Decision-support system for domestic water demand forecasting and management

PhD ThesisA generic but flexible decision-support system for domestic water demand forecasting and management (DFMS) has been developed as part of a highlyintegrated decision-support system for river-basin management. Its purpose is to provide water-resources planners with the facilities for estimating future water demand for any demand region and time period, having regard to the possibility of introducing demand-management measures. The system has the capability of predicting domestic-water demand by various methods according to the data availability, computing conservation effectiveness due to the implementation of various demand-management measures, forecasting the number of customers for different consumption units (person, household, water connection) and facilitating the development of demand-scenarios for eveluating various options. The system is designed in such a way that makes it easy to use for both novice and experienced users since it is driven by a menu system which relies on a mouse rather than the keyboard. Moreover, the communication between user and the system is by means of a user-friendly interface which makes extensive use of hypertext and colour graphics in presenting the results. Briefly, DFMS comprises the following components: a GIS that stores, displays and analyses all geo-coded information such as satellite imagery, urban areas, cities and towns, etc.; • a database which provides access to non-spatial data such as demand-area location and characteristics including top-level descriptors such as population, total demand, per-capita consumption, etc.; • an expert system which uses the rule-based inference for data entry and predicting values (quantitative or qualitative) of variables from the knowledgebase; . four methods of demand forecasting ranging from superficial to detailed, namely time extrapolation, econometric variables, end-uses variables and households classification; a multi-objective decision component which helps the user to determine the most appropriate forecasting method and conservation measures; • a set of mathematical models to provide the analytical capability for quantifying descriptors, producing multiple outputs etc.; • a user-interface with access to the various functional components of the system and the various help/explain files; • a set of pre- and post-processors which support editing of the inputs data and the visualisation or analysis of model output, in addition to handling scenarios for each of the models or variables; • a set of help files which are used to provide the user with the necessary assistance if for any reason, a more detailed explanation is required, based on a hypertext; In order to demonstrate the system capability, DFMS has been applied to the Swindon demand area of Thames Water Utilities Ltd.Department of Civil Engineering, University of Newcastle upon Tyne, World Bank (Joint/Japan Scholarship Program) British Embassy, Amma

Haploinsufficiency of PRR12 causes a spectrum of neurodevelopmental, eye, and multisystem abnormalities

Purpose: Proline Rich 12 (PRR12) is a gene of unknown function with suspected DNA-binding activity, expressed in developing mice and human brains. Predicted loss-of-function variants in this gene are extremely rare, indicating high intolerance of haploinsufficiency. Methods: Three individuals with intellectual disability and iris anomalies and truncating de novo PRR12 variants were described previously. We add 21 individuals with similar PRR12 variants identified via matchmaking platforms, bringing the total number to 24. Results: We observed 12 frameshift, 6 nonsense, 1 splice-site, and 2 missense variants and one patient with a gross deletion involving PRR12. Three individuals had additional genetic findings, possibly confounding the phenotype. All patients had developmental impairment. Variable structural eye defects were observed in 12/24 individuals (50%) including anophthalmia, microphthalmia, colobomas, optic nerve and iris abnormalities. Additional common features included hypotonia (61%), heart defects (52%), growth failure (54%), and kidney anomalies (35%). PrediXcan analysis showed that phecodes most strongly associated with reduced predicted PRR12 expression were enriched for eye- (7/30) and kidney- (4/30) phenotypes, such as wet macular degeneration and chronic kidney disease. Conclusion: These findings support PRR12 haploinsufficiency as a cause for a novel disorder with a wide clinical spectrum marked chiefly by neurodevelopmental and eye abnormalities. Graphic Abstract: [Figure not available: see fulltext.

Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): Current status and its characteristics

Butterflyfish are among the most iconic of the coral reef fishes and represent a model system to study general questions of biogeography, evolution and population genetics. We assembled and annotated the genome sequence of the blacktail butterflyfish (Chaetodon austriacus), an Arabian region endemic species that is reliant on coral reefs for food and shelter. Using available bony fish (superclass Osteichthyes) genomes as a reference, a total of 28 926 high-quality protein-coding genes were predicted from 13 967 assembled scaffolds. The quality and completeness of the draft genome of C. austriacus suggest that it has the potential to serve as a resource for studies on the co-evolution of reef fish adaptations to the unique Red Sea environment, as well as a comparison of gene sequences between closely related congeneric species of butterflyfish distributed more broadly across the tropical Indo-Pacific

Haploinsufficiency of PRR12 causes a spectrum of neurodevelopmental, eye, and multisystem abnormalities

PURPOSE: Proline Rich 12 (PRR12) is a gene of unknown function with suspected DNA-binding activity, expressed in developing mice and human brains. Predicted loss-of-function variants in this gene are extremely rare, indicating high intolerance of haploinsufficiency. METHODS: Three individuals with intellectual disability and iris anomalies and truncating de novo PRR12 variants were described previously. We add 21 individuals with similar PRR12 variants identified via matchmaking platforms, bringing the total number to 24. RESULTS: We observed 12 frameshift, 6 nonsense, 1 splice-site, and 2 missense variants and one patient with a gross deletion involving PRR12. Three individuals had additional genetic findings, possibly confounding the phenotype. All patients had developmental impairment. Variable structural eye defects were observed in 12/24 individuals (50%) including anophthalmia, microphthalmia, colobomas, optic nerve and iris abnormalities. Additional common features included hypotonia (61%), heart defects (52%), growth failure (54%), and kidney anomalies (35%). PrediXcan analysis showed that phecodes most strongly associated with reduced predicted PRR12 expression were enriched for eye- (7/30) and kidney- (4/30) phenotypes, such as wet macular degeneration and chronic kidney disease. CONCLUSION: These findings support PRR12 haploinsufficiency as a cause for a novel disorder with a wide clinical spectrum marked chiefly by neurodevelopmental and eye abnormalities

A review of contemporary patterns of endemism for shallow water reef fauna in the Red Sea

Aim: The Red Sea is characterised by a unique fauna and historical periods of desiccation, hypersalinity and intermittent isolation. The origin and contemporary composition of reef-associated taxa in this region can illuminate biogeographical principles about vicariance and the establishment (or local extirpation) of existing species. Here we aim to: (1) outline the distribution of shallow water fauna between the Red Sea and adjacent regions, (2) explore mechanisms for maintaining these distributions and (3) propose hypotheses to test these mechanisms. Location: Red Sea, Gulf of Aden, Arabian Sea, Arabian Gulf and Indian Ocean. Methods: Updated checklists for scleractinian corals, fishes and non-coral invertebrates were used to determine species richness in the Red Sea and the rest of the Arabian Peninsula and assess levels of endemism. Fine-scale diversity and abundance of reef fishes within the Red Sea were explored using ecological survey data. Results: Within the Red Sea, we recorded 346 zooxanthellate and azooxanthellate scleractinian coral species of which 19 are endemic (5.5%). Currently 635 species of polychaetes, 211 echinoderms and 79 ascidians have been documented, with endemism rates of 12.6%, 8.1% and 16.5% respectively. A preliminary compilation of 231 species of crustaceans and 137 species of molluscs include 10.0% and 6.6% endemism respectively. We documented 1071 shallow fish species, with 12.9% endemic in the entire Red Sea and 14.1% endemic in the Red Sea and Gulf of Aden. Based on ecological survey data of endemic fishes, there were no major changes in species richness or abundance across 1100 km of Saudi Arabian coastline. Main conclusions: The Red Sea biota appears resilient to major environmental fluctuations and is characterized by high rates of endemism with variable degrees of incursion into the Gulf of Aden. The nearby Omani and Arabian Gulfs also have variable environments and high levels of endemism, but these are not consistently distinct across taxa. The presence of physical barriers does not appear to explain species distributions, which are more likely determined by ecological plasticity and genetic diversity

Bipartite life cycle of coral reef fishes promotes increasing shape disparity of the head skeleton during ontogeny: an example from damselfishes (Pomacentridae)

Background: Quantitative studies of the variation of disparity during ontogeny exhibited by the radiation of coral reef fishes are lacking. Such studies dealing with the variation of disparity, i.e. the diversity of organic form, over ontogeny could be a first step in detecting evolutionary mechanisms in these fishes. The damselfishes (Pomacentridae) have a bipartite life-cycle, as do the majority of demersal coral reef fishes. During their pelagic dispersion phase, all larvae feed on planktonic prey. On the other hand, juveniles and adults associated with the coral reef environment show a higher diversity of diets. Using geometric morphometrics, we study the ontogenetic dynamic of shape disparity of different head skeletal units (neurocranium, suspensorium and opercle, mandible and premaxilla) in this fish family. We expected that larvae of different species might be relatively similar in shapes. Alternatively, specialization may become notable even in the juvenile and adult phase. Results: The disparity levels increase significantly throughout ontogeny for each skeletal unit. At settlement, all larval shapes are already species-specific. Damselfishes show high levels of ontogenetic allometry during their postsettlement growth. The divergence of allometric patterns largely explains the changes in patterns and levels of shape disparity over ontogeny. The rate of shape change and the length of ontogenetic trajectories seem to be less variable among species. We also show that the high levels of shape disparity at the adult stage are correlated to a higher level of ecological and functional diversity in this stage. Conclusion: Diversification throughout ontogeny of damselfishes results from the interaction among several developmental novelties enhancing disparity. The bipartite life-cycle of damselfishes exemplifies a case where the variation of environmental factors, i.e. the transition from the more homogeneous oceanic environment to the coral reef offering a wide range of feeding habits, promotes increasing shape disparity of the head skeleton over the ontogeny of fishes

Genetic population structure, gene flow, and evolutionary history of selected ornamental fish in the Red Sea

The ornamental fishery is expanding rapidly in the Red Sea, and concerns about the possibility of overexploitation were raised. Marine protected areas (MPAs) were addressed as a potential solution to prevent overexploitation. However, the sources of stock recruitment are not well understood. This thesis aims to reveal the genetic population structure and the demographic connectivity in the endemic fish species of the Red Sea Larabicus quadrilineatus, and in the two common fish species Chromis viridis and Pseudanthias squamipinnis. The fish samples were obtained from five locations in the Red Sea. For comparison, additional samples of the two common species were obtained from two locations in the Indo-Malay Archipelago. Partial sequence of the mitochondrial control region was used as a molecular marker in the three studied species. The studied species exhibited high genetic diversity as inferred from the haplotype and nucleotide indices. Analysis of molecular variance (AMOVA) detected significant genetic variation between northern and central/southern populations of L. quadrilineatus (ΦCT = 0.01; P < 0.01), and between the populations in the Gulf of Aqaba and the Red Sea proper of P. squamipinnis (ΦST = 0.02; P < 0.01). In addition, AMOVA detected significant genetic variation between the Red Sea and the Indo-Malay Archipelago for both C. viridis (ΦCT = 0.462; P < 0.001) and P. squamipinnis (ΦST = 0.78; P < 0.001). Migration analysis in the Red Sea revealed (1) higher migration into the Gulf of Aqaba for all species; (2) higher northward migration for C. viridis and L. quadrilineatus; and higher southward migration in the Red Sea proper for P. squamipinnis. A significant relationship between the genetic versus the geographic distances was shown only for L. quadrilineatus, and as a consequence the mean larval dispersal distance based on the isolation-by-distance model was estimated to be between 0.44 and 5 km. Estimates of the effective population size were the highest (1) in Hodeidah (southern Red Sea) for both L. quadrilineatus and C. viridis; and (2) in Tor (northern Red Sea) for P. squamipinnis. The results in this thesis were discussed in relation to the oceanographic factors and the biological features of the studied fishes. The historical event Last Glacial Maximum proved its influence on the population demographic history and the currents effective population size of the studied species. In order to enable a sustainable ornamental fishery on the studied species in the Red Sea, the results of this thesis suggest that (1) populations in the Red Sea should be managed as one stock for C. viridis; (2) populations of L. quadrilineatus northern and southern Red Sea should be managed as two stocks; and (3) populations in the Gulf of Aqaba and in the Red Sea proper should be managed separately for P. squamipinnis. The rather low larval dispersal distance of about 5 km needs to be considered in the design of MPAs to enable connectivity and self-seeding in L. quadrilineatus

First Record Mutations in the Genes ASPA and ARSA Causing Leukodystrophy in Jordan

Leukodystrophies (LDs) are heterogeneous genetic disorders characterized by abnormal white matter in the central nervous system. Some of the LDs are progressive and often fatal. In general, LD is primarily diagnosed based on the neuroimaging; however, definitive diagnosis of the LD type is done using genetic testing such as next-generation sequencing. The aim of this study is to identify the genetic causes of LD in two independent Jordanian cases that exhibit MRI findings confirming LD with no definitive diagnosis using whole exome sequencing (WES). The most likely causative variants were identified. In one case, the homozygous pathogenic variant NM_000049.2:c.914C>A;p.Ala305Glu, which is previously reported in ClinVar, in the gene ASPA was identified causing Canavan disease. In the second case, the homozygous novel variant NM_000487.5:c.256C>G;p.Arg86Gly in the gene ARSA was identified causing metachromatic leukodystrophy. The two variants segregate in their families. The phenotypes of the two studied cases overlap with assigned diseases. The present study raises the importance of using WES to identify the precise neurodevelopmental diseases in Jordan

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