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Selected AbstractsBreast cancer incidence among American Indian and Alaska Native women: US, 1999,2004,,§CANCER, Issue S5 2008Phyllis A. Wingo PhD Abstract BACKGROUND. Breast cancer is a leading cause of cancer morbidity and mortality among American Indian and Alaska Native (AI/AN) women. Although published studies have suggested that breast cancer rates among AI/AN women are lower than those among other racial and ethnic populations, accurate determinations of the breast cancer burden have been hampered by misclassification of AI/AN race. METHODS. Cancer incidence data from the National Program of Cancer Registries and the Surveillance, Epidemiology, and End Results Program were combined to estimate age-adjusted rates for the diagnosis years 1999 through 2004. Several steps were taken to reduce the misclassification of AI/AN race: linking cases to Indian Health Service (IHS) patient services database, restricting analyses to Contract Health Service Delivery Area counties, and stratifying results by IHS region. RESULTS. Breast cancer incidence rates among AI/AN women varied nearly 3-fold across IHS regions. The highest rates were in Alaska (134.8) and the Plains (Northern, 115.9; Southern, 115.7), and the lowest rates were in the Southwest (50.8). The rate in Alaska was similar to the rate among non-Hispanic white (NHW) women in Alaska. Overall, AI/AN women had lower rates of breast cancer than NHW women, but AI/AN women were more likely to be diagnosed with late-stage disease. CONCLUSIONS. To the authors' knowledge, this report provides the most comprehensive breast cancer incidence data for AI/AN women to date. The wide regional variation indicates an important need for etiologic and health services research, and the large percentage of AI/AN women with late-stage disease demands innovative approaches for increasing access to screening. Cancer 2008;113(5 suppl):1191,202. Published 2008 by the American Cancer Society. [source] FAST AND ROBUST INCREMENTAL ACTION PREDICTION FOR INTERACTIVE AGENTSCOMPUTATIONAL INTELLIGENCE, Issue 1 2005Jonathan Dinerstein The ability for a given agent to adapt on-line to better interact with another agent is a difficult and important problem. This problem becomes even more difficult when the agent to interact with is a human, because humans learn quickly and behave nondeterministically. In this paper, we present a novel method whereby an agent can incrementally learn to predict the actions of another agent (even a human), and thereby can learn to better interact with that agent. We take a case-based approach, where the behavior of the other agent is learned in the form of state,action pairs. We generalize these cases either through continuous k -nearest neighbor, or a modified bounded minimax search. Through our case studies, our technique is empirically shown to require little storage, learn very quickly, and be fast and robust in practice. It can accurately predict actions several steps into the future. Our case studies include interactive virtual environments involving mixtures of synthetic agents and humans, with cooperative and/or competitive relationships. [source] Streaming Surface Reconstruction Using WaveletsCOMPUTER GRAPHICS FORUM, Issue 5 2008J. Manson Abstract We present a streaming method for reconstructing surfaces from large data sets generated by a laser range scanner using wavelets. Wavelets provide a localized, multiresolution representation of functions and this makes them ideal candidates for streaming surface reconstruction algorithms. We show how wavelets can be used to reconstruct the indicator function of a shape from a cloud of points with associated normals. Our method proceeds in several steps. We first compute a low-resolution approximation of the indicator function using an octree followed by a second pass that incrementally adds fine resolution details. The indicator function is then smoothed using a modified octree convolution step and contoured to produce the final surface. Due to the local, multiresolution nature of wavelets, our approach results in an algorithm over 10 times faster than previous methods and can process extremely large data sets in the order of several hundred million points in only an hour. [source] An optimal method of DNA silver staining in polyacrylamide gelsELECTROPHORESIS, Issue 8 2007Yun-Tao Ji Abstract A silver staining technique has widely been used to detect DNA fragments with high sensitivity on polyacrylamide gels. The conventional procedure of the silver staining is tedious, which takes about 40,60,min and needs five or six kinds of chemicals and four kinds of solutions. Although our previous improved method reduced several steps, it still needed six kinds of chemicals. The objective of this study was to improve further the existing procedures and develop an optimal method for DNA silver staining on polyacrylamide gels. The novel procedure could be completed with only four chemicals and two solutions within 20,min. The steps of ethanol, acetic acid, and nitric acid precession before silver impregnation have been eliminated and the minimal AgNO3 dose has been used in this up-to-date method. The polyacrylamide gel of the DNA sliver staining displayed a golden yellow and transparent background with high sensitivity. The minimum 0.44 and 3.5,ng of DNA amount could be detected in denaturing and nondenaturing polyacrylamide gel, respectively. This result indicated that our optimal method can save time and cost, and still keep a high sensitivity for DNA staining in polyacrylamide gels. [source] Efficient and sensitive method of DNA silver staining in polyacrylamide gelsELECTROPHORESIS, Issue 1 2005Lujiang Qu Abstract DNA silver staining is widely used to detect DNA fragment in polyacrylamide gel with high sensitivity. Conventional procedures of the silver staining involve several steps, which take about 40 min to 2 h in total. To improve the efficiency of DNA silver staining, a more efficient protocol is developed in this study. The procedure comprises only four steps including impregnating, rinsing, developing, and stopping, and could be completed within 20 min. Nitric acid and ethanol in the silver-impregnation step of the new procedure eliminates the need for prior treatment of gels with a fixing solution and following rinse prior to impregnation with silver. The procedure has high sensitivity and long storage lifetime. The minimum detectable mass of DNA is 0.44 and 3.5 ng in denaturing and nondenaturing polyacrylamide gel, respectively. [source] Data analysis of environmental air pollutant monitoring systems in EuropeENVIRONMETRICS, Issue 6 2004Kristina Voigt Abstract Public access to information about the environment is being strengthened across Europe. The concept of public's right to information gives the basis for the access to environmental information. In this paper the quality of air pollutant monitoring systems in the 15 European member states is analyzed. For pragmatic reasons only the capitals are looked upon. Comprehensive data on environmental monitoring programs concerning air pollutants like ozone (O3), nitrogen dioxide (NO2), nitrogen oxide (NO), carbon dioxide (CO2) and carbon monoxide (CO), and sometimes suspended dust, benzene and other environmental chemicals are available on the free Internet. As different monitoring information systems exist in the European member states a comparison of these systems with their pros and cons is of great interest to the public. Environmental air pollutant monitoring systems in the capitals of the 15 EEC member countries (objects) are evaluated by applying 5 evaluation criteria for the differentiation of these systems. The scores run from 0,=,insufficient, 1,=,medium, to 2,=,excellent. Different data-analysis methods will be applied. As order theory is still not sufficiently presented in the scientific literature, a short overview about the so-called Hasse diagram technique and POSAC method is outlined. In several steps the data-matrix is analyzed coming to the conclusion that all methods (additionally PCA is used) identify one criterion as specifically important. Not unexpected, each method has its own advantage. The aim of this data-analysis is the evaluation of the publicly available air quality monitoring systems in Europe with their pros and cons. This might help the interested public to find and understand the information given on the Internet. Furthermore our evaluation approach might give some recommendations for an improvement of the air quality monitoring systems. Copyright © 2004 John Wiley & Sons, Ltd. [source] Synthesis of Enantiopure Ruthenium Tricarbonyl Complexes of a Bicyclic Cyclopentadienone DerivativeEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 16 2008Min-soo Kim Abstract (,)-Menthone was converted stereoselectively into 3-menthylpropargyl alcohol 8 in several steps and subsequently converted into enantiopure cyclopentadienone ruthenium carbonyl complexes. In the malonate cases, ruthenacycle 15 was also formed during the cyclization reaction. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Val-Ala Dipeptide Isosteres by Hydrocyanation of ,,-Amino ,,,-Unsaturated Ketones , Control of Stereoselectivity by the N -Protecting GroupEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2003Fabio Benedetti Abstract Three diastereoisomeric hydroxyethylene isosters of the Val-Ala dipeptide were synthesized from ,,,-unsaturated ketones 1 derived from N -Boc- and N,N -dibenzyl- L -valine. The enones were hydrocyanated with diethylaluminum cyanide to give the corresponding ,-cyano ketones with the stereoselectivity depending on the protecting group. N -Boc protected enone 1a gave a 1:1 mixture of anti and syn adducts 4a, 5a while the corresponding N,N -dibenzyl compound 1c gave a 6:1 mixture of anti, syn adducts 4c, 5c. Borohydride reduction of the resulting cyano ketones is also controlled by the protecting group, resulting in opposite stereoselectivities for N -Boc and N,N -dibenzyl compounds. The cyano alcohols thus obtained were converted, in several steps, into two series of enantiomerically pure hydroxyethylene isosters of the Val-Ala dipeptide. In the first series the hydroxy group and the N -terminal of the isoster are internally protected through the formation of an oxazolidine; in the second series the hydroxy group and the C-terminal are protected as lactone. Two oxazolidines (28, 29), corresponding to syn,syn and syn,anti 4-hydroxy-5-amino acid isosters, and three lactones (23,25), corresponding to syn,syn, syn,anti, and anti,anti isosters were obtained by this approach. (© Wiley-VCH Verlag GmbH & Co KGaA, 69451 Weinheim, Germany, 2003) [source] Chemotactic response of plant-growth-promoting bacteria towards roots of vesicular-arbuscular mycorrhizal tomato plantsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2003Sushma Gupta Sood Abstract The chemotactic responses of the plant-growth-promoting rhizobacteria Azotobacter chroococcum and Pseudomonas fluorescens to roots of vesicular-arbuscular mycorrhizal (Glomus fasciculatum) tomato plants were determined. A significantly (P=0.05) greater number of bacterial cells of wild strains were attracted towards vesicular-arbuscular mycorrhizal tomato roots compared to non-vesicular-arbuscular mycorrhizal tomato roots. Substances exuded by roots served as chemoattractants for these bacteria. P. fluorescens was strongly attracted towards citric and malic acids, which were predominant constituents in root exudates of tomato plants. A. chroococcum showed a stronger response towards sugars than amino acids, but the response was weakest towards organic acids. The effects of temperature, pH, and soil water matric potential on bacterial chemotaxis towards roots were also investigated. In general, significantly (P=0.05) greater chemotactic responses of bacteria were observed at higher water matric potentials (0, ,1, and ,5 kPa), slightly acidic to neutral pH (6, 6.5 and 7), and at 20,30°C (depending on the bacterium) than in other environmental conditions. It is suggested that chemotaxis of P. fluorescens and A. chroococcum towards roots and their exudates is one of the several steps in the interaction process between bacteria and vesicular-arbuscular mycorrhizal roots. [source] Synthesis and Biological Evaluation of 14-Alkoxymorphinans.HELVETICA CHIMICA ACTA, Issue 7 2003Part 1 The 14- O -benzylnaltrexones 3,6 were prepared from naltrexone (2) in several steps. The novel compounds were biologically evaluated in radioligand binding and in [35S]GTP,S functional assays in comparison to the reference compound naltrexone. In the binding assay, compounds 3,6 exhibited preference for , opioid receptors, while the parent compound naltrexone shows preference for , receptors. In the functional assay, , antagonist potency of compounds 3,6 was in the range of naltrexone, while , antagonist potency was considerably higher for most novel compounds in comparison to naltrexone. [source] Patients' experiences of hope and suffering during the first year following acute spinal cord injuryJOURNAL OF CLINICAL NURSING, Issue 3 2005Vibeke Lohne MNSc Aims and objectives., The aim of this study was to explore patients' experiences of hope during the first year suffering from spinal cord injury. Background., There is a lack of substantial precision with regard to the concept of hope. Very few qualitative studies focusing on experiences of hope in spinal cord-injured patients have been identified in the literature. In this study, ,hope' was defined as future oriented towards improvement. Design and methods., Data were collected by means of personal interviews (n = 10) at the participants' homes in Norway. A phenomenological-hermeneutic approach, inspired by Ricoeur, was used to extract the meaning of the patients' experiences. The analysis was performed in several steps, as a hermeneutic process. Results., In this study, the findings revealed two main themes: ,The Vicious Circle' and ,Longing'. The vicious circle constituted aspects of suffering, and the common hope experienced by the subjects was therefore to leave the vicious circle. Experiences of suffering were experienced as feelings of loneliness, impatience, disappointment, bitterness and dependency. The ,Longing' was based on the subject's former life and was the source of awaked new hopes, which again was experienced comforting. Conclusions., Experiences of suffering created hope and longing. The meaning of hope was to find a possible way out of the circle and the hoping was experienced as a comfort. Relevance to clinical practice., Implications to nursing practice are listening to the suffering and longing individual and comforting the suffering by pointing towards possible future roads of hope. [source] Identifying and reducing error in cluster-expansion approximations of protein energiesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2010Seungsoo Hahn Abstract Protein design involves searching a vast space for sequences that are compatible with a defined structure. This can pose significant computational challenges. Cluster expansion is a technique that can accelerate the evaluation of protein energies by generating a simple functional relationship between sequence and energy. The method consists of several steps. First, for a given protein structure, a training set of sequences with known energies is generated. Next, this training set is used to expand energy as a function of clusters consisting of single residues, residue pairs, and higher order terms, if required. The accuracy of the sequence-based expansion is monitored and improved using cross-validation testing and iterative inclusion of additional clusters. As a trade-off for evaluation speed, the cluster-expansion approximation causes prediction errors, which can be reduced by including more training sequences, including higher order terms in the expansion, and/or reducing the sequence space described by thecluster expansion. This article analyzes the sources of error and introduces a method whereby accuracy can be improved by judiciously reducing the described sequence space. The method is applied to describe the sequence,stability relationship for several protein structures: coiled-coil dimers and trimers, a PDZ domain, and T4 lysozyme as examples with computationally derived energies, and SH3 domains in amphiphysin-1 and endophilin-1 as examples where the expanded pseudo-energies are obtained from experiments. Our open-source software package Cluster Expansion Version 1.0 allows users to expand their own energy function of interest and thereby apply cluster expansion to custom problems in protein design. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Clinical Update on the Use of Niacin for the Treatment of DyslipidemiaJOURNAL OF THE AMERICAN ACADEMY OF NURSE PRACTITIONERS, Issue 12 2004Kathy Berra MSN Purpose To provide nurse practitioners (NPs) with clinical and practical information about the use of niacin in the treatment of dyslipidemia. Data Sources Research-based and review articles in the medical literature and National Cholesterol Education Program guidelines. Conclusions Niacin provides beneficial effects on all major lipid fractions, particularly high-density lipoprotein cholesterol and triglycerides. Niacin also reduces low-density lipoprotein (LDL) cholesterol; lipoprotein (a); and the number of highly atherogenic small, dense LDL particles. Niacin promotes angiographic regression when used in combination with other drugs that lower LDL cholesterol and can reduce cardiovascular risk in patients with coronary heart disease. Several niacin formulations are available, but the safety (i.e., from hepato-toxicity) and tolerability (i.e., severity of flushing) of these niacin formulations may differ. Implications for Practice Niacin therapy is appropriate for many types of lipid abnormalities, including complex dyslipidemias. NPs can take several steps to minimize potential side effects of niacin therapy and to ensure that patients adhere to this important intervention. [source] A simple DNA extraction method suitable for PCR detection of genetically modified maizeJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 14 2007Manuel Porcar Abstract BACKGROUND: The polymerase chain reaction (PCR) is a powerful tool that is being increasingly used for detection of transgenic DNA. PCR requires only a minute quantity of template, but sensitive and accurate testing requires DNA of sufficient purity and free from inhibitors such as plant polysaccharides. Several standard protocols are available for this purpose, but they usually involve several steps, imply destruction of the maize kernel, or are time-consuming. Our aim was to develop a fast and simple extraction method to isolate a raw DNA-containing solution from maize tissues suitable for use as a template in a PCR-based detection assay with specific oligonucleotides directed to the identification of event MON810. RESULTS: The NaOH-based DNA extraction method we report here is time-saving (5 min) and can be used to isolate DNA-containing solutions from a small maize leaf portion (down to 1 mg) or from a single overnight-germinated kernel. PCR performed with selected primers yielded reproducible detection of transgenic DNA. CONCLUSION: The main advantages of the procedure are the quick extraction step, the possibility of non-destructive testing of maize kernels, and the robustness of the PCR-based detection, a consequence of the selection of MON810-matching oligonucleotides yielding intense and highly specific amplicons. Copyright © 2007 Society of Chemical Industry [source] The effects of dynein inhibition on the autophagic pathway in glioma cellsNEUROPATHOLOGY, Issue 1 2010Midori Yamamoto Autophagy has multiple physiological functions, including protein degradation, organelle turnover and the response of cancer cells to chemotherapy. Because autophagy is implicated in a number of diseases, a better understanding of the molecular mechanisms of autophagy is needed for therapeutic purposes, including rational design of drugs. Autophagy is a process that occurs in several steps as follows: formation of phagophores, formation of mature autophagosomes, targeting and trafficking of autophagosomes to lysosomes, formation of autolysosomes by fusion between autophagosomes and lysosomes, and finally, degradation of the autophagic bodies within the lysosomes. It has been suggested that autophagosome formation is driven by molecular motor machineries, and, once formed, autophagosomes need to reach lysosomes, enriched perinuclearly around the microtubule-organizing centre. While it is recognized that all these steps require the cytoskeletal network, little is known about the mechanisms involved. Here we assessed the role of cytoplasmic dynein in the autophagic process of human glioma cells to determine the part played by dynein in autophagy. We observed that chemical interference with dynein function led to an accumulation of autophagosomes, suggesting impaired autophagosome-lysosome fusion. In contrast, we found that overexpression of dynamitin, which disrupts the dynein complex, reduced the number of autophagosomes, suggesting the requirement of the dynein-dynactin interaction in the early membrane trafficking step in autophagosome formation. These results suggest that dynein plays a variety of crucial roles during the autophagic process in glioma cells. [source] Development of the cell covering in the dinoflagellate Scrippsiella hexapraecingula (Peridiniales, Dinophyceae)PHYCOLOGICAL RESEARCH, Issue 3 2001Satoko Sekida SUMMARY The organization and development of cell coverings in two alternate phases of the life cycle in a marine dinoflagellate, Scrippsiella hexapraecingula Horiguchi et Chihara, were investigated by thin sectioning and freeze-fracture electron microscopy. In one of these phases, the motile phase, cells have an outermost plasma membrane that is lined with flattened amphiesmal vesicles. Groups of microtubules lie beneath these vesicles. In mature motile cells, thecal plates are completely enclosed in individual amphiesmal vesicles. After settling, the cells enter the second, non-motile phase. Here, ecdysis occurs, resulting in several steps including formation of the first pellicle layer (PI), fusion of the inner amphiesmal vesicle membranes to form the new plasma membrane, deposition of the second pellicle layer (PM) under PI, and the appearance and fusion of juvenile amphiesmal vesicles to form new territories, which eventually give rise to new thecal plates in the next motile phase. Thus, the pattern in which thecal plates are arranged in motile cells is determined at the time when the amphiesmal vesicles develop into non-motile cells. [source] Elevated carbon dioxide increases nitrate uptake and nitrate reductase activity when tobacco is growing on nitrate, but increases ammonium uptake and inhibits nitrate reductase activity when tobacco is growing on ammonium nitratePLANT CELL & ENVIRONMENT, Issue 11 2001P. Matt Abstract The influence of elevated [CO2] on the uptake and assimilation of nitrate and ammonium was investigated by growing tobacco plants in hydroponic culture with 2 mm nitrate or 1 mm ammonium nitrate and ambient or 800 p.p.m. [CO2]. Leaves and roots were harvested at several times during the diurnal cycle to investigate the levels of the transcripts for a high-affinity nitrate transporter (NRT2), nitrate reductase (NIA), cytosolic and plastidic glutamine synthetase (GLN1, GLN2), the activity of NIA and glutamine synthetase, the rate of 15N-nitrate and 15N-ammonium uptake, and the levels of nitrate, ammonium, amino acids, 2-oxoglutarate and carbohydrates. (i) In source leaves of plants growing on 2 mm nitrate in ambient [CO2], NIA transcript is high at the end of the night and NIA activity increases three-fold after illumination. The rate of nitrate reduction during the first part of the light period is two-fold higher than the rate of nitrate uptake and exceeds the rate of ammonium metabolism in the glutamate: oxoglutarate aminotransferase (GOGAT) pathway, resulting in a rapid decrease of nitrate and the accumulation of ammonium, glutamine and the photorespiratory intermediates glycine and serine. This imbalance is reversed later in the diurnal cycle. The level of the NIA transcript falls dramatically after illumination, and NIA activity and the rate of nitrate reduction decline during the second part of the light period and are low at night. NRT2 transcript increases during the day and remains high for the first part of the night and nitrate uptake remains high in the second part of the light period and decreases by only 30% at night. The nitrate absorbed at night is used to replenish the leaf nitrate pool. GLN2 transcript and glutamine synthetase activity rise to a maximum at the end of the day and decline only gradually after darkening, and ammonium and amino acids decrease during the night. (ii) In plants growing on ammonium nitrate, about 30% of the nitrogen is derived from ammonium. More ammonium accumulates in leaves during the day, and glutamine synthetase activity and glutamine levels remain high through the night. There is a corresponding 30% inhibition of nitrate uptake, a decrease of the absolute nitrate level, and a 15,30% decrease of NIA activity in the leaves and roots. The diurnal changes of leaf nitrate and the absolute level and diurnal changes of the NIA transcript are, however, similar to those in nitrate-grown plants. (iii) Plants growing on nitrate adjust to elevated [CO2] by a coordinate change in the diurnal regulation of NRT2 and NIA, which allows maximum rates of nitrate uptake and maximum NIA activity to be maintained for a larger part of the 24 h diurnal cycle. In contrast, tobacco growing on ammonium nitrate adjusts by selectively increasing the rate of ammonium uptake, and decreasing the expression of NRT2 and NIA and the rate of nitrate assimilation. In both conditions, the overall rate of inorganic nitrogen utilization is increased in elevated [CO2] due to higher rates of uptake and assimilation at the end of the day and during the night, and amino acids are maintained at levels that are comparable to or even higher than in ambient [CO2]. (iv) Comparison of the diurnal changes of transcripts, enzyme activities and metabolite pools across the four growth conditions reveals that these complex diurnal changes are due to transcriptional and post-transcriptional mechanisms, which act several steps and are triggered by various signals depending on the condition and organ. The results indicate that nitrate and ammonium uptake and root NIA activity may be regulated by the sugar supply, that ammonium uptake and assimilation inhibit nitrate uptake and root NIA activity, that the balance between the influx and utilization of nitrate plays a key role in the diurnal changes of the NIA transcript in leaves, that changes of glutamine do not play a key role in transcriptional regulation of NIA in leaves but instead inhibit NIA activity via uncharacterized post-transcriptional or post-translational mechanisms, and that high ammonium acts via uncharacterized post-transcriptional or post-translational mechanisms to stabilize glutamine synthetase activity during the night. [source] Proteomics of human cerebrospinal fluid , the good, the bad, and the uglyPROTEOMICS - CLINICAL APPLICATIONS, Issue 8 2007Jing Zhang ProfessorArticle first published online: 13 JUL 200 Abstract The development of MALDI ESI in the late 1980s has revolutionized the biological sciences and facilitated the emergence of a new discipline called proteomics. Application of proteomics to human cerebrospinal fluid (CSF) has greatly hastened the advancement of characterizing the CSF proteome as well as revealing novel protein biomarkers that are diagnostic of various neurological diseases. While impressive progressions have been made in this field, it has become increasingly clear that proteomics results generated by various laboratories are highly variable. The underlying issues are vast, including limitations and complications with heterogeneity of patients/testing subjects, experimental design, sample processing, as well as current proteomics technology. Accordingly, this review not only summarizes the current status of characterization of the human CSF proteome and biomarker discovery for major neurodegenerative disorders, i.e., Alzheimer's disease and Parkinson's disease, but also addresses a few essential caveats involved in several steps of CSF proteomics that may contribute to the variable/contradicting results reported by different laboratories. The potential future directions of CSF proteomics are also discussed with this analysis. [source] Technical note: An R program for automating bone cross section reconstructionAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2010Adam D. Sylvester Abstract Many recent studies have used long bone cross-sectional geometric properties in various comparative analyses. Methods have been described for reconstructing diaphyseal cross sections from external molds and biplanar radiographs that produce accurate results (within 5% of true values on average). The manual image processing required, however, is both time and labor intensive. A new freely available program developed here for the computational freeware, R, automates much of the process. This study compares cross-sectional properties calculated using the new R program to those from peripheral quantitative CT (pQCT) and the original manual method. We find that the R program works aswell as the original manual image processing for most cross sections eliminates the chance for entry errors at several steps and greatly speeds up data collection. Am J Phys Anthropol 142:665,669, 2010. © 2010 Wiley-Liss, Inc. [source] Modeling and analysis of disease and risk factors through learning Bayesian networks from observational dataQUALITY AND RELIABILITY ENGINEERING INTERNATIONAL, Issue 3 2008Jing Li Abstract This paper focuses on identification of the relationships between a disease and its potential risk factors using Bayesian networks in an epidemiologic study, with the emphasis on integrating medical domain knowledge and statistical data analysis. An integrated approach is developed to identify the risk factors associated with patients' occupational histories and is demonstrated using real-world data. This approach includes several steps. First, raw data are preprocessed into a format that is acceptable to the learning algorithms of Bayesian networks. Some important considerations are discussed to address the uniqueness of the data and the challenges of the learning. Second, a Bayesian network is learned from the preprocessed data set by integrating medical domain knowledge and generic learning algorithms. Third, the relationships revealed by the Bayesian network are used for risk factor analysis, including identification of a group of people who share certain common characteristics and have a relatively high probability of developing the disease, and prediction of a person's risk of developing the disease given information on his/her occupational history. Copyright © 2007 John Wiley & Sons, Ltd. [source] Inter-laboratory comparison of elemental analysis and gas chromatography/combustion/isotope ratio mass spectrometry.RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 7 200915N measurements of selected compounds for the development of an isotopic Grob test An inter-laboratory exercise was carried out by a consortium of five European laboratories to establish a set of compounds, suitable for calibrating gas chromatography/combustion/isotope ratio mass spectrometry (GC-C-IRMS) devices, to be used as isotopic reference materials for hydrogen, carbon, nitrogen and oxygen stable isotope measurements. The set of compounds was chosen with the aim of developing a mixture of reference materials to be used in analytical protocols to check for food and beverage authentication. The exercise was organized in several steps to achieve the certification level: the first step consisted of the a priori selection of chemical compounds on the basis of the scientific literature and successive GC tests to set the analytical conditions for each single compound and the mixture. After elimination of the compounds that turned out to be unsuitable in a multi-compound mixture, some additional oxygen- and nitrogen-containing substances were added to complete the range of calibration isotopes. The results of ,13C determinations for the entire set of reference compounds have previously been published, while the ,D and ,18O determinations were unsuccessful and after statistical analysis of the data the results did not reach the level required for certification. In the present paper we present the results of an inter-laboratory exercise to identify and test the set of nitrogen-containing compounds present in the mixture developed for use as reference materials for the validation of GC-C-IRMS analyses in individual laboratories. Copyright © 2009 John Wiley & Sons, Ltd. [source] Monitoring of Cochlear Function During Cochlear ImplantationTHE LARYNGOSCOPE, Issue 6 2006Oliver Adunka MD Abstract Objective: To report the feasibility of monitoring cochlear function during cochlear implantation. Study Design: Case report. Setting: Tertiary care referral center. Methods: A child with audiologic features typical of bilateral auditory neuropathy underwent cochlear implantation. The scala tympani was entered inferior and slightly anterior to the round window membrane margin and smooth electrode insertion was achieved. Using single polarity click stimuli, the cochlear microphonic was measured at several steps during surgery. Results: Cochlear microphonics were present at all stages during the implantation process and were clearly distinguished from neural responses by stimulus polarity inversion and constant latencies, despite changes in stimulus level. With the electrode in situ, amplitudes were smaller but persisted until the final measurement at 10 minutes after insertion. At follow-up 2 weeks after surgery, behavioral audiometry results indicated profound hearing loss in the operated ear. Conclusions: This paper demonstrates the feasibility of monitoring cochlear function during cochlear implantation. The routine surgical approach did not appear to adversely affect the functional measurements. Standard size, full electrode insertion did diminish the amplitude of the cochlear microphonics, possibly as a result of intracochlear mechanical impairment. Ultimately, profound hearing loss was documented, indicating that factors other than immediate changes induced by electrode insertion were likely responsible for the loss of cochlear function. [source] A simple method for purifying the White Spot Syndrome Virus using ultrafiltrationAQUACULTURE RESEARCH, Issue 6 2009Martina Hilda Gracia-Valenzuela Abstract A very simple and efficient method was developed for isolating intact White Spot Syndrome Virus (WSSV) particles from infected Litopenaeus vannamei tissue. No density gradient centrifugation, ultracentrifugation or protease inhibitors were required for the purification of intact WSSV virions using microfilters (100 kDa cut-off) combined with several steps of conventional centrifugation procedures. A mortality assay was run using healthy shrimp to prove that the virions obtained were infective. The concentrated viral preparations were further studied using polyacrylamide gel electrophoresis (PAGE). At least five distinct protein bands were detected when intact purified WSSV virions were found by sodium dodecyl sulphate-PAGE, followed by Coomassie Brilliant R-250 staining. The estimated molecular weights of these proteins were 23, 24, 29, 32 and 42-kDa, which could correspond to viral protein. Using this method, the virus does not lose its ability to infect healthy shrimp. [source] Eicosanoids influence in vitro elongation of plasmatocytes from the tobacco hornworm, Manduca sextaARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 1 2005Jon S. Miller Abstract Nodule formation is the predominant insect cellular defense reaction to bacterial challenges, responsible for clearing the largest proportion of infecting bacteria from hemolymph circulation. Hemocyte spreading behavior is a critical step in the nodulation process. It has been suggested that eicosanoids mediate several steps in the process. However, the influence of eicosanoids on hemocyte spreading has not been investigated in detail. To test the hypothesis that eicosanoids mediate hemocyte spreading behavior, I treated larvae of the tobacco hornworm, Manduca sexta, with eicosanoid biosynthesis inhibitors and later assessed plasmatocyte elongation on glass slides. Plasmatocytes from larvae treated with dexamethasone did not elongate to the extent of plasmatocytes from untreated control larvae. The dexamethasone effect on plasmatocyte elongation was expressed in a dose-dependent manner and was reversed by injecting dexamethasone-treated larvae with the eicosanoid-precursor fatty acid, arachidonic acid. Palmitic acid, which is not substrate for eicosanoid biosynthesis, did not reverse the influence of dexamethasone on plasmatocyte elongation. Finally, plasmatocytes from larvae treated with a range of eicosanoid biosynthesis inhibitors did not elongate to the extent of plasmatocytes from control larvae. Plasmatocyte width did not appear to be influenced in this study. These findings strongly support the idea that insect plasmatocyte elongation is influenced by eicosanoids. Arch. Insect Biochem. Physiol. 59:42,51, 2005. © 2005 Wiley-Liss, Inc. [source] Influence of the Weißenberg number on the stability of Oldroyd kind fluidsASIA-PACIFIC JOURNAL OF CHEMICAL ENGINEERING, Issue 4 2010N. Scurtu Abstract This paper is concerned with nonlinear rheological fluids of Oldroyd type. We present a (formal) stability analysis of the corresponding system of equations, showing stability limits on the Weißenberg number in certain cases. To this end, we proceed in several steps, thus separating the possible sources for instabilities. First, a spectral analysis of the linearized Oldroyd system is presented. Then, the influence of the ,a -term on the stability of the constitutive stress equation and of the full Oldroyd system is examined. Moreover, because this stability analysis is of formal and linear nature, we complement it by numerical simulations for the system showing that the upper limit of the Weißenberg number found by the stability analysis is fairly sharp. We thereby try to shed some light on the high Weißenberg number problem, that is, the problem why in certain cases there seem to exist no solutions to the Oldroyd problem for large Weißenberg numbers. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd. [source] Treatment of Distal Colitis with Local Anaesthetic AgentsBASIC AND CLINICAL PHARMACOLOGY & TOXICOLOGY, Issue 4 2002Stellan Björck The original observation was an adrenergic hyperinnervation of the inflamed mucosa (hyperinnervation hypothesis). In order to silence local nervous reflexes, the mucosa was treated topically with 2% lidocaine gel. The clinical results are promising and no side effects have been observed. The relapse rate is relatively high and related to the duration of treatment. In studies of experimental colitis a potential antagonism between harmful adrenergic nerves (vasoconstrictor substances and proinflammatory cytokines) and mucosa-protective visceral afferents (antiinflammatory cytokines) in the pathogenesis of colitis is intriguing. Other studies have emphasized the importance of neutrophils for causing damage to the colon epithelium (neutrophil hypothesis) and local anaesthetics have potent effects on several steps of the inflammatory response in addition to the nervous blockade. [source] Characterization of cryogel monoliths for extraction of minor proteins from milk by cation exchangeBIOTECHNOLOGY & BIOENGINEERING, Issue 6 2009Jagan M. Billakanti Abstract Extraction and purification of high-value minor proteins directly from milk without pre-treatment is a challenge for the dairy industry. Pre-treatment of milk before extraction of proteins by conventional packed-bed chromatography is usually necessary to prevent column blockage but it requires several steps that result in significant loss of yield and activity for many minor proteins. In this paper, we demonstrate that it is possible to pass 40,50 column volumes of various milk samples (raw whole milk, homogenized milk, skim milk and acid whey) through a 5 mL cryogel chromatographic column at 550 cm/h without exceeding its pressure limits if the processing temperature is maintained above 35°C. The dynamic binding capacity obtained for the cryogel matrix (2.1 mg/mL) was similar to that of the binding capacity (2.01 mg/mL) at equilibrium with 0.1 mg/mL of lactoferrin in the feed samples. The cryogel column selectively binds lactoferrin and lactoperoxidase with only minor leakage in flowthrough fractions. Lactoferrin was recovered from elution fractions with a yield of over 85% and a purity of more than 90%. These results, together with the ease of manufacture, low cost and versatile surface chemistry of cryogels suggest that they may be a good alternative to packed-bed chromatography for direct capture of proteins from milk. Biotechnol. Bioeng. 2009;103: 1155,1163. © 2009 Wiley Periodicals, Inc. [source] Purification of homogeneous forms of fungal peroxygenaseBIOTECHNOLOGY JOURNAL, Issue 11 2009René Ullrich Abstract Extracellular peroxygenase from the agaric fungus Agrocybe aegerita is a versatile biocatalyst that oxygenates various substrates by means of hydrogen peroxide. The enzyme is routinely produced in suspensions of soybean meal and has until now been purified by several steps of fast protein liquid chromatography (FPLC) using different ion exchangers. The final protein fraction had a molecular mass of 46 kDa but still consisted of several incompletely separated proteins with slightly differing isoelectric points (pI 5.2, 5.6, 6.1), probably representing differently glycosylated isoforms. This made it difficult to further purify the individual protein forms. Since homogeneous protein fractions are a pre-requisite for X-ray crystallography and specific structure-function studies, an appropriate FPLC procedure was developed starting with pre-purification of crude peroxygenase on SP Sepharose followed by chromatofocusing on a Mono P column and elution with a pH gradient. Three sufficiently separated main protein peaks were eluted from the Mono P column and confirmed to be distinct forms of aromatic peroxygenase with different pIs. All A. aegerita peroxygenase forms oxygenated toluene and naphthalene and no catalytic differences were observed between them. We tested also two devices for preparative isoelectric focusing (Rotofor, IsoPrime systems) for peroxygenase separation but resolution and protein recovery were not sufficient. [source] Effects of 7,8-dihydro-8-oxo-deoxyguanosine on antigen challenge in ovalbumin-sensitized mice may be mediated by suppression of RacBRITISH JOURNAL OF PHARMACOLOGY, Issue 7 2009JY Ro Background and purpose:, Earlier we reported that 7,8-dihydro-8-oxo-deoxyguanosine (8-oxo-dG), an oxidatively modified guanine nucleoside, exerted anti-inflammatory activity through inactivation of the GTP binding protein, Rac. In the present study, the effects of 8-oxo-dG were investigated on responses to antigen challenge in sensitized mice, as Rac is also involved at several steps of the immune process including antigen-induced release of mediators from mast cells. Experimental approach:, Mice were sensitized and challenged with ovalbumin without or with oral administration of 8-oxo-dG during the challenge. Effects of 8-oxo-dG were assessed by measuring lung function, cells and cytokines in broncho-alveolar lavage fluid (BALF) and serum levels of antigen-specific IgE. Rac activity in BALF cells was also measured. Key results:, 8-oxo-dG inhibited the increased airway resistance and decreased lung compliance of sensitized and challenged mice to the levels of non-sensitized control mice and lowered the increased leukocytes particularly, eosinophils, in BALF. Furthermore, 8-oxo-dG suppressed allergy-associated immune responses, such as raised anti- ovalbumin IgE antibody in serum, increased expression of CD40 and CD40 ligand in lung, increased interleukin-4, -5, -13, interferon-, and tumour necrosis factor-, in BALF and mRNA levels of these cytokines in BALF cells, dose-dependently. The corresponding purine, 8-oxo-guanine, showed no effects in the same experiments. Finally, 8-oxo-dG, but not 8-oxo-guanine, inhibited the increased Rac activity in sensitized and challenged mice. Conclusion and implications:, 8-Oxo-dG had anti-allergic actions that might be mediated by Rac inactivation. This compound merits further evaluation of its therapeutic potential in allergic asthma. [source] Extracellular and intracellular mechanisms that mediate the metastatic activity of exogenous osteopontinCANCER, Issue 8 2009Jami Mandelin PhD Abstract BACKGROUND: Osteopontin affects several steps of the metastatic cascade. Despite direct correlation with metastasis in experimental systems and in patient studies, the extracellular and intracellular basis for these observations remains unsolved. In this study, the authors used human melanoma and sarcoma cell lines to evaluate the effects of soluble osteopontin on metastasis. METHODS: Exogenous osteopontin or negative controls, including a site-directed mutant osteopontin, were used in functional assays in vitro, ex vivo, and in vivo that were designed to test the extracellular and intracellular mechanisms involved in experimental metastasis. RESULTS: In the extracellular environment, the results confirmed that soluble osteopontin is required for its prometastatic effects; this phenomenon is specific, arginine-glycine-aspartic acid (RGD)-dependent, and evident in experimental models of metastasis. In the intracellular environment, osteopontin initially induced rapid tyrosine 418 (Tyr-418) dephosphorylation of the cellular homolog of the Rous sarcoma virus (c-Src), with decreases in actin stress fibers and increased binding to the vascular endothelium. This heretofore undescribed Tyr dephosphorylation was followed by a tandem c-Src phosphorylation after tumor cell attachment to the metastatic site. CONCLUSIONS: The results of this study revealed a complex molecular interaction as well as a dual role for osteopontin in metastasis that depends on whether tumor cells are in circulation or attached. Such context-dependent functional insights may contribute to antimetastasis strategies. Cancer 2009. © 2009 American Cancer Society. [source] | ||||||||||||||||||||||