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We have analyzed a total of 12 different global and local multiple
protein-sequence alignment methods. The purpose of this study is to
evaluate each method's ability to correctly identify the ordered series of
motifs found among all members of a given protein family. Four
phylogenetically distributed sets of sequences from the hemoglobin, kinase,
aspartic acid protease, and ribonuclease H protein families were used to
test the methods. The performance of all 12 methods was affected by (1) the
number of sequences in the test sets, (2) the degree of similarity among
the sequences, and (3) the number of indels required to produce a multiple
alignment. Global methods generally performed better than local methods in
the detection of motif patterns.
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Ekatherina Serysheva Hebist Berhane Luca Grumolato Kubilay Demir Sophie Balmer Maxime Bodak Michael Boutros Stuart Aaronson Marek Mlodzik Andreas Jenny 《EMBO reports》2013,14(8):718-725
Wnt/β-catenin signalling is central to development and its regulation is essential in preventing cancer. Using phosphorylation of Dishevelled as readout of pathway activation, we identified Drosophila Wnk kinase as a new regulator of canonical Wnt/β-catenin signalling. WNK kinases are known for regulating ion co-transporters associated with hypertension disorders. We demonstrate that wnk loss-of-function phenotypes resemble canonical Wnt pathway mutants, while Wnk overexpression causes gain-of-function canonical Wnt-signalling phenotypes. Importantly, knockdown of human WNK1 and WNK2 also results in decreased Wnt signalling in mammalian cell culture, suggesting that Wnk kinases have a conserved function in ensuring peak levels of canonical Wnt signalling. 相似文献
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Background
Malaria elimination requires successful nationwide control efforts. Detecting the spatiotemporal distribution and mapping high-risk areas are useful to effectively target pockets of malaria endemic regions for interventions.Objective
The aim of the study was to identify patterns of malaria distribution by space and time in unstable malaria transmission areas in northwest Ethiopia.Methods
Data were retrieved from the monthly reports stored in the district malaria offices for the period between 2003 and 2012. Eighteen districts in the highland and fringe malaria areas were included and geo-coded for the purpose of this study. The spatial data were created in ArcGIS10 for each district. The Poisson model was used by applying Kulldorff methods using the SaTScan™ software to analyze the purely temporal, spatial and space-time clusters of malaria at a district levels.Results
The study revealed that malaria case distribution has spatial, temporal, and spatiotemporal heterogeneity in unstable transmission areas. Most likely spatial malaria clusters were detected at Dera, Fogera, Farta, Libokemkem and Misrak Este districts (LLR =197764.1, p<0.001). Significant spatiotemporal malaria clusters were detected at Dera, Fogera, Farta, Libokemkem and Misrak Este districts (LLR=197764.1, p<0.001) between 2003/1/1 and 2012/12/31. A temporal scan statistics identified two high risk periods from 2009/1/1 to 2010/12/31 (LLR=72490.5, p<0.001) and from 2003/1/1 to 2005/12/31 (LLR=26988.7, p<0.001).Conclusion
In unstable malaria transmission areas, detecting and considering the spatiotemporal heterogeneity would be useful to strengthen malaria control efforts and ultimately achieve elimination. 相似文献5.
Silvia Pineiro Ashvini Chauhan Timkhite-kulu Berhane Rana Athar Guili Zheng Cynthia Wang Tamar Dickerson Xiaobing Liang Despoina S. Lymperopoulou Huan Chen Mary Christman Clifford Louime Wisal Babiker O. Colin Stine Henry N. Williams 《Microbial ecology》2013,65(3):652-660
The predatory Bacteriovorax are Gram-negative bacteria ubiquitous in saltwater systems that prey upon other Gram-negative bacteria in a similar manner to the related genus Bdellovibrio. Among the phylogenetically defined clusters of Bacteriovorax, cluster V has only been isolated from estuaries suggesting that it may be a distinct estuarine phylotype. To assess this hypothesis, the spatial and temporal distribution of cluster V and other Bacteriovorax phylogenetic assemblages along the salinity gradient of Chesapeake Bay were determined. Cluster V was expected to be found in significantly greater numbers in low to moderate salinity waters compared to high salinity areas. The analyses of water and sediment samples from sites in the bay revealed cluster V to be present at the lower salinity and not high salinity sites, consistent with it being an estuarine phylotype. Cluster IV had a similar distribution pattern and may also be specifically adapted to estuaries. While the distribution of clusters V and IV were similar for salinity, they were distinct on temperature gradients, being found in cooler and in warmer temperatures, respectively. The differentiation of phylotype populations along the salinity and temporal gradients in Chesapeake Bay revealed distinct niches inhabited by different phylotypes of Bacteriovorax and unique estuarine phylotypes. 相似文献
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Background
Diabetes mellitus is becoming one of the major causes of premature adult mortality in developing countries. However, there is a very little documentation of the morbidity trend in such countries.Objective
To assess the ten-year trend of diabetes mellitus at Gondar University Teaching Referral Hospital, northwest Ethiopia.Methods
A hospital-based retrospective record review was done at the main referral hospital in northwest Ethiopia. Data were obtained from medical records of all registered diabetic patients in the Diabetic Follow up Clinic between 2000 and 2009. An Extended Mantel-Haenzel chi-square test for the linear trend was used to examine the trend over time.Result
Out of the total 354,524 patients who visited the Outpatient Department of the hospital during the study period, 1553 (4.4/1000) were diabetes patients, of which 50.1% was type 1 and 49.9% type 2 diabetes mellitus. The average increase in the proportion of both Type 1 and Type 2 diabetes mellitus cases between 2000 and 2009 was 125%. The mean (±SD) age for Type 1 diabetes mellitus was 29.1 (±12), and 53.5 (±12) for Type 2 diabetes. Overall 42.5% of the diabetes mellitus patients were female and 31.7% were rural residents. The mean body mass index for both type of diabetes mellitus increased from 15.9 to 18.3 kg for type 1 and from 23.8 to 24.6 for type 2 between 2000 and 2009, respectively.Conclusion
The number of diabetes mellitus cases seen at Gondar Referral Hospital is rising steadily. A comprehensive diabetes prevention, treatment, and care program is needed to improve the quality of life of the increasing diabetes mellitus cases in Ethiopia. 相似文献7.
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The African Black Oystercatcher Haematopus moquini is a charismatic, southern African near-endemic, wader species, that is often seen as a flagship species for coastal bird conservation, as it was recently down-listed regionally to Least Concern on the IUCN Red List of Threatened Species. To celebrate this rare conservation success story, BirdLife South Africa named it the 2018 Bird of the Year and ran a year-long programme in collaboration with the Nature’s Valley Trust highlighting aspects of the species’ biology, current threats, and conservation success. We used data collected by the Southern African Bird Atlas Project (SABAP1 and SABAP2) to examine changes in the species’ range and relative abundance, both in the records between the two projects, as well as trends within the SABAP2 sampling period (2008–2017). This case study enabled us to assess whether such metrics can accurately reflect abundance and distributional changes in a species. We found increases in the reported range and the reporting rates between the two Atlas projects, and that the SABAP2 reporting rate was stable. Regionally, across four coastal categories, the reporting rate was lowest in KwaZulu-Natal, though this region also showed an increase in the probability of reporting during the SABAP2 period. While corroborating the recent change in the species’ conservation status, we also provide good evidence that the long-term SABAP data can be used successfully to assess population trends and range changes over time. 相似文献
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We propose a two-stage model for time series data of counts from multiple locations. This method fits first-stage model(s) using the technique of iteratively weighted filtered least squares (IWFLS) to obtain location-specific intercepts and slopes, with possible lagged effects via polynomial distributed lag modeling. These slopes and/or intercepts are then taken to a second-stage mixed-effects meta-regression model in order to stabilize results from various locations. The representation of the models from the stages into a combined mixed-effects model, issues of inference and choices of the parameters in modeling the lag structure are discussed. We illustrate this proposed model via detailed analysis on the effect of air pollution on school absenteeism based on data from the Southern California Children's Health Study. 相似文献