Optimization of the RNeasy Mini Kit to obtain high-quality total RNA from sessile cells of Staphylococcus aureus

Biofilm formed by Staphylococcus aureus is considered an important virulence trait in the pathogenesis of infections associated with implantable medical devices. Gene expression analyses are important strategies for determining the mechanisms involved in production and regulation of biofilm. Obtaining intact RNA preparations is the first and most critical step for these studies. In this article, we describe an optimized protocol for obtaining total RNA from sessile cells of S. aureus using the RNeasy Mini Kit. This method essentially consists of a few steps, as follows: 1) addition of acetone-ethanol to sessile cells, 2) lysis with lysostaphin at 37°C/10 min, 3) vigorous mixing, 4) three cycles of freezing and thawing, and 5) purification of the lysate in the RNeasy column. This simple pre-kit procedure yields high-quality total RNA from planktonic and sessile cells of S. aureus.

Synthesis of Short Oligonucleotides on a Soluble Support by the Phosphoramidite Method

In the last decades, the chemical synthesis of short oligonucleotides has become an important aspect of study due to the discovery of new functions for nucleic acids such as antisense oligonucleotides (ASOs), aptamers, DNAzymes, microRNA (miRNA) and small interfering RNA (siRNA). The applications in modern therapies and fundamental medicine on the treatment of different cancer diseases, viral infections and genetic disorders has established the necessity to develop scalable methods for their cheaper and easier industrial manufacture. While small scale solid-phase oligonucleotide synthesis is the method of choice in the field, various challenges still remain associated with the production of short DNA and RNA-oligomers in very large quantities. On the other hand, solution phase synthesis of oligonucleotides offers a more predictable scaling-up of the synthesis and is amenable to standard industrial manufacture techniques. In the present thesis, various protocols for the synthesis of short DNA and RNA oligomers have been studied on a peracetylated and methylated β-cyclodextrin, and also on a pentaerythritol-derived support. On using the peracetylated and methylated β-cyclodextrin soluble supports, the coupling cycle was simplified by replacement of the typical 5′-O-(4,4′-dimethoxytrityl) protecting group with an acid-labile acetal-protected 5′-O-(1-methoxy-1-methylethyl) group, which upon acid-catalyzed methanolysis released easily removable volatile products. For this reason monomeric building blocks 5′-O-(1-methoxy-1-methylethyl) 3′-(2-cyano-ethyl-N,N-diisopropylphosphoramidite) were synthesized. Alternatively, on using the precipitative pentaerythritol support, novel 2´-O-(2-cyanoethyl)-5´-O-(1-methoxy-1-methylethyl) protected phosphoramidite building blocks for RNA synthesis have been prepared and their applicability by the synthesis of a pentamer was demonstrated. Similarly, a method for the preparation of short RNAs from commercially available 5´-O-(4,4´-dimethoxytrityl)-2´-O-(tert-butyldimethyl-silyl)ribonucleoside 3´-(2-cyanoethyl-N,N-diisopropylphosphoramidite) building blocks has been developed

Preparation of powdered egg yolk using a mini spray dryer

Powdered egg is used as an emulsifying agent in emulsion formulations. It is an excellent source of high quality protein, of which the yolk contains 44% and the egg white 56%. Spray drying is a widely applied method for drying aqueous or organic solutions and emulsions in the chemical and food industries. Spray drying can be used to preserve food or simply as a rapid drying method. The objective of this work was to study the viability of obtaining powdered egg yolk powder using a Büchi B-190 Mini Spray Dryer. The egg yolk protein was evaluated by the semi-micro Kjeldahl method. It was concluded that the use of the Büchi B-190 Mini Spray Dryer to produce powdered egg yolk is perfectly feasible.

Capillary electrophoresis: Applicability and method validation for biorefinery analytics

Wood-based bioprocesses present one of the fields of interest with the most potential in the circular economy. Expanding the use of wood raw material in sustainable industrial processes is acknowledged on both a global and a regional scale. This thesis concerns the application of a capillary zone electrophoresis (CZE) method with the aim of monitoring wood-based bioprocesses. The range of detectable carbohydrate compounds is expanded to furfural and polydatin in aquatic matrices. The experimental portion has been conducted on a laboratory scale with samples imitating process samples. This thesis presents a novel strategy for the uncertainty evaluation via in-house validation. The focus of the work is on the uncertainty factors of the CZE method. The CZE equipment is sensitive to ambient conditions. Therefore, a proper validation is essential for robust application. This thesis introduces a tool for process monitoring of modern bioprocesses. As a result, it is concluded that the applied CZE method provides additional results to the analysed samples and that the profiling approach is suitable for detecting changes in process samples. The CZE method shows significant potential in process monitoring because of the capability of simultaneously detecting carbohydrate-related compound clusters. The clusters can be used as summary terms, indicating process variation and drift.

What children value : a scale to guide health promotion programs

Objective. Physical activity is important for the health of all human beings. Although it is important to develop good health promotion programs for children to increase participation in physical activity, to date there appear to be no programs based on what kids value beyond health and physical activity itself. This study proposed to create a scale with strong content and face validity that could uncover what any given population of children value in life regardless of their participation in physical activity and that experts feel could be related to physical activity. These findings will allow the development of targeted health promotion programs to increase children's participation in regular physical activity. Method In this study, a combination of qualitative and quantitative approaches was used. Data were gathered from seven experts in the field, sixty-seven children in grades three to five, five parents, and three teachers. From these data response groupings were created and sent to four experts to be given single word names. The resulting nine theme names were re-worked into "child-friendly" language. Four children were then asked to discuss theme names to see if they liked and understood them. The next step involved asking children and experts to rank order the nine themes, the children in general and the experts in terms of relevance to physical activity. From these results, possible versions of the scale were then created using the combined expert/children rankings. Each version was examined for content validity. Two versions of a scale resulted. These were sent to experts, parents, teachers and children in order to determine which one they liked better and to suggest any foreseeable problems. Once this information was collected, a beta (final prototype) version of the scale was created. Results. Nine common theme names were created from the response groupings. All four children agreed that they did understand and like each of the nine theme names. Experts and teachers agreed that full coverage of the content had been achieved. Children suggested a single wording change from "Being Accepted" to "Being Included". Five themes were selected for inclusion. The beta version of the scale included 12 forced choice statements, the first ten comparing all themes against one another followed by two anchor statements. Conclusion. At the outset it was recognized that it is essential to know what children think is important in their lives in order to serve as potential benefits in the development of effective physical activity promotion programs. This study developed a scale which could be used to determine what a population of children feel is important in order to focus health promotion programs for physical activity. The scale has strong face and content validity.

Method and truth in MÄ dhyamika

Abstract The study was undertaken to identify what motivates registered nurses to participate in continuing education activities. The primary questions were whether basic nursing education, employment status, clinical area, and position, as well as readiness for selfdirected learning influenced Canadian nurses' motivational orientations when deciding to participate in continuing education activities. Other individual differences (e.g., age) were also examined. The sample included 142 registered nurses employed at an urban community hospital. Three instruments were used for data collection: the Education Participation Scale, the Self-Directed Learning Readiness Scale, and a nursing survey consisting of demographic questions. Basic nursing education and employment status did not effect motivational orientation or self-directed learning readiness. Clinical area and level of position significantly influenced nurses' decisions to participate in continuing education activities. Motivational orientation had a significant relationship with selfdirected learning readiness. Implications for practice as a result of this study involves program planning and delivery. The identification of the motivational orientations of participants may assist in the development and delivery of continuing education programs that are beneficial, relevant, and address the identified learning needs of participants. Implications for future research also exist in relation to studying different groups of nurses, for example, registered nursing assistants, and investigating related issues, for example, what are the deterrents to participation in continuing education?

Statistical evaluation of texture analysis from the biocrystallization method

The consumers are becoming more concerned about food quality, especially regarding how, when and where the foods are produced (Haglund et al., 1999; Kahl et al., 2004; Alföldi, et al., 2006). Therefore, during recent years there has been a growing interest in the methods for food quality assessment, especially in the picture-development methods as a complement to traditional chemical analysis of single compounds (Kahl et al., 2006). The biocrystallization as one of the picture-developing method is based on the crystallographic phenomenon that when crystallizing aqueous solutions of dihydrate CuCl2 with adding of organic solutions, originating, e.g., from crop samples, biocrystallograms are generated with reproducible crystal patterns (Kleber & Steinike-Hartung, 1959). Its output is a crystal pattern on glass plates from which different variables (numbers) can be calculated by using image analysis. However, there is a lack of a standardized evaluation method to quantify the morphological features of the biocrystallogram image. Therefore, the main sakes of this research are (1) to optimize an existing statistical model in order to describe all the effects that contribute to the experiment, (2) to investigate the effect of image parameters on the texture analysis of the biocrystallogram images, i.e., region of interest (ROI), color transformation and histogram matching on samples from the project 020E170/F financed by the Federal Ministry of Food, Agriculture and Consumer Protection(BMELV).The samples are wheat and carrots from controlled field and farm trials, (3) to consider the strongest effect of texture parameter with the visual evaluation criteria that have been developed by a group of researcher (University of Kassel, Germany; Louis Bolk Institute (LBI), Netherlands and Biodynamic Research Association Denmark (BRAD), Denmark) in order to clarify how the relation of the texture parameter and visual characteristics on an image is. The refined statistical model was accomplished by using a lme model with repeated measurements via crossed effects, programmed in R (version 2.1.0). The validity of the F and P values is checked against the SAS program. While getting from the ANOVA the same F values, the P values are bigger in R because of the more conservative approach. The refined model is calculating more significant P values. The optimization of the image analysis is dealing with the following parameters: ROI(Region of Interest which is the area around the geometrical center), color transformation (calculation of the 1 dimensional gray level value out of the three dimensional color information of the scanned picture, which is necessary for the texture analysis), histogram matching (normalization of the histogram of the picture to enhance the contrast and to minimize the errors from lighting conditions). The samples were wheat from DOC trial with 4 field replicates for the years 2003 and 2005, “market samples”(organic and conventional neighbors with the same variety) for 2004 and 2005, carrot where the samples were obtained from the University of Kassel (2 varieties, 2 nitrogen treatments) for the years 2004, 2005, 2006 and “market samples” of carrot for the years 2004 and 2005. The criterion for the optimization was repeatability of the differentiation of the samples over the different harvest(years). For different samples different ROIs were found, which reflect the different pictures. The best color transformation that shows efficiently differentiation is relied on gray scale, i.e., equal color transformation. The second dimension of the color transformation only appeared in some years for the effect of color wavelength(hue) for carrot treated with different nitrate fertilizer levels. The best histogram matching is the Gaussian distribution. The approach was to find a connection between the variables from textural image analysis with the different visual criteria. The relation between the texture parameters and visual evaluation criteria was limited to the carrot samples, especially, as it could be well differentiated by the texture analysis. It was possible to connect groups of variables of the texture analysis with groups of criteria from the visual evaluation. These selected variables were able to differentiate the samples but not able to classify the samples according to the treatment. Contrarily, in case of visual criteria which describe the picture as a whole there is a classification in 80% of the sample cases possible. Herewith, it clearly can find the limits of the single variable approach of the image analysis (texture analysis).

Aplicación de una técnica mínimamente invasiva para la reparación de ruptura del tendón de Aquiles

Introducción Las rupturas agudas del tendón de Aquiles se presentan en pacientes entre 40 y 50 años. Las causas más comunes son actividades deportivas. Se han descrito técnicas mínimamente invasivas, con complicaciones como infección del sitio operatorio, adherencias y la lesión del nervio sural. El propósito de este estudio es determinar el desenlace clínico y funcional, de los pacientes con rupturas agudas del tendón de Aquiles llevados a reparación quirúrgica mínimamente invasiva entre 2011 y 2013 en nuestra institución. Materiales y métodos. Estudio tipo Serie de casos. Se realizó evaluación de fuerza muscular, fatiga muscular, arcos de movilidad con respecto a la extremidad contralateral, la escala AOFAS y se describieron las complicaciones. Resultados. Se evaluaron 21 pacientes de 31 elegibles, diecisiete hombres y cuatro mujeres. Edad promedio de 42,7 años, duración promedio de seguimiento de 17,47 meses. Como complicación hubo una dehiscencia de sutura treinta días después del procedimiento. Los pacientes regresaron a actividades laborales 48 días después de cirugía. El tiempo promedio de retorno a actividades deportivas fue de 8.47 meses. El puntaje promedio en la escala AOFAS fue 90. Los arcos de movilidad del tobillo fueron en promedio de 52° para el lado afectado y 56° en el no intervenido. El número de repeticiones de elevación de talón de la extremidad afectada fue de 58 en promedio. Discusión. Estos resultados sugieren que la técnica mínimamente invasiva para reparación del tendón de Aquiles provee resultados funcionales satisfactorios a corto y mediano plazo con bajas tasas de complicación.

Prevalencia de delirium en población adulta en cuidado intensivo.

Introducción: El delirium es un trastorno de conciencia de inicio agudo asociado a confusión o disfunción cognitiva, se puede presentar hasta en 42% de pacientes, de los cuales hasta el 80% ocurren en UCI. El delirium aumenta la estancia hospitalaria, el tiempo de ventilación mecánica y la morbimortalidad. Se pretendió evaluar la prevalencia de periodo de delirium en adultos que ingresaron a la UCI en un hospital de cuarto nivel durante 2012 y los factores asociados a su desarrollo. Metodología Se realizó un estudio transversal con corte analítico, se incluyeron pacientes hospitalizados en UCI médica y UCI quirúrgica. Se aplicó la escala de CAM-ICU y el Examen Mínimo del Estado Mental para evaluar el estado mental. Las asociaciones significativas se ajustaron con análisis multivariado. Resultados: Se incluyeron 110 pacientes, el promedio de estancia fue 5 días; la prevalencia de periodo de delirium fue de 19.9%, la mediana de edad fue 64.5 años. Se encontró una asociación estadísticamente significativa entre el delirium y la alteración cognitiva de base, depresión, administración de anticolinérgicos y sepsis (p< 0,05). Discusión Hasta la fecha este es el primer estudio en la institución. La asociación entre delirium en la UCI y sepsis, uso de anticolinérgicos, y alteración cognitiva de base son consistentes y comparables con factores de riesgo descritos en la literatura mundial.

Efficient topology estimation for large scale optical mapping

Large scale image mosaicing methods are in great demand among scientists who study different aspects of the seabed, and have been fostered by impressive advances in the capabilities of underwater robots in gathering optical data from the seafloor. Cost and weight constraints mean that lowcost Remotely operated vehicles (ROVs) usually have a very limited number of sensors. When a low-cost robot carries out a seafloor survey using a down-looking camera, it usually follows a predetermined trajectory that provides several non time-consecutive overlapping image pairs. Finding these pairs (a process known as topology estimation) is indispensable to obtaining globally consistent mosaics and accurate trajectory estimates, which are necessary for a global view of the surveyed area, especially when optical sensors are the only data source. This thesis presents a set of consistent methods aimed at creating large area image mosaics from optical data obtained during surveys with low-cost underwater vehicles. First, a global alignment method developed within a Feature-based image mosaicing (FIM) framework, where nonlinear minimisation is substituted by two linear steps, is discussed. Then, a simple four-point mosaic rectifying method is proposed to reduce distortions that might occur due to lens distortions, error accumulation and the difficulties of optical imaging in an underwater medium. The topology estimation problem is addressed by means of an augmented state and extended Kalman filter combined framework, aimed at minimising the total number of matching attempts and simultaneously obtaining the best possible trajectory. Potential image pairs are predicted by taking into account the uncertainty in the trajectory. The contribution of matching an image pair is investigated using information theory principles. Lastly, a different solution to the topology estimation problem is proposed in a bundle adjustment framework. Innovative aspects include the use of fast image similarity criterion combined with a Minimum spanning tree (MST) solution, to obtain a tentative topology. This topology is improved by attempting image matching with the pairs for which there is the most overlap evidence. Unlike previous approaches for large-area mosaicing, our framework is able to deal naturally with cases where time-consecutive images cannot be matched successfully, such as completely unordered sets. Finally, the efficiency of the proposed methods is discussed and a comparison made with other state-of-the-art approaches, using a series of challenging datasets in underwater scenarios

Large-Scale Surface registration

The first part of this work presents an accurate analysis of the most relevant 3D registration techniques, including initial pose estimation, pairwise registration and multiview registration strategies. A new classification has been proposed, based on both the applications and the approach of the methods that have been discussed. The main contribution of this thesis is the proposal of a new 3D multiview registration strategy. The proposed approach detects revisited regions obtaining cycles of views that are used to reduce the inaccuracies that may exist in the final model due to error propagation. The method takes advantage of both global and local information of the registration process, using graph theory techniques in order correlate multiple views and minimize the propagated error by registering the views in an optimal way. The proposed method has been tested using both synthetic and real data, in order to show and study its behavior and demonstrate its reliability.

Patch Scale Nest-Site Selection by Marbled Murrelets (Brachyramphus marmoratus)

The Marbled Murrelet (Brachyramphus marmoratus) is a threatened alcid that nests almost exclusively in old-growth forests along the Pacific coast of North America. Nesting habitat has significant economic importance. Murrelet nests are extremely difficult and costly to find, which adds uncertainty to management and conservation planning. Models based on air photo interpretation of forest cover maps or assessments by low-level helicopter flights are currently used to rank presumed Marbled Murrelet nesting habitat quality in British Columbia. These rankings are assumed to correlate with nest usage and murrelet breeding productivity. Our goal was to find the models that best predict Marbled Murrelet nesting habitat in the ground-accessible portion of the two regions studied. We generated Resource Selection Functions (RSF) using logistic regression models of ground-based forest stand variables gathered at plots around 64 nests, located using radio-telemetry, versus 82 random habitat plots. The RSF scores are proportional to the probability of nests occurring in a forest patch. The best models differed somewhat between the two regions, but include both ground variables at the patch scale (0.2-2.0 ha), such as platform tree density, height and trunk diameter of canopy trees and canopy complexity, and landscape scale variables such as elevation, aspect, and slope. Collecting ground-based habitat selection data would not be cost-effective for widespread use in forestry management; air photo interpretation and low-level aerial surveys are much more efficient methods for ranking habitat suitability on a landscape scale. This study provides one method for ground-truthing the remote methods, an essential step made possible using the numerical RSF scores generated herein.

Sensitivity of large-scale atmospheric analyses to humidity observations and its impact on the global water cycle and tropical and extratropical weather systems in ERA40

Reanalysis data obtained from data assimilation are increasingly used for diagnostic studies of the general circulation of the atmosphere, for the validation of modelling experiments and for estimating energy and water fluxes between the Earth surface and the atmosphere. Because fluxes are not specifically observed, but determined by the data assimilation system, they are not only influenced by the utilized observations but also by model physics and dynamics and by the assimilation method. In order to better understand the relative importance of humidity observations for the determination of the hydrological cycle, in this paper we describe an assimilation experiment using the ERA40 reanalysis system where all humidity data have been excluded from the observational data base. The surprising result is that the model, driven by the time evolution of wind, temperature and surface pressure, is able to almost completely reconstitute the large-scale hydrological cycle of the control assimilation without the use of any humidity data. In addition, analysis of the individual weather systems in the extratropics and tropics using an objective feature tracking analysis indicates that the humidity data have very little impact on these systems. We include a discussion of these results and possible consequences for the way moisture information is assimilated, as well as the potential consequences for the design of observing systems for climate monitoring. It is further suggested, with support from a simple assimilation study with another model, that model physics and dynamics play a decisive role for the hydrological cycle, stressing the need to better understand these aspects of model parametrization. .

On the generation mechanisms of short-scale unbalanced modes in rotating two-layer flows with vertical shear

We report on the results of a laboratory investigation using a rotating two-layer annulus experiment, which exhibits both large-scale vortical modes and short-scale divergent modes. A sophisticated visualization method allows us to observe the flow at very high spatial and temporal resolution. The balanced long-wavelength modes appear only when the Froude number is supercritical (i.e. $F\,{>}\,F_\mathrm{critical}\,{\equiv}\, \upi^2/2$), and are therefore consistent with generation by a baroclinic instability. The unbalanced short-wavelength modes appear locally in every single baroclinically unstable flow, providing perhaps the first direct experimental evidence that all evolving vortical flows will tend to emit freely propagating inertia–gravity waves. The short-wavelength modes also appear in certain baroclinically stable flows. We infer the generation mechanisms of the short-scale waves, both for the baro-clinically unstable case in which they co-exist with a large-scale wave, and for the baroclinically stable case in which they exist alone. The two possible mechanisms considered are spontaneous adjustment of the large-scale flow, and Kelvin–Helmholtz shear instability. Short modes in the baroclinically stable regime are generated only when the Richardson number is subcritical (i.e. $\hbox{\it Ri}\,{<}\,\hbox{\it Ri}_\mathrm{critical}\,{\equiv}\, 1$), and are therefore consistent with generation by a Kelvin–Helmholtz instability. We calculate five indicators of short-wave generation in the baroclinically unstable regime, using data from a quasi-geostrophic numerical model of the annulus. There is excellent agreement between the spatial locations of short-wave emission observed in the laboratory, and regions in which the model Lighthill/Ford inertia–gravity wave source term is large. We infer that the short waves in the baroclinically unstable fluid are freely propagating inertia–gravity waves generated by spontaneous adjustment of the large-scale flow.

Comparing sampling needs for variograms of soil properties computed by the method of moments and residual maximum likelihood

It has been generally accepted that the method of moments (MoM) variogram, which has been widely applied in soil science, requires about 100 sites at an appropriate interval apart to describe the variation adequately. This sample size is often larger than can be afforded for soil surveys of agricultural fields or contaminated sites. Furthermore, it might be a much larger sample size than is needed where the scale of variation is large. A possible alternative in such situations is the residual maximum likelihood (REML) variogram because fewer data appear to be required. The REML method is parametric and is considered reliable where there is trend in the data because it is based on generalized increments that filter trend out and only the covariance parameters are estimated. Previous research has suggested that fewer data are needed to compute a reliable variogram using a maximum likelihood approach such as REML, however, the results can vary according to the nature of the spatial variation. There remain issues to examine: how many fewer data can be used, how should the sampling sites be distributed over the site of interest, and how do different degrees of spatial variation affect the data requirements? The soil of four field sites of different size, physiography, parent material and soil type was sampled intensively, and MoM and REML variograms were calculated for clay content. The data were then sub-sampled to give different sample sizes and distributions of sites and the variograms were computed again. The model parameters for the sets of variograms for each site were used for cross-validation. Predictions based on REML variograms were generally more accurate than those from MoM variograms with fewer than 100 sampling sites. A sample size of around 50 sites at an appropriate distance apart, possibly determined from variograms of ancillary data, appears adequate to compute REML variograms for kriging soil properties for precision agriculture and contaminated sites. (C) 2007 Elsevier B.V. All rights reserved.