New Shuttle Vector-Based Expression System To Generate Polyhistidine-Tagged Fusion Proteins in Staphylococcus aureus and Escherichia coli.

Four Staphylococcus aureus-Escherichia coli shuttle vectors were constructed for gene expression and production of tagged fusion proteins. Vectors pBUS1-HC and pTSSCm have no promoter upstream of the multiple cloning site (MCS), and this allows study of genes under the control of their native promoters, and pBUS1-Pcap-HC and pTSSCm-Pcap contain the strong constitutive promoter of S. aureus type 1 capsule gene 1A (Pcap) upstream of a novel MCS harboring codons for the peptide tag Arg-Gly-Ser-hexa-His (rgs-his6). All plasmids contained the backbone derived from pBUS1, including the E. coli origin ColE1, five copies of terminator rrnB T1, and tetracycline resistance marker tet(L) for S. aureus and E. coli. The minimum pAMα1 replicon from pBUS1 was improved through either complementation with the single-strand origin oriL from pUB110 (pBUS1-HC and pBUS1-Pcap-HC) or substitution with a pT181-family replicon (pTSSCm and pTSSCm-Pcap). The new constructs displayed increased plasmid yield and segregational stability in S. aureus. Furthermore, pBUS1-Pcap-HC and pTSSCm-Pcap offer the potential to generate C-terminal RGS-His6 translational fusions of cloned genes using simple molecular manipulation. BcgI-induced DNA excision followed by religation converts the TGA stop codon of the MCS into a TGC codon and links the rgs-his6 codons to the 3' end of the target gene. The generation of the rgs-his6 codon-fusion, gene expression, and protein purification were demonstrated in both S. aureus and E. coli using the macrolide-lincosamide-streptogramin B resistance gene erm(44) inserted downstream of Pcap. The new His tag expression system represents a helpful tool for the direct analysis of target gene function in staphylococcal cells.

Distributions and Variability of Particulate Organic Matter in a Coastal Upwelling System

In this study we examined the spatial and temporal variability of particulate organic material (POM) off Oregon during the upwelling season. High-resolution vertical profiling of beam attenuation was conducted along two cross-shelf transects. One transect was located in a region where the shelf is relatively uniform and narrow (off Cascade Head (CH)); the second transect was located in a region where the shelf is shallow and wide (off Cape Perpetua (CP)). In addition, water samples were collected for direct analysis of chlorophyll, particulate organic carbon (POC), and particulate organic nitrogen (PON). Beam attenuation was highly correlated with POC and PON. Striking differences in distribution patterns and characteristics of POM were observed between CH and CP. Off CH, elevated concentrations of chlorophyll and POC were restricted to the inner shelf and were highly variable in time. The magnitude of the observed short-term temporal variability was of the same order as that of the seasonal variability reported in previous studies. Elevated concentrations of nondegraded chlorophyll and POM were observed near the bottom. Downwelling and rapid sinking are two mechanisms by which phytoplankton cells can be delivered to the bottom before being degraded. POM may be then transported across the shelf via the benthic nepheloid layer. Along the CP transect, concentrations of POM were generally higher than they were along the CH transect and extended farther across the shelf. Characteristics of surface POM, namely, C: N ratios and carbon: chlorophyll ratios, differed between the two sites. These differences can be attributed to differences in shelf circulation.

Effects of Study Area Size on Geographic Characterizations of Health Events: Prostate Cancer Incidence in Southern New England, USA, 1994-1998.

ABSTRACT : BACKGROUND : We consider how representations of geographic variation in prostate cancer incidence across Southern New England, USA may be affected by selection of study area and/or properties of the statistical analysis. METHOD : A spatial scan statistic was used to monitor geographic variation among 35,167 incident prostate cancer cases diagnosed in Massachusetts, Connecticut and Rhode Island from 1994 to 1998, in relation to the 1990 populations of men 20+ years of age living in that region. Results from the combined-states analysis were compared to those from single-states. Impact of scanning procedures set to examine up to 50% or no more than10% of at-risk populations also was evaluated. RESULTS : With scanning set to 50%, 5 locations in the combined-states analysis were identified with markedly distinct incidence rates. Fewer than expected cases were estimated for nearly all Connecticut, Rhode Island and West Central Massachusetts, whereas census tracts on and around Cape Cod, and areas of Southwestern Connecticut and adjacent to greater Boston were estimated to have yielded more than expected incidence. Results of single-state analyses exhibited several discrepancies from the combined-states analysis. More conservative scanning found many more locations with varying incidence, but discrepancies between the combined- and single-state analysis were fewer. CONCLUSION : It is important to acknowledge the conditional nature of spatial analyses and carefully consider whether a true cluster of events is identified or artifact stemming from selection of study area size and/or scanning properties.

Validity and reliability of using MVP 4 Function Walk4Life digital pedometers to assess physical activity levels among preschool-aged Head Start children

The Surgeon General recommends preschoolers 3-5 years old accumulate 60 minutes of moderate-to-vigorous physical activity (MVPA) per day. However, there is limited data measuring physical activity (PA) and MVPA amongst this population. The purpose of this cross-sectional study is to determine the validity, reliability, and feasibility of using MVP 4 Function Walk4Life digital pedometers (MVP-4) in measuring MVPA among preschoolers using the newly modified direct observational technique, System for Observing Fitness Instruction Time-Preschool Version (SOFIT-P) as the gold standard. An ethnically diverse population of 3-5 year old underserved children were recruited from two Harris County Department of Education (HCDE) Head Start centers. For 2 days at baseline and 2 days at post-test, 75 children enrolled wore MVP-4 pedometers for approximately 6-hours per observation day and were observed using SOFIT-P during predominantly active times. Statistical analyses used Pearson "r" correlation coefficients to determine mean minutes of PA and MVPA, convergent and criterion validity, and reliability. Significance was set at p = <0.05. Feasibility was determined through process evaluation information collected during this study via observations from data collectors and teacher input. Results show mean minutes of PA and MVPA ranged between 30-42 and 11-14 minutes, respectively. Convergent validity comparing BMI percentiles with MVP-4 PA outcomes show no significance at pre-test; however, each measurement at post-test showed significance for MVPA (p = 0.0247, p = 0.0056), respectively. Criterion validity comparing percent MVPA time between SOFIT-P and MVP-4 pedometers was determined; however, results deemed insufficient due to inconsistency in observation times while using the newly developed SOFIT-P. Reliability measures show no significance at pre-test, yet show significant results for all PA outcomes at post-test (p = 0.001, p = 0.001, p = 0.0010, p = 0.003), respectively. Finally, MVP-4 pedometers lacked feasibility due to logistical barriers in design. Researchers feel the significant results at post-test are secondary to increased familiarity and more accurate placement of pedometers across time. Researchers suggest manufacturers of MVP-4 pedometers further modify the instrument for ease of use with this population, following which future studies ought to determine validity using objective measures or all-day direct observation techniques.^

Extracto de semillas de vid (Vitis vinifera L.) con actividad antioxidante : eficiencia de diferentes solventes en el proceso de extracción

Los objetivos de este trabajo fueron comparar la eficiencia de diferentes solventes en la extracción de compuestos fenólicos a partir de las semillas de vid; evaluar la actividad antioxidante a través del poder reductor de los extractos obtenidos y analizar el proceso de extracción a diferentes temperaturas, utilizando el solvente más eficiente. Se emplearon semillas de vid cv. Cabernet Sauvignon provenientes de vinificaciones. Los solventes ensayados y las temperaturas de tratamiento fueron los siguientes: agua destilada a 90°C, alcohol metílico al 70% a 30°C, acetona al 75% a 30°C y alcohol etílico al 20% a 30°C. La concentración de los compuestos fenólicos fue determinada por el método de Folin-Ciocalteu. La actividad antioxidante se determinó midiendo el poder reductor, por el método de Oyaizu. El agua a 90°C fue el solvente más eficiente para la extracción de compuestos fenólicos de las semillas de la vid (12,587 mg/g de materia seca). La acetona 75% a 30°C extrajo 7,268 mg de compuestos fenólicos / g de materia seca, el metanol al 70% a 30°C extrajo 0,963 mg de compuestos fenólicos / g de materia seca y el etanol al 20% a 30°C extrajo 0,799 mg de compuestos fenólicos / g de materia seca. Se estudió el proceso de extracción empleando agua a 60 y a 90°C. El agua a 90°C extrajo aproximadamente cinco veces más polifenoles que el agua a 60°C, después de cinco horas de tratamiento.

Extracto de semillas de vid (Vitis vinifera L.) con actividad antioxidante : concentración, deshidratación y comparación con antioxidantes de uso comercial

Los objetivos de este trabajo fueron: 1) Evaluar un proceso de concentración y deshidratación de un extracto polifenólico de semillas de vid (Vitis vinifera L.). El proceso debía conservar el poder reductor del extracto. 2) Valorar la eficiencia del antioxidante obtenido por comparación con antioxidantes de uso habitual en un producto vegetal susceptible de ser oxidado, tal como el jugo de manzanas. El extracto de semillas de vid fue concentrado a 60°C en un concentrador rotativo al vacío de laboratorio. La concentración de los compuestos fenólicos fue determinada por el método de Folin-Ciocalteu modificado. La actividad antioxidante se determinó midiendo el poder reductor, por el método de Oyaizu. La oxidación del jugo de manzanas se determinó por el método de Özoglu. El extracto concentrado obtenido fue deshidratado por dos métodos: liofilización y secado en lecho de espuma. A igual concentración fenólica, el extracto concentrado mostró mayor capacidad antioxidante que el extracto simple. El extracto secado en lecho de espuma conservó la misma capacidad antioxidante que el extracto concentrado. El extracto liofilizado experimentó una pérdida significativa de la actividad antioxidante. El extracto concentrado de semillas de vid inhibió la oxidación del jugo de manzanas en un 31,51%, el ácido ascórbico en un 2,60% y el dióxido de azufre en un 97,40%.

Effect of Prosopis flexuosa on understory species and its importance to pastoral management in woodlands of the Central Monte Desert

In the Monte Biogeographic Province, located in the arid region of Argentina, the presence of Prosopis flexuosa DC. produces spatial heterogeneity through edaphic modifications and microclimate changes. This results in vegetation patches differing in species composition and abundance. However, this interaction can be modified by the occurrence of gradients of biotic stress or disturbance intensity. In particular, grazing has been observed to enhance or reduce vegetation heterogeneity. Such complex of interactions could determine forage availability for cattle in one of the driest areas of the Monte Desert. We assessed the effect of Prosopis on understory species and analyzed whether the outcomes of this interaction differed with distance to watering points, as a proxy of grazing intensity, in the Northeast of Mendoza Province, Argentina. We used a two-way factorial design including the following factors: 1) microsite (under the cover of P. flexuosa trees and in intercanopy microsites) and 2) distance to watering points ("near the watering point", 500-700 m away, and "far from the watering point", 3-4 km away). Cover of each species, total cover, bare soil, and litter were recorded, and plant diversity, richness, and evenness were estimated with the modified Point Quadrat method. Results showed that P. flexuosa cover, distance from watering points, and the interaction between them determined species composition, abundance and spatial distribution of understory species, and were, consequently, a determining factor for forage availability. The presence of P. flexuosa enhances carrying capacity by supporting higher abundance of grasses under its canopy. Near watering points, high grazing intensity appears to disrupt the patches formed under P. flexuosa canopies, reducing the differences between microsites.

Estimation of the normal boiling point of organic compounds via group contributions

The normal boiling point is a fundamental thermo-physical property, which is important in describing the transition between the vapor and liquid phases. Reliable method which can predict it is of great importance, especially for compounds where there are no experimental data available. In this work, an improved group contribution method, which is second order method, for determination of the normal boiling point of organic compounds based on the Joback functional first order groups with some changes and added some other functional groups was developed by using experimental data for 632 organic components. It could distinguish most of structural isomerism and stereoisomerism, which including the structural, cis- and trans- isomers of organic compounds. First and second order contributions for hydrocarbons and hydrocarbon derivatives containing carbon, hydrogen, oxygen, nitrogen, sulfur, fluorine, chlorine and bromine atoms, are given. The fminsearch mathematical approach from MATLAB software is used in this study to select an optimal collection of functional groups (65 functional groups) and subsequently to develop the model. This is a direct search method that uses the simplex search method of Lagarias et al. The results of the new method are compared to the several currently used methods and are shown to be far more accurate and reliable. The average absolute deviation of normal boiling point predictions for 632 organic compounds is 4.4350 K; and the average absolute relative deviation is 1.1047 %, which is of adequate accuracy for many practical applications.

Code and readme of a MATLAB-based graphical user interface program for computing functionals of the geopotential

We present a novel graphical user interface program GrafLab (GRAvity Field LABoratory) for spherical harmonic synthesis (SHS) created in MATLAB®. This program allows to comfortably compute 38 various functionals of the geopotential up to ultra-high degrees and orders of spherical harmonic expansion. For the most difficult part of the SHS, namely the evaluation of the fully normalized associated Legendre functions (fnALFs), we used three different approaches according to required maximum degree: (i) the standard forward column method (up to maximum degree 1800, in some cases up to degree 2190); (ii) the modified forward column method combined with Horner's scheme (up to maximum degree 2700); (iii) the extended-range arithmetic (up to an arbitrary maximum degree). For the maximum degree 2190, the SHS with fnALFs evaluated using the extended-range arithmetic approach takes only approximately 2-3 times longer than its standard arithmetic counterpart, i.e. the standard forward column method. In the GrafLab, the functionals of the geopotential can be evaluated on a regular grid or point-wise, while the input coordinates can either be read from a data file or entered manually. For the computation on a regular grid we decided to apply the lumped coefficients approach due to significant time-efficiency of this method. Furthermore, if a full variance-covariance matrix of spherical harmonic coefficients is available, it is possible to compute the commission errors of the functionals. When computing on a regular grid, the output functionals or their commission errors may be depicted on a map using automatically selected cartographic projection.

Ice thickness distribution and glacier bed of Hallstätter Gletscher

Hallstätter Glacier is the northernmost glacier of Austria. Appendant to the northern Limestone Alps, the glacier is located at 47°28'50'' N, 13°36'50'' E in the Dachstein-region. At the same time with its advance linked to the Little Ice Age (LIA), research on changes in size and mass of Hallstätter glacier was started in 1842 by Friedrich Simony. He observed and documented the glacier retreat related to its last maximum extension in 1856. In addition, Hallstätter Glacier is a subject to scientific research to date. In this thesis methods and results of ongoing mass balance measurements are presented and compared to long term volume changes and meteorological observations. The current mass balance monitoring programm using the direct glaciological method was started 2006. In this context, 2009 the ice thickness was measured with ground penetrating radar. The result are used with digital elevation models reconstucted from historical maps and recent digital elevation models to calculate changes in shape and volume of Hallstätter Glacier. Based on current meteorological measurements near the glacier and longtime homogenized climate data provided by HISTALP, time series of precipitation and temperature beginning at the LIA are produced. These monthly precipitation and monthly mean temperature data are used to compare results of a simple degree day model with the volume change calculated from the difference of the digital elevation models. The two years of direct mass balance measurements are used to calibrate the degree day model. A number of possible future scenarios are produced to indicate prospective changes. Within the 150-year-period between 1856 and 2007 the Hallstätter Glacier lost 1940 meters of its length and 2.23 km**2 in area. 37% of the initial volume of 1856 remained. This retreat came along with a change in climate. The application of a running avarage of 30 years shows an increase in precipitation of 18.5% and a warming of 1.3°C near the glacier between 1866 and 1993. The mass loss was continued in the hydrological years 2006/2007 and 2007/2008 showing mean specific mass balance of -376 mm and -700 mm, respectively. Applying a temperature correction for the different minimum elevations of the glacier, the degree day approach based on the two measured mass balances can reproduce sign and order of magnitude of the volume change of Hallstätter Glacier since 1856. Nevertheless, the relative deviation is significant. Future scenarios show, that 30% of the entire glacier volume remains after subtracting the elevation changes between the digital elevation models of 2002 and 2007 ten times from the surface of 2007. The past and present mass changes of Hallstätter Glacier are showing a retreating glacier as a consequence of rising temperatures. Due to high precepitation, increased with previous warming, the Hallstätter Glacier can and will exist in lower elevation compared to inner alpine glaciers.

Temperature, precipitation and Normalized Difference Vegetation Index (NDVI) from 1982 to 2009 in the Koshi River Basin of the Middle Himalayas

The aim of this paper is to find out if there is a significant difference in using NDVI dataset processed by harmonic analysis method to evaluate its dynamic and response to climate change, compared with the original data.

Two way clustering of Microarray Data using a Hybrid Approach

The Microarray technique is rather powerful, as it allows to test up thousands of genes at a time, but this produces an overwhelming set of data files containing huge amounts of data, which is quite difficult to pre-process, separate, classify and correlate for interesting conclusions to be extracted. Modern machine learning, data mining and clustering techniques based on information theory, are needed to read and interpret the information contents buried in those large data sets. Independent Component Analysis method can be used to correct the data affected by corruption processes or to filter the uncorrectable one and then clustering methods can group similar genes or classify samples. In this paper a hybrid approach is used to obtain a two way unsupervised clustering for a corrected microarray data.

Comparison of dynamic effects of high-speed traffic load on ballasted track using a simplified two-dimensional and full three-dimensional model.

The vertical dynamic actions transmitted by railway vehicles to the ballasted track infrastructure is evaluated taking into account models with different degree of detail. In particular, we have studied this matter from a two-dimensional (2D) finite element model to a fully coupled three-dimensional (3D) multi-body finite element model. The vehicle and track are coupled via a non-linear Hertz contact mechanism. The method of Lagrange multipliers is used for the contact constraint enforcement between wheel and rail. Distributed elevation irregularities are generated based on power spectral density (PSD) distributions which are taken into account for the interaction. The numerical simulations are performed in the time domain, using a direct integration method for solving the transient problem due to the contact nonlinearities. The results obtained include contact forces, forces transmitted to the infrastructure (sleeper) by railpads and envelopes of relevant results for several track irregularities and speed ranges. The main contribution of this work is to identify and discuss coincidences and differences between discrete 2D models and continuum 3D models, as wheel as assessing the validity of evaluating the dynamic loading on the track with simplified 2D models

MEDVIR: 3D visual interface applied to gene profile analisys.

The origins for this work arise in response to the increasing need for biologists and doctors to obtain tools for visual analysis of data. When dealing with multidimensional data, such as medical data, the traditional data mining techniques can be a tedious and complex task, even to some medical experts. Therefore, it is necessary to develop useful visualization techniques that can complement the expert’s criterion, and at the same time visually stimulate and make easier the process of obtaining knowledge from a dataset. Thus, the process of interpretation and understanding of the data can be greatly enriched. Multidimensionality is inherent to any medical data, requiring a time-consuming effort to get a clinical useful outcome. Unfortunately, both clinicians and biologists are not trained in managing more than four dimensions. Specifically, we were aimed to design a 3D visual interface for gene profile analysis easy in order to be used both by medical and biologist experts. In this way, a new analysis method is proposed: MedVir. This is a simple and intuitive analysis mechanism based on the visualization of any multidimensional medical data in a three dimensional space that allows interaction with experts in order to collaborate and enrich this representation. In other words, MedVir makes a powerful reduction in data dimensionality in order to represent the original information into a three dimensional environment. The experts can interact with the data and draw conclusions in a visual and quickly way.

A new approach to change detection in multispectral images by means of ERGAS index

In this letter, we propose a novel method for unsupervised change detection (CD) in multitemporal Erreur Relative Globale Adimensionnelle de Synthese (ERGAS) satellite images by using the relative dimensionless global error in synthesis index locally. In order to obtain the change image, the index is calculated around a pixel neighborhood (3x3 window) processing simultaneously all the spectral bands available. With the objective of finding the binary change masks, six thresholding methods are selected. A comparison between the proposed method and the change vector analysis method is reported. The accuracy CD showed in the experimental results demonstrates the effectiveness of the proposed method.