Full Length Research Paper LTR-retrotransposons-based molecular markers in cultivated Egyptian cottons G. barbadense L.

Long terminal repeat (LTR)-retrotransposons are mobile genetic elements that are ubiquitous in plants and constitute a major portion of their nuclear genomes. LTR-retrotransposons possess unique properties that make them appropriate for investigating relationships between closely related species and populations. The aim of the current study was to employ Ty1-copia group retrotransposons as molecular markers in cultivated Egyptian cottons, G. barbadense L. Restriction site analysis of PCRamplified Ty1-copia RT domain promoted the construction of a restriction map for each Egyptian cultivar. These maps display distinctive patterns of restriction site variation. Furthermore, these patterns are capable of differentiating even between cultivars that appear to have diverged only in the past 50 years. These results demonstrate that retrotransposon-based molecular markers are particularly valuable tools for plant molecular phylogenetic and population genetic studie

Molecular epidemiology of antibiotic-associated diarrhoea due to Clostridium difficile and clostridium perfringens in Ain Shams University Hospitals

Background: As we are living in the era of antibiotic overuse, antibiotic associated diarrhea (AAD) is considered now a distinct health problem with a need for more attention. Aim of the Study: was to perform a highly specific detection and definition of pathogenic Clostridium perfringens and Clostridium difficile related AAD in children compared to adults and geriatircs. Patients and Methods: One hundred and fifty patients diagnosed for AAD were included in this study (50 children, 50 adults and 50 geriatric patients). All of them were subjected to full medical history including complete therapeutic history of antibiotics and collection of stool sample during the attack for detection of Clostridium perfringenes enterotoxin (CPEnt) and Clostridium difficile cytotoxin by (EIA) kit. PCR detection of Clostridium perfringenes cpe gene (Coding gene for CPEnt) was performed as well. Results: Results showed that prevalence of Clostridium difficile cytotoxin was 24% while Clostridium perfringenes enterotoxin was 12% as detected by EIA in faecal specimens as a whole. Detection of cpe gene by PCR was positive in 16% of all cases. Children (OR: 4.2, 95% CI: 1.3-14.8, P_0.01) and geriatric patients (OR: 3.4, 95% CI: 1.2-13.5, P_0.02) were significantly more prone to Clostridium difficile AAD compared to adults. Also, childhood was a significant risk for Clostridium perfringens AAD (OR: 2.1, 95% CI: 0.54-7.4, P_0.04). In Conclusion: children and geriatric patients are more vulnerable to develop AAD with antibiotic abuse compared to adults. Abbreviations: AAD=Antibiotic associated diarrhea, CI=Confidence interval, ELISA=Enzyme-linked immunosorbent assay, OR=Odd ratio, PCR=Polymerase chain reaction. Keywords: Antibiotic-associated diarrhea, children, Clostridium perfringens, Clostridium difficile. Egypt. J. Hum. Genet Vol. 8 (2) 2007: pp. 121-13

The role of hepatic progenitor cells in predicting response to therapy in Egyptian patients with chronic hepatitis C, genotype 4

Background: Interferon therapy is used as a line of treatment of chronic hepatitis C virus (HCV) in several areas of the world including Egypt.Objective: Our aim was to investigate the value of hepatic progenitor cells (HPCs) in predicting response of patients with chronic HCV, genotype 4 to pegylated interferon (PEGIFN) plus ribavirin (RBV) therapy.Methods: Pre-treatment liver biopsies obtained from 110 patients with chronic HCV, genotype 4 were examined immunohisto- chemically for HPCs using cytokeratin19. The mean number of HPCs as ductular reaction (DR) and as isolated progenitor cells (IPCs) was counted in each case. The patients were classified into: those with sustained virological response (SVR) and those who did not achieve SVR. The results were compared between the two groups. Also, the relationships between HPCs and other clinico-pathologic variables were estimated using multivariate analysis.Results: The mean number of HPCs was the only independent predictor of therapeutic response, being significantly higher in non-responders (P = 0 for DR and P = 0.03 for IPCs). On the other hand, fibrosis stage and steatosis were the only independent factors which showed a significant direct association with the mean number of HPCs in the form of DR and IPCs (P = 0 for each).Conclusion: The number of HPCs provides prognostic information in chronic HCV since it is significantly associated with stage of fibrosis. More importantly, it can be used as a marker to predict response of patients with chronic HCV to PEGIFN plus RBV therapy.Keywords: Chronic hepatitis C, genotype 4, response to therapy, hepatic progenitor cells

Adsorption and reaction of CO on (Pd–)Al2O3 and (Pd–)ZrO2: vibrational spectroscopy of carbonate formation

γ-Alumina is widely used as an oxide support in catalysis, and palladium nanoparticles supported by alumina represent one of the most frequently used dispersed metals. The surface sites of the catalysts are often probed via FTIR spectroscopy upon CO adsorption, which may result in the formation of surface carbonate species. We have examined this process in detail utilizing FTIR to monitor carbonate formation on γ-alumina and zirconia upon exposure to isotopically labelled and unlabelled CO and CO2. The same was carried out for well-defined Pd nanoparticles supported on Al2O3 or ZrO2. A water gas shift reaction of CO with surface hydroxyls was detected, which requires surface defect sites and adjacent OH groups. Furthermore, we have studied the effect of Cl synthesis residues, leading to strongly reduced carbonate formation and changes in the OH region (isolated OH groups were partly replaced or were even absent). To corroborate this finding, samples were deliberately poisoned with Cl to an extent comparable to that of synthesis residues, as confirmed by Auger electron spectroscopy. For catalysts prepared from Cl-containing precursors a new CO band at 2164 cm−1 was observed in the carbonyl region, which was ascribed to Pd interacting with Cl. Finally, the FTIR measurements were complemented by quantification of the amount of carbonates formed via chemisorption, which provides a tool to determine the concentration of reactive defect sites on the alumina surface

The role of hepatic progenitor cells in predicting response to therapy in Egyptian patients with chronic hepatitis C, genotype 4

Background: Interferon therapy is used as a line of treatment of chronic hepatitis C virus (HCV) in several areas of the world including Egypt. Objective: Our aim was to investigate the value of hepatic progenitor cells (HPCs) in predicting response of patients with chronic HCV, genotype 4 to pegylated interferon (PEGIFN) plus ribavirin (RBV) therapy. Methods: Pre-treatment liver biopsies obtained from 110 patients with chronic HCV, genotype 4 were examined immunohistochemically for HPCs using cytokeratin19. The mean number of HPCs as ductular reaction (DR) and as isolated progenitor cells (IPCs) was counted in each case. The patients were classified into: those with sustained virological response (SVR) and those who did not achieve SVR. The results were compared between the two groups. Also, the relationships between HPCs and other clinico-pathologic variables were estimated using multivariate analysis. Results: The mean number of HPCs was the only independent predictor of therapeutic response, being significantly higher in non-responders (P = 0 for DR and P = 0.03 for IPCs). On the other hand, fibrosis stage and steatosis were the only independent factors which showed a significant direct association with the mean number of HPCs in the form of DR and IPCs (P = 0 for each). Conclusion: The number of HPCs provides prognostic information in chronic HCV since it is significantly associated with stage of fibrosis. More importantly, it can be used as a marker to predict response of patients with chronic HCV to PEGIFN plus RBV therapy. DOI: https://dx.doi.org/10.4314/ahs.v19i1.14 Cite as: Helal T El A, Radwan NA, Mahmoud HA, Zaki AME, Ahmed NS, Wahib AAA, et al. The role of hepatic progenitor cells in predicting response to therapy in Egyptian patients with chronic hepatitis C, genotype 4. Afri Health Sci. 2019;19(1). 1411-1421. https://dx.doi.org/10.4314/ahs.v19i1.1

Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method

BACKGROUND: Data mining can be utilized to automate analysis of substantial amounts of data produced in many organizations. However, data mining produces large numbers of rules and patterns, many of which are not useful. Existing methods for pruning uninteresting patterns have only begun to automate the knowledge acquisition step (which is required for subjective measures of interestingness), hence leaving a serious bottleneck. In this paper we propose a method for automatically acquiring knowledge to shorten the pattern list by locating the novel and interesting ones. METHODS: The dual-mining method is based on automatically comparing the strength of patterns mined from a database with the strength of equivalent patterns mined from a relevant knowledgebase. When these two estimates of pattern strength do not match, a high "surprise score" is assigned to the pattern, identifying the pattern as potentially interesting. The surprise score captures the degree of novelty or interestingness of the mined pattern. In addition, we show how to compute p values for each surprise score, thus filtering out noise and attaching statistical significance. RESULTS: We have implemented the dual-mining method using scripts written in Perl and R. We applied the method to a large patient database and a biomedical literature citation knowledgebase. The system estimated association scores for 50,000 patterns, composed of disease entities and lab results, by querying the database and the knowledgebase. It then computed the surprise scores by comparing the pairs of association scores. Finally, the system estimated statistical significance of the scores. CONCLUSION: The dual-mining method eliminates more than 90% of patterns with strong associations, thus identifying them as uninteresting. We found that the pruning of patterns using the surprise score matched the biomedical evidence in the 100 cases that were examined by hand. The method automates the acquisition of knowledge, thus reducing dependence on the knowledge elicited from human expert, which is usually a rate-limiting step

People with higher interoceptive sensitivity are more altruistic, but improving interoception does not increase altruism

People consistently show preferences and behaviors that benefit others at a cost to themselves, a phenomenon termed altruism. We investigated if perception of one’s body signals – interoception - may be underlying such behaviors. We tested if participants’ sensitivity to their own heartbeat predicted their decision on a choice between self-interest and altruism, and if improving this sensitivity through training would make participants more altruistic. Across these two experiments, interoceptive sensitivity predicted altruism measured through monetary generosity. Improving interoceptive sensitivity did, however, not lead to more altruistic behaviour. We conclude that there is a unique link between interoception and altruistic behaviour, likely established over an individual’s history of altruistic acts, and the body responses they elicit. The findings suggest that humans might literally ‘listen to their heart’ to guide their altruistic behavior

The global burden of viral hepatitis from 1990 to 2013: findings from the Global Burden of Disease Study 2013

BACKGROUND: With recent improvements in vaccines and treatments against viral hepatitis, an improved understanding of the burden of viral hepatitis is needed to inform global intervention strategies. We used data from the Global Burden of Disease (GBD) Study to estimate morbidity and mortality for acute viral hepatitis, and for cirrhosis and liver cancer caused by viral hepatitis, by age, sex, and country from 1990 to 2013. METHODS: We estimated mortality using natural history models for acute hepatitis infections and GBD's cause-of-death ensemble model for cirrhosis and liver cancer. We used meta-regression to estimate total cirrhosis and total liver cancer prevalence, as well as the proportion of cirrhosis and liver cancer attributable to each cause. We then estimated cause-specific prevalence as the product of the total prevalence and the proportion attributable to a specific cause. Disability-adjusted life-years (DALYs) were calculated as the sum of years of life lost (YLLs) and years lived with disability (YLDs). FINDINGS: Between 1990 and 2013, global viral hepatitis deaths increased from 0·89 million (95% uncertainty interval [UI] 0·86–0·94) to 1·45 million (1·38–1·54); YLLs from 31·0 million (29·6–32·6) to 41·6 million (39·1–44·7); YLDs from 0·65 million (0·45–0·89) to 0·87 million (0·61–1·18); and DALYs from 31·7 million (30·2–33·3) to 42·5 million (39·9–45·6). In 2013, viral hepatitis was the seventh (95% UI seventh to eighth) leading cause of death worldwide, compared with tenth (tenth to 12th) in 1990. INTERPRETATION: Viral hepatitis is a leading cause of death and disability worldwide. Unlike most communicable diseases, the absolute burden and relative rank of viral hepatitis increased between 1990 and 2013. The enormous health loss attributable to viral hepatitis, and the availability of effective vaccines and treatments, suggests an important opportunity to improve public health. FUNDING: Bill & Melinda Gates Foundation

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015

SummaryBackground The Global Burden of Diseases, Injuries, and Risk Factors Study 2015 provides an up-to-date synthesis of the evidence for risk factor exposure and the attributable burden of disease. By providing national and subnational assessments spanning the past 25 years, this study can inform debates on the importance of addressing risks in context. Methods We used the comparative risk assessment framework developed for previous iterations of the Global Burden of Disease Study to estimate attributable deaths, disability-adjusted life-years (DALYs), and trends in exposure by age group, sex, year, and geography for 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks from 1990 to 2015. This study included 388 risk-outcome pairs that met World Cancer Research Fund-defined criteria for convincing or probable evidence. We extracted relative risk and exposure estimates from randomised controlled trials, cohorts, pooled cohorts, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. We developed a metric that allows comparisons of exposure across risk factors—the summary exposure value. Using the counterfactual scenario of theoretical minimum risk level, we estimated the portion of deaths and DALYs that could be attributed to a given risk. We decomposed trends in attributable burden into contributions from population growth, population age structure, risk exposure, and risk-deleted cause-specific DALY rates. We characterised risk exposure in relation to a Socio-demographic Index (SDI). Findings Between 1990 and 2015, global exposure to unsafe sanitation, household air pollution, childhood underweight, childhood stunting, and smoking each decreased by more than 25%. Global exposure for several occupational risks, high body-mass index (BMI), and drug use increased by more than 25% over the same period. All risks jointly evaluated in 2015 accounted for 57·8% (95% CI 56·6–58·8) of global deaths and 41·2% (39·8–42·8) of DALYs. In 2015, the ten largest contributors to global DALYs among Level 3 risks were high systolic blood pressure (211·8 million [192·7 million to 231·1 million] global DALYs), smoking (148·6 million [134·2 million to 163·1 million]), high fasting plasma glucose (143·1 million [125·1 million to 163·5 million]), high BMI (120·1 million [83·8 million to 158·4 million]), childhood undernutrition (113·3 million [103·9 million to 123·4 million]), ambient particulate matter (103·1 million [90·8 million to 115·1 million]), high total cholesterol (88·7 million [74·6 million to 105·7 million]), household air pollution (85·6 million [66·7 million to 106·1 million]), alcohol use (85·0 million [77·2 million to 93·0 million]), and diets high in sodium (83·0 million [49·3 million to 127·5 million]). From 1990 to 2015, attributable DALYs declined for micronutrient deficiencies, childhood undernutrition, unsafe sanitation and water, and household air pollution; reductions in risk-deleted DALY rates rather than reductions in exposure drove these declines. Rising exposure contributed to notable increases in attributable DALYs from high BMI, high fasting plasma glucose, occupational carcinogens, and drug use. Environmental risks and childhood undernutrition declined steadily with SDI; low physical activity, high BMI, and high fasting plasma glucose increased with SDI. In 119 countries, metabolic risks, such as high BMI and fasting plasma glucose, contributed the most attributable DALYs in 2015. Regionally, smoking still ranked among the leading five risk factors for attributable DALYs in 109 countries; childhood underweight and unsafe sex remained primary drivers of early death and disability in much of sub-Saharan Africa. Interpretation Declines in some key environmental risks have contributed to declines in critical infectious diseases. Some risks appear to be invariant to SDI. Increasing risks, including high BMI, high fasting plasma glucose, drug use, and some occupational exposures, contribute to rising burden from some conditions, but also provide opportunities for intervention. Some highly preventable risks, such as smoking, remain major causes of attributable DALYs, even as exposure is declining. Public policy makers need to pay attention to the risks that are increasingly major contributors to global burden. Funding Bill & Melinda Gates Foundation

Relative judgement is relatively difficult: evidence against the role of relative judgement in absolute identification

A variety of processes have been put forward to explain absolute identification performance. One difference between current models of absolute identification is the extent to which the task involves accessing stored representations in long-term memory (e.g. exemplars in memory, Kent & Lamberts, Journal of Experimental Psychology: Learning Memory and Cognition, 31, 289–305, 2005) or relative judgement (comparison of the current stimulus to the stimulus on the previous trial, Stewart, Brown & Chater, Psychological Review, 112, 881–911, 2005). In two experiments we explored this by tapping into these processes. In Experiment 1 participants completed an absolute identification task using eight line lengths whereby a single stimulus was presented on each trial for identification. They also completed a matching task aimed at mirroring exemplar comparison in which eight line lengths were presented in a circular array and the task was to report which of these matched a target presented centrally. Experiment 2 was a relative judgement task and was similar to Experiment 1 except that the task was to report the difference (jump-size) between the current stimulus and that on the previous trial. The absolute identification and matching data showed clear similarities (faster and more accurate responding for stimuli near the edges of the range and similar stimulus-response confusions). In contrast, relative judgment performance was poor suggesting relative judgement is not straightforward. Moreover, performance as a function of jump-size differed considerably between the relative judgement and absolute identification tasks. Similarly, in the relative judgement task, predicting correct stimulus identification based on successful relative judgement yielded the reverse pattern of performance observed in the absolute identification task. Overall, the data suggest that relative judgement does not underlie absolute identification and that the task is more likely reliant on an exemplar comparison process