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Current Methods (current + methods)
Selected AbstractsAmplification of low quantity bacterial RNA for microarray studies: time-course analysis of Leptospirillum ferrooxidans under nitrogen-fixing conditions,ENVIRONMENTAL MICROBIOLOGY, Issue 6 2006Mercedes Moreno-Paz Summary We have developed a method for the amplification of low quantity total bacterial RNA for DNA microarrays analysis. Current methods are based on the linear amplification by the in vitro transcription from the T7 promoter, similar to that used for eukaryotic mRNA amplification. For the incorporation of T7 promoter, the prokaryotic RNA must be enzymatically modified for the incorporation of a polyA tail at the 3, end to emulate the eukaryotic mRNA. The method we describe and validate herein avoids this step by the direct and random incorporation of the T7 promoter. From 500 ng of total bacterial RNA, we obtained 130,150 µg of antisense RNA, such products being good substrate for fluorescent labelling and DNA microarray analysis. The method was validated with bacterial samples from which it is very difficult to obtain sufficient amounts and quality of total RNA for global gene expression analysis. This is critical for low cell density growing microorganisms, environmental samples, or many extremophiles where the composition of the cultural media severely affects the RNA yield, like in the case of the acidophile and iron oxidizer Gram-negative bacterium Leptospirillum ferrooxidans. We further validated our amplification method in parallel experiments with non-amplified RNA by following the expression of the L. ferrooxidans nif regulon along the time-course of growth. [source] Synchrony of spontaneous calcium activity in mouse neocortex before synaptogenesisEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 4 2007Jean-Claude Platel Abstract Spontaneous calcium activity can be detected in embryonic mouse cortical slices as fluorescence intensity variations, in the presence of a fluorescent calcium indicator. Current methods to detect and quantify these variations depend heavily on experimenters whose judgement may interfere with measurement. In the present work, we developed new software called CalSignal for automatic detection and tracking of cellular bodies and quantification of spontaneous calcium activity on time-series of confocal fluorescence images. Analysis of 28 neocortical slices revealed that 21.0% of detected cells displayed peaks of fluorescence corresponding to spontaneous activity, with a mean frequency of one peak per 4 min. This activity was blocked in the absence of extracellular calcium but was not modified after depletion of calcium stores with thapsigargin or blockade of voltage-gated calcium channels with Ni2+. Further, statistical analysis of calcium activity revealed concomitant activation of distant cells in 24 slices, and the existence of a significant network of synchrony based on such coactivations in 17 slices out of 28. These networks enclosed 84.3% of active cells, scattered throughout the neocortical wall (mean distance between cellular bodies, 111.7 µm). Finally, it was possible to identify specific cells which were synchronously active with more neighbouring cells than others. The identity of these nodal cells remains to be investigated to fully comprehend the role of spontaneous calcium activity, before synaptogenesis, in shaping cortical neurogenesis. [source] Ammonium fluoride extraction for determining inorganic sulphur in acid forest soilsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 2 2000J. Prietzel Summary Current methods for determining inorganic sulphur (S) in aerated mineral soil horizons often result in underestimates. To overcome this defect we developed a new method combining a batch extraction with 0.5 m NH4F solution at a soil:solution ratio of 1:5 with a subsequent analysis of the mobilized SO42, by ion chromatography. The ammonium fluoride extraction enables us to characterize inorganic sulphate in non-calcareous forest soils. It is more efficient than conventional procedures in which inorganic S is extracted with phosphate or bicarbonate solution. In contrast to the extraction with strongly alkaline reagents (NaOH, KOH, LiOH), the NH4+,NH3 buffer system in NH4F prevents the pH of the suspension from exceeding 9.0 and thus the undesired conversion of organic S into SO42, by auto-oxidation and hydrolysis of ester sulphate. In a comparison we demonstrated that the inorganic S in six German forest soils is underestimated by up to 50% or 200 kg S ha,1 in the uppermost 60 cm, if it is assessed by extraction with 0.016 m KH2PO4 or 0.5 m NaHCO3 instead of 0.5 m NH4F. Conversely, the pool of ester sulphate is overestimated almost threefold. [source] The smear layer in endodontics , a reviewINTERNATIONAL ENDODONTIC JOURNAL, Issue 1 2010D. R. Violich Abstract Root canal instrumentation produces a layer of organic and inorganic material called the smear layer that may also contain bacteria and their by-products. It can prevent the penetration of intracanal medicaments into dentinal tubules and influence the adaptation of filling materials to canal walls. This article provides an overview of the smear layer, focusing on its relevance to endodontics. The PubMed database was used initially; the reference list for smear layer featured 1277 articles, and for both smear layer dentine and smear layer root canal revealed 1455 publications. Smear layer endodontics disclosed 408 papers. A forward search was undertaken on selected articles and using some author names. Potentially relevant material was also sought in contemporary endodontic texts, whilst older books revealed historic information and primary research not found electronically, such that this paper does not represent a ,classical' review. Data obtained suggests that smear layer removal should enhance canal disinfection. Current methods of smear removal include chemical, ultrasonic and laser techniques , none of which are totally effective throughout the length of all canals or are universally accepted. If smear is to be removed, the method of choice seems to be the alternate use of ethylenediaminetetraacetic acid and sodium hypochlorite solutions. Conflict remains regarding the removal of the smear layer before filling root canals, with investigations required to determine the role of the smear layer in the outcomes of root canal treatment. [source] Current methods for assaying angiogenesis in vitro and in vivoINTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY, Issue 5 2004Carolyn A. Staton Summary Angiogenesis, the development of new blood vessels from an existing vasculature, is essential in normal developmental processes and in numerous pathologies, including diabetic retinopathy, psoriasis and tumour growth and metastases. One of the problems faced by angiogenesis researchers has been the difficulty of finding suitable methods for assessing the effects of regulators of the angiogenic response. The ideal assay would be reliable, technically straightforward, easily quantifiable and, most importantly, physiologically relevant. Here, we review the advantages and limitations of the principal assays in use, including those for the proliferation, migration and differentiation of endothelial cells in vitro, vessel outgrowth from organ cultures and in vivo assays such as sponge implantation, corneal, chamber, zebrafish, chick chorioallantoic membrane (CAM) and tumour angiogenesis models. [source] An improved method for detecting red cells with hemoglobin H inclusions that does not require glass capillary tubesINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 2 2003D.E. Sabath Summary, -Thalassemia trait is the most common inherited abnormality worldwide. Diagnosis of , -thalassemia trait can be difficult as there are no abnormalities detectable by hemoglobin electrophoresis or high-performance liquid chromatography. Detection of individuals with , -thalassemia trait, particularly the type present in many Asian populations, is important for genetic counseling purposes, because these individuals are at risk for having offspring with hemoglobin Bart's hydrops fetalis, a fatal condition. The best routine diagnostic method to detect individuals with , -thalassemia trait is staining reticulocyte-enriched red cell preparations with brilliant cresyl blue to detect hemoglobin H inclusions. Current methods use centrifugation of microhematocrit tubes to enrich for reticulocytes, which presents a laboratory safety hazard. In this report, we describe an alternative technique to enrich for reticulocytes that does not require glass capillary tubes, but is as effective as the capillary tube method for reticulocyte enrichment and detection of cells containing hemoglobin H inclusions. [source] On Reading MacKinnon WoodsJOURNAL OF ARCHITECTURAL EDUCATION, Issue 3 2004MARY CATHERINE KILCOYNE Consensus is growing among climatologists and environmentalists that the ground on which we walk and the air through which we move are in a heightened, constant, and inexorable state of redefinition through the accelerated northward movement of ecosystems. Current methods of climate change research convey an abstraction of landscape through information gathering that is remote, anonymous, and general. Through the medium of the architectural intervention, this work explores a shift in perception so as to register landscapes in flux at a level of intimacy. The attentive reading of change across MacKinnon Woods becomes an act of emplacement. [source] Titration methodologies for monitoring of anaerobic digestion in developing countries,a reviewJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 12 2004O Lahav Abstract An increase in volatile fatty acids (VFA) concentration (or the proportional decrease in carbonate alkalinity concentration) is the first practical measurable indication that an anaerobic treatment system is in a state of stress. If the system is not rectified at this early stage, failure is likely. Current methods for VFA measurement include distillation, colorimetry, gas chromatography and various titration techniques. In terms of simplicity, speed and cost-effectiveness it is generally accepted that titration methods are superior for the purpose of on-site routine monitoring and control, particularly in developing countries. This paper reviews the methods published in the last four decades concerning on-site titration measurement of VFA and carbonate alkalinity concentrations. The review encompasses the following: aquatic chemistry related to the theory on which most of the methods are based, and a detailed description of each of the principal methods published followed by critical and comparative evaluation. Copyright © 2004 Society of Chemical Industry [source] Binding of anti-HLA class I antibody to endothelial cells produce an inflammatory cytokine secretory pattern,JOURNAL OF CLINICAL LABORATORY ANALYSIS, Issue 3 2009Eduardo Reyes-Vargas Abstract Current methods are inadequate for the diagnosis of early chronic allograft rejection. The goal of this study was to determine whether ligation of anti-HLA antibodies to endothelial cells is associated with a distinctive cytokine secretory pattern. Human iliac artery endothelial cells (HIAEC) cultured in vitro were incubated with w6/32, an anti-HLA class I mAb. Culture supernatants collected daily for up to 4 days were tested for secretion of 13 cytokines using a multiplexed fluorescent microsphere immunoassay. Culture of HIAEC with medium containing mAb w6/32 supported the growth of HIAEC during the 4-day study period. Levels of the pro-inflammatory cytokines IL-1,, IL-6, IL-8, and TNF-, became significantly increased in supernatants of HIAEC incubated with the mAb w6/32. We conclude that ligation of anti-HLA class I antibodies to HLA class I antigens in endothelial cells initiates an acute inflammatory process and detecting an inflammatory cytokine secretory pattern might be useful to diagnose sub-clinical chronic allograft rejection. J. Clin. Lab. Anal. 23:157,160, 2009. © 2009 Wiley-Liss, Inc. [source] Biomechanical evaluation of healing in a non-critical defect in a large animal model of osteoporosisJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 5 2003C. A. Lill Abstract Current methods for fracture treatment in osteoporosis are not always sufficient. To develop new fixation strategies (both mechanical and biological) requires pre-clinical testing utilizing appropriate models. The aim of this study was to apply a recently developed sheep model of osteoporosis to the study of healing in a non-critical long bone defect. A standardized transverse mid-shaft tibial osteotomy (with a fracture gap of 3 mm) was performed in seven osteoporotic and seven normal sheep and stabilized with a special external fixator for 8 weeks. The fixator was used for weekly in vivo bending stiffness measurements. Ex vivo bending stiffness and torsional stiffness of the callus zone were also determined. Callus area, callus density, and osteoporosis status were determined at 0, 4, and 8 weeks using peripheral quantitative computed tomography. The increase of in vivo bending stiffness of the callus was delayed approximately 2 weeks in osteoporotic animals. A significant difference (33%) in torsional stiffness was found between the osteotomized and contralateral intact tibia in osteoporotic animals, but no significant difference occurred in normal sheep (2%). In osteoporotic animals, ex vivo bending stiffness was reduced 21% (p = 0.05). Bending stiffness was correlated with callus density (r = 0.76, r = 0.53); torsional stiffness was correlated with callus area (r = 0.60) and to a lesser extent with callus density (r = 0.53). This study demonstrated a delay of fracture healing in osteoporotic sheep tibiae with respect to callus formation, mineralization, and mechanical properties. © 2003 Orthopaedic Research Society. Published by Elsevier Science Ltd. All rights reserved. [source] Microparticulate formulations for the controlled release of interleukin-2JOURNAL OF PHARMACEUTICAL SCIENCES, Issue 5 2004Tommy T. Thomas Abstract Interleukin 2 (IL-2) is a pleotropic growth factor essential to immune system function. Current methods of administration are limited by the necessity of hospitalization as well as dose-limiting toxicities and side effects. There is also the issue of low therapeutic concentrations at the desired site of action; for instance, in the case of solid tumor treatment. Here we describe the design of controlled-release vehicles for the local administration of IL-2 based on single (SE) and double emulsion (DE) poly(lactic- co -glycolic acid) (PLGA) systems and a newly developed class of spray-dried lipid,protein,sugar systems composed of L -,-dipalmitoylphosphatidylcholine (DPPC) and 0.2% Eudragit E 100. All three systems demonstrated the release of therapeutic drug quantities. Totals of 2.0, 0.5, and 2.8 ,g of IL-2 (per mg of solid) were encapsulated in the SE, DE, and spray-dried formulations, respectively. The SE and DE released of 30 and 15% of the encapsulated protein, respectively, with delivery of biologically active IL-2 during the first 5 to 10 days. The lipid,protein,sugar-based system demonstrated extended sustained release of biologically active IL-2 for a period of 4 months. These systems provide a potential framework for long-term loco-regional immunotherapeutic treatment regimens. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:1100,1109, 2004 [source] Using Real-time PCR to Discriminate and Quantify the Closely Related Wheat Pathogens Oculimacula yallundae and Oculimacula acuformisJOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2005K. Walsh Abstract Oculimacula yallundae and O. acuformis are the causal agents of eyespot disease of wheat and other cereals. The two fungi react differently to the application of fungicides, but they cannot be distinguished visually and their occurrence is often masked by other less damaging pathogens. Current methods to detect and distinguish Oculimacula species are impractical when testing large numbers of samples. A real-time polymerase chain reaction (PCR) assay, suitable for large-scale testing, was developed and used for quantitative detection and discrimination of O. yallundae and O. acuformis. As the available DNA sequences differ by only a small number of conserved nucleotide polymorphisms, three different methods were investigated to achieve the desired specificity. A combination of mutagenically separated PCR and a shortened primer gave the best specificity for O. yallundae and O. acuformis, respectively. Although the comparison illustrated the practicalities of each method, it was not possible to devise a fixed set of rules for the design of primers to discriminate two closely related sequences; it is assumed that sequence context is an overriding and difficult to predict factor, and that a range of empirical approaches may need to be taken to reach the specificity required. [source] Immunological Detection of in Vitro Formed Phosphatidylethanol,An Alcohol Biomarker,With Monoclonal AntibodiesALCOHOLISM, Issue 6 2008Antti E. Nissinen Background:, Phosphatidylethanol (PEth) is a promising new marker for detecting long-term alcohol abuse with excellent sensitivity and specificity. Current methods are based on the high performance liquid chromatography,mass spectrometric method and therefore require high levels of expertise and expensive instrumentation. This study was designed to generate PEth-specific monoclonal antibodies for PEth immunoassay development. Methods:, C57/BL6 mice were immunized with PEth in 3 different carriers, mouse serum albumin, mouse high-density lipoproteins, and human low-density lipoprotein (LDL). Mouse splenocytes were fused with a mouse myeloma cell line using the hybridoma technique. Mouse IgM-producing cell lines were selected by limiting dilutions. Binding characteristics of the anti-PEth antibodies were studied using luminometric immunoassays and sequence analysis of the variable region mRNA sequences of the antibodies. Produced antibodies were purified by chromatographic methods. PEth was detected with these antibodies in fluorescence immunoassay and flow cytometric analysis. Results:, We generated monoclonal cell lines (2B1 and 2E9) that produce IgM antibodies binding specifically to PEth but not to structurally or chemically similar phospholipids, such as phosphatidylcholine, phosphatidic acid, and cardiolipin. We show here that these anti-PEth antibodies can be used to detect PEth in a fluorescent PEth assay and FACS analysis of human red blood cell samples spiked with PEth. Conclusions:, The present study shows that PEth-specific monoclonal antibodies can be generated using traditional hybridoma technique. Immunogenicity of PEth was enhanced using human LDL as an immunization carrier. The generated monoclonal anti-PEth antibodies, 2B1 and 2E9 bind to PEth in fluid phase and in biological membranes. [source] Parameter estimation for differential equations: a generalized smoothing approachJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 5 2007J. O. Ramsay Summary., We propose a new method for estimating parameters in models that are defined by a system of non-linear differential equations. Such equations represent changes in system outputs by linking the behaviour of derivatives of a process to the behaviour of the process itself. Current methods for estimating parameters in differential equations from noisy data are computationally intensive and often poorly suited to the realization of statistical objectives such as inference and interval estimation. The paper describes a new method that uses noisy measurements on a subset of variables to estimate the parameters defining a system of non-linear differential equations. The approach is based on a modification of data smoothing methods along with a generalization of profiled estimation. We derive estimates and confidence intervals, and show that these have low bias and good coverage properties respectively for data that are simulated from models in chemical engineering and neurobiology. The performance of the method is demonstrated by using real world data from chemistry and from the progress of the autoimmune disease lupus. [source] Additive angle method for fast large-tip-angle RF pulse design in parallel excitationMAGNETIC RESONANCE IN MEDICINE, Issue 4 2008William A. Grissom Abstract Current methods for parallel excitation RF pulse design are based on the small-tip-angle approximation, which provides a computationally efficient means of pulse calculation. In general, pulses designed with those methods are inaccurate when scaled to produce large-tip angles, and methods for large-tipangle pulse design are more computationally demanding. This paper introduces a fast iterative method for large-tip-angle parallel pulse design that is formulated as a small number of Bloch equation simulations and fast small-tip-angle pulse designs, the results of which add to produce large-tip-angle pulses. Simulations and a phantom experiment demonstrate that the method is effective in designingmultidimensional large-tip-angle pulses of high excitation accuracy, compared to pulses designed with small-tip-angle methods. Magn Reson Med 59:779,787, 2008. © 2008 Wiley-Liss, Inc. [source] Nondestructive optical determination of fiber organization in intact myocardial wallMICROSCOPY RESEARCH AND TECHNIQUE, Issue 7 2008Rebecca M. Smith Abstract Mapping the myocardial fiber organization is important for assessing the electrical and mechanical properties of normal and diseased hearts. Current methods to determine the fiber organization have several limitations: histological sectioning mechanically distorts the tissue and is labor-intensive, while diffusion tensor imaging has low spatial resolution and requires expensive MRI scanners. Here, we utilized optical clearing, a fluorescent dye, and confocal microscopy to create three-dimensional reconstructions of the myocardial fiber organization of guinea pig and mouse hearts. We have optimized the staining and clearing procedure to allow for the nondestructive imaging of whole hearts with a thickness up to 3.5 mm. Myocardial fibers could clearly be identified at all depths in all preparations. We determined the change of fiber orientation across strips of guinea pig left ventricular wall. Our study confirms the qualitative result that there is a steady counterclockwise fiber rotation across the ventricular wall. Quantitatively, we found a total fiber rotation of 105.7 ± 14.9° (mean ± standard error of the mean); this value lies within the range reported by previous studies. These results show that optical clearing, in combination with a fluorescent dye and confocal microscopy, is a practical and accurate method for determining myocardial fiber organization. Microsc. Res. Tech., 2008. © 2008 Wiley-Liss, Inc. [source] 3D CT angiography of abdominal wall vascular perforators to plan DIEAP flaps,,MICROSURGERY, Issue 8 2007Gedge D. Rosson M.D. Purpose: Since the first report of TRAM flap reconstruction, there have been numerous studies to reduce complications of elective breast reconstruction. Current methods of preoperative perforator localization can be time-consuming, inaccurate, and imprecise. Thus, we sought to evaluate ultra-high resolution 3D CT angiography for the preoperative mapping of DIEAP flap perforating vessels. Methods: We reviewed all perforator-based breast reconstructions performed over a 5-month period. Candidates for DIEAP flap reconstruction were sent for a focused CT scan of the abdominal wall, using the 64 slice multi-detector CT scanner. Results: This article presents our first 23 flaps in 17 patients with preoperative ultra-high resolution 3D CT angiography. The reconstruction plan changed in three patients (18%). There was one take-back for venous congestion, but no partial or total flap loss. Conclusions: Preoperative perforator flap planning for breast reconstruction utilizing 3D CT angiogram is safe, easy to read, and can change the operative plan. © 2007 Wiley-Liss, Inc. Microsurgery, 2007. [source] Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickensMOLECULAR ECOLOGY, Issue 11 2007JEFF A. JOHNSON Abstract Current methods of DNA sequence analysis attempt to reconstruct historical patterns of population structure and growth from contemporary samples. However, these techniques may be influenced by recent population bottlenecks, which have the potential to eliminate lineages that reveal past changes in demography. One way to examine the performance of these demographic methods is to compare samples from populations before and after recent bottlenecks. We compared estimates of demographic history from populations of greater prairie-chickens (Tympanuchus cupido) before and after recent bottlenecks using four common methods (nested clade analysis [NCA], Tajima's D, mismatch distribution, and mdiv). We found that NCA did not perform well in the presence of bottleneck events, although it did recover some genetic signals associated with increased isolation and the extinction of intermediate populations. The majority of estimates for Tajima's D, including those from bottlenecked populations, were not significantly different from zero, suggesting our data conformed to neutral expectations. In contrast, mismatch distributions including the raggedness index were more likely to identify recently bottlenecked populations with this data set. Estimates of population mutation rate (,), population divergence time (t), and time to the most recent common ancestor (TMRCA) from mdiv were similar before and after bottlenecks; however, estimates of gene flow (M) were significantly lower in a few cases following a bottleneck. These results suggest that caution should be used when assessing demographic history from contemporary data sets, as recently fragmented and bottlenecked populations may have lost lineages that affect inferences of their demographic history. [source] Comparison of breath testing with fructose and high fructose corn syrups in health and IBSNEUROGASTROENTEROLOGY & MOTILITY, Issue 5 2008S. M. Skoog Abstract, Although incomplete fructose absorption has been implicated to cause gastrointestinal symptoms, foods containing high fructose corn syrup (HFCS) contain glucose. Glucose increases fructose absorption in healthy subjects. Our hypothesis was that fructose intolerance is less prevalent after HFCS consumption compared to fructose alone in healthy subjects and irritable bowel syndrome (IBS). Breath hydrogen levels and gastrointestinal symptoms were assessed after 40 g of fructose (12% solution) prepared either in water or as HFCS, administered in double-blind randomized order on 2 days in 20 healthy subjects and 30 patients with IBS. Gastrointestinal symptoms were recorded on 100-mm Visual Analogue Scales. Breath hydrogen excretion was more frequently abnormal (P < 0.01) after fructose (68%) than HFCS (26%) in controls and patients. Fructose intolerance (i.e. abnormal breath test and symptoms) was more prevalent after fructose than HFCS in healthy subjects (25%vs 0%, P = 0.002) and patients (40%vs 7%, P = 0.062). Scores for several symptoms (e.g. bloating r = 0.35) were correlated (P , 0.01) to peak breath hydrogen excretion after fructose but not HFCS; in the fructose group, this association did not differ between healthy subjects and patients. Symptoms were not significantly different after fructose compared to HFCS. Fructose intolerance is more prevalent with fructose alone than with HFCS in health and in IBS. The prevalence of fructose intolerance is not significantly different between health and IBS. Current methods for identifying fructose intolerance should be modified to more closely reproduce fructose ingestion in daily life. [source] Climate variables as predictors of basal metabolic rate: New equationsAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 5 2008Andrew W. Froehle Estimation of basal metabolic rate (BMR) and daily energy expenditure (DEE) in living humans and in fossil hominins can be used to understand the way populations adapt to different environmental and nutritional circumstances. One variable that should be considered in such estimates is climate, which may influence between-population variation in BMR. Overall, populations living in warmer climates tend to have lower BMR than those living in colder climates, even after controlling for body size and composition. Current methods of estimating BMR ignore climate, or deal with its effects in an insufficient manner. This may affect studies that use the factorial method to estimate DEE from BMR, when BMR is not measured but predicted using an equation. The present meta-analysis of published BMR uses stepwise regression to investigate whether the inclusion of climate variables can produce a generally applicable model for human BMR. Regression results show that mean annual temperature and high heat index temperature have a significant effect on BMR, along with body size, age and sex. Based on the regression analysis, equations predicting BMR from body size and climate variables were derived and compared with existing equations. The new equations are generally more accurate and more consistent across climates than the older ones. Estimates of DEE in living and fossil humans using the new equations are compared with estimates using previously published equations, illustrating the utility of including climate variables in estimates of BMR. The new equations derived here may prove useful for future studies of human energy expenditure. Am. J. Hum. Biol., 2008. © 2008 Wiley-Liss, Inc. [source] Work-related amputations in Washington state, 1997,2005AMERICAN JOURNAL OF INDUSTRIAL MEDICINE, Issue 7 2010Naomi J. Anderson MPH Abstract Background Work-related amputations are infrequent but devastating injuries. Attempts to more accurately estimate the burden of amputations and industries at risk have led the Washington State occupational surveillance program to explore new methods for case identification in Washington State workers' compensation data. Methods Two methods were utilized for case identification of work-related amputations. The first method used the ANSI Z16 nature code for amputation. An alternative method utilized medical, hospital, and claim administration coding of medical bills and bill payment systems. After identifying suspected amputation claims, a sample of the medical records associated with different case identification methods were reviewed to verify that an amputation likely occurred. Results From 1997 to 2005, 2,528 amputations were identified using the ANSI Z16 code for amputation (Nature,=,100) and an additional 3,912 amputations were identified using the alternative method. There was an increasing trend of amputation injuries over the time period using the ANSI amputation definition; however, the trend in amputation injuries captured by the alternative method was decreasing. This may indicate a bias in estimating a trend due to misclassification of amputation injuries. The sectors with the highest amputation claims rates were Manufacturing; Construction; Agriculture, Forestry, Fishing and Hunting; Accommodation and Food Services; and Wholesale and Retail Trade. Conclusions Current methods to identify work-related amputations in the workers' compensation data system underestimate the burden of amputations in Washington State. By utilizing alternative case identification methods, we estimate that there were about 150% more amputations in Washington State over the time period. Am. J. Ind. Med. 53:693,705, 2010. © 2010 Wiley-Liss, Inc. [source] Multivariate phase combination improves automated crystallographic model buildingACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Pavol Skubák Density modification is a standard technique in macromolecular crystallography that can significantly improve an initial electron-density map. To obtain optimal results, the initial and density-modified map are combined. Current methods assume that these two maps are independent and propagate the initial map information and its accuracy indirectly through previously determined coefficients. A multivariate equation has been derived that no longer assumes independence between the initial and density-modified map, considers the observed diffraction data directly and refines the errors that can occur in a single-wavelength anomalous diffraction experiment. The equation has been implemented and tested on over 100 real data sets. The results are dramatic: the method provides significantly improved maps over the current state of the art and leads to many more structures being built automatically. [source] Membrane bioreactors: overview of the effects of module geometry on mixing energyASIA-PACIFIC JOURNAL OF CHEMICAL ENGINEERING, Issue 3 2009Yuan Wang Abstract Membranes used in municipal membrane bioreactor (MBR) plants can be configured as flat sheet (FS) membranes or hollow fibre (HF) membranes. The HFs can be mounted either horizontally or vertically. The membranes can be immersed in their own vessel or within the aerobic vessel. These various configurations combine to give a unique reactor design. Current methods of design assume the mixing characteristics (e.g. each reactor vessel is completely mixed); hence the energy necessary to achieve complete mixing cannot be optimised. This paper presents an overview of mixing studies undertaken by the authors' research group on pilot- and full-scale MBRs through residence time distribution (RTD) analysis and computational fluid dynamics (CFD) modelling. The drawbacks of current technique for the sizing of MBRs (e.g. compartmental modelling) are highlighted. The use of CFD as a design tool to evaluate the mixing and energy of MBRs with different configurations (e.g. HF vs FS, inside submerged vs outside submerged) is presented. The MBR CFD model was validated using field-measured RTD data and compared with compartmental model. Results from mixing studies suggest that HF membranes are more energy efficient in terms of creating completely mixed conditions than the FS membranes. Copyright © 2009 Curtin University of Technology and John Wiley & Sons, Ltd. [source] Bias in cross-validated free R factors: mitigation of the effects of non-crystallographic symmetryACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2006Felcy Fabiola Current methods of free R factor cross-validation assume that the structure factors of the test and working sets are independent of one another. This assumption is only an approximation when the modeled structure occupies anything less than the full asymmetric unit. Through progressive elimination of reflections from the working set, starting with those expected to be most correlated to the test set, small biases in free R can be measured, presumably because of over-sampling of the Fourier transform owing to bulk solvent in the crystal. This level of bias may be of little practical importance, but it rises to significant levels with increasing non-crystallographic symmetry owing to wider correlations between structure factors than hitherto appreciated. In the presence of 15-fold non-crystallographic symmetry, with resolutions commonly attainable in macromolecular crystallography, it may not be possible to calculate an unbiased free R factor. Methods are developed for the calculation of reduced-bias free R factors through elimination of the strongest correlations between test and working sets. With 180-fold non-crystallographic symmetry they may not be an accurate indicator of absolute quality, but they do yield the correct optimal weighting for stereochemical restraints. [source] Electrically heated cables protect vines from frost damage at early floweringAUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH, Issue 1 2009D.W. LAMB Abstract Background and Aims:, Current methods of frost protection in vineyards involve fans, air heaters or sprinklers; each is limited by environmental constraints or available water. An alternative, all-electrical technique offers growers wider choice to match options with their vineyard operations. This study evaluates the ability of electrical heating cables, wrapped around the vine cordons, to protect inflorescences from frost damage. Methods and Results:, Five heating cable treatments in six replicates were applied to a 2-ha block of Sauvignon Blanc in the southern New England Region of Australia. Vines were subjected to a single ,3°C frost event in November 2006 when at approximately 30% capfall. Non-heated vines suffered 41% (Control) and 46% (No heat) inflorescence loss. Those subjected to Low heat suffered a 28% loss, Medium-heated vines suffered a 16% loss and High-heated vines suffered a 13% loss. Qualitative scoring of the vines indicated that more than half of the Medium-/High-heated vines suffered no appreciate damage, whereas all non-heated vines suffered some form of potential crop loss or damage. Conclusion:, Electrical heating cables of minimum 10 W/m power rating were found to significantly reduce frost damage to inflorescences at 30% capfall. Significance of the Study:, At approximately 43 kW/ha, electrical heating cable offers an alternative frost protection method for small vineyards. [source] AID in reprogramming: Quick and efficientBIOESSAYS, Issue 5 2010Identification of a key enzyme called AID, its activity in DNA demethylation, may help to overcome a pivotal epigenetic barrier in reprogramming somatic cells toward pluripotency Abstract Current methods of reprogramming differentiated cells into induced pluripotent stem cells remain slow and inefficient. In a recent report published online in Nature, Bhutani et al.1 developed a cell fusion strategy, achieving quick and efficient reprogramming toward pluripotency. Using this assay, they identified an immune system protein called activation-induced cytidine deaminase, or AID, which unexpectedly is actually able to "aid" in reprogramming due to its involvement in DNA demethylation that is required for induction of the two key pluripotency genes, Oct4 and Nanog. More recently, Popp et al.2 also reported online in Nature that AID is important for complete cell reprogramming in mammals. Together, these findings provide new insights into how cells are reprogrammed, identify the specific role of AID in cell fate reversal, and advance the field of regenerative medicine. [source] Bayesian Adaptive Regression Splines for Hierarchical DataBIOMETRICS, Issue 3 2007Jamie L. Bigelow Summary This article considers methodology for hierarchical functional data analysis, motivated by studies of reproductive hormone profiles in the menstrual cycle. Current methods standardize the cycle lengths and ignore the timing of ovulation within the cycle, both of which are biologically informative. Methods are needed that avoid standardization, while flexibly incorporating information on covariates and the timing of reference events, such as ovulation and onset of menses. In addition, it is necessary to account for within-woman dependency when data are collected for multiple cycles. We propose an approach based on a hierarchical generalization of Bayesian multivariate adaptive regression splines. Our formulation allows for an unknown set of basis functions characterizing the population-averaged and woman-specific trajectories in relation to covariates. A reversible jump Markov chain Monte Carlo algorithm is developed for posterior computation. Applying the methods to data from the North Carolina Early Pregnancy Study, we investigate differences in urinary progesterone profiles between conception and nonconception cycles. [source] Diffusion properties of transurethral intraprostatic injectionBJU INTERNATIONAL, Issue 9 2004Mark K. Plante OBJECTIVES To evaluate the location and extent of diffusion that occurs when liquid is injected transurethrally into the prostate gland, by correlating real-time fluoroscopy and gross pathology, and to quantify the variables that influence intraprostatic diffusion during chemoablation of the prostate. MATERIALS AND METHODS A solution of diatrizoate meglumine (HypaqueTM, Nycomed, Princeton, NJ) gentamicin and methylene-blue dye (HGM) was injected transurethrally into the prostate in six dogs, using a passive-deflection needle injection system. The intraprostatic diffusion characteristics were evaluated during each injection using real-time C-arm fluoroscopy, and following each injection by gross examination of methylene blue staining within the prostatic tissues. HGM back-flow into the urethra at the time of injection was assessed by measuring gentamicin levels in the collected bladder irrigant after each injection, using a standard dilution formula. RESULTS There was variability in the intraprostatic diffusion both fluoroscopically and grossly. The needle occasionally assumed a straighter trajectory than its intended curve. Intraprostatic diffusion was detected in 12 of 36 injections (33%). Using standard manipulations of various devices increased the intraprostatic diffusion in these injections to almost 80%. There was less intraprostatic diffusion when the injection resistance was either extremely high or absent. There was no extraprostatic extravasation of HGM beyond the prostatic capsule. CONCLUSION Current methods of transurethral intraprostatic injection are variable for both the diffusion of HGM solution and in needle deployment. The gross diffusion patterns with the HGM solution were consistent with the diffusion patterns documented in our previous research using absolute ethanol. These and other factors may partly explain the variability of the lesions produced with ethanol injection. Therefore, more research is needed to further elucidate the diffusion characteristics of solutions injected intraprostatically using the transurethral approach. [source] Instant Volumetric Understanding with Order-Independent Volume RenderingCOMPUTER GRAPHICS FORUM, Issue 3 2004Benjamin Mora Rapid, visual understanding of volumetric datasets is a crucial outcome of a good volume rendering application, but few current volume rendering systems deliver this result. Our goal is to reduce the volumetric surfing that is required to understand volumetric features by conveying more information in fewer images. In order to achieve this goal, and in contrast with most current methods which still use optical models and alpha blending, our approach reintroduces the order-independent contribution of every sample along the ray in order to have an equiprobable visualization of all the volume samples. Therefore, we demonstrate how order independent sampling can be suitable for fast volume understanding, show useful extensions to MIP and X-ray like renderings, and, finally, point out the special advantage of using stereo visualization in these models to circumvent the lack of depth cues. Categories and Subject Descriptors: I.3.3 [Computer Graphics]: Picture/Image, Generation, I.3.7 [Computer Graphics]: Three-Dimensional graphics and realism. [source] Efficient resource discovery in self-organized unstructured peer-to-peer networksCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 2 2009Lu Liu Abstract In unstructured peer-to-peer (P2P) networks, two autonomous peer nodes can be connected if users in those nodes are interested in each other's data. Owing to the similarity between P2P networks and social networks, where peer nodes can be regarded as people and connections can be regarded as relationships, social strategies are useful for improving the performance of resource discovery by self-organizing autonomous peers on unstructured P2P networks. In this paper, we present an efficient social-like peer-to-peer (ESLP) method for resource discovery by mimicking different human behaviours in social networks. ESLP has been simulated in a dynamic environment with a growing number of peer nodes. From the simulation results and analysis, ESLP achieved better performance than current methods. Copyright © 2008 John Wiley & Sons, Ltd. [source] | |||||||||||||||||||||||||||||||||||||