An optimized relational database for querying structural patterns in proteins.

A database is an essential component in almost any software system, and its creation involves more than just data modeling and schema design. It also includes query optimization and tuning. This paper focuses on a web system called GSP4PDB, which is used for searching structural patterns in proteins. The system utilizes a normalized relational database, which has proven to be inefficient even for simple queries. This article discusses the optimization of the GSP4PDB database by implementing two techniques: denormalization and indexing. The empirical evaluation described in the article shows that combining these techniques enhances the efficiency of the database when querying both real and artificial graph-based structural patterns.

Determining future aflatoxin contamination risk scenarios for corn in Southern Georgia, USA using spatio-temporal modelling and future climate simulations.

Aflatoxins (AFs) are produced by fungi in crops and can cause liver cancer. Permitted levels are legislated and batches of grain are rejected based on average concentrations. Corn grown in Southern Georgia (GA), USA, which experiences drought during the mid-silk growth period in June, is particularly susceptible to infection by Aspergillus section Flavi species which produce AFs. Previous studies showed strong association between AFs and June weather. Risk factors were developed: June maximum temperatures > 33 °C and June rainfall < 50 mm, the 30-year normals for the region. Future climate data were estimated for each year (2000-2100) and county in southern GA using the RCP 4.5 and RCP 8.5 emissions scenarios. The number of counties with June maximum temperatures > 33 °C and rainfall < 50 mm increased and then plateaued for both emissions scenarios. The percentage of years thresholds were exceeded was greater for RCP 8.5 than RCP 4.5. The spatial distribution of high-risk counties changed over time. Results suggest corn growth distribution should be changed or adaptation strategies employed like planting resistant varieties, irrigating and planting earlier. There were significantly more counties exceeding thresholds in 2010-2040 compared to 2000-2030 suggesting that adaptation strategies should be employed as soon as possible.

Investigation of the Environmental and Socio-Economic Characteristics of Counties with a High Asthma Burden to Focus Asthma Action in Utah.

Rising adult asthma prevalence (AAP) rates and asthma emergency room (AER) visits constitute a large burden on public health in Utah (UT), a high-altitude state in the Great Basin Desert, USA. This warrants an investigation of the characteristics of the counties with the highest asthma burden within UT to improve allocation of health resources and for planning. The relations between several predictor environmental, health behavior and socio-economic variables and two health outcome variables, AAP and AER visits, were investigated for UT's 29 counties. Non-parametric statistical comparison tests, correlation and linear regression analysis were used to determine the factors significantly associated with AER visits and AAP. Regression kriging with Utah small area data (USAD) as well as socio-economic and pollution data enabled local Moran's I cluster analysis and the investigation of moving correlations between health outcomes and risk factors. Results showed the importance of desert/mining dust and socio-economic status as AAP and AER visits were greatest in the south of the state, highlighting a marked north-south divide in terms of these factors within the state. USAD investigations also showed marked differences in pollution and socio-economic status associated with AAP within the most populous northern counties. Policies and interventions need to address socio-economic inequalities within counties and between the north and south of the state. Fine (PM2.5) and coarse (PM10) particulate matter monitors should be installed in towns in central and southern UT to monitor air quality as these are sparse, but in the summer, air quality can be worse here. Further research into spatiotemporal variation in air quality within UT is needed to inform public health interventions such as expanding clean fuel programs and targeted land-use policies. Efforts are also needed to examine barriers to routine asthma care.

Spatial analysis of drug poisoning deaths in the American west: A comparison study using profile regression to adjust for collinearity and spatial correlation.

BACKGROUND: The USA has seen dramatic increases in drug poisoning deaths (DPD) recently. State-level rates have responded to federal and state initiatives, yet the counties with the highest rates are stable. Spatial analysis enables investigators to identify the highest risk counties and most important risk factors, although results are often confounded by spatial autocorrelation and multicollinearity. METHODS: Profile regression (PR) is an integrated method for cluster and regression analysis, which adjusts for spatial-autocorrelation and multi-collinearity. RESULTS: With PR, three clusters were identified in the Western USA with most of NM, NV and UT and several counties in AZ, CO, ID and WY being high-risk. Cluster analysis in a previous study only identified high-risk counties in northern CA, NM and NV. Elevation, suicide and LDS population were positively, and population density was negatively linked with DPD for PR and standard regression (SR) showing differences between the mountain west and coastal areas. Complex relationships between DPD and several variables were identified by PR which was not possible with SR. CONCLUSIONS: Statistically principled methods like PR are needed for appropriate identification of the highest risk counties and important risk factors given the complex relationships with DPD. Funding for prevention, education and medical services should be targeted at rural, mountain communities in the west which have high %LDS and suicide rates. Counties with high %poverty and %Hispanic were also at high-risk. Individual-level studies are needed to confirm important risk factors in high-risk counties.

Modeling the spatial distribution of African buffalo (Syncerus caffer) in the Kruger National Park, South Africa.

The population density of wildlife reservoirs contributes to disease transmission risk for domestic animals. The objective of this study was to model the African buffalo distribution of the Kruger National Park. A secondary objective was to collect field data to evaluate models and determine environmental predictors of buffalo detection. Spatial distribution models were created using buffalo census information and archived data from previous research. Field data were collected during the dry (August 2012) and wet (January 2013) seasons using a random walk design. The fit of the prediction models were assessed descriptively and formally by calculating the root mean square error (rMSE) of deviations from field observations. Logistic regression was used to estimate the effects of environmental variables on the detection of buffalo herds and linear regression was used to identify predictors of larger herd sizes. A zero-inflated Poisson model produced distributions that were most consistent with expected buffalo behavior. Field data confirmed that environmental factors including season (P = 0.008), vegetation type (P = 0.002), and vegetation density (P = 0.010) were significant predictors of buffalo detection. Bachelor herds were more likely to be detected in dense vegetation (P = 0.005) and during the wet season (P = 0.022) compared to the larger mixed-sex herds. Static distribution models for African buffalo can produce biologically reasonable results but environmental factors have significant effects and therefore could be used to improve model performance. Accurate distribution models are critical for the evaluation of disease risk and to model disease transmission.

Spatial analysis of drug poisoning deaths in the American West, particularly Utah.

BACKGROUND: Most states in the Western US have high rates of drug poisoning death (DPD), especially New Mexico, Nevada, Arizona and Utah (UT). This seems paradoxical in UT where illicit drug use, smoking and drinking rates are low. To investigate this, spatial analysis of county level DPD data and other relevant factors in the Western US and UT was undertaken. METHODS: Poisson kriging was used to smooth the DPD data, populate data gaps and improve the reliability of rates recorded in sparsely populated counties. Links between DPD and economic, environmental, health, lifestyle, and demographic factors were investigated at four scales using multiple linear regression. LDS church membership and altitude, factors not previously considered, were included. Spatial change in the strength and sign of relationships was investigated using geographically weighted regression and significant DPD clusters were identified using the Local Moran's I. RESULTS: Economic factors, like the sharp social gradient between rural and urban areas were important to DPD throughout the west. Higher DPD rates were also found in areas of higher elevation and the desert rural areas in the south. The unique characteristics of DPD in UT in terms of health and lifestyle factors, as well as the demographic structure of DPD in the most LDS populous states (UT, Idaho, Wyoming), suggest that high DPD in heavily LDS areas are predominantly prescription opioid related whereas in other Western states a larger proportion of DPD might come from illicit drugs. CONCLUSION: Drug policies need to be adapted to the geographical differences in the dominant type of drug causing death. Educational materials need to be marketed to the demographic groups at greatest risk and take into account differences in population characteristics between and within States. Some suggestions about how such adaptations can be made are given and future research needs outlined.

A comparison of multiple indicator kriging and area-to-point Poisson kriging for mapping patterns of herbivore species abundance in Kruger National Park, South Africa.

Kruger National Park (KNP), South Africa, provides protected habitats for the unique animals of the African savannah. For the past 40 years, annual aerial surveys of herbivores have been conducted to aid management decisions based on (1) the spatial distribution of species throughout the park and (2) total species populations in a year. The surveys are extremely time consuming and costly. For many years, the whole park was surveyed, but in 1998 a transect survey approach was adopted. This is cheaper and less time consuming but leaves gaps in the data spatially. Also the distance method currently employed by the park only gives estimates of total species populations but not their spatial distribution. We compare the ability of multiple indicator kriging and area-to-point Poisson kriging to accurately map species distribution in the park. A leave-one-out cross-validation approach indicates that multiple indicator kriging makes poor estimates of the number of animals, particularly the few large counts, as the indicator variograms for such high thresholds are pure nugget. Poisson kriging was applied to the prediction of two types of abundance data: spatial density and proportion of a given species. Both Poisson approaches had standardized mean absolute errors (St. MAEs) of animal counts at least an order of magnitude lower than multiple indicator kriging. The spatial density, Poisson approach (1), gave the lowest St. MAEs for the most abundant species and the proportion, Poisson approach (2), did for the least abundant species. Incorporating environmental data into Poisson approach (2) further reduced St. MAEs.