Representation of evidence: An approach to uncertainty handling in knowledge-based systems

Many knowledge based systems (KBS) transform a situation information into an appropriate decision using an in built knowledge base. As the knowledge in real world situation is often uncertain, the degree of truth of a proposition provides a measure of uncertainty in the underlying knowledge. This uncertainty can be evaluated by collecting `evidence' about the truth or falsehood of the proposition from multiple sources. In this paper we propose a simple framework for representing uncertainty in using the notion of an evidence space.

Combustion and heat transfer characteristics of nanofluid fuel droplets: A short review

With the pressing need to meet an ever-increasing energy demand, the combustion systems utilizing fossil fuels have been the major contributors to carbon footprint. As the combustion of conventional energy resources continue to produce significant Green House gas (GHG) emissions, there is a strong emphasis to either upgrade or find an energy-efficient eco-friendly alternative to the traditional hydrocarbon fuels. With recent developments in nanotechnology, the ability to manufacture materials with custom tailored properties at nanoscale has led to the discovery of a new class of high energy density fuels containing reactive metallic nanoparticles (NPs). Due to the high reactive interfacial area and enhanced thermal and mass transport properties of nanomaterials, the high heat of formation of these metallic fuels can now be released rapidly, thereby saving on specific fuel consumption and hence reducing GHG emissions. In order to examine the efficacy of nanofuels in energetic formulations, it is imperative to first study their combustion characteristics at the droplet scale that form the fundamental building block for any combustion system utilizing liquid fuel spray. During combustion of such multiphase, multicomponent droplets, the phenomenon of diffusional entrapment of high volatility species leads to its explosive boiling (at the superheat limit) thereby leading to an intense internal pressure build-up. This pressure upsurge causes droplet fragmentation either in form of a microexplosion or droplet puffing followed by atomization (with formation of daughter droplets) featuring disruptive burning. Both these atomization modes represent primary mechanisms for extracting the high oxidation energies of metal NP additives by exposing them to the droplet flame (with daughter droplets acting as carriers of NPs). Atomization also serves as a natural mechanism for uniform distribution and mixing of the base fuel and enhancing burning rates (due to increase in specific surface area through formation of smaller daughter droplets). However, the efficiency of atomization depends on the thermo-physical properties of the base fuel, NP concentration and type. For instance, at dense loading NP agglomeration may lead to shell formation which would sustain the pressure upsurge and hence suppress atomization thereby reducing droplet gasification rate. Contrarily, the NPs may act as nucleation sites and aid boiling and the radiation absorption by NPs (from the flame) may lead to enhanced burning rates. Thus, nanoadditives may have opposing effects on the burning rate depending on the relative dominance of processes occurring at the droplet scale. The fundamental idea in this study is to: First, review different thermo-physical processes that occur globally at the droplet and sub-droplet scale such as surface regression, shell formation due to NP agglomeration, internal boiling, atomization/NP transport to flame zone and flame acoustic interaction that occur at the droplet scale and second, understand how their interaction changes as a function of droplet size, NP type, NP concentration and the type of base fuel. This understanding is crucial for obtaining phenomenological insights on the combustion behavior of novel nanofluid fuels that show great promise for becoming the next-generation fuels. (C) 2016 Elsevier Ltd. All rights reserved.

Genetics of Type III Bartter Syndrome in Spain, Proposed Diagnostic Algorithm

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Evidence for classification of c.1852_1853AA > GC in MLH1 as a neutral variant for Lynch syndrome

Background: Lynch syndrome (LS) is an autosomal dominant inherited cancer syndrome characterized by early onset cancers of the colorectum, endometrium and other tumours. A significant proportion of DNA variants in LS patients are unclassified. Reports on the pathogenicity of the c.1852_1853AA>GC (p.Lys618Ala) variant of the MLH1 gene are conflicting. In this study, we provide new evidence indicating that this variant has no significant implications for LS. Methods: The following approach was used to assess the clinical significance of the p.Lys618Ala variant: frequency in a control population, case-control comparison, co-occurrence of the p.Lys618Ala variant with a pathogenic mutation, co-segregation with the disease and microsatellite instability in tumours from carriers of the variant. We genotyped p.Lys618Ala in 1034 individuals (373 sporadic colorectal cancer [CRC] patients, 250 index subjects from families suspected of having LS [revised Bethesda guidelines] and 411 controls). Three well-characterized LS families that fulfilled the Amsterdam II Criteria and consisted of members with the p.Lys618Ala variant were included to assess co-occurrence and co-segregation. A subset of colorectal tumour DNA samples from 17 patients carrying the p.Lys618Ala variant was screened for microsatellite instability using five mononucleotide markers. Results: Twenty-seven individuals were heterozygous for the p.Lys618Ala variant; nine had sporadic CRC (2.41%), seven were suspected of having hereditary CRC (2.8%) and 11 were controls (2.68%). There were no significant associations in the case-control and case-case studies. The p.Lys618Ala variant was co-existent with pathogenic mutations in two unrelated LS families. In one family, the allele distribution of the pathogenic and unclassified variant was in trans, in the other family the pathogenic variant was detected in the MSH6 gene and only the deleterious variant co-segregated with the disease in both families. Only two positive cases of microsatellite instability (2/17, 11.8%) were detected in tumours from p.Lys618Ala carriers, indicating that this variant does not play a role in functional inactivation of MLH1 in CRC patients. Conclusions: The p.Lys618Ala variant should be considered a neutral variant for LS. These findings have implications for the clinical management of CRC probands and their relatives.

Regulation of the fitness of Atlantic salmon (Salmo salar) by intra-specific competition amongst the juveniles

Factors affecting the fitness of juvenile salmon are discussed. Although fitness from the genetic point of view is defined as the relative capacity of carriers of a given genotype to transmit their genes to the gene pool of the following generations, growth and survival of individuals are also components of fitness, and are influenced by responses to competition, which is the major topic of this article including implications for management. In order to better understand the relationships of density-dependent survival in Newfoundland, egg depositions were manipulated experimentally in the Freshwater River. Figures demonstrate the relationship between stock (number of eggs per 100 m2 of river) and recruitment (number of smolts per l00 m2 of Atlantic salmon, and also the percentage survival from egg to smolt stage related to potential egg depositions.

Serological and Genetic Evidence for Altered Complement System Functionality in Systemic Lupus Erythematosus: Findings of the GAPAID Consortium

Systemic lupus erythematosus is a chronic autoimmune disease with multifactorial ethiopathogenesis. The complement system is involved in both the early and late stages of disease development and organ damage. To better understand autoantibody mediated complement consumption we examined ex vivo immune complex formation on autoantigen arrays. We recruited patients with SLE (n = 211), with other systemic autoimmune diseases (n = 65) and non-autoimmune control subjects (n = 149). Standard clinical and laboratory data were collected and serum complement levels were determined. The genotype of SNP rs1143679 in the ITGAM gene was also determined. Ex vivo formation of immune complexes, with respect to IgM, IgG, complement C4 and C3 binding, was examined using a functional immunoassay on autoantigen microarray comprising nucleic acids, proteins and lipids. Complement consumption of nucleic acids increased upon binding of IgM and IgG even when serum complement levels were decreased due to consumption in SLE patients. A negative correlation between serum complement levels and ex vivo complement deposition on nucleic acid autoantigens is demonstrated. On the contrary, complement deposition on tested protein and lipid autoantigens showed positive correlation with C4 levels. Genetic analysis revealed that the non-synonymous variant rs1143679 in complement receptor type 3 is associated with an increased production of anti-dsDNA IgG antibodies. Notwithstanding, homozygous carriers of the previously reported susceptible allele (AA) had lower levels of dsDNA specific IgM among SLE patients. Both the non-synonymous variant rs1143679 and the high ratio of nucleic acid specific IgG/IgM were associated with multiple organ involvement. In summary, secondary complement deficiency in SLE does not impair opsonization of nucleic-acid-containing autoantigens but does affect other antigens and potentially other complement dependent processes. Dysfunction of the receptor recognizing complement opsonized immune complexes promotes the development of class-switched autoantibodies targeting nucleic acids.

Synthesis Gas Generation by Chemical-Looping Reforming Using Ce-Based Oxygen Carriers Modified with Fe, Cu, and Mn Oxides

Chemical-looping reforming (CLR) is a technology that can be used for partial oxidation and steam reforming of hydrocarbon fuels. It involves the use of a metal oxide as an oxygen carrier, which transfers oxygen from combustion air to the fuel. Composite oxygen carriers of cerium oxide added with Fe, Cu, and Mn oxides were prepared by co-precipitation and investigated in a thermogravimetric analyzer and a fixed-bed reactor using methane as fuel and air as oxidizing gas. It was revealed that the addition of transition-metal oxides into cerium oxide can improve the reactivity of the Ce-based oxygen carrier. The three kinds of mixed oxides showed high CO and H-2 selectivity at above 800 degrees C. As for the Ce-Fe-O oxygen carrier, methane was converted to synthesis gas at a H-2/CO molar ratio close to 2:1 at a temperature of 800-900 degrees C; however, the methane thermolysis reaction was found on Ce-Cu-O and Ce-Mn-O oxygen carriers at 850-900 degrees C. Among the three kinds of oxygen carriers, Ce-Fe-O presented the best performance for methane CLR. On Ce-Fe-O oxygen carriers, the CO and H-2 selectivity decreased as the Fe content increased in the carrier particles. An optimal range of the Ce/Fe molar ratio is Ce/Fe > 1 for Ce-Fe-O oxygen carriers. Scanning electron microscopy (SEM) analysis revealed that the microstructure of the Ce-Fe-O oxides was not dramatically changed before and after 20 cyclic reactions. A small amount of Fe3C was found in the reacted Ce-Fe-O oxides by X-ray diffraction (XRD) analysis.

PHOTOLUMINESCENCE AND SURFACE PHOTOVOLTAIC SPECTRA OF STRAINED INP ON GAAS

A high energy shift of the band-band recombination has been observed in the photoluminescence (PL) spectra of the strained InP epilayer on GaAs by metalorganic chemical vapor deposit. The strain determined by PL peak is in good agreement with calculated thermal strain. The surface photovoltalic spectra gives the information about energy gap, lattice mismatching, and composition of heteroepilayers, diffusion length, surface, and interface recombination velocity of minority carriers of heteroepitaxy layers.

Preparation of porous chitosan/agarose microsphere and its R-phycoerythrin release properties

The chitosan microspheres (CS-CL) were prepared by suspension crosslinking method and used as carriers of R-phycoerythrin (R-PE). In this study, R-PE was loaded in the microspheres and released in vitro. The effects of pH value, temperature, ionic strength, and R-PE concentration on loading efficiency and release behavior were discussed. A novel microsphere that contained agarose (CS-AR MP) was prepared and the basic loading and releasing behavior for R-PE of this kind of new micro-spheres were also investigated. The results showed that all these chitosan microspheres have the ability to control-release R-PE. The addition of agarose may somewhat accelerate the release rate of R-PE from microspheres and reduce the capacity of adsorption for R-PE. (c) 2006 Wiley Periodicals, Inc.

Studies on the transmission of WSSV (white spot syndrome virus) in juvenile Marsupenaeus japonicus via marine microalgae

We studied the possible role that marine microalgae may play during the outbreaks of WSS (white spot syndrome). In order to elucidate the possibility of marine microalgae carrying WSSV (white spot syndrome virus), six marine microallgae (Isochr.vsis galbana, Skeletonema costatum, Chlorella sp., Heterosigma akashiwo, Scrippsiella trochoidea, Dunaliella salina) were co-cultured with adult Marsupenaeus japollicus infected with WSSV and were assayed daily by nested-PCR to study whether they could carry WSSV. Further experiments were conducted to investigate whether the virus carried by microalgae could re-infect juvenile M. japonicus. Results showed that all of the experimental microalgae, except H. akashiwo could carry WSSV, and among them, Chlorella sp. and S. trochoidea had the strongest WSSV-carrying ability. Unlike other invertebrate carriers of WSSV, the WSSV detections in microalgae, which were positive after I and 3 days, were negative after 10 days of incubation. WSSV detection results in juvenile M. japonicus showed that the juvenile shrimp were re-infected by co-cultured Chlorella sp., although the juvenile M. japonicus carried so small an amount of WSSV that it could only be detected by nested-PCR. The results of this experiment suggest that microalgae might be one possible horizontal transmission pathway for WSSV. Further research, however, is required to better understand the factors behind the different carrying abilities and virus-carrying mechanisms of different microalgae. (c) 2007 Elsevier Inc. All rights reserved.

The use of fluorescence microscopy to define polymer localisation to the late endocytic compartments in cells that are targets for drug delivery

Macromolecular therapeutics and nano-sized drug delivery systems often require localisation to specific intracellular compartments. In particular, efficient endosomal escape, retrograde trafficking, or late endocytic/lysosomal activation are often prerequisites for pharmacological activity. The aim of this study was to define a fluorescence microscopy technique able to confirm the localisation of water-soluble polymeric carriers to late endocytic intracellular compartments. Three polymeric carriers of different molecular weight and character were studied: dextrin (Mw~50,000 g/mol), a N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer (Mw approximately 35,000 g/mol) and polyethylene glycol (PEG) (Mw 5000 g/mol). They were labelled with Oregon Green (OG) (0.3-3 wt.%; <3% free OG in respect of total). A panel of relevant target cells were used: THP-1, ARPE-19, and MCF-7 cells, and primary bovine chondrocytes (currently being used to evaluate novel polymer therapeutics) as well as NRK and Vero cells as reference controls. Specific intracellular compartments were marked using either endocytosed physiological standards, Marine Blue (MB) or Texas-red (TxR)-Wheat germ agglutinin (WGA), TxR-Bovine Serum Albumin (BSA), TxR-dextran, ricin holotoxin, C6-7-nitro-2,1,3-benzoxadiazol-4-yl (NBD)-labelled ceramide and TxR-shiga toxin B chain, or post-fixation immuno-staining for early endosomal antigen 1 (EEA1), lysosomal-associated membrane proteins (LAMP-1, Lgp-120 or CD63) or the Golgi marker GM130. Co-localisation with polymer-OG conjugates confirmed transfer to discreet, late endocytic (including lysosomal) compartments in all cells types. The technique described here is a particularly powerful tool as it circumvents fixation artefacts ensuring the retention of water-soluble polymers within the vesicles they occupy.

Pharmacogenomic studies of the anticancer and immunosuppressive thiopurines mercaptopurine and azathioprine.

AIMS
To examine the allelic variation of three enzymes involved in 6-mercaptopurine/azathioprine (6-MP/AZA) metabolism and evaluate the in?uence of these polymorphisms on toxicity, haematological parameters and metabolite levels in patients with acute lymphoblastic leukaemia (ALL) or in?ammatory bowel disease (IBD).
METHODS
Clinical data and blood samples were collected from 19 ALL paediatric patients and 35 IBD patients who were receiving 6-MP/AZA therapy. All patients were screened for seven genetic polymorphisms in three enzymes involved in mercaptopurine metabolism [xanthine oxidase, inosine triphosphatase (C94?A and IVS2+21A?C) and thiopurine methyltransferase]. Erythrocyte and plasma metabolite concentrations were also determined. The associations between the various genotypes and myelotoxicity, haematological parameters and metabolite concentrations were determined.
RESULTS
Thiopurine methyltransferase variant alleles were associated with a preferential metabolism away from 6-methylmercaptopurine nucleotides (P = 0.008 in ALL patients,P = 0.038 in IBD patients) favouring 6-thioguanine nucleotides (6-TGNs) (P = 0.021 in ALL patients). Interestingly, carriers of inosine triphosphatase IVS2+21A?C variants among ALL and IBD patients had signi?cantly higher concentrations of the active cytotoxic metabolites, 6-TGNs (P = 0.008 in ALL patients,P = 0.047 in IBD patients). The study con?rmed the association of thiopurine methyltransferase heterozygosity with leucopenia and neutropenia in ALL patients and reported a signi?cant association between inosine triphosphatase IVS2+21A?C variants with thrombocytopenia (P = 0.012).
CONCLUSIONS
Pharmacogenetic polymorphisms in the 6-MP pathway may help identify patients at risk for associated toxicities and may serve as a guide for dose
individualization.

Influence of ABCB1 polymorphisms and haplotypes on tacrolimus nephrotoxicity and dosage requirements in children with liver transplant

AIMS
The aim of this study was to investigate the in?uence of genetic polymorphisms in ABCB1 on the incidence of nephrotoxicity and tacrolimus dosage-requirements in paediatric patients following liver transplantation.
METHODS
Fifty-one paediatric liver transplant recipients receiving tacrolimus were genotyped for ABCB1 C1236>T, G2677>T and C3435>T polymorphisms. Dose-adjusted tacrolimus trough concentrations and estimated glomerular ?ltration rates (EGFR) indicative of renal toxicity were determined and correlated with the corresponding genotypes.
RESULTS
The present study revealed a higher incidence of the ABCB1 variant-alleles examined among patients with renal dysfunction (30% reduction in EGFR) at 6 months post-transplantation (1236T allele: 63.3% vs 37.5% in controls,P = 0.019; 2677T allele: 63.3% vs. 35.9%, p = 0.012; 3435T allele: 60% vs. 39.1%,P = 0.057). Carriers of the G2677->T variant allele also had a signi?cant reduction (%) in EGFR at 12 months post-transplant (mean difference = 22.6%; P = 0.031). Haplotype analysis showed a signi?cant association between T-T-T haplotypes and an increased incidence of nephrotoxicity at 6 months post-transplantation (haplotype-frequency = 52.9% in nephrotoxic patients vs 29.4% in controls; P = 0.029). Furthermore, G2677->T and C3435->T polymorphisms and T-T-T haplotypes were signi?cantly correlated with higher tacrolimus dose-adjusted pre-dose concentrations at various time points examined long after drug initiation.
CONCLUSIONS
These ?ndings suggest that ABCB1 polymorphisms in the native intestine signi?cantly in?uence tacrolimus dosage-requirement in the stable phase after transplantation. In addition, ABCB1 polymorphisms in paediatric liver transplant recipients may predispose them to nephrotoxicity over the ?rst year posttransplantation. Genotyping future transplant recipients for ABCB1 polymorphisms, therefore, could have the potential to individualize better tacrolimus immunosuppressive therapy and enhance drug safety

Lack of Association Between the Trp719Arg Polymorphism in Kinesin-Like Protein-6 and Coronary Artery Disease in 19 Case-Control Studies

Objectives: We sought to replicate the association between the kinesin-like protein 6 (KIF6) Trp719Arg polymorphism (rs20455), and clinical coronary artery disease (CAD).
Background: Recent prospective studies suggest that carriers of the 719Arg allele in KIF6 are at increased risk of clinical CAD compared with noncarriers.
Methods: The KIF6 Trp719Arg polymorphism (rs20455) was genotyped in 19 case-control studies of nonfatal CAD either as part of a genome-wide association study or in a formal attempt to replicate the initial positive reports.
Results: A total of 17,000 cases and 39,369 controls of European descent as well as a modest number of South Asians, African Americans, Hispanics, East Asians, and admixed cases and controls were successfully genotyped. None of the 19 studies demonstrated an increased risk of CAD in carriers of the 719Arg allele compared with noncarriers. Regression analyses and fixed-effects meta-analyses ruled out with high degree of confidence an increase of <2% in the risk of CAD among European 719Arg carriers. We also observed no increase in the risk of CAD among 719Arg carriers in the subset of Europeans with early-onset disease (younger than 50 years of age for men and younger than 60 years of age for women) compared with similarly aged controls as well as all non-European subgroups.
Conclusions: The KIF6 Trp719Arg polymorphism was not associated with the risk of clinical CAD in this large replication study.

Plasma HDL cholesterol and risk of myocardial infarction: A mendelian randomisation study

Background: High plasma HDL cholesterol is associated with reduced risk of myocardial infarction, but whether this association is causal is unclear. Exploiting the fact that genotypes are randomly assigned at meiosis, are independent of non-genetic confounding, and are unmodified by disease processes, mendelian random isation can be used to test the hypothesis that the association of a plasma biomarker with disease is causal.
Methods: We performed two mendelian randomisation analyses. First, we used as an instrument a single nucleotide polymorphism (SNP) in the endothelial lipase gene (LIPG Asn396Ser) and tested this SNP in 20 studies (20 913 myocardial infarction cases, 95 407 controls). Second, we used as an instrument a genetic score consisting of 14 common SNPs that exclusively associate with HDL cholesterol and tested this score in up to 12 482 cases of myocardial infarction and 41 331 controls. As a positive control, we also tested a genetic score of 13 common SNPs exclusively associated with LDL cholesterol.
Findings: Carriers of the LIPG 396Ser allele (2·6% frequency) had higher HDL cholesterol (0·14 mmol/L higher p=8×10-13) but similar levels of other lipid and non-lipid risk factors for myocardial infarction compared with noncarriers. This difference in HDL cholesterol is expected to decrease risk of myocardial infarction by 13% (odds ratio [OR] 0·87, 95% CI 0·84-0·91). However, we noted that the 396Ser allele was not associated with risk of myocardial infarction (OR 0·99, 95% CI 0·88-1·11, p=0·85). From observational epidemiology, an increase of 1 SD in HDL cholesterol was associated with reduced risk of myocardial infarction (OR 0·62, 95% CI 0·58-0·66). However, a 1 SD increase in HDL cholesterol due to genetic score was not associated with risk of myocardial infarction (OR 0·93 95% CI 0·68-1·26, p=0·63). For LDL cholesterol, the estimate from observational epidemiology (a 1 SD increase in LDL cholesterol associated with OR 1·54, 95% CI 1·45-1·63) was concordant with that from genetic score (OR 2·13 95% CI 1·69-2·69, p=2×10 -10).
Interpretation: Some genetic mechanisms that raise plasma HDL cholesterol do not seem to lower risk of myocardial infarction. These data challenge the concept that raising of plasma HDL cholesterol will uniformly translate into reductions in risk of myocardial infarction.