydrogen sulphide in shrimp culture

This thesis entitled Development of nitrifying ans photosynthetic sulfur bacteria based bioaugmentation systems for the bioremediation of ammonia and hydregen sulphide in shrimp culture. the thesis is to propose a sustainable, low cost option for the mitigation of toxic ammonia and hydrogen sulphide in shrimp culture systems. Use of ‘bioaugmentors’ as pond additives is an emerging field in aquaculture. Understanding the role of organisms involved in the ‘bioaugmentor’ will obviously help to optimize conditions for their activity.The thesis describes the use of wood powder immobilization of nitrifying consortia.Shrimp grow out systems are specialized and highly dynamic aquaculture production units which when operated under zero exchange mode require bioremediation of ammonia, nitrite nitrogen and hydrogen sulphide to protect the crop. The research conducted here is to develop an economically viable and user friendly technology for addressing the above problem. The nitrifying bacterial consortia (NBC) generated earlier (Achuthan et al., 2006) were used for developing the technology.Clear demonstration of better quality of immobilized nitrifiers generated in this study for field application.

Pyocyanin (5-methyl-1-hydroxyphenazine) produced by Pseudomonas aeruginosa as antagonist to vibrios in aquaculture: overexpression, downstream process and toxicity

Pyocyanin is a versatile and multifunctional phenazine, widely used as a bio-control agent. Besides its toxicity in higher concentration, it has been applied as bio-control agents against many pathogens including the Vibrio spp. in aquaculture systems. The exact mechanism of the production of pyocyanin in Pseudomonas aeruginosa is well known, but the genetic modification of pyocyanin biosynthetic pathways in P. aeruginosa is not yet experimented to improve the yield of pyocyanin production. In this context, one of the aims of this work was to improve the yield of pyocyanin production in P. aeruginosa by way of increasing the copy number of pyocyanin pathway genes and their over expression. The specific aims of this work encompasses firstly, the identification of probiotic effect of P. aeruginosa isolated from various ecological niches, the overexpression of pyocyanin biosynthetic genes, development of an appropriate downstream process for large scale production of pyocyanin and its application in aquaculture industries. In addition, this work intends to examine the toxicity of pyocyanin on various developmental stages of tiger shrimp (Penaeus monodon), Artemia nauplii, microbial consortia of nitrifying bioreactors (Packed Bed Bioreactor, PBBR and Stringed Bed Suspended Bioreactor, SBSBR) and in vitro cell culture systems from invertebrates and vertebrates. The present study was undertaken with a vision to manage the pathogenic vibrios in aquaculture through eco-friendly and sustainable management strategies with the following objectives: Identification of Pseudomonas isolated from various ecological niches and its antagonism to pathogenic vibrios in aquaculture.,Saline dependent production of pyocyanin in Pseudomonas aeruginosa originated from different ecological niches and their selective application in aquaculture,Cloning and overexpression of Phz genes encoding phenazine biosynthetic pathway for the enhanced production of pyocyanin in Pseudomonas aeruginosa MCCB117,Development of an appropriate downstream process for large scale production of pyocyanin from PA-pUCP-Phz++; Structural elucidation and functional analysis of the purified compoundToxicity of pyocyanin on various biological systems.

Development of bioreactors for nitrifying sewage

Nitrification is the biological oxidation of ammonium, first to nitrite and then to nitrate by two groups of aerobic, chemolithotrophic bacteria belonging to the family Nitrobacteriaceae. The biological nitrification in municipal wastewater treatment is important in those cases were ammonia removal requirement specially exist. In a trickling filter or in an activated sludge system nitrification is rate limiting and thus necessitates longer detention time. The combined carbon oxidation-nitrification processes generally have low population of nitrifiers due to a high ratio of BOD to total nitrogen in the effluent. This necessitates, separate carbon and nitrogen oxidation processes, which thus minimizes wash out ofthe nitrifiers. Therefore, a separate stage nitrification has become essential to achieve faster and efficient removal of ammonia from the wastewater. The present work deals with the development of bio reactor for nitrifying of sewage as the tertiary process so that the treated wastewater can be used for irrigation, algal culture or fish culture

Activated packed bed bioreactor for rapid nitrification in brackish water hatchery systems

A packed bed bioreactor (PBBR) was developed for rapid establishment of nitrification in brackish water hatchery systems in the tropics. The reactors were activated by immobilizing ammonia-oxidizing (AMONPCU- 1) and nitrite-oxidizing (NIONPCU-1) bacterial consortia on polystyrene and low-density polyethylene beads, respectively. Fluorescence in situ hybridization demonstrated the presence of autotrophic nitrifiers belong to Nitrosococcus mobilis, lineage of b ammonia oxidizers and nitrite oxidizer Nitrobacter sp. in the consortia. The activated reactors upon integration to the hatchery system resulted in significant ammonia removal (P\0.01) culminating to its undetectable levels. Consequently, a significantly higher percent survival of larvae was observed in the larval production systems. With spent water the reactors could establish nitrification with high percentage removal of ammonia (78%), nitrite (79%) and BOD (56%) within 7 days of initiation of the process. PBBR is configured in such a way to minimize the energy requirements for continuous operation by limiting the energy inputs to a single stage pumping of water and aeration to the aeration cells. The PBBR shall enable hatchery systems to operate under closed recirculating mode and pave the way for better water management in the aquaculture industry.

Nitrification in a packed bed bioreactor integrated into amarine recirculating maturation system under different substrate concentrations and flow rates

BACKGROUND: A packed bed bioreactor (PBBR) activated with an indigenous nitrifying bacterial consortia was developed and commercialized for rapid establishment of nitrification in brackish water and marine hatchery systems in the tropics. The present study evaluated nitrification in PBBR integrated into a Penaeus monodon recirculating maturation system under different substrate concentrations and flow rates. RESULTS:Instantnitrificationwasobservedafter integration ofPBBRinto thematuration system.TANandNO2-Nconcentrations were always maintained below0.5 mg L−1 during operation. The TANandNO2-N removalwas significant (P < 0.001) in all the six reactor compartments of the PBBR having the substrates at initial concentrations of 2, 5 and 10 mg L−1. The average volumetric TAN removal rates increased with flow rates from 43.51 (250 L h−1) to 130.44 (2500 L h−1) gTAN m−3 day−1 (P < 0.05). FISH analysis of the biofilms after 70 days of operation gave positive results with probes NSO 190 ((β ammonia oxidizers), NsV 443 (Nitrosospira spp.) NEU (halophilic Nitrosomonas), Ntspa 712 (Phylum Nitrospira) indicating stability of the consortia. CONCLUSION: The PBBR integrated into the P. monodon maturation system exhibited significant nitrification upon operation for 70 days as well as at different substrate concentrations and flow rates. This system can easily be integrated into marine and brackish water aquaculture systems, to establish instantaneous nitrification

Stringed bed suspended bioreactors (SBSBR)for in situ nitrification in penaeid and non-penaeid hatchery systems

For establishing nitrification in prawn (non-penaeid, salinity 10–15 ppt) and shrimp (penaeid, salinity 30–35 ppt) larval production systems, a stringed bed suspended bioreactor (SBSBR) was designed, fabricated, and validated. It was fabricated with 5 mm polystyrene and low density polyethylene beads as the substrata for ammonia and nitrite oxidizing bacterial consortia, respectively, with an overall surface area of 684 cm2. The reactors were activated in a prototype activator and were transported in polythene bags to the site of testing. Performance of the reactors activated with the nitrifying bacterial consortia AMONPCU-1 (ammonia oxidizers for non-penaeid culture) and NIONPCU-1 (nitrite oxidizers for non-penaeid culture) was evaluated in a Macrobrachium rosenbergii larval rearing system and those activated with AMOPCU-1 (ammonia oxidizers for penaeid culture) and NIOPCU-1 (nitrite oxidizers for penaeid culture) in a Penaeus monodon seed production system. Rapid setting up of nitrification could be observed in both the static systems which resulted in a higher relative per cent survival of larvae