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Sample records for optimizing staining protocols

  1. Optimized Protocol of Methanol Treatment for Immunofluorescent Staining in Fixed Brain Slices

    Science.gov (United States)

    Yuan, Feng; Cohen, Noam A.; Cohen, Akiva S.

    2017-01-01

    We optimized methanol treatment in paraformaldehyde-fixed slices for immunofluorescent staining of ependymal basal bodies in brain ventricles. As 100% methanol induced severe deformations to the slices (including rolling and folding over), we tried to decrease methanol concentration. We found that 33.3% to 75% methanol could result in ideal immunostaining of basal bodies without inducing obvious deformations. Instead of treating slices at −20°C (without proper cryoprotection measurements) as suggested in previous studies, we carried out methanol treatment at room temperature. Our modified protocol can not only raise immunostaining efficiency in tissue slices, it may also prevent potential freezing damages to the samples. PMID:26509907

  2. Optimizing Staining Protocols for Laser Microdissection of Specific Cell Types from the Testis Including Carcinoma In Situ

    DEFF Research Database (Denmark)

    Sonne, Si Brask; Dalgaard, Marlene D; Nielsen, John Erik;

    2009-01-01

    protocols, and present two staining protocols for frozen sections, one for fast and specific staining of fetal germ cells, testicular carcinoma in situ cells, and other cells with embryonic stem cell-like properties that express the alkaline phosphatase, and one for specific staining of lipid droplet......Microarray and RT-PCR based methods are important tools for analysis of gene expression; however, in tissues containing many different cells types, such as the testis, characterization of gene expression in specific cell types can be severely hampered by noise from other cells. The laser...... microdissection technology allows for enrichment of specific cell types. However, when the cells are not morphologically distinguishable, it is necessary to use a specific staining method for the target cells. In this study we have tested different fixatives, storage conditions for frozen sections and staining...

  3. Morphology and structure of lipoproteins revealed by an optimized negative-staining protocol of electron microscopy[S

    Science.gov (United States)

    Zhang, Lei; Song, James; Cavigiolio, Giorgio; Ishida, Brian Y.; Zhang, Shengli; Kane, John P.; Weisgraber, Karl H.; Oda, Michael N.; Rye, Kerry-Anne; Pownall, Henry J.; Ren, Gang

    2011-01-01

    Plasma lipoprotein levels are predictors of risk for coronary artery disease. Lipoprotein structure-function relationships provide important clues that help identify the role of lipoproteins in cardiovascular disease. The compositional and conformational heterogeneity of lipoproteins are major barriers to the identification of their structures, as discovered using traditional approaches. Although electron microscopy (EM) is an alternative approach, conventional negative staining (NS) produces rouleau artifacts. In a previous study of apolipoprotein (apo)E4-containing reconstituted HDL (rHDL) particles, we optimized the NS method in a way that eliminated rouleaux. Here we report that phosphotungstic acid at high buffer salt concentrations plays a key role in rouleau formation. We also validate our protocol for analyzing the major plasma lipoprotein classes HDL, LDL, IDL, and VLDL, as well as homogeneously prepared apoA-I-containing rHDL. High-contrast EM images revealed morphology and detailed structures of lipoproteins, especially apoA-I-containing rHDL, that are amenable to three-dimensional reconstruction by single-particle analysis and electron tomography. PMID:20978167

  4. Optimizing Staining Protocols for Laser Microdissection of Specific Cell Types from the Testis Including Carcinoma In Situ

    DEFF Research Database (Denmark)

    Sonne, Si Brask; Dalgaard, Marlene D; Nielsen, John Erik

    2009-01-01

    Microarray and RT-PCR based methods are important tools for analysis of gene expression; however, in tissues containing many different cells types, such as the testis, characterization of gene expression in specific cell types can be severely hampered by noise from other cells. The laser...... microdissection technology allows for enrichment of specific cell types. However, when the cells are not morphologically distinguishable, it is necessary to use a specific staining method for the target cells. In this study we have tested different fixatives, storage conditions for frozen sections and staining...

  5. A Staining Protocol for Identifying Secondary Compounds in Myrtaceae

    Directory of Open Access Journals (Sweden)

    Hernan A. Retamales

    2014-10-01

    Full Text Available Premise of the study: Here we propose a staining protocol using toluidine blue (TBO and ruthenium red to reliably identify secondary compounds in the leaves of some species of Myrtaceae. Methods and Results: Leaves of 10 species representing 10 different genera of Myrtaceae were processed and stained using five different combinations of ruthenium red and TBO. Optimal staining conditions were determined as 1 min of ruthenium red (0.05% aqueous and 45 s of TBO (0.1% aqueous. Secondary compounds clearly identified under this treatment include mucilage in the mesophyll, polyphenols in the cuticle, lignin in fibers and xylem, tannins and carboxylated polysaccharides in the epidermis, and pectic substances in the primary cell walls. Conclusions: Potential applications of this protocol include systematic, phytochemical, and ecological investigations in Myrtaceae. It might be applicable to other plant families rich in secondary compounds and could be used as a preliminary screening method for extraction of these elements.

  6. Optimization of Picrosirius red staining protocol to determine collagen fiber orientations in vaginal and uterine cervical tissues by Mueller polarized microscopy.

    Science.gov (United States)

    Nazac, André; Bancelin, Stéphane; Teig, Benjamin; Ibrahim, Bicher Haj; Fernandez, Hervé; Schanne-Klein, Marie-Claire; De Martino, Antonello

    2015-08-01

    Polarized microscopy provides unique information on anisotropic samples. In its most complete implementation, namely Mueller microscopy, this technique is well suited for the visualization of fibrillar proteins orientations, with collagen in the first place. However, the intrinsic optical anisotropy of unstained tissues has to be enhanced by Picrosirius Red (PR) staining to enable Mueller measurements. In this work, we compared the orientation mapping provided by Mueller and second harmonic generation (SHG) microscopies on PR stained samples of vaginal and uterine cervix tissues. SHG is a multiphoton technique that is highly specific to fibrillar collagen, and was taken as the "gold standard" for its visualization. We showed that Mueller microscopy can be safely used to determine collagen orientation in PR stained cervical tissue. In contrast, in vaginal samples, Mueller microscopy revealed orientations not only of collagen but also of other anisotropic structures. Thus PR is not fully specific to collagen, which necessitates comparison to SHG microscopy in every type of tissue. In addition to this study of PR specificity, we determined the optimal values of the staining parameters. We found that staining times of 5 min, and sample thicknesses of 5 µm were sufficient in cervical and vaginal tissues.

  7. Staining protocol for organotypic hippocampal slice cultures.

    Science.gov (United States)

    Gogolla, Nadine; Galimberti, Ivan; DePaola, Vincenzo; Caroni, Pico

    2006-01-01

    This protocol details a method to immunostain organotypic slice cultures from mouse hippocampus. The cultures are based on the interface method, which does not require special equipment, is easy to execute and yields slice cultures that can be imaged repeatedly, from the time of isolation at postnatal day 6-9 up to 6 months in vitro. The preserved tissue architecture facilitates the analysis of defined hippocampal synapses, cells and entire projections. Time-lapse imaging is based on transgenes expressed in the mice or on constructs introduced through transfection or viral vectors; it can reveal processes that develop over periods ranging from seconds to months. Subsequent to imaging, the slices can be processed for immunocytochemistry to collect further information about the imaged structures. This protocol can be completed in 3 d.

  8. A pipeline for developing and testing staining protocols for flow cytometry, demonstrated with SYBR Green I and propidium iodide viability staining.

    Science.gov (United States)

    Nescerecka, Alina; Hammes, Frederik; Juhna, Talis

    2016-12-01

    The increasing use of flow cytometry (FCM) for analyses of environmental samples has resulted in a large variety of staining protocols with varying results and limited comparability. Viability assessment with FCM is in this context of particular interest because incorrect staining could severely affect the outcome/interpretation of the results. Here we propose a pipeline for the development and optimization of staining protocols for environmental samples, demonstrated with the common viability dye combination of SYBR Green I (SG) and propidium iodide (PI). Optimization steps included the assessment of dye solvents, determination of suitable PI concentration, and determining the optimal staining temperature and staining time. We demonstrated that dimethyl sulfoxide (DMSO) could impair membrane integrity, when used for SGPI stock solution preparation, and TRIS buffer was chosen as an alternative. Moreover we selected 6μM as optimal PI final concentration: less than 3μM resulted in incomplete staining of damaged cells, while concentrations higher that 12μM resulted in false PI-positive staining of intact cells. Low temperatures (25°C) resulted in a slow reaction and did not enable the staining of all bacteria, while high temperatures (44°C) caused damage to cells and false PI-positive results. Hence, 35°C was selected as optimal staining temperature. We further showed that a minimum of 15min were necessary to obtain stable staining results. Moreover, we showed that addition of EDTA resulted in 1-39% more PI-positive results compared to an EDTA-free sample, and argue that insufficient evidence currently exist in favor of adding EDTA to all samples in general. Altogether, the data clearly shows the need to be careful, precise and reproducible when staining cells for flow cytometric analyses, and the need to assess and optimize staining protocols with both viable and non-viable bacteria. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. An Eco-friendly, Scaled-down Gram Stain Protocol

    Directory of Open Access Journals (Sweden)

    Ruth A. Gyure

    2010-04-01

    Full Text Available Currently, flushing large volumes of Gram stain reagents into sanitary sewage systems is no longer acceptable. These chemical wastes are highly regulated and must be collected, labeled, and disposed of in a responsible manner, usually by paying a commercial service to remove them to an authorized off-site facility. Such services are costly and, as expected, costs are proportional to volume of collected waste. This “old” method of Gram staining, even if effluent is collected, generates a high volume of liquid waste which is unnecessarily diluted with additional large volumes of water from the rinsing steps. The purpose of using this scaled-down and eco-friendly protocol is to dramatically reduce the amount of liquid waste produced without sacrificing quality of results. This protocol is flexible, practical, and easy to implement. It does not require students to work at a bench sink, reduces user cost, and lowers environmental impact overall.

  10. Zebrafish embryology and cartilage staining protocols for high school students.

    Science.gov (United States)

    Emran, Farida; Brooks, Jacqueline M; Zimmerman, Steven R; Johnson, Susan L; Lue, Robert A

    2009-06-01

    The Life Sciences-Howard Hughes Medical Institute Outreach Program at Harvard University supports high school science education by offering an on-campus program for students and their teachers to participate in investigative, hands-on laboratory sessions. The outreach program has recently designed and launched a successful zebrafish embryology protocol that we present here. The main objectives of this protocol are to introduce students to zebrafish as a model research organism and to provide students with direct experience with current techniques used in embryological research. The content of the lab is designed to generate discussions on embryology, genetics, fertilization, natural selection, and animal adaptation. The protocol produces reliable results in a time-efficient manner using a minimum of reagents. The protocol presented here consists of three sections: observations of live zebrafish larvae at different developmental stages, cartilage staining of zebrafish larvae, and a mutant hunt involving identification of two zebrafish mutants (nacre and chokh). Here, we describe the protocol, show the results obtained for each section, and suggest possible alternatives for different lab settings.

  11. Optimized Negative-Staining Electron Microscopy for Lipoprotein Studies

    Science.gov (United States)

    Zhang, Lei; Tong, Huimin; Garewal, Mark; Ren, Gang

    2012-01-01

    Background Negative-staining (NS), a rapid, simple and conventional technique of electron microscopy (EM), has been commonly used to initially study the morphology and structure of proteins for half a century. Certain NS protocols however can cause artifacts, especially for structurally flexible or lipid-related proteins, such as lipoproteins. Lipoproteins were often observed in the form of rouleau as lipoprotein particles appeared to be stacked together by conventional NS protocols. The flexible components of lipoproteins, i.e. lipids and amphipathic apolipoproteins, resulted in the lipoprotein structure being sensitive to the NS sample preparation parameters, such as operational procedures, salt concentrations, and the staining reagents. Scope of review The most popular NS protocols that have been used to examine lipoprotein morphology and structure were reviewed. Major conclusions The comparisons show that an optimized NS (OpNS) protocol can eliminate the rouleau artifacts of lipoproteins, and that the lipoproteins are similar in size and shape as statistically measured from two EM methods, OpNS and cryo-electron microscopy (cryo-EM). OpNS is a high-throughput, high-contrast and high-resolution (near 1 nm, but rarely better than 1 nm) method which has been used to discover the mechanics of a small protein, 53 kDa cholesterol ester transfer protein (CETP), and the structure of an individual particle of a single protein by individual-particle electron tomography (IPET), i.e. a 14 Å-resolution IgG antibody three-dimensional map. General significance It is suggested that OpNS can be used as a general protocol to study the structure of proteins, especially highly dynamic proteins with equilibrium-fluctuating structures. PMID:23032862

  12. CT protocol review and optimization.

    Science.gov (United States)

    Kofler, James M; Cody, Dianna D; Morin, Richard L

    2014-03-01

    To reduce the radiation dose associated with CT scans, much attention is focused on CT protocol review and improvement. In fact, annual protocol reviews will soon be required for ACR CT accreditation. A major challenge in the protocol review process is determining whether a current protocol is optimal and deciding what steps to take to improve it. In this paper, the authors describe methods for pinpointing deficiencies in CT protocols and provide a systematic approach for optimizing them. Emphasis is placed on a team approach, with a team consisting of at least one radiologist, one physicist, and one technologist. This core team completes a critical review of all aspects of a CT protocol and carefully evaluates proposed improvements. Changes to protocols are implemented only with consensus of the core team, with consideration of all aspects of the CT examination, including image quality, radiation dose, patient care and safety, and workflow.

  13. Optimalization Of Port-Wine Stain Treatment With Lasers

    Science.gov (United States)

    Lahaye, C. T.; van Gemert, M. J.; Henning, J. P. H.

    1985-03-01

    To optimalize laser-parameters for therapy of port-wine stains temperature calculations have been performed on a skin model. The optimal values of these numerically evaluated variables are: wavelength λ= 415,577 or 540 nm., pulse-time t1 a few milliseconds and beam radius wi> 0.1 mm. Based on these theoretical results some experiments have been carried out which confirm the calculations. Thus laser-therapy for port-wine stains can be ameliorated.

  14. Establishing a protocol for immunocytochemical staining and chromogenic in situ hybridization of Giemsa and Diff-Quick prestained cytological smears

    Directory of Open Access Journals (Sweden)

    Elsa Beraki

    2012-01-01

    Full Text Available Background: Protocols for immunocytochemical staining (ICC and in situ hybridization (ISH of air-dried Diff-Quick or May-Grünwald Giemsa (MGG-stained smears have been difficult to establish. An increasing need to be able to use prestained slides for ICC and ISH in specific cases led to this study, aiming at finding a robust protocol for both methods. Materials and Methods: The material consisted of MGG- and Diff-Quick-stained smears. After diagnosis, one to two diagnostic smears were stored in the department. Any additional smear(s containing diagnostic material were used for this study. The majority were fine needle aspirates (FNAC from the breast, comprising materials from fibroadenomas, fibrocystic disease, and carcinomas. A few were metastatic lesions (carcinomas and malignant melanomas. There were 64 prestained smears. Ten smears were Diff-Quick stained, and 54 were MGG stained. The antibodies used for testing ICC were Ki-67, ER, and PgR, CK MNF116 (pancytokeratin and E-cadherin. HER-2 Dual SISH was used to test ISH. Citrate, TRS, and TE buffers at pH6 and pH9 were tested, as well as, different heating times, microwave powers and antibody concentrations. The ICC was done on the Dako Autostainer (Dako®, Glostrup, Denmark, and HER-2 Dual SISH was done on the Ventana XT-machine (Ventana / Roche® , Strasbourg, France. Results: Optimal results were obtained with the TE buffer at pH 9, for both ICC and ISH. Antibody concentrations generally had to be higher than in the immunohistochemistry (IHC. The optimal microwave heat treatment included an initial high power boiling followed by low power boiling. No post fixation was necessary for ICC, whereas, 20 minutes post fixation in formalin (4% was necessary for ISH. Conclusions: Microwave heat treatment, with initial boiling at high power followed by boiling at low power and TE buffer at pH 9 were the key steps in the procedure. Antibody concentrations has to be adapted for each ICC marker. Post

  15. Nucleic acid protocols: Extraction and optimization

    Directory of Open Access Journals (Sweden)

    Saeed El-Ashram

    2016-12-01

    Full Text Available Yield and quality are fundamental features for any researchers during nucleic acid extraction. Here, we describe a simplified, semi-unified, effective, and toxic material free protocol for extracting DNA and RNA from different prokaryotic and eukaryotic sources exploiting the physical and chemical properties of nucleic acids. Furthermore, this protocol showed that DNA and RNA are under triple protection (i.e. EDTA, SDS and NaCl during lysis step, and this environment is improper for RNase to have DNA liberated of RNA and even for DNase to degrade the DNA. Therefore, the complete removal of RNA under RNase influence is achieved when RNase is added after DNA extraction, which gives optimal quality with any protocols. Similarly, DNA contamination in an isolated RNA is degraded by DNase to obtain high-quality RNA. Our protocol is the protocol of choice in terms of simplicity, recovery time, environmental safety, amount, purity, PCR and RT-PCR applicability.

  16. Dual phylogenetic staining protocol for simultaneous analysis of yeast and bacteria in artworks

    Science.gov (United States)

    González-Pérez, Marina; Brinco, Catarina; Vieira, Ricardo; Rosado, Tânia; Mauran, Guilhem; Pereira, António; Candeias, António; Caldeira, Ana Teresa

    2017-02-01

    The detection and analysis of metabolically active microorganisms are useful to determine those directly involved in the biodeterioration of cultural heritage (CH). Fluorescence in situ hybridization with oligonucleotide probes targeted at rRNA (RNA-FISH) has demonstrated to be a powerful tool for signaling them. However, more efforts are required for the technique to become a vital tool for the analysis of CH's microbiological communities. Simultaneous analysis of microorganisms belonging to different kingdoms, by RNA-FISH in-suspension approach, could represent an important progress: it could open the door for the future use of the technique to analyze the microbial communities by flow cytometry, which has shown to be a potent tool in environmental microbiology. Thus, in this work, various already implemented in-suspension RNA-FISH protocols for ex situ analysis of yeast and bacteria were investigated and adapted for allowing the simultaneous detection of these types of microorganisms. A deep investigation of the factors that can affect the results was carried out, focusing particular attention on the selection of the fluorochromes used for labelling the probe set. The resultant protocol, involving the use of EUK516-6-FAM/EUB338-Cy3 probes combination, was validated using artificial consortia and gave positive preliminary results when applied in samples from a real case study: the Paleolithic archaeological site of Escoural Cave (Alentejo, Portugal). This approach represents the first dual-staining RNA-FISH in-suspension protocol developed and applied for the simultaneous investigation of CH biodeteriogenic agents belonging to different kingdoms.

  17. A Bayesian approach to optimizing cryopreservation protocols

    Directory of Open Access Journals (Sweden)

    Sammy Sambu

    2015-06-01

    Full Text Available Cryopreservation is beset with the challenge of protocol alignment across a wide range of cell types and process variables. By taking a cross-sectional assessment of previously published cryopreservation data (sample means and standard errors as preliminary meta-data, a decision tree learning analysis (DTLA was performed to develop an understanding of target survival using optimized pruning methods based on different approaches. Briefly, a clear direction on the decision process for selection of methods was developed with key choices being the cooling rate, plunge temperature on the one hand and biomaterial choice, use of composites (sugars and proteins as additional constituents, loading procedure and cell location in 3D scaffolding on the other. Secondly, using machine learning and generalized approaches via the Naïve Bayes Classification (NBC method, these metadata were used to develop posterior probabilities for combinatorial approaches that were implicitly recorded in the metadata. These latter results showed that newer protocol choices developed using probability elicitation techniques can unearth improved protocols consistent with multiple unidimensionally-optimized physical protocols. In conclusion, this article proposes the use of DTLA models and subsequently NBC for the improvement of modern cryopreservation techniques through an integrative approach.

  18. An optimized transformation protocol for Lipomyces starkeyi.

    Science.gov (United States)

    Calvey, Christopher H; Willis, Laura B; Jeffries, Thomas W

    2014-08-01

    We report the development of an efficient genetic transformation system for Lipomyces starkeyi based on a modified lithium acetate transformation protocol. L. starkeyi is a highly lipogenic yeast that grows on a wide range of substrates. The initial transformation rate for this species was extremely low, and required very high concentrations of DNA. A systematic approach for optimizing the protocol resulted in an increase in the transformation efficiency by four orders of magnitude. Important parameters included cell density, the duration of incubation and recovery periods, the heat shock temperature, and the concentration of lithium acetate and carrier DNA within the transformation mixture. We have achieved efficiencies in excess of 8,000 transformants/µg DNA, which now make it possible to screen libraries in the metabolic engineering of this yeast. Metabolic engineering based on this transformation system could improve lipogenesis and enable formation of higher value products.

  19. Efficient Protocols for Distributed Classification and Optimization

    CERN Document Server

    Daume, Hal; Saha, Avishek; Venkatasubramanian, Suresh

    2012-01-01

    In distributed learning, the goal is to perform a learning task over data distributed across multiple nodes with minimal (expensive) communication. Prior work (Daume III et al., 2012) proposes a general model that bounds the communication required for learning classifiers while allowing for $\\eps$ training error on linearly separable data adversarially distributed across nodes. In this work, we develop key improvements and extensions to this basic model. Our first result is a two-party multiplicative-weight-update based protocol that uses $O(d^2 \\log{1/\\eps})$ words of communication to classify distributed data in arbitrary dimension $d$, $\\eps$-optimally. This readily extends to classification over $k$ nodes with $O(kd^2 \\log{1/\\eps})$ words of communication. Our proposed protocol is simple to implement and is considerably more efficient than baselines compared, as demonstrated by our empirical results. In addition, we illustrate general algorithm design paradigms for doing efficient learning over distribute...

  20. A novel staining protocol for multiparameter assessment of cell heterogeneity in Phormidium populations (cyanobacteria employing fluorescent dyes.

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    Daria Tashyreva

    Full Text Available Bacterial populations display high heterogeneity in viability and physiological activity at the single-cell level, especially under stressful conditions. We demonstrate a novel staining protocol for multiparameter assessment of individual cells in physiologically heterogeneous populations of cyanobacteria. The protocol employs fluorescent probes, i.e., redox dye 5-cyano-2,3-ditolyl tetrazolium chloride, 'dead cell' nucleic acid stain SYTOX Green, and DNA-specific fluorochrome 4',6-diamidino-2-phenylindole, combined with microscopy image analysis. Our method allows simultaneous estimates of cellular respiration activity, membrane and nucleoid integrity, and allows the detection of photosynthetic pigments fluorescence along with morphological observations. The staining protocol has been adjusted for, both, laboratory and natural populations of the genus Phormidium (Oscillatoriales, and tested on 4 field-collected samples and 12 laboratory strains of cyanobacteria. Based on the mentioned cellular functions we suggest classification of cells in cyanobacterial populations into four categories: (i active and intact; (ii injured but active; (iii metabolically inactive but intact; (iv inactive and injured, or dead.

  1. The effects of different decalcification protocols on TUNEL and general cartilage staining

    NARCIS (Netherlands)

    Emans, PJ; Bulstra, SK; Kuijer, R

    2005-01-01

    Apoptosis is characterized by DNA strand breaks with a 3'-OH terminus, which are analyzed by terminal deoxy(d)-UTP nick end labeling (TUNEL). Proteinase K digestion is thought to be an essential step in the TUNEL procedure. The effects of decalcifying reagents on general staining and the TUNEL assay

  2. Weighted optimization of irradiance for photodynamic therapy of port wine stains

    Science.gov (United States)

    He, Linhuan; Zhou, Ya; Hu, Xiaoming

    2016-10-01

    Planning of irradiance distribution (PID) is one of the foremost factors for on-demand treatment of port wine stains (PWS) with photodynamic therapy (PDT). A weighted optimization method for PID was proposed according to the grading of PWS with a three dimensional digital illumination instrument. Firstly, the point clouds of lesions were filtered to remove the error or redundant points, the triangulation was carried out and the lesion was divided into small triangular patches. Secondly, the parameters such as area, normal vector and orthocenter for optimization of each triangular patch were calculated, and the weighted coefficients were determined by the erythema indexes and areas of patches. Then, the optimization initial point was calculated based on the normal vectors and orthocenters to optimize the light direction. In the end, the irradiation can be optimized according to cosine values of irradiance angles and weighted coefficients. Comparing the irradiance distribution before and after optimization, the proposed weighted optimization method can make the irradiance distribution match better with the characteristics of lesions, and has the potential to improve the therapeutic efficacy.

  3. Routing Protocol Design and Performance Optimization in Cognitive Radio Networks

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    Zhenguo Wu

    2013-10-01

    Full Text Available Routing protocol is an important issue in cognitive radio networks. This paper explored the issues and challenges of routing protocol in cognitive radio network from five aspects: hidden terminal, exposed terminal, deafness, cross-layer design, and topology. The existed protocols are classified by the metrics: the establishment of active routing, cross-layer routing, and network performance indicators. Focusing on analyzing performance of routing protocols and design optimized schemes in cognitive radio networks, the advantage and disadvantage of related work were discussed in detail.

  4. Optimization of irradiance for photodynamic therapy of port-wine stain

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    Zhang, Feng-juan; Hu, Xiao-ming; Zhou, Ya; Li, Qin

    2015-04-01

    Controllable and effective irradiation of lesions is among the key factors that affect the potency of photodynamic therapy (PDT). An optimization method for the irradiance distribution of treatment was proposed which can be used to improve the efficacy of PDT and allow more lesions to receive the desired irradiance level in a single therapy session. With the proposed digital illumination binocular treatment system, the preferred surface normal vectors, irradiation angles, as well as area and weight coefficients of lesions can be achieved and used as characteristic parameters to optimize the irradiation direction. Two port-wine stain phantom experiments were performed. The comparison of the illumination area between preoptimization and postoptimization showed that the proposed method can effectively guide the light source control, improve the distribution of light dose, and increase the effective treatment area.

  5. An optimized color transformation for the analysis of digital images of hematoxylin & eosin stained slides.

    Science.gov (United States)

    Zarella, Mark D; Breen, David E; Plagov, Andrei; Garcia, Fernando U

    2015-01-01

    Hematoxylin and eosin (H&E) staining is ubiquitous in pathology practice and research. As digital pathology has evolved, the reliance of quantitative methods that make use of H&E images has similarly expanded. For example, cell counting and nuclear morphometry rely on the accurate demarcation of nuclei from other structures and each other. One of the major obstacles to quantitative analysis of H&E images is the high degree of variability observed between different samples and different laboratories. In an effort to characterize this variability, as well as to provide a substrate that can potentially mitigate this factor in quantitative image analysis, we developed a technique to project H&E images into an optimized space more appropriate for many image analysis procedures. We used a decision tree-based support vector machine learning algorithm to classify 44 H&E stained whole slide images of resected breast tumors according to the histological structures that are present. This procedure takes an H&E image as an input and produces a classification map of the image that predicts the likelihood of a pixel belonging to any one of a set of user-defined structures (e.g., cytoplasm, stroma). By reducing these maps into their constituent pixels in color space, an optimal reference vector is obtained for each structure, which identifies the color attributes that maximally distinguish one structure from other elements in the image. We show that tissue structures can be identified using this semi-automated technique. By comparing structure centroids across different images, we obtained a quantitative depiction of H&E variability for each structure. This measurement can potentially be utilized in the laboratory to help calibrate daily staining or identify troublesome slides. Moreover, by aligning reference vectors derived from this technique, images can be transformed in a way that standardizes their color properties and makes them more amenable to image processing.

  6. Hardware Abstraction and Protocol Optimization for Coded Sensor Networks

    DEFF Research Database (Denmark)

    Nistor, Maricica; Roetter, Daniel Enrique Lucani; Barros, João

    2015-01-01

    -efficient protocols that use such an abstraction, as well as mechanisms to optimize a communication protocol in terms of energy consumption. The problem is modeled for different feedback-based techniques, where sensors are connected to a base station, either directly or through relays. We show that for four example......The design of the communication protocols in wireless sensor networks (WSNs) often neglects several key characteristics of the sensor's hardware, while assuming that the number of transmitted bits is the dominating factor behind the system's energy consumption. A closer look at the hardware...... platforms, the use of relays may decrease up to 4.5 times the total energy consumption when the protocol and the hardware are carefully matched. We conclude that: 1) the energy budget for a communication protocol varies significantly on different sensor platforms; and 2) the protocols can be judiciously...

  7. A protocol for collecting and staining hemocytes from the yellow fever mosquito Aedes aegypti.

    Science.gov (United States)

    Qayum, Amina A; Telang, Aparna

    2011-05-16

    not necessary if the downstream goal is to collect, fix and stain hemocytes for diagnostics. Here, we demonstrate our method of collecting mosquito hemolymph that combines the simplicity of perfusion, using anticoagulant buffers in place of saline solution, with the accuracy of high injection techniques to isolate clean preparations of hemocytes in Aedes mosquitoes.

  8. OPTIMIZING LISTENING SKILLS TO IMPROVE THE TOEFL SCORE OF STAIN PEKALONGAN STUDENTS

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    Riskiana .

    2015-10-01

    Full Text Available The fact that the students have problems in the three micro-skills of listening namely recognizing the English stress patterns, the reduced forms of words, and words boundaries and that the teachers never teach the students how to listen have made them get low TOEFL scores on listening section. This research aims at: (1 finding out whether optimizing listening skills can improve the students’ TOEFL scores on listening; and (2 describing the class situation during the teaching of toefl listening by optimizing listening skills. This action research is conducted in two cycles each of which is divided into planning, acting, observing, and reflecting. There are two kinds of data. The qualitative data taken from observation, interview, and questionnaire are analyzed by using Constant Comparative Method. The quantitative data taken from the pre-test in the pre-research, post-test in cycle 1, and post-test in cycle 2 are analyzed by using descriptive statistics. The subjects of the research are the STAIN Pekalongan students taking English 3 class, the TOEFL Preparation Class, in the Academic Year 2014/2015. The result of the research shows that: (1 teaching toefl listening section by optimizing listening skills is able to overcome the students’ problems in the three micro-skills of listening and consequently improve the students’ TOEFL scores on listening. Their average scores improve from 101 in the pre-test to 118 in the post-test of cycle 1 and 129 in the post-test of cycle 2; (2 The class situation is attractive and the students are actively involved in the various activities done during the teaching and learning process. In line with the success of optimizing listening skills in teaching TOEFL listening, it is suggested that teachers should examine their students’ listening problems so as to be able to teach them what they need in listening to English.

  9. Optimal Medium Access Protocols for Cognitive Radio Networks

    CERN Document Server

    Lai, Lifeng; Jiang, Hai; Poor, H Vincent

    2008-01-01

    This paper focuses on the design of medium access control protocols for cognitive radio networks. The scenario in which a single cognitive user wishes to opportunistically exploit the availability of empty frequency bands within parts of the radio spectrum having multiple bands is first considered. In this scenario, the availability probability of each channel is unknown a priori to the cognitive user. Hence efficient medium access strategies must strike a balance between exploring (learning) the availability probability of the channels and exploiting the knowledge of the availability probability identified thus far. For this scenario, an optimal medium access strategy is derived and its underlying recursive structure is illustrated via examples. To avoid the prohibitive computational complexity of this optimal strategy, a low complexity asymptotically optimal strategy is developed. Next, the multi-cognitive user scenario is considered and low complexity medium access protocols, which strike an optimal balanc...

  10. Evolutionary and principled search strategies for sensornet protocol optimization.

    Science.gov (United States)

    Tate, Jonathan; Woolford-Lim, Benjamin; Bate, Iain; Yao, Xin

    2012-02-01

    Interactions between multiple tunable protocol parameters and multiple performance metrics are generally complex and unknown; finding optimal solutions is generally difficult. However, protocol tuning can yield significant gains in energy efficiency and resource requirements, which is of particular importance for sensornet systems in which resource availability is severely restricted. We address this multi-objective optimization problem for two dissimilar routing protocols and by two distinct approaches. First, we apply factorial design and statistical model fitting methods to reject insignificant factors and locate regions of the problem space containing near-optimal solutions by principled search. Second, we apply the Strength Pareto Evolutionary Algorithm 2 and Two-Archive evolutionary algorithms to explore the problem space, with each iteration potentially yielding solutions of higher quality and diversity than the preceding iteration. Whereas a principled search methodology yields a generally applicable survey of the problem space and enables performance prediction, the evolutionary approach yields viable solutions of higher quality and at lower experimental cost. This is the first study in which sensornet protocol optimization has been explicitly formulated as a multi-objective problem and solved with state-of-the-art multi-objective evolutionary algorithms.

  11. Choosing optimal wavelength for photodynamic therapy of port wine stains by mathematic simulation

    Science.gov (United States)

    Wang, Ying; Gu, Ying; Zuo, Zhaohui; Huang, Naiyan

    2011-09-01

    Many laser wavelengths have been used in photodynamic therapy (PDT) for port wine stains (PWS). However, how these wavelengths result in different PDT outcomes has not been clearly illuminated. This study is designed to analyze which wavelengths would be the most advantageous for use in PDT for PWS. The singlet oxygen yield in PDT-treated PWS skin under different wavelengths at the same photosensitizer dosage was simulated and the following three situations were simulated and compared: 1. PDT efficiency of 488, 532, 510, 578, and 630 nm laser irradiation at clinical dosage (100 mW/cm2, 40 min); 2. PDT efficiency of different wavelength for PWS with hyperpigmentation after previous PDT; 3. PDT efficiency of different wavelengths for PWS, in which only deeply located ectatic vessels remained. The results showed that singlet oxygen yield is the highest at 510 nm, it is similar at 532 nm and 488 nm, and very low at 578 nm and 630 nm. This result is identical to the state in clinic. According to this theoretical study, the optimal wavelength for PDT in the treatment of PWS should near the absorption peaks of photosensitizer and where absorption from native chromophores (haemoglobin and melanin) is diminished.

  12. An optimized protocol for the production of high purity maltose.

    Science.gov (United States)

    Nehete, P N; Shah, N K; Ramamurthy, V; Kothari, R M

    1992-07-01

    An economical protocol, which is simple, rapid and reproducible for the production of maltose by enzymatic hydrolysis of tapioca starch, has been optimized. The protocol involves liquefaction of 35% (w/w) tapioca starch by bacterial α-amylase at 78±2°C to 3 to 5% (w/w) reducing sugars, followed by maximal (85±3% w/w maltose equivalent) saccharification with barley β-amylase and pullulanase at 50°C for 24 to 30 h. The post-saccharification recovery protocol comprised decolourization by charcoal, de-dextrinization by denatured spirit precipitation, de-ionization by passage through cation and anion exchangers and dehydration by vacuum drying. A white crystalline maltose powder was obtained with specifications comparable to commercial high purity maltose. The protocol yields at least 60% (w/w) recovery of maltose and is suitable for use by the pharmaceutical industry. The protocol is unique in that it utilizes cheap and easily hydrolysed tapioca starch, leaves no mother liquor, enabling higher recovery of maltose, and allows almost quantitative recovery of limit maltodextrins, a value-added marketable by-product.

  13. FOXP3-stained image analysis for follicular lymphoma: optimal adaptive thresholding with maximal nucleus coverage

    Science.gov (United States)

    Senaras, C.; Pennell, M.; Chen, W.; Sahiner, B.; Shana'ah, A.; Louissaint, A.; Hasserjian, R. P.; Lozanski, G.; Gurcan, M. N.

    2017-03-01

    Immunohistochemical detection of FOXP3 antigen is a usable marker for detection of regulatory T lymphocytes (TR) in formalin fixed and paraffin embedded sections of different types of tumor tissue. TR plays a major role in homeostasis of normal immune systems where they prevent auto reactivity of the immune system towards the host. This beneficial effect of TR is frequently "hijacked" by malignant cells where tumor-infiltrating regulatory T cells are recruited by the malignant nuclei to inhibit the beneficial immune response of the host against the tumor cells. In the majority of human solid tumors, an increased number of tumor-infiltrating FOXP3 positive TR is associated with worse outcome. However, in follicular lymphoma (FL) the impact of the number and distribution of TR on the outcome still remains controversial. In this study, we present a novel method to detect and enumerate nuclei from FOXP3 stained images of FL biopsies. The proposed method defines a new adaptive thresholding procedure, namely the optimal adaptive thresholding (OAT) method, which aims to minimize under-segmented and over-segmented nuclei for coarse segmentation. Next, we integrate a parameter free elliptical arc and line segment detector (ELSD) as additional information to refine segmentation results and to split most of the merged nuclei. Finally, we utilize a state-of-the-art super-pixel method, Simple Linear Iterative Clustering (SLIC) to split the rest of the merged nuclei. Our dataset consists of 13 region-ofinterest images containing 769 negative and 88 positive nuclei. Three expert pathologists evaluated the method and reported sensitivity values in detecting negative and positive nuclei ranging from 83-100% and 90-95%, and precision values of 98-100% and 99-100%, respectively. The proposed solution can be used to investigate the impact of FOXP3 positive nuclei on the outcome and prognosis in FL.

  14. Analysis of Energy Optimized Hierarchical Routing Protocols in WSN

    Directory of Open Access Journals (Sweden)

    Er. Shelly Jain

    2013-05-01

    Full Text Available Modern wireless sensor network can be expanded into large geographical areas via cheap sensor devices which can sustain themselves with limited energy and developing an energy efficient protocol is a major challenge. Currently, routing in the wireless sensor network faces multiple challenges, such as new scalability, coverage, packet loss, interference, real-time audio and real time video streaming, weather reports, energy constraints and so forth. Clustering sensor nodes is an effective topology control approach. LEACH is an energy efficient clustering protocol because of its nodes distribution capabilities but still it has limitations because it leads to uneven energy distribution. PEGASIS is an enhancement of LEACH using chain-based technique to optimize the energy consumption. This protocol also has certain disadvantages like delays in larger networks etc. HEED is an advanced version of protocol which removes the disadvantages of LEACH and PEGASIS by using distributed algorithm for selecting the cluster heads (CH. It does not make any assumptions about the infrastructure or capabilities of nodes. LEACH, PEGASIS and HEED routing algorithms are compared using Matlab simulation on a Wi-Max network and the results & analysis are based upon the simulation experiments. Simulation results demonstrate that HEED is effective in prolonging the network lifetime and also overcomes the disadvantages of both LEACH & PEGASIS

  15. Monitoring Plasmodium falciparum growth and development by UV flow cytometry using an optimized Hoechst-thiazole orange staining strategy.

    Science.gov (United States)

    Grimberg, Brian T; Erickson, John J; Sramkoski, R Michael; Jacobberger, James W; Zimmerman, Peter A

    2008-06-01

    The complex life cycle of Plasmodium falciparum (Pf) makes it difficult to limit infections and reduce the risk of severe malaria. Improved understanding of Pf blood-stage growth and development would provide new opportunities to evaluate and interfere with successful completion of the parasite's life cycle. Cultured blood stage Pf was incubated with Hoechst 33342 (HO) and thiazole orange (TO) to stain DNA and total nucleic acids, respectively. Correlated HO and TO fluorescence emissions were then measured by flow cytometry. Complex bivariate data patterns were analyzed by manual cluster gating to quantify parasite life cycle stages. The permutations of viable staining with both reagents were tested for optimal detection of parasitized RBC (pRBC). Pf cultures were exposed to HO and TO simultaneously to achieve optimal staining of pRBC and consistent quantification of early and late stages of the replicative cycle (rings through schizonts). Staining of Pf nucleic acids allows for analysis of parasite development in the absence of fixatives, lysis, or radioactivity to enable examination of erythrocytes from parasite invasion through schizont rupture using sensitive and rapid assay procedures. Investigation of the mechanisms by which anti-malarial drugs and antibodies act against different Pf lifecycle stages will be aided by this cytometric strategy. (c) 2008 International Society for Advancement of Cytometry.

  16. Boosting bioluminescence neuroimaging: an optimized protocol for brain studies.

    Science.gov (United States)

    Aswendt, Markus; Adamczak, Joanna; Couillard-Despres, Sebastien; Hoehn, Mathias

    2013-01-01

    Bioluminescence imaging is widely used for optical cell tracking approaches. However, reliable and quantitative bioluminescence of transplanted cells in the brain is highly challenging. In this study we established a new bioluminescence imaging protocol dedicated for neuroimaging, which increases sensitivity especially for noninvasive tracking of brain cell grafts. Different D-Luciferin concentrations (15, 150, 300 and 750 mg/kg), injection routes (i.v., i.p., s.c.), types of anesthesia (Isoflurane, Ketamine/Xylazine, Pentobarbital) and timing of injection were compared using DCX-Luc transgenic mice for brain specific bioluminescence. Luciferase kinetics was quantitatively evaluated for maximal photon emission, total photon emission and time-to-peak. Photon emission followed a D-Luciferin dose-dependent relation without saturation, but with delay in time-to-peak increasing for increasing concentrations. The comparison of intravenous, subcutaneous and intraperitoneal substrate injection reflects expected pharmacokinetics with fastest and highest photon emission for intravenous administration. Ketamine/Xylazine and Pentobarbital anesthesia showed no significant beneficial effect on maximal photon emission. However, a strong difference in outcome was observed by injecting the substrate pre Isoflurane anesthesia. This protocol optimization for brain specific bioluminescence imaging comprises injection of 300 mg/kg D-Luciferin pre Isoflurane anesthesia as an efficient and stable method with a signal gain of approx. 200% (compared to 150 mg/kg post Isoflurane). Gain in sensitivity by the novel imaging protocol was quantitatively assessed by signal-to-noise calculations of luciferase-expressing neural stem cells grafted into mouse brains (transplantation of 3,000-300,000 cells). The optimized imaging protocol lowered the detection limit from 6,000 to 3,000 cells by a gain in signal-to-noise ratio.

  17. Optimal linear detectors for nonorthogonal amplify-and-forward protocol

    KAUST Repository

    Ahmed, Qasim Zeeshan

    2013-06-01

    In this paper, we propose optimal linear detectors for non-orthogonal amplify-and-forward cooperative protocol when considering a single-relay scenario. Two types of detectors are proposed based on the principles of minimum mean square error (MMSE) and minimum bit error rate (MBER). The MMSE detector minimizes the mean square error, while the MBER minimizes the system bit error rate (BER). Both detectors exhibit excellent BER performance with relatively low complexity as compared to the maximal likelihood (ML) detector. The BER performance of both detectors is superior to the channel inversion, the maximal ratio combining, and the biased ML detectors. © 2013 IEEE.

  18. Optimizing otoacoustic emission protocols for a UNHS program.

    Science.gov (United States)

    Hatzopoulos, S; Petruccelli, J; Ciorba, A; Martini, A

    2009-01-01

    To identify the optimal test protocol to screen for hearing problems in newborns, an evaluation of three distortion product otoacoustic emission (DPOAE) protocols was conducted in neonates, from a well-baby nursery (WBN) and from a neonatal intensive care unit (NICU) and compared to the performance in newborns of a more standard protocol based on transient-evoked OAEs (TEOAEs). The DPOAE protocols used asymmetrical stimulus intensities (L(1) > L(2)) with a frequency ratio of 1.22, in the following format: (P1), L(1) = 60, L(2) = 50 dB SPL; (P2), L(1) = 65, L(2) = 55 dB SPL, and (P3), L(1) = 75, L(2) = 65 dB SPL. Linear TEOAE responses, evoked by click stimuli of 75 dB peSPL, were used as controls of normal cochlear function. Five frequencies at 1.5, 2.0, 3.0, 4.0 and 5.0 kHz were tested with a common commercially available macro-based software subroutine (Otodynamics Corp, ILO-92). The project evaluated the responses from 1200 WBN infants (average age 48 h) and 350 low-birth-weight NICU infants, all randomly selected. Statistical analyses comparing the signal-to-noise ratios (S/N), at the predefined f(2) frequencies, indicated that the P1 and P2 DPOAE protocols generated similar responses. Significant S/N differences were observed in the P3 to P2 dataset comparisons. DPOAE scoring criteria were estimated from the P3 dataset using a one-sided, distribution-free confidence intervals. The scoring criteria for a 'pass' were estimated as a minimum S/N of 6.0, 7.0 and 6.0 dB at 2.0, 3.0 and 4.0 kHz, respectively. In terms of feasibility, the P3 protocol generated responses in 98% of the WBN and 94.8% of the NICU infants. All three DPOAE protocols demonstrated shorter time-recording requirements than the standard TEOAE test. The false-positive and false-negative rates for the NICU infants were estimated as 0.0028 and 0.003%, respectively.

  19. Sub-optimal Specificity of Modified Ziehl-Neelsen Staining for Quick Identification of Tuberculous Meningitis

    Science.gov (United States)

    Wang, Ting; Feng, Guo-Dong; Pang, Yu; Yang, Yi-Ning; Dai, Wen; Zhang, Lin; Zhou, Lin-Fu; Yang, Jia-Lei; Zhan, Li-Ping; Marais, Ben J.; Zhao, Yan-Lin; Zhao, Gang

    2016-01-01

    Background: Microbiological confirmation of tuberculous meningitis (TBM) remains problematic. We assessed the diagnostic performance of a modified Ziehl-Neelsen (MZN) staining method that showed promise in earlier studies. Methods: Patients evaluated for TBM in Shaanxi province, China, were prospectively enrolled from May, 2011 to April, 2013. Cerebrospinal fluid (CSF) specimens were evaluated using the Xpert MTB/RIF® assay, MZN staining, and standard biochemical and microbiological tests, together with detailed clinical and radiological assessment. Results: Among 316 patients included in the study, 38 had definite TBM, 66 probable TBM, 163 possible TBM and 49 “no TBM,” using consensus uniform research case definition criteria. Comparing “definite or probable TBM” to “no TBM” MZN staining had higher sensitivity than Xpert MTB/RIF® (88.5 vs. 36.5%), but greatly reduced specificity (71.4 vs. 100.0%); 14/49 (28.6%) cases with “no TBM” tested positive on MZN. Mycobacterium tuberculosis culture was performed in 104/179 (58.1%) of MZN positive samples; 12.5% (13/104) were positive. Using Xpert MTB/RIF® as the reference standard, MZN had a sensitivity of 92.1% (95% CI 79.2–97.3) and specificity of 71.4% (95% CI 57.6–82.2). Conclusion: Xpert MTB/RIF® offered a rapid and specific TBM diagnosis, but sensitivity was poor. MZN was mainly hampered by false positives. Strategies to enhance the sensitivity of Xpert MTB/RIF® or improve the diagnostic accuracy of MZN should be explored. PMID:28082963

  20. iTOUGH2 Universal Optimization Using the PEST Protocol

    Energy Technology Data Exchange (ETDEWEB)

    Finsterle, S.A.

    2010-07-01

    application models, the PEST protocol [Doherty, 2007] has been implemented into iTOUGH2. This protocol enables communication between the application (which can be a single 'black-box' executable or a script or batch file that calls multiple codes) and iTOUGH2. The concept requires that for the application model: (1) Input is provided on one or more ASCII text input files; (2) Output is returned to one or more ASCII text output files; (3) The model is run using a system command (executable or script/batch file); and (4) The model runs to completion without any user intervention. For each forward run invoked by iTOUGH2, select parameters cited within the application model input files are then overwritten with values provided by iTOUGH2, and select variables cited within the output files are extracted and returned to iTOUGH2. It should be noted that the core of iTOUGH2, i.e., its optimization routines and related analysis tools, remains unchanged; it is only the communication format between input parameters, the application model, and output variables that are borrowed from PEST. The interface routines have been provided by Doherty [2007]. The iTOUGH2-PEST architecture is shown in Figure 1. This manual contains installation instructions for the iTOUGH2-PEST module, and describes the PEST protocol as well as the input formats needed in iTOUGH2. Examples are provided that demonstrate the use of model-independent optimization and analysis using iTOUGH2.

  1. Investigation of photodynamic therapy optimization for port wine stain using modulation of photosensitizer administration methods.

    Science.gov (United States)

    Wang, Ying; Zuo, Zhaohui; Liao, Xiaohua; Gu, Ying; Qiu, Haixia; Zeng, Jing

    2013-12-01

    To raise photosensitizer concentration level during the photodynamic therapy process, two new methods of photosensitizer administration were investigated. The first method involves the slow intravenous injection of photosensitizer throughout the first 15 min of irradiation, and the second method involves 30 min fomentation before photosensitizer injection and irradiation. The fluorescence spectra of port wine stain skin were monitored and the therapeutic effect correlated index was calculated with a previously published spectral algorithm. Thirty cases were divided into group A (slow injection of photosensitizer during the first 15 min), group B (fomentation), and group C (control group, traditional injection method), with 10 cases in each group. To analyze the effect of these two new methods, the change of therapeutic effect correlated index values of two photodynamic therapy sessions for each patient were calculated, and the photodynamic therapy outcome was compared. The results showed that the change of therapeutic effect correlated index in group A was slightly more remarkable than that in the control group. The change of therapeutic effect correlated index in group B was similar to that in the control group. Slow injection of photosensitizer during photodynamic therapy has a potential to increase photosensitizer concentration level during photodynamic therapy. However, fomentation before photodynamic therapy has no such potential. There is a need for new methods to be attempted.

  2. Optimized protocol for derivation of human embryonic stem cell lines.

    Science.gov (United States)

    Camarasa, María Vicenta; Galvez, Víctor Miguel; Brison, Daniel Roy; Bachiller, Daniel

    2012-09-01

    For the past 12 years, the biology and applications of human embryonic stem cells (hESCs) have received great attention from the scientific community. Derivatives of the first hESC line obtained by J. Thomson's group (Science 282(5391):1145-1147, 1998) have been used in clinical trials in patients with spinal cord injury, and other hESC lines have now been used to generate cells for use in treating blindness (Lancet 379(9817):713-720, 2012). In addition to the classical protocol based on mouse or human feeder layers using open culture methods (In Vitro Cellular & Developmental Biology - Animal 46(3-4):386-394, 2010; Stem Cells 23(9):1221-1227, 2005; Nature Biotechnology 24(2):185-187, 2006; Human Reproduction 21(2):503-511, 2006; Human Reproduction 20(8):2201-2206, 2005; Fertility and Sterility 83(5):1517-1529, 2005), novel hESC lines have been derived xeno-free (without using animal derived reagents) (PLoS One 5 (4):1024-1026, 2010), feeder-free (without supporting cell monolayers) (Lancet 365(9471):1601-1603, 2005), in microdrops under oil (In Vitro Cellular & Developmental Biology - Animal 46(3-4):236-41, 2010) and in suspension with ROCK inhibitor (Nature Biotechnology 28(4):361-4, 2010). Regardless of the culture system, successful hESC derivation usually requires optimization of embryo culture, the careful and timely isolation of its inner cell mass (ICM), and precise culture conditions up to the establishment of pluripotent cell growth during hESC line derivation. Herein we address the crucial steps of the hESC line derivation protocol, and provide tips to apply quality control to each step of the procedure.

  3. A critical assessment for the value of markers to gate-out undesired events in HLA-peptide multimer staining protocols

    Directory of Open Access Journals (Sweden)

    Odunsi Kunle

    2011-07-01

    Full Text Available Abstract Background The introduction of antibody markers to identify undesired cell populations in flow-cytometry based assays, so called DUMP channel markers, has become a practice in an increasing number of labs performing HLA-peptide multimer assays. However, the impact of the introduction of a DUMP channel in multimer assays has so far not been systematically investigated across a broad variety of protocols. Methods The Cancer Research Institute's Cancer Immunotherapy Consortium (CRI-CIC conducted a multimer proficiency panel with a specific focus on the impact of DUMP channel use. The panel design allowed individual laboratories to use their own protocol for thawing, staining, gating, and data analysis. Each experiment was performed twice and in parallel, with and without the application of a dump channel strategy. Results The introduction of a DUMP channel is an effective measure to reduce the amount of non-specific MULTIMER binding to T cells. Beneficial effects for the use of a DUMP channel were observed across a wide range of individual laboratories and for all tested donor-antigen combinations. In 48% of experiments we observed a reduction of the background MULTIMER-binding. In this subgroup of experiments the median background reduction observed after introduction of a DUMP channel was 0.053%. Conclusions We conclude that appropriate use of a DUMP channel can significantly reduce background staining across a large fraction of protocols and improve the ability to accurately detect and quantify the frequency of antigen-specific T cells by multimer reagents. Thus, use of a DUMP channel may become crucial for detecting low frequency antigen-specific immune responses. Further recommendations on assay performance and data presentation guidelines for publication of MULTIMER experimental data are provided.

  4. Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies.

    Science.gov (United States)

    Lorenz, Todd C

    2012-05-22

    In the biological sciences there have been technological advances that catapult the discipline into golden ages of discovery. For example, the field of microbiology was transformed with the advent of Anton van Leeuwenhoek's microscope, which allowed scientists to visualize prokaryotes for the first time. The development of the polymerase chain reaction (PCR) is one of those innovations that changed the course of molecular science with its impact spanning countless subdisciplines in biology. The theoretical process was outlined by Keppe and coworkers in 1971; however, it was another 14 years until the complete PCR procedure was described and experimentally applied by Kary Mullis while at Cetus Corporation in 1985. Automation and refinement of this technique progressed with the introduction of a thermal stable DNA polymerase from the bacterium Thermus aquaticus, consequently the name Taq DNA polymerase. PCR is a powerful amplification technique that can generate an ample supply of a specific segment of DNA (i.e., an amplicon) from only a small amount of starting material (i.e., DNA template or target sequence). While straightforward and generally trouble-free, there are pitfalls that complicate the reaction producing spurious results. When PCR fails it can lead to many non-specific DNA products of varying sizes that appear as a ladder or smear of bands on agarose gels. Sometimes no products form at all. Another potential problem occurs when mutations are unintentionally introduced in the amplicons, resulting in a heterogeneous population of PCR products. PCR failures can become frustrating unless patience and careful troubleshooting are employed to sort out and solve the problem(s). This protocol outlines the basic principles of PCR, provides a methodology that will result in amplification of most target sequences, and presents strategies for optimizing a reaction. By following this PCR guide, students should be able to: • Set up reactions and thermal cycling

  5. Routing Protocol with Optimal Location of Aggregation Point in Wireless Sensor Networks

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A wireless sensor network is typically composed of hundreds, even thousands of tiny sensors used to monitor physical phenomena. As data collected by the sensors are often redundant, data aggregation is important for conserving energy. In this paper, we present a new routing protocol with optimal data aggregation. This routing protocol has good performance due to its optimal selection of aggregation point locations. This paper details the optimal selection of aggregation point locations.

  6. Automation of sample preparation for mass cytometry barcoding in support of clinical research: protocol optimization.

    Science.gov (United States)

    Nassar, Ala F; Wisnewski, Adam V; Raddassi, Khadir

    2017-03-01

    Analysis of multiplexed assays is highly important for clinical diagnostics and other analytical applications. Mass cytometry enables multi-dimensional, single-cell analysis of cell type and state. In mass cytometry, the rare earth metals used as reporters on antibodies allow determination of marker expression in individual cells. Barcode-based bioassays for CyTOF are able to encode and decode for different experimental conditions or samples within the same experiment, facilitating progress in producing straightforward and consistent results. Herein, an integrated protocol for automated sample preparation for barcoding used in conjunction with mass cytometry for clinical bioanalysis samples is described; we offer results of our work with barcoding protocol optimization. In addition, we present some points to be considered in order to minimize the variability of quantitative mass cytometry measurements. For example, we discuss the importance of having multiple populations during titration of the antibodies and effect of storage and shipping of labelled samples on the stability of staining for purposes of CyTOF analysis. Data quality is not affected when labelled samples are stored either frozen or at 4 °C and used within 10 days; we observed that cell loss is greater if cells are washed with deionized water prior to shipment or are shipped in lower concentration. Once the labelled samples for CyTOF are suspended in deionized water, the analysis should be performed expeditiously, preferably within the first hour. Damage can be minimized if the cells are resuspended in phosphate-buffered saline (PBS) rather than deionized water while waiting for data acquisition.

  7. An Almost-Surely Terminating Polynomial Protocol for Asynchronous Byzantine Agreement with Optimal Resilience

    CERN Document Server

    Abraham, Ittai; Halpern, Joseph Y

    2008-01-01

    Consider an asynchronous system with private channels and $n$ processes, up to $t$ of which may be faulty. We settle a longstanding open question by providing a Byzantine agreement protocol that simultaneously achieves three properties: 1. (optimal) resilience: it works as long as $n>3t$ 2. (almost-sure) termination: with probability one, all nonfaulty processes terminate 3. (polynomial) efficiency: the expected computation time, memory consumption, message size, and number of messages sent are all polynomial in $n$. Earlier protocols have achieved only two of these three properties. In particular, the protocol of Bracha is not polynomially efficient, the protocol of Feldman and Micali is not optimally resilient, and the protocol of Canetti and Rabin does not have almost-sure termination. Our protocol utilizes a new primitive called shunning (asynchronous) verifiable secret sharing (SVSS), which ensures, roughly speaking, that either a secret is successfully shared or a new faulty process is ignored from this...

  8. Power Saving MAC Protocols for WSNs and Optimization of S-MAC Protocol

    Directory of Open Access Journals (Sweden)

    Simarpreet Kaur

    2012-11-01

    Full Text Available Low power MAC protocols have received a lot of consideration in the last few years because of their influence on the lifetime of wireless sensor networks. Since, sensors typically operate on batteries, replacement of which is often difficult. A lot of work has been done to minimize the energy expenditure and prolong the sensor lifetime through energy efficient designs, across layers. Meanwhile, the sensor network should be able to maintain a certain throughput in order to fulfill the QoS requirements of the end user, and to ensure the constancy of the network. This paper introduces different types of MAC protocols used for WSNs and proposes S‐MAC, a Medium‐Access Control protocol designed for Wireless Sensor Networks. S‐MAC uses a few innovative techniques to reduce energy consumption and support selfconfiguration. A new protocol is suggested to improve the energy efficiency, latency and throughput of existing MAC protocol for WSNs. A modification of the protocol is then proposed to eliminate the need for some nodes to stay awake longer than the other nodes which improves the energy efficiency, latency and throughput and hence increases the life span of a wireless sensor network.

  9. Numerical optimization of sequential cryogen spray cooling and laser irradiation for improved therapy of port wine stain.

    Science.gov (United States)

    Milanič, Matija; Jia, Wangcun; Nelson, J Stuart; Majaron, Boris

    2011-02-01

    Despite application of cryogen spray (CS) precooling, customary treatment of port wine stain (PWS) birthmarks with a single laser pulse does not result in complete lesion blanching for a majority of patients. One obvious reason is nonselective absorption by epidermal melanin, which limits the maximal safe radiant exposure. Another possible reason for treatment failure is screening of laser light within large PWS vessels, which prevents uniform heating of the entire vessel lumen. Our aim is to identify the parameters of sequential CS cooling and laser irradiation that will allow optimal photocoagulation of various PWS blood vessels with minimal risk of epidermal thermal damage. Light and heat transport in laser treatment of PWS are simulated using a custom 3D Monte Carlo model and 2D finite element method, respectively. Protein denaturation in blood and skin are calculated using the Arrhenius kinetic model with tissue-specific coefficients. Simulated PWS vessels with diameters of 30-150 µm are located at depths of 200-600 µm, and shading by nearby vessels is accounted for according to PWS histology data from the literature. For moderately pigmented and dark skin phototypes, PWS blood vessel coagulation and epidermal thermal damage are assessed for various parameters of sequential CS cooling and 532-nm laser irradiation, i.e. the number of pulses in a sequence (1-5), repetition rate (7-30 Hz), and radiant exposure. Simulations of PWS treatment in darker skin phototypes indicate specific cooling/irradiation sequences that provide significantly higher efficacy and safety as compared to the customary single-pulse approach across a wide range of PWS blood vessel diameters and depths. The optimal sequences involve three to five laser pulses at repetition rates of 10-15 Hz. Application of the identified cooling/irradiation sequences may offer improved therapeutic outcome for patients with resistant PWS, especially in darker skin phototypes. Copyright © 2011

  10. Optimal path for a quantum teleportation protocol in entangled networks

    OpenAIRE

    Di Franco, C.; Ballester, D.

    2010-01-01

    Bellman's optimality principle has been of enormous importance in the development of whole branches of applied mathematics, computer science, optimal control theory, economics, decision making, and classical physics. Examples are numerous: dynamic programming, Markov chains, stochastic dynamics, calculus of variations, and the brachistochrone problem. Here we show that Bellman's optimality principle is violated in a teleportation problem on a quantum network. This implies that finding the opt...

  11. Optimal path for a quantum teleportation protocol in entangled networks

    Science.gov (United States)

    di Franco, C.; Ballester, D.

    2012-01-01

    Bellman's optimality principle has been of enormous importance in the development of whole branches of applied mathematics, computer science, optimal control theory, economics, decision making, and classical physics. Examples are numerous: dynamic programming, Markov chains, stochastic dynamics, calculus of variations, and the brachistochrone problem. Here we show that Bellman's optimality principle is violated in a teleportation problem on a quantum network. This implies that finding the optimal fidelity route for teleporting a quantum state between two distant nodes on a quantum network with bipartite entanglement will be a tough problem and will require further investigation.

  12. Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil

    Science.gov (United States)

    Silvestri, Erin E.; Feldhake, David; Griffin, Dale; Lisle, John T.; Nichols, Tonya L.; Shah, Sanjiv; Pemberton, A; Schaefer III, Frank W

    2016-01-01

    Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological impurities that can interfere with microbiological detection. This study aimed to optimize a previously used indirect processing protocol, which included a series of washing and centrifugation steps. Optimization of the protocol included: identifying an ideal extraction diluent, variation in the number of wash steps, variation in the initial centrifugation speed, sonication and shaking mechanisms. The optimized protocol was demonstrated at two laboratories in order to evaluate the recovery of spores from loamy and sandy soils. The new protocol demonstrated an improved limit of detection for loamy and sandy soils over the non-optimized protocol with an approximate matrix limit of detection at 14 spores/g of soil. There were no significant differences overall between the two laboratories for either soil type, suggesting that the processing protocol will be robust enough to use at multiple laboratories while achieving comparable recoveries.

  13. Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil.

    Science.gov (United States)

    Silvestri, Erin E; Feldhake, David; Griffin, Dale; Lisle, John; Nichols, Tonya L; Shah, Sanjiv R; Pemberton, Adin; Schaefer, Frank W

    2016-11-01

    Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological impurities that can interfere with microbiological detection. This study aimed to optimize a previously used indirect processing protocol, which included a series of washing and centrifugation steps. Optimization of the protocol included: identifying an ideal extraction diluent, variation in the number of wash steps, variation in the initial centrifugation speed, sonication and shaking mechanisms. The optimized protocol was demonstrated at two laboratories in order to evaluate the recovery of spores from loamy and sandy soils. The new protocol demonstrated an improved limit of detection for loamy and sandy soils over the non-optimized protocol with an approximate matrix limit of detection at 14spores/g of soil. There were no significant differences overall between the two laboratories for either soil type, suggesting that the processing protocol will be robust enough to use at multiple laboratories while achieving comparable recoveries. Copyright © 2016. Published by Elsevier B.V.

  14. Final rinse optimization: influence of different agitation protocols.

    Science.gov (United States)

    Paragliola, Raffaele; Franco, Vittorio; Fabiani, Cristiano; Mazzoni, Annalisa; Nato, Fernando; Tay, Franklin R; Breschi, Lorenzo; Grandini, Simone

    2010-02-01

    This study examined the effect of different root canal irrigant agitation protocols in the penetration of an endodontic irrigant into dentinal tubules. Fifty-six human single-rooted teeth were shaped with nickel-titanium instruments, and a final rinse of 5% sodium hypochlorite labeled with 0.2% alizarin red was performed. Specimens were assigned to 7 groups (N = 8) and submitted to the following rinse activation protocols: no agitation (control group), K-File or gutta-percha agitation, or different sonic (EndoActivator [Advanced Endodontics, Santa Barbara, CA] and Plastic Endo, Lincolnshire, IL) and ultrasonic (Satelec [Acteongroup, Merignac, France] and EMS, Nyon, Switzerland) agitations. Specimens were sectioned at 1, 3, and 5 mm from the apex in 1-mm-thick slabs, ground, and prepared for fluorescence microscopy at 100x with a wavelength of 450 milliseconds. Irrigant penetration into dentinal tubules was analyzed by using Kruskal-Wallis analysis of variance followed by post-hoc comparisons. Groups were ranked in the following order: control = K-file = gutta-percha ultrasonic agitation to increase the effectiveness of the final rinse procedure in the apical third of the canal walls. Copyright 2010 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  15. CT dose minimization using personalized protocol optimization and aggressive bowtie

    Science.gov (United States)

    Wang, Hui; Yin, Zhye; Jin, Yannan; Wu, Mingye; Yao, Yangyang; Tao, Kun; Kalra, Mannudeep K.; De Man, Bruno

    2016-03-01

    In this study, we propose to use patient-specific x-ray fluence control to reduce the radiation dose to sensitive organs while still achieving the desired image quality (IQ) in the region of interest (ROI). The mA modulation profile is optimized view by view, based on the sensitive organs and the ROI, which are obtained from an ultra-low-dose volumetric CT scout scan [1]. We use a clinical chest CT scan to demonstrate the feasibility of the proposed concept: the breast region is selected as the sensitive organ region while the cardiac region is selected as IQ ROI. Two groups of simulations are performed based on the clinical CT dataset: (1) a constant mA scan adjusted based on the patient attenuation (120 kVp, 300 mA), which serves as baseline; (2) an optimized scan with aggressive bowtie and ROI centering combined with patient-specific mA modulation. The results shows that the combination of the aggressive bowtie and the optimized mA modulation can result in 40% dose reduction in the breast region, while the IQ in the cardiac region is maintained. More generally, this paper demonstrates the general concept of using a 3D scout scan for optimal scan planning.

  16. Optimization and comparative evaluation of nucleic acids extraction protocols

    Directory of Open Access Journals (Sweden)

    Lucian Negura

    2011-12-01

    Full Text Available Modern molecular applications have grown the need of biobanks, which contain DNA and RNA of high purety, quality, and quantity. Nucleic acid extraction methods have widely variate and evolve in time, from methods using toxic reagents to enzymatic protocols, and furthermore to DNA or RNA-binding polymers, separating membranes or highly eulogized commercially kits. In order to establish a constant, reproducible and ergonomic system in generating biobanks, we compared different available methods for the extraction of genomic DNA and total RNA, from peripheram blood or solid tumoral tissues. We evaluated the cost/effectiveness and time consumption of each method, tracking RNA/DNA quantity, quality and integrity. We imagined a “E-ratio” value to define these parameters, and a “NA- estimation” to integrate “E-ratio” with quality and integrity data.

  17. Optimizing amniotic membrane tissue banking protocols for ophthalmic use.

    Science.gov (United States)

    Hettiarachchi, D; Dissanayake, V H W; Goonasekera, H W W

    2016-09-01

    Amniotic membrane (AM) due to its anti-inflammatory, anti-scarring and anti-angiogenic properties is used as corneal and wound grafts. When developing AM tissue banks, cell viability, membrane morphology and genomic stability should be preserved following cryopreservation. To analyze the changes rendered to the AM during the process of cryopreservation by comparing different combinations of standard cryopreservation media; fetal bovine serum (FBS), dimethyl sulfoxide (DMSO), Dulbecco's modified eagle's medium (DMEM) and glycerol at -80 °C and at -196 °C for a period of 6 weeks and at 4 °C in 70 % alcohol for 6 weeks. Following informed consent, placentae of healthy term pregnancies delivered by elective Cesarean section were collected and AM separated into 5 × 5 cm size sections and under sterile conditions stored in 9:1 DMSO:FBS and 1:1 DMEM:Glycerol at -196 and -80 °C for 6 weeks. Similar sections were also stored at 4 °C in 70 % alcohol for 6 weeks. After storage periods following were assessed; AM epithelial cell viability by trypan blue vital stain, epithelial cell proliferation capacity by cell doubling time, membrane morphology by haematoxylin and eosin (H&E) stain and genomic stability by conventional G-banded karyotyping. Human amniotic epithelial cells were cultured in DMEM and 10 % FBS in humidified atmosphere of 5 % carbon dioxide at 37 °C and were characterized using RT-PCR for Octamer-binding protein 4 (Oct-4) and glucose-6-phosphate dehydrogenase (G6PD) genes. All the above parameters were also assessed in fresh AM. AM obtained from 4 term placentae. Mean cell count and mean cell doubling times in days respectively; for fresh AM 3.8 × 10(6); 1.59, after 6 weeks in DMSO:FBS at -196 °C 3.0 × 10(6); 2.38 and at -80 °C 2.1 × 10(6); 1.60, in DMEM:Glycerol at -196 °C 3.6 × 10(6); 2.33 at -80 °C 23 × 10(6); 1.66 and at 4 °C 3.3 × 10(6); 2.14. Histology analysis of the fresh AM showed an intact epithelial

  18. Optimizing stimulation and analysis protocols for neonatal fMRI.

    Science.gov (United States)

    Cusack, Rhodri; Wild, Conor; Linke, Annika C; Arichi, Tomoki; Lee, David S C; Han, Victor K

    2015-01-01

    The development of brain function in young infants is poorly understood. The core challenge is that infants have a limited behavioral repertoire through which brain function can be expressed. Neuroimaging with fMRI has great potential as a way of characterizing typical development, and detecting abnormal development early. But, a number of methodological challenges must first be tackled to improve the robustness and sensitivity of neonatal fMRI. A critical one of these, addressed here, is that the hemodynamic response function (HRF) in pre-term and term neonates differs from that in adults, which has a number of implications for fMRI. We created a realistic model of noise in fMRI data, using resting-state fMRI data from infants and adults, and then conducted simulations to assess the effect of HRF of the power of different stimulation protocols and analysis assumptions (HRF modeling). We found that neonatal fMRI is most powerful if block-durations are kept at the lower range of those typically used in adults (full on/off cycle duration 25-30s). Furthermore, we show that it is important to use the age-appropriate HRF during analysis, as mismatches can lead to reduced power or even inverted signal. Where the appropriate HRF is not known (for example due to potential developmental delay), a flexible basis set performs well, and allows accurate post-hoc estimation of the HRF.

  19. A Systematic Design Method for Large-Scale Wireless Ad Hoc Network Protocol Based on Optimization Decomposition Theory

    OpenAIRE

    Chaonong Xu; Chi Zhang; Yongjun Xu; Zhiguang Wang

    2015-01-01

    The idea of network protocol design based on optimization theory has been proposed and used practically in Internet for about 15 years. However, for large-scale wireless ad hoc network, although protocol could be viewed as a recursive solving of a global optimization problem, protocol design is still facing huge challenge because an effective distributed algorithm for solving global optimization problem is still lacking. We solve the problem by putting forward a systematic design method based...

  20. Optimization and Evaluation Strategy of Esophageal Tissue Preparation Protocols for Metabolomics by LC-MS.

    Science.gov (United States)

    Wang, Huiqing; Xu, Jing; Chen, Yanhua; Zhang, Ruiping; He, Jiuming; Wang, Zhonghua; Zang, Qingce; Wei, Jinfeng; Song, Xiaowei; Abliz, Zeper

    2016-04-01

    Sample preparation is a critical step in tissue metabolomics. Therefore, a comprehensive and systematic strategy for the screening of tissue preparation protocols is highly desirable. In this study, we developed an Optimization and Evaluation Strategy based on LC-MS to screen for a high-extractive efficiency and reproducible esophageal tissue preparation protocol for different types of endogenous metabolites (amino acids, carnitines, cholines, etc.), with a special focus on low-level metabolites. In this strategy, we first selected a large number of target metabolites based on literature survey, previous work in our lab, and known metabolic pathways. For these target metabolites, we tested different solvent extraction methods (biphasic solvent extraction, two-step [TS], stepwise [SW], all-in one [AO]; single-phase solvent extraction, SP) and esophageal tissue disruption methods (homogenized wet tissue [HW], ground wet tissue [GW], and ground dry tissue [GD]). A protocol involving stepwise addition of solvents and a homogenized wet tissue protocol (SWHW) was superior to the others. Finally, we evaluated the stability of endogenous metabolites in esophageal tissues and the sensitivity, reproducibility, and recovery of the optimal protocol. The results proved that the SWHW protocol was robust and adequate for bioanalysis. This strategy will provide important guidance for the standardized and scientific investigation of tissue metabolomics.

  1. Optimizing sonication protocols for transthoracic focused ultrasound surgery

    Science.gov (United States)

    Gao, J.; Volovick, A.; Cao, R.; Nabi, G.; Cochran, S.; Melzer, A.; Huang, Z.

    2012-11-01

    During transthoracic focused ultrasound surgery (TFUS), the intervening ribs absorb and reflect the majority of the ultrasound energy excited by an acoustic source, resulting in pain, bone injuries and insufficient energy delivered to the target organs of liver, kidney, and pancreas. Localized hot spots may also exist at the interfaces between the ribs and soft tissue and in the highly absorptive regions such as the skin and connective tissue. The aims of this study were to clarify the effects of focal beam distortion and frequency-dependent rib heating in TFUS and to propose possible techniques to reduce the side-effects of rib heating and increase ultrasound efficacy. Frequency-dependent heating at the target and the ribs were estimated using finite element analysis (PZFlex, Weidlinger Associates Inc, USA) along with experimental verification on a range of different phantoms. The ratio of ultrasonic power density at the target and the ribs, the time-varying spatial distribution of temperature, and the ablated focus of each sonication were taken as key indicators to determine the optimal operating frequency. Comparison with a patient specific model was also made. TFUS seems to be useful to treat tumours that are small and near the surface of the abdominal organs. For targets deep inside these organs, severe attenuation of energy occurs, suggesting that purely ultrasound thermal ablation with advanced heating patterns will have limited effects in improving the treatment efficacy. Results demonstrate that the optimal ultrasound frequency is around 0.8 MHz for the configurations considered, but this may shift to higher frequencies with changes in the axial and lateral positions of the tumours relative to the ribs. To date, we have elucidated the most important effects and correlated these with idealised anatomical geometry. The changes in frequency and other techniques such as selection of excited element patterns in FUS arrays had some effect. However, more advanced

  2. Optimization of Micropropagation Protocol for Goji Berry (Lycium barbarum L.

    Directory of Open Access Journals (Sweden)

    Alexandru Fira

    2016-11-01

    Full Text Available Micropropagation of Lycium barbarum cv. 'Ningxia N1' was achieved. The cultures were by initiated by axenical seed germination. The highest shoot proliferation was obtained on the MS media with 1.33 or 2.22 µM benzyl adenine, gelled with wheat starch as an agar alternative. The treatments with 2.22 µM benzyl adenine ensured proliferation rates superior to the ones with 1.33 μM benzyl adenine, but the latter provided longer and more robust shoots. Use of large microcuttings as an explant onto the multiplication media ensured higher in vitro explant survival, higher number of shoots regeneration and more vigorous plantlets. The microcuttings inserted vertically into the media yielded superior growth and multiplication as compared to the microcuttings placed horizontally. The non-rooted, elongated shoots from the treatment 1.33 μM benzyl adenine were either rooted in vitro on a hormone-free MS medium with starch or used for direct ex vitro rooting and acclimatization. The optimal number of microcuttings/vessel for in vitro rooting was 40 and the rooted plantlets were efficiently acclimatized ex vitro by three methods: float hydroculture in floating cell trays, floating perlite, and in Jiffy7 pellets.

  3. Construction of optimal resources for concatenated quantum protocols

    Science.gov (United States)

    Pirker, A.; Wallnöfer, J.; Briegel, H. J.; Dür, W.

    2017-06-01

    We consider the explicit construction of resource states for measurement-based quantum information processing. We concentrate on special-purpose resource states that are capable to perform a certain operation or task, where we consider unitary Clifford circuits as well as non-trace-preserving completely positive maps, more specifically probabilistic operations including Clifford operations and Pauli measurements. We concentrate on 1 →m and m →1 operations, i.e., operations that map one input qubit to m output qubits or vice versa. Examples of such operations include encoding and decoding in quantum error correction, entanglement purification, or entanglement swapping. We provide a general framework to construct optimal resource states for complex tasks that are combinations of these elementary building blocks. All resource states only contain input and output qubits, and are hence of minimal size. We obtain a stabilizer description of the resulting resource states, which we also translate into a circuit pattern to experimentally generate these states. In particular, we derive recurrence relations at the level of stabilizers as key analytical tool to generate explicit (graph) descriptions of families of resource states. This allows us to explicitly construct resource states for encoding, decoding, and syndrome readout for concatenated quantum error correction codes, code switchers, multiple rounds of entanglement purification, quantum repeaters, and combinations thereof (such as resource states for entanglement purification of encoded states).

  4. Protocol description and optimization scheduling for multi-fieldbus integration system.

    Science.gov (United States)

    Zhong, Chongquan; Chen, Chen

    2015-11-01

    Device integration technique is applied to integrate different fieldbus devices into one control system. At present mature integration techniques use appropriative software to support corresponding protocols. New software must be developed when a new fieldbus is integrated. In this research, a universal protocol description method is proposed. It focuses on the packets encapsulation description, and different protocol messages can be encapsulated and parsed by the interpreter in a unified way. Moreover, in order to ensure the communication efficiency and QoS of different kinds of messages, packets encapsulated via protocol description are optimized and scheduled before transmission inside the interpreter. The approaches have been applied in the prototype of a software product and verified in a power monitoring project.

  5. European project HOPE (Health Optimization Protocol for Energy-efficient Buildings)

    NARCIS (Netherlands)

    Bluyssen, P.M.; Cox, C.W.J.; Maroni, M.; Boschi, N.; Raw, G.; Roulet, C.A.; Foradini, F.

    2003-01-01

    In January 2002, a new European project named HOPE (Health Optimization Protocol for Energy-efficient Buildings) started with 14 participants from nine European countries. The final goal of the project is to provide the means to increase the number of energy-efficient buildings, i.e. buildings that

  6. European project HOPE (Health Optimization Protocol for Energy-efficient Buildings)

    NARCIS (Netherlands)

    Bluyssen, P.M.; Cox, C.W.J.; Maroni, M.; Boschi, N.; Raw, G.; Roulet, C.A.; Foradini, F.

    2003-01-01

    In January 2002, a new European project named HOPE (Health Optimization Protocol for Energy-efficient Buildings) started with 14 participants from nine European countries. The final goal of the project is to provide the means to increase the number of energy-efficient buildings, i.e. buildings that

  7. Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels

    Directory of Open Access Journals (Sweden)

    Mergeai G.

    2006-01-01

    Full Text Available A reliable, fast, cheap and sensitive silver staining method to detect nucleic acids in polyacrylamide gels was developed from two standard stain procedures. The main differences between the three methods concerned (i the preexposure with formaldehyde during silver nitrate impregnation, (ii the addition of sodium thiosulfate and sodium carbonate instead of sodium hydroxide during development; (iii the removal of the stop reaction or the inclusion of absolute ethanol with acetic acid in the stop solution and (iv the duration of the different reaction steps. All methods allowed the detection of similar polymorphisms for single sequence repeats with different cotton genotypes but important differences regarding the contrast, background and conservation duration of the gels were observed. Two methods gave superior sensitivity. The improved method was sensitive, fast (20 min, gave lower backgrounds, produced gels with long-term conservation ability, and allowed a reutilization of all the solutions used in the staining procedure from fi ve to seven times, making it quite cheap.

  8. Optimized protocols for Mycobacterium leprae strain management: frozen stock preservation and maintenance in athymic nude mice.

    Science.gov (United States)

    Trombone, Ana Paula Fávaro; Pedrini, Sílvia Cristina Barbosa; Diório, Suzana Madeira; Belone, Andréa de Faria Fernandes; Fachin, Luciana Raquel Vicenzi; do Nascimento, Dejair Caitano; Rosa, Patricia Sammarco

    2014-03-23

    Leprosy, caused by Mycobacterium leprae, is an important infectious disease that is still endemic in many countries around the world, including Brazil. There are currently no known methods for growing M. leprae in vitro, presenting a major obstacle in the study of this pathogen in the laboratory. Therefore, the maintenance and growth of M. leprae strains are preferably performed in athymic nude mice (NU-Foxn1(nu)). The laboratory conditions for using mice are readily available, easy to perform, and allow standardization and development of protocols for achieving reproducible results. In the present report, we describe a simple protocol for purification of bacilli from nude mouse footpads using trypsin, which yields a suspension with minimum cell debris and with high bacterial viability index, as determined by fluorescent microscopy. A modification to the standard method for bacillary counting by Ziehl-Neelsen staining and light microscopy is also demonstrated. Additionally, we describe a protocol for freezing and thawing bacillary stocks as an alternative protocol for maintenance and storage of M. leprae strains.

  9. Hybridization of Meta-heuristics for Optimizing Routing protocol in VANETs

    Directory of Open Access Journals (Sweden)

    R.R Sedamkar

    2016-02-01

    Full Text Available The goal of VANET is to establish a vehicular communication system which is reliable and fast which caters to road safety and road safety. In VANET where network fragmentation is frequent with no central control, routing becomes a challenging task. Planning an optimal routing plan for tuning parameter configuration of routing protocol for setting up VANET is very crucial. This is done by defining an optimization problem where hybridization of meta-heuristics is defined. The paper contributes the idea of combining meta-heuristic algorithm to enhance the performance of individual search method for optimization problem

  10. Optimization of a plasmid electroporation protocol for Aeromonas salmonicida subsp. salmonicida.

    Science.gov (United States)

    Dallaire-Dufresne, Stéphanie; Emond-Rheault, Jean-Guillaume; Attéré, Sabrina A; Tanaka, Katherine H; Trudel, Mélanie V; Frenette, Michel; Charette, Steve J

    2014-03-01

    Aeromonas salmonicida subsp. salmonicida is a major fish pathogen. Molecular tools are required to study the virulence and genomic stability of this bacterium. An efficient electroporation-mediated transformation protocol for A. salmonicida subsp. salmonicida would make genetic studies faster and easier. In the present study, we designed the 4.1-kb pSDD1 plasmid as a tool for optimizing an electroporation protocol for A. salmonicida subsp. salmonicida. We systematically tested the electroporation conditions to develop a protocol that generates the maximum number of transformants. Under these optimal conditions (25 kV/cm, 200 Ω, 25 μF), we achieved an electroporation efficiency of up to 1×10(5) CFU/μg DNA. The electroporation protocol was also tested using another plasmid of 10.6-kb and three different strains of A. salmonicida subsp. salmonicida. The strains displayed significant differences in their electro-transformation competencies. Strain 01-B526 was the easiest to electroporate, especially with the pSDD1 plasmid. This plasmid was stably maintained in the 01-B526 transformants, as were the native plasmids, but could be easily cured by removing the selection conditions. This is the first efficient electroporation protocol reported for A. salmonicida subsp. salmonicida, and offers new possibilities for studying this bacterium.

  11. A Green Clustering Protocol for Mobile Sensor Network Using Particle Swarm Optimization

    Institute of Scientific and Technical Information of China (English)

    Nurul Mu’azzah Abdul Latiff; NikNoordini NikAbdMalik; Abdul Halim Abdul Latiff

    2016-01-01

    Abstract-Energy consumption of sensor nodes is one of the crucial issues in prolonging the lifetime of wireless sensor networks. One of the methods that can improve the utilization of sensor nodes batteries is the clustering method. In this paper, we propose a green clustering protocol for mobile sensor networks using particle swarm optimization (PSO) algorithm. We define a new fitness function that can optimize the energy consumption of the whole network and minimize the relative distance between cluster heads and their respective member nodes. We also take into account the mobility factor when defining the cluster membership, so that the sensor nodes can join the cluster that has the similar mobility pattern. The performance of the proposed protocol is compared with well-known clustering protocols developed for wireless sensor networks such as LEACH (low-energy adaptive clustering hierarchy) and protocols designed for sensor networks with mobile nodes called CM-IR (clustering mobility-invalid round). In addition, we also modify the improved version of LEACH called MLEACH-C, so that it is applicable to the mobile sensor nodes environment. Simulation results demonstrate that the proposed protocol using PSO algorithm can improve the energy consumption of the network, achieve better network lifetime, and increase the data delivered at the base station.

  12. Determination of optimal rehydration, fixation and staining methods for histological and immunohistochemical analysis of mummified soft tissues.

    Science.gov (United States)

    Mekota, A-M; Vermehren, M

    2005-01-01

    During an excavation headed by the German Institute for Archaeology, Cairo, at the tombs of the nobles in Thebes-West, Upper Egypt, three types of tissues from different mummies were sampled to compare 13 well known rehydration methods for mummified tissue with three newly developed methods. Furthermore, three fixatives were tested with each of the rehydration fluids. Meniscus (fibrocartilage), skin, and a placenta were used for this study. The rehydration and fixation procedures were uniform for all methods. The stains used were standard hematoxylin and eosin, elastica van Gieson, periodic acid-Schiff, and Grocott, and five commercially obtained immunohistochemical stains including pancytokeratin, vimentin, alpha-smooth-muscle-actin, basement membrane collagen type IV, and S-100 protein. The sections were examined by transmitted light microscopy. Our study showed that preservation of the tissue is dependent on the quality and effectiveness of the combination of the rehydration and fixation solutions, and that the quality of the histological and histochemical stains is dependent on the tissue quality. In addition, preservation of the antigens in the tissues is dependent on tissue quality, and fungal permeation had no influence on the tissue. Finally, the results are tissue specific. For placenta the best solution combination was Sandison and solution III (both fixed with formaldehyde) while results for skin were best with Ruffer I (using formaldehyde and Schaffer as fixatives), Grupe et al. (using formaldehyde as a fixative) and solution III (in combination with formaldehyde and Bouin fixatives). Ruffer II (using formaldehyde as a fixative) and solution III (in combination with Schaffer fixative) gave the best results for fibrocartilage.

  13. A Multiple-Dimensional Tree Routing Protocol for Multisink Wireless Sensor Networks Based on Ant Colony Optimization

    OpenAIRE

    Hui Zhou; Dongliang Qing; Xiaomei Zhang; Honglin Yuan; Chen Xu

    2012-01-01

    Routing protocol is an important topic in the wireless sensor networks. For MultiSink wireless sensor networks, the routing protocol designs and implementations are more difficult due to the structure complexity. The paper deals with the problem of a multiple-dimensional tree routing protocol for multisink wireless sensor networks based on ant colony optimization. The proposed protocol is as follows: (1) listening mechanism is used to establish and maintain multidimensional tree routing topol...

  14. Energy Constrained Reliable Routing Optimized Cluster Head Protocol for Multihop under Water Acoustic Sensor Networks

    Directory of Open Access Journals (Sweden)

    Padmavathy.T.V

    2012-06-01

    Full Text Available Underwater acoustic sensor network is an emerging technique consisting of sensor nodes, and AUVs all working together to sense various phenomenon, converts the sensed information into digital data, storethe digital data and communicate to the base stations through the intermediate nodes. Also UnderwaterAcoustic Sensor Networks are playing a main role in ocean applications. Unfortunately the efficiency of underwater Acoustic Sensor Networks is inferior to that of terrestrial sensor networks due to the longpropagation delay, narrow bandwidth and high error rates. Also battery life and storage capacity of node is limited. Many routing protocols are proposed to improve the efficiency of Under Water Acoustic Sensor Networks. However their improvement is not enough, so there is a need of suitable routing protocol that consider all these limitations and makes communication in underwater network viable. In this paper, we propose a protocol called Reliable Routing Optimized Cluster Head (RROCH protocol, a network coding approach for multihop topologies. We used performance metrics like packet delivery ratio, energy consumption, end-to-end delay and throughput of sensor nodes. LEACH, HMR-LEACH, LEACH-M are compared for their performance at different traffic conditions, number of nodes and depth. By analyzing our simulation results we found that RROCH protocol may be used for denser network with low traffic and HMR- LEACH protocol is suitable for higher traffic with less number of nodes.

  15. A Self-organizing Location and Mobility-Aware Route Optimization Protocol for Bluetooth Wireless

    Directory of Open Access Journals (Sweden)

    Sheikh Tahir Bakhsh

    2016-06-01

    Full Text Available Bluetooth allows multi-hop ad-hoc networks that contain multiple interconnected piconets in a common area to form a scatternet. Routing is one of the technical issues in a scatternet because nodes can arrive and leave at arbitrary times; hence node mobility has a serious impact on network performance. Bluetooth network is built in an ad-hoc fashion, therefore, a fully connected network does not guarantee. Moreover, a partially connected network may not find the shortest route between source and destination. In this paper, a new Self-organizing Location and Mobility-aware Route Optimization (LMRO protocol is proposed for Bluetooth scatternet, which is based on node mobility and location. The proposed protocol considered the shortest route ahead of the source and destination nodes through nodes location information. In addition, proposed protocol guarantees network connectivity through executing Self-organizing procedure for the damaged route by considering signal strength. The proposed LMRO protocol predicts node mobility through the signal strength and activates an alternate link before the main link breaks. Simulation results show that the LMRO protocol has reduced the average hop count by 20%-50% and increased network throughput by 30%-40% compared to existing protocols.

  16. Analytical approach to cross-layer protocol optimization in wireless sensor networks

    Science.gov (United States)

    Hortos, William S.

    2008-04-01

    In the distributed operations of route discovery and maintenance, strong interaction occurs across mobile ad hoc network (MANET) protocol layers. Quality of service (QoS) requirements of multimedia service classes must be satisfied by the cross-layer protocol, along with minimization of the distributed power consumption at nodes and along routes to battery-limited energy constraints. In previous work by the author, cross-layer interactions in the MANET protocol are modeled in terms of a set of concatenated design parameters and associated resource levels by multivariate point processes (MVPPs). Determination of the "best" cross-layer design is carried out using the optimal control of martingale representations of the MVPPs. In contrast to the competitive interaction among nodes in a MANET for multimedia services using limited resources, the interaction among the nodes of a wireless sensor network (WSN) is distributed and collaborative, based on the processing of data from a variety of sensors at nodes to satisfy common mission objectives. Sensor data originates at the nodes at the periphery of the WSN, is successively transported to other nodes for aggregation based on information-theoretic measures of correlation and ultimately sent as information to one or more destination (decision) nodes. The "multimedia services" in the MANET model are replaced by multiple types of sensors, e.g., audio, seismic, imaging, thermal, etc., at the nodes; the QoS metrics associated with MANETs become those associated with the quality of fused information flow, i.e., throughput, delay, packet error rate, data correlation, etc. Significantly, the essential analytical approach to MANET cross-layer optimization, now based on the MVPPs for discrete random events occurring in the WSN, can be applied to develop the stochastic characteristics and optimality conditions for cross-layer designs of sensor network protocols. Functional dependencies of WSN performance metrics are described in

  17. Optimal hop position-based minimum energy routing protocol for underwater acoustic sensor networks

    Directory of Open Access Journals (Sweden)

    K.S. Geethu

    2015-05-01

    Full Text Available Development of energy-efficient routing protocols is a major concern in the design of underwater acoustic sensor networks (UASNs since UASN nodes are typically powered by batteries, which are difficult to replace or recharge in aquatic environments. This study proposes an optimal hop position-based energy-efficient routing protocol for UASNs. Initially, the authors present an analytical model to compute the total energy consumption in a multi-hop UASN for deep water scenario, taking into account dependence of usable bandwidth on transmission distance and propagation characteristics of underwater acoustic channel. They derive analytical solution for the optimal hop distance that minimises total energy consumption in the network. They then propose an energy-efficient routing protocol that relies on the computation of optimal hop distance. In their routing scheme, selection of forwarding nodes are based on their depth, residual energy and closeness to the computed optimal hop position corresponding to source node. Simulation results show that total energy consumption of the network gets reduced drastically, leading to improvement in network lifetime. Moreover, the proposed routing scheme makes use of courier nodes to handle coverage-hole problem. The efficient movement of courier nodes improves packet delivery ratio and network throughput.

  18. Size-specific optimization of CT protocols based on minimum detectability.

    Science.gov (United States)

    Zhang, Yakun; Smitherman, Christopher; Samei, Ehsan

    2017-04-01

    To develop a comprehensive model of task-based performance of CT across a broad library of CT protocols, so that radiation dose and image quality can be optimized within a large multivendor clinical facility. Eighty adult CT protocols from the Duke University Medical Center were grouped into 23 protocol groups with similar acquisition characteristics. A size-based image quality phantom (Duke Mercury Phantom 2.0) was imaged using these protocol groups for a range of clinically relevant dose levels on two CT manufacturer platforms (Siemens SOMATOM Definition Flash and GE CT750 HD). For each protocol group, phantom size, and dose level, the images were analyzed to extract task-based image quality metrics, the task transfer function (TTF), and the noise power spectrum (NPS). The TTF and NPS were further combined with generalized models of lesion task functions to predict the detectability of the lesions in terms of areas under the receiver operating characteristic curve (Az ). A graphical user interface (GUI) was developed to present Az as a function of lesion size and contrast, dose, patient size, and protocol, as well as to derive the necessary dose to achieve a detection threshold for a targeted lesion. The GUI provided the prediction of Az values modeling detection confidence for a targeted lesion, patient size, and dose. As an example, an abdomen pelvis exam for one scanner, with a reference task size/contrast of 5-mm/50-HU, and an Az of 0.9 indicated a dose requirement of 4.0, 8.9, and 16.9 mGy for patient diameters of 25, 30, and 35 cm, respectively. For a constant patient diameter of 30 cm and 50-HU lesion contrast, the minimum detected lesion size at those dose levels were predicted to be 8.4, 5.0, and 3.9 mm, respectively. A CT protocol optimization platform was developed by combining task-based detectability calculations with a GUI that demonstrates the tradeoff between dose and image quality. The platform can be used to improve individual protocol dose

  19. Explicit solutions to analytical models of cross-layer protocol optimization in wireless sensor networks

    Science.gov (United States)

    Hortos, William S.

    2009-05-01

    The work is based on the interactions among the nodes of a wireless sensor network (WSN) to cooperatively process data from multiple sensors. Quality-of-service (QoS) metrics are associated with the quality of fused information: throughput, delay, packet error rate, etc. A multivariate point process (MVPP) model of discrete random events in WSNs establishes stochastic characteristics of optimal cross-layer protocols. In previous work by the author, discreteevent, cross-layer interactions in the MANET protocol are modeled in very general analytical terms with a set of concatenated design parameters and associated resource levels by multivariate point processes (MVPPs). Characterization of the "best" cross-layer designs for the MANET is formulated by applying the general theory of martingale representations to controlled MVPPs. Performance is described in terms of concatenated protocol parameters and controlled through conditional rates of the MVPPs. Assumptions on WSN characteristics simplify the dynamic programming conditions to yield mathematically tractable descriptions for the optimal routing protocols. Modeling limitations on the determination of closed-form solutions versus iterative explicit solutions for ad hoc WSN controls are presented.

  20. Feasibility of an optimized MR enterography protocol in the evaluation of pediatric inflammatory bowel disease

    OpenAIRE

    Bosemani, T; Ozturk, A.; Tekes, A.; Hemker, MO; Huisman, TAGM

    2013-01-01

    Cross-sectional imaging forms an important alternative and complimentary tool to endoscopy in aiding the clinician with diagnosis and management of pediatric inflammatory bowel disease (IBD). The purpose of the study was to evaluate the feasibility of an optimized Magnetic Resonance Enterography (MRE) protocol in the evaluation of patients with suspected IBD. 31 children (18 boys and 13 girls) were evaluated by a pediatric gastroenterologist prior to MRE and given a grading for clinical sever...

  1. Single-cell qPCR on dispersed primary pituitary cells -an optimized protocol

    Directory of Open Access Journals (Sweden)

    Haug Trude M

    2010-11-01

    Full Text Available Abstract Background The incidence of false positives is a potential problem in single-cell PCR experiments. This paper describes an optimized protocol for single-cell qPCR measurements in primary pituitary cell cultures following patch-clamp recordings. Two different cell harvesting methods were assessed using both the GH4 prolactin producing cell line from rat, and primary cell culture from fish pituitaries. Results Harvesting whole cells followed by cell lysis and qPCR performed satisfactory on the GH4 cell line. However, harvesting of whole cells from primary pituitary cultures regularly produced false positives, probably due to RNA leakage from cells ruptured during the dispersion of the pituitary cells. To reduce RNA contamination affecting the results, we optimized the conditions by harvesting only the cytosol through a patch pipette, subsequent to electrophysiological experiments. Two important factors proved crucial for reliable harvesting. First, silanizing the patch pipette glass prevented foreign extracellular RNA from attaching to charged residues on the glass surface. Second, substituting the commonly used perforating antibiotic amphotericin B with β-escin allowed efficient cytosol harvest without loosing the giga seal. Importantly, the two harvesting protocols revealed no difference in RNA isolation efficiency. Conclusion Depending on the cell type and preparation, validation of the harvesting technique is extremely important as contaminations may give false positives. Here we present an optimized protocol allowing secure harvesting of RNA from single cells in primary pituitary cell culture following perforated whole cell patch clamp experiments.

  2. Design and Analysis of Optimization Algorithms to Minimize Cryptographic Processing in BGP Security Protocols.

    Science.gov (United States)

    Sriram, Vinay K; Montgomery, Doug

    2017-07-01

    The Internet is subject to attacks due to vulnerabilities in its routing protocols. One proposed approach to attain greater security is to cryptographically protect network reachability announcements exchanged between Border Gateway Protocol (BGP) routers. This study proposes and evaluates the performance and efficiency of various optimization algorithms for validation of digitally signed BGP updates. In particular, this investigation focuses on the BGPSEC (BGP with SECurity extensions) protocol, currently under consideration for standardization in the Internet Engineering Task Force. We analyze three basic BGPSEC update processing algorithms: Unoptimized, Cache Common Segments (CCS) optimization, and Best Path Only (BPO) optimization. We further propose and study cache management schemes to be used in conjunction with the CCS and BPO algorithms. The performance metrics used in the analyses are: (1) routing table convergence time after BGPSEC peering reset or router reboot events and (2) peak-second signature verification workload. Both analytical modeling and detailed trace-driven simulation were performed. Results show that the BPO algorithm is 330% to 628% faster than the unoptimized algorithm for routing table convergence in a typical Internet core-facing provider edge router.

  3. Optimization and comparison of simultaneous and separate acquisition protocols for dual isotope myocardial perfusion SPECT

    Science.gov (United States)

    Ghaly, Michael; Links, Jonathan M.; Frey, Eric C.

    2015-07-01

    Dual-isotope simultaneous-acquisition (DISA) rest-stress myocardial perfusion SPECT (MPS) protocols offer a number of advantages over separate acquisition. However, crosstalk contamination due to scatter in the patient and interactions in the collimator degrade image quality. Compensation can reduce the effects of crosstalk, but does not entirely eliminate image degradations. Optimizing acquisition parameters could further reduce the impact of crosstalk. In this paper we investigate the optimization of the rest Tl-201 energy window width and relative injected activities using the ideal observer (IO), a realistic digital phantom population and Monte Carlo (MC) simulated Tc-99m and Tl-201 projections as a means to improve image quality. We compared performance on a perfusion defect detection task for Tl-201 acquisition energy window widths varying from 4 to 40 keV centered at 72 keV for a camera with a 9% energy resolution. We also investigated 7 different relative injected activities, defined as the ratio of Tc-99m and Tl-201 activities, while keeping the total effective dose constant at 13.5 mSv. For each energy window and relative injected activity, we computed the IO test statistics using a Markov chain Monte Carlo (MCMC) method for an ensemble of 1,620 triplets of fixed and reversible defect-present, and defect-absent noisy images modeling realistic background variations. The volume under the 3-class receiver operating characteristic (ROC) surface (VUS) was estimated and served as the figure of merit. For simultaneous acquisition, the IO suggested that relative Tc-to-Tl injected activity ratios of 2.6-5 and acquisition energy window widths of 16-22% were optimal. For separate acquisition, we observed a broad range of optimal relative injected activities from 2.6 to 12.1 and acquisition energy window of widths 16-22%. A negative correlation between Tl-201 injected activity and the width of the Tl-201 energy window was observed in these ranges. The results

  4. Simple Protocol for Secondary School Hands-On Activity: Electrophoresis of Pre-Stained Nucleic Acids on Agar-Agar Borate Gels

    Science.gov (United States)

    Britos, Leticia; Goyenola, Guillermo; Orono, Silvia Umpierrez

    2004-01-01

    An extremely simple, inexpensive, and safe method is presented, which emulates nucleic acids isolation and electrophoretic analysis as performed in a research environment, in the context of a secondary school hands-on activity. The protocol is amenable to an interdisciplinary approach, taking into consideration the electrical and chemical…

  5. Optimization of an Efficient and Sustainable Sonogashira Cross-Coupling Protocol

    KAUST Repository

    Walter, Philipp E.

    2012-12-01

    Cross coupling reactions are a well-established tool in modern organic synthesis and play a crucial role in the synthesis of a high number of organic compounds. Their importance is highlighted by the Nobel Prize in chemistry to Suzuki, Heck and Negishi in 2010. The increasing importance of sustainability requirements in chemical production has furthermore promoted the development of cross-coupling protocols that comply with the principles of “Green Chemistry”1. The Sonogashira reaction is today the most versatile and powerful way to generate aryl alkynes, a moiety recurring in many pharmaceutical and natural products. Despite many improvements to the original reaction, reports on generally applicable protocols that work under sustainable conditions are scarce. Our group recently reported an efficient protocol for a copperfree Sonogashira cross-coupling at low temperature, in aqueous medium and with no addition of organic solvents or additives2. The goal of this work was to further investigate the effects of different reaction parameters on the catalytic activity in order to optimize the protocol. Limitations of the protocol were tested in respect to reaction temperature, heating method, atmosphere, base type and amount, catalyst loading, reaction time and work up procedure. The reaction worked successfully under air and results were not affected by the presence of oxygen in the water phase. Among a variety of bases tested, triethylamine was confirmed to give the best results and its required excess could be reduced from nine to four equivalents. Catalyst loading could also be reduced by up to 90%: Good to near quantitative yields for a broad range of substrates were achieved using a catalyst concentration of 0.25mol% and 5 eq of Et3N at 50°C while more reactive substrates could be coupled with a catalyst concentration as low as 0.025mol%. Filtration experiments showed the possibility of a simplified work up procedure and a protocol completely free of organic

  6. AN APPROACH TO OPTIMIZE QOS ROUTING PROTOCOL USING GENETIC ALGORITHM IN MANET

    Directory of Open Access Journals (Sweden)

    Vikas Siwach

    2012-09-01

    Full Text Available Quality of Service support for Mobile Ad hoc Networks is an exigenttask due to dynamic topology and limited resource. To support QoS,the link state information such as delay, bandwidth, jitter, cost, errorrate and node energy in the network should be available andmanageable. QOS is one the basic requirement of a network andwhen we talk about the Mobile Network this is the highly constraintrequirement of a user. To improve the quality of service we usedifferent changes in MANET protocols, its parameter, routingalgorithm etc. The proposed work is to define a genetic based routingapproach to optimize the routing in MANETs. The genetic approachwill generate an optimized path on the basic of congestion over thenetwork. The result path will improve the data delivery over thenetwork. The focus of the paper is to study about MANET, QOS andtries to develop a network on which genetic algorithm is applied togenerate an optimized path.

  7. Optimization on fixed low latency implementation of GBT protocol in FPGA

    CERN Document Server

    Chen, Kai; Wu, Weihao; Xu, Hao; Yao, Lin

    2016-01-01

    For accelerator physics experiment, the Front-End (FE) electronics components are subjected to a radiation background. GigaBit Transceiver (GBT) architecture is a protocol developed by CERN, to provide high-speed (4.8 Gbps) radiation hard optical link for data transmission. To use GBT protocol on the FE detector, GBTX ASIC is designed. For the back-end side, GBT-FPGA is a project launched by CERN, to provide the implementation of GBT protocol in different types of Field Programmable Gate Arrays (FPGA). For ATLAS experiment, GBT protocol is used by FE electronics of several sub-detectors. Back-End exchanges data and commands like TTC information with FE. The low-latency requirement is important especially for the trigger data path. In this paper, we report several changes to the GBT-FPGA IP core. Some optimizations are applied to achieve a lower latency. The adding of multiplexer let GBT mode can be switched between forward error correction mode and wide mode, without FPGA reprogramming. The clock distribution...

  8. Optimized energy-delay sub-network routing protocol development and implementation for wireless sensor networks

    Science.gov (United States)

    Fonda, James W.; Zawodniok, Maciej; Jagannathan, S.; Watkins, Steve E.

    2008-08-01

    The development and the implementation issues of a reactive optimized energy-delay sub-network routing (OEDSR) protocol for wireless sensor networks (WSN) are introduced and its performance is contrasted with the popular ad hoc on-demand distance vector (AODV) routing protocol. Analytical results illustrate the performance of the proposed OEDSR protocol, while experimental results utilizing a hardware testbed under various scenarios demonstrate improvements in energy efficiency of the OEDSR protocol. A hardware platform constructed at the University of Missouri-Rolla (UMR), now the Missouri University of Science and Technology (MST), based on the Generation 4 Smart Sensor Node (G4-SSN) prototyping platform is also described. Performance improvements are shown in terms of end-to-end (E2E) delay, throughput, route-set-up time and drop rates and energy usage is given for three topologies, including a mobile topology. Additionally, results from the hardware testbed provide valuable lessons for network deployments. Under testing OEDSR provides a factor of ten improvement in the energy used in the routing session and extends network lifetime compared to AODV. Depletion experiments show that the time until the first node failure is extended by a factor of three with the network depleting and network lifetime is extended by 6.7%.

  9. Optimizing a dynamical decoupling protocol for solid-state electronic spin ensembles in diamond

    Science.gov (United States)

    Farfurnik, D.; Jarmola, A.; Pham, L. M.; Wang, Z. H.; Dobrovitski, V. V.; Walsworth, R. L.; Budker, D.; Bar-Gill, N.

    2015-08-01

    We demonstrate significant improvements of the spin coherence time of a dense ensemble of nitrogen-vacancy (NV) centers in diamond through optimized dynamical decoupling (DD). Cooling the sample down to 77 K suppresses longitudinal spin relaxation T1 effects and DD microwave pulses are used to increase the transverse coherence time T2 from ˜0.7 ms up to ˜30 ms . We extend previous work of single-axis (Carr-Purcell-Meiboom-Gill) DD towards the preservation of arbitrary spin states. Following a theoretical and experimental characterization of pulse and detuning errors, we compare the performance of various DD protocols. We identify that the optimal control scheme for preserving an arbitrary spin state is a recursive protocol, the concatenated version of the XY8 pulse sequence. The improved spin coherence might have an immediate impact on improvements of the sensitivities of ac magnetometry. Moreover, the protocol can be used on denser diamond samples to increase coherence times up to NV-NV interaction time scales, a major step towards the creation of quantum collective NV spin states.

  10. Scanning protocol optimization and dose evaluation in coronary stenosis using multi-slices computed tomography

    Science.gov (United States)

    Huang, Yung-hui; Chen, Chia-lin; Sheu, Chin-yin; Lee, Jason J. S.

    2007-02-01

    Cardiovascular diseases are the most common incidence for premature death in developed countries. A major fraction is attributable to atherosclerotic coronary artery disease, which may result in sudden cardiac failure. A reduction of mortality caused by myocardial infarction may be achieved if coronary atherosclerosis can be detected and treated at an early stage before symptoms occur. Therefore, there is need for an effective tool that allows identification of patients at increased risk for future cardiac events. The current multi-detector CT has been widely used for detection and quantification of coronary calcifications as a sign of coronary atherosclerosis. The aim of this study is to optimize the diagnostic values and radiation exposure in coronary artery calcium-screening examination using multi-slice CT (MSCT) with different image scan protocols. The radiation exposure for all protocols is evaluated by using computed tomography dose index (CTDI) phantom measurements. We chose an optimal scanning protocol and evaluated patient radiation dose in the MSCT coronary artery screenings and preserved its expecting diagnostic accuracy. These changes make the MSCT have more operation flexibility and provide more diagnostic values in current practice.

  11. Feasibility of an optimized MR enterography protocol in the evaluation of pediatric inflammatory bowel disease.

    Science.gov (United States)

    Bosemani, T; Ozturk, A; Tekes, A; Hemker, M O; Huisman, T A G M

    2013-01-01

    Cross-sectional imaging forms an important alternative and complimentary tool to endoscopy in aiding the clinician with diagnosis and management of pediatric inflammatory bowel disease (IBD). The purpose of the study was to evaluate the feasibility of an optimized Magnetic Resonance Enterography (MRE) protocol in the evaluation of patients with suspected IBD. 31 children (18 boys and 13 girls) were evaluated by a pediatric gastroenterologist prior to MRE and given a grading for clinical severity of disease. Imaging was then performed with oral contrast and a tailored protocol using fast T1/T2 weighted pulse sequences. Additionally, contrast and glucagon were administered intravenously. Imaging findings were then correlated with the clinical data. Excellent distension was achieved in the small bowel. The majority of the studies were of diagnostic quality with no motion artifacts. Imaging findings showed statistically significant correlation with disease activity. An optimized pediatric MRE protocol is feasible and correlates well with clinical disease activity. This in turn aids the clinician in the management of children with this chronic debilitating disease.

  12. Use of C-Arm Cone Beam CT During Hepatic Radioembolization : Protocol Optimization for Extrahepatic Shunting and Parenchymal Enhancement

    NARCIS (Netherlands)

    van den Hoven, Andor F.; Prince, Jip F.; de Keizer, Bart; Vonken, Evert Jan P A; Bruijnen, Rutger C G; Verkooijen, Helena M.; Lam, Marnix G E H; van den Bosch, Maurice A A J

    2016-01-01

    Purpose: To optimize a C-arm computed tomography (CT) protocol for radioembolization (RE), specifically for extrahepatic shunting and parenchymal enhancement. Materials and Methods: A prospective development study was performed per IDEAL recommendations. A literature-based protocol was applied in pa

  13. Low radiation dose protocol in cardiac CT with 100 kVp: usefulness of display preset optimization.

    Science.gov (United States)

    Nakaura, Takeshi; Kidoh, Masafumi; Sakaino, Naritsugu; Nakamura, Shota; Nozaki, Toshimitsu; Izumi, Akari; Harada, Kazunori; Yamashita, Yasuyuki

    2013-08-01

    To evaluate the radiation dose and image quality of 100 kVp cardiac CT, and the effects of display setting optimization. We randomly assigned 100 patients undergoing cardiac CT to one of following two protocols. Fifty patients underwent our conventional protocol with 120 kVp, and the other 50 patients underwent our low radiation dose protocol with 100 kVp. We compared effective dose (ED); CT number, image noise, and contrast noise ratio (CNR) of ascending aorta at 120 and 100 kVp protocol. We also performed quantitative analysis and qualitative analysis for bitmap image of 120, 100 kVp, and display preset optimization for 100 kVp images. The estimated ED was 48 % lower with the 100 kVp protocol than the 120 kVp protocol (2.8 vs. 5.5 mSv, p protocol (18.5 ± 3.6 vs. 18.6 ± 3.8, p = 0.84). Display preset optimization significantly improved image quality of 100 kVp cardiac CT, and there is no significant difference in qualitative analysis and quantitative analysis between 100 kVp scan with optimized display preset and 120 kVp scan (p > 0.05). The 100 kVp scanning with optimized display preset offers almost same image quality at cardiac CT of thin adults under 48 % decreased radiation dose.

  14. Solving iTOUGH2 simulation and optimization problems using the PEST protocol

    Energy Technology Data Exchange (ETDEWEB)

    Finsterle, S.A.; Zhang, Y.

    2011-02-01

    The PEST protocol has been implemented into the iTOUGH2 code, allowing the user to link any simulation program (with ASCII-based inputs and outputs) to iTOUGH2's sensitivity analysis, inverse modeling, and uncertainty quantification capabilities. These application models can be pre- or post-processors of the TOUGH2 non-isothermal multiphase flow and transport simulator, or programs that are unrelated to the TOUGH suite of codes. PEST-style template and instruction files are used, respectively, to pass input parameters updated by the iTOUGH2 optimization routines to the model, and to retrieve the model-calculated values that correspond to observable variables. We summarize the iTOUGH2 capabilities and demonstrate the flexibility added by the PEST protocol for the solution of a variety of simulation-optimization problems. In particular, the combination of loosely coupled and tightly integrated simulation and optimization routines provides both the flexibility and control needed to solve challenging inversion problems for the analysis of multiphase subsurface flow and transport systems.

  15. Diffusion weighted magnetic resonance imaging of the breast: protocol optimization, interpretation, and clinical applications.

    Science.gov (United States)

    Partridge, Savannah C; McDonald, Elizabeth S

    2013-08-01

    Diffusion-weighted magnetic resonance (MR) imaging (DWI) has shown promise for improving the positive predictive value of breast MR imaging for detection of breast cancer, evaluating tumor response to neoadjuvant chemotherapy, and as a noncontrast alternative to MR imaging in screening for breast cancer. However, data quality varies widely. Before implementing DWI into clinical practice, one must understand the pertinent technical considerations and current evidence regarding clinical applications of breast DWI. This article provides an overview of basic principles of DWI, optimization of breast DWI protocols, imaging features of benign and malignant breast lesions, promising clinical applications, and potential future directions.

  16. Optimized IMAC-IMAC protocol for phosphopeptide recovery from complex biological samples

    DEFF Research Database (Denmark)

    Ye, Juanying; Zhang, Xumin; Young, Clifford

    2010-01-01

    under three different conditions. Fe(III)-nitrilotriacetic acid (NTA) IMAC resin was chosen due to its superior performance in all tests. We further investigated the solution ionization efficiency change of the phosphoryl group and carboxylic group in different acetonitrile-water solutions and observed...... that the ionization efficiencies of the phosphoryl group and carboxylic group changed differently when the acetonitrile concentration was increased. A magnified difference was achieved in high acetonitrile content solutions. On the basis of this concept, an optimized phosphopeptide enrichment protocol was established...

  17. Discrete Particle Swarm Optimization Routing Protocol for Wireless Sensor Networks with Multiple Mobile Sinks

    Directory of Open Access Journals (Sweden)

    Jin Yang

    2016-07-01

    Full Text Available Mobile sinks can achieve load-balancing and energy-consumption balancing across the wireless sensor networks (WSNs. However, the frequent change of the paths between source nodes and the sinks caused by sink mobility introduces significant overhead in terms of energy and packet delays. To enhance network performance of WSNs with mobile sinks (MWSNs, we present an efficient routing strategy, which is formulated as an optimization problem and employs the particle swarm optimization algorithm (PSO to build the optimal routing paths. However, the conventional PSO is insufficient to solve discrete routing optimization problems. Therefore, a novel greedy discrete particle swarm optimization with memory (GMDPSO is put forward to address this problem. In the GMDPSO, particle’s position and velocity of traditional PSO are redefined under discrete MWSNs scenario. Particle updating rule is also reconsidered based on the subnetwork topology of MWSNs. Besides, by improving the greedy forwarding routing, a greedy search strategy is designed to drive particles to find a better position quickly. Furthermore, searching history is memorized to accelerate convergence. Simulation results demonstrate that our new protocol significantly improves the robustness and adapts to rapid topological changes with multiple mobile sinks, while efficiently reducing the communication overhead and the energy consumption.

  18. Discrete Particle Swarm Optimization Routing Protocol for Wireless Sensor Networks with Multiple Mobile Sinks.

    Science.gov (United States)

    Yang, Jin; Liu, Fagui; Cao, Jianneng; Wang, Liangming

    2016-07-14

    Mobile sinks can achieve load-balancing and energy-consumption balancing across the wireless sensor networks (WSNs). However, the frequent change of the paths between source nodes and the sinks caused by sink mobility introduces significant overhead in terms of energy and packet delays. To enhance network performance of WSNs with mobile sinks (MWSNs), we present an efficient routing strategy, which is formulated as an optimization problem and employs the particle swarm optimization algorithm (PSO) to build the optimal routing paths. However, the conventional PSO is insufficient to solve discrete routing optimization problems. Therefore, a novel greedy discrete particle swarm optimization with memory (GMDPSO) is put forward to address this problem. In the GMDPSO, particle's position and velocity of traditional PSO are redefined under discrete MWSNs scenario. Particle updating rule is also reconsidered based on the subnetwork topology of MWSNs. Besides, by improving the greedy forwarding routing, a greedy search strategy is designed to drive particles to find a better position quickly. Furthermore, searching history is memorized to accelerate convergence. Simulation results demonstrate that our new protocol significantly improves the robustness and adapts to rapid topological changes with multiple mobile sinks, while efficiently reducing the communication overhead and the energy consumption.

  19. SSR-Patchwork: An Optimized Protocol to Obtain a Rapid and Inexpensive SSR Library Using First-Generation Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Antonietta Di Maio

    2013-01-01

    Full Text Available Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS is not readily available. Methods and Results: We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30000 Mbp, and a third with an undetermined genome size (Kochia saxicola. Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. Conclusions: The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  20. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology.

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  1. Agrobacterium-mediated transformation of cauliflower: optimization of protocol and development of Bt-transgenic cauliflower

    Indian Academy of Sciences (India)

    R Chakrabarty; N Viswakarma; S R Bhat; P B Kirti; B D Singh; V L Chopra

    2002-09-01

    A number of factors that are known to influence genetic transformation were evaluated to optimize Agrobacterium-mediated transformation of hypocotyl explants of cauliflower variety Pusa Snowball K-1. The binary vector p35SGUSINT mobilized into Agrobacterium strain GV2260 was used for transformation and transient GUS expression was used as the basis for identifying the most appropriate conditions for transformation. Explant age, preculture period, bacterial strain and density were found to be critical determinants of transformation efficiency. Using the optimized protocol, the synthetic cryIA(b) gene was mobilized into cauliflower. Molecular analyses of transgenics established the integration and expression of the transgene. Insect bioassays indicated the effectiveness of the transgene against infestation by diamondback moth (Plutella xylostella) larvae.

  2. Optimal Relay Selection using Efficient Beaconless Geographic Contention-Based Routing Protocol in Wireless Adhoc Networks

    Directory of Open Access Journals (Sweden)

    G. Srimathy

    2012-04-01

    Full Text Available In Wireless Ad hoc network, cooperation of nodes can be achieved by more interactions at higher protocol layers, particularly the MAC (Medium Access Control and network layers play vital role. MAC facilitates a routing protocol based on position location of nodes at network layer specially known as Beacon-less geographic routing (BLGR using Contention-based selection process. This paper proposes two levels of cross-layer framework -a MAC network cross-layer design for forwarder selection (or routing and a MAC-PHY for relay selection. CoopGeo; the proposed cross-layer protocol provides an efficient, distributed approach to select next hops and optimal relays to form a communication path. Wireless networks suffers huge number of communication at the same time leads to increase in collision and energy consumption; hence focused on new Contention access method that uses a dynamical change of channel access probability which can reduce the number of contention times and collisions. Simulation result demonstrates the best Relay selection and the comparative of direct mode with the cooperative networks. And Performance evaluation of contention probability with Collision avoidance.

  3. Improving the Performance of Dynamic Source Routing Protocol by Optimization of Neural Networks

    Directory of Open Access Journals (Sweden)

    Rajesh Gargi

    2012-07-01

    Full Text Available Dynamic Source Routing protocol is one of the most promising among on demand category of protocols for MANETs. Demands of network performance conflict with the demands of mobile networks . To enhance the QoS in a protocol like DSR we used ANN which helps to preserve the resources of the MANET leading to improvement in performance of DSR. While routing the data, If a legitimate node is mistaken as rogue node then also the QoS suffers and if a rogue node is not detected then also it can consume the resources of the network and deteriorate the QoS . In this work a neural network has been further optimized to improve its accuracy by varying the number of layers in it. A typical wireless network scenario of DSR has been simulated in NS2 and then a rogue node has been introduced to mimic attack. The parameters from the trace files have been used to train a neural network simulated in Matlab and its effectiveness has been improved to make the detection of intrusion more accurate. Although previous work has been reported in the area of application of neural networks for intrusion detection but there is a scope of improvement in this technique by varying the number of layers of ANN, making it more effective and improving the QoS of MANET.

  4. Security Issues in the Optimized Link State Routing Protocol Version 2 (OLSRV2

    Directory of Open Access Journals (Sweden)

    Ulrich Herberg

    2010-04-01

    Full Text Available Mobile Ad hoc NETworks (MANETs are leaving the confines of research laboratories, to find place in real-world deployments. Outside specialized domains (military, vehicular, etc., city-wide communitynetworks are emerging, connecting regular Internet users with each other, and with the Internet, via MANETs. Growing to encompass more than a handful of “trusted participants”, the question of preserving the MANET network connectivity, even when faced with careless or malicious participants, arises, and must be addressed. A first step towards protecting a MANET is to analyze the vulnerabilities of the routing protocol, managing the connectivity. By understanding how the algorithms of the routing protocol operate,and how these can be exploited by those with ill intent, countermeasures can be developed, readying MANETs for wider deployment and use.This paper takes an abstract look at the algorithms that constitute the Optimized Link State Routing Protocolversion 2 (OLSRv2, and identifies for each protocol element the possible vulnerabilities and attacks in a certain way, provides a “cookbook” for how to best attack an operational OLSRv2 network, or for how to proceed with developing protective countermeasures against these attacks

  5. Port-Wine Stains

    Science.gov (United States)

    ... Child Natural Disasters: How Families Can Help Port-Wine Stains KidsHealth > For Parents > Port-Wine Stains Print ... Manchas de vino de oporto What Are Port-Wine Stains? A port-wine stain is a type ...

  6. Multihopping Multilevel Clustering Heterogeneity-Sensitive Optimized Routing Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Muhammad Aslam

    2017-01-01

    Full Text Available Effective utilization of energy resources in Wireless Sensor Networks (WSNs has become challenging under uncertain distributed cluster-formation and single-hop intercluster communication capabilities. So, sensor nodes are forced to operate at expensive full rate transmission power level continuously during whole network operation. These challenging network environments experience unwanted phenomena of drastic energy consumption and packet drop. In this paper, we propose an adaptive immune Multihopping Multilevel Clustering (MHMLC protocol that executes a Hybrid Clustering Algorithm (HCA to perform optimal centralized selection of Cluster-Heads (CHs within radius of centrally located Base Station (BS and distributed CHs selection in the rest of network area. HCA of MHMLC also produces optimal intermediate CHs for intercluster multihop communications that develop heterogeneity-aware economical links. This hybrid cluster-formation facilitates the sensors to function at short range transmission power level that enhances link quality and avoids packet drop. The simulation environments produce fair comparison among proposed MHMLC and existing state-of-the-art routing protocols. Experimental results give significant evidence of better performance of the proposed model in terms of network lifetime, stability period, and data delivery ratio.

  7. Whatever works: a systematic user-centered training protocol to optimize brain-computer interfacing individually.

    Directory of Open Access Journals (Sweden)

    Elisabeth V C Friedrich

    Full Text Available This study implemented a systematic user-centered training protocol for a 4-class brain-computer interface (BCI. The goal was to optimize the BCI individually in order to achieve high performance within few sessions for all users. Eight able-bodied volunteers, who were initially naïve to the use of a BCI, participated in 10 sessions over a period of about 5 weeks. In an initial screening session, users were asked to perform the following seven mental tasks while multi-channel EEG was recorded: mental rotation, word association, auditory imagery, mental subtraction, spatial navigation, motor imagery of the left hand and motor imagery of both feet. Out of these seven mental tasks, the best 4-class combination as well as most reactive frequency band (between 8-30 Hz was selected individually for online control. Classification was based on common spatial patterns and Fisher's linear discriminant analysis. The number and time of classifier updates varied individually. Selection speed was increased by reducing trial length. To minimize differences in brain activity between sessions with and without feedback, sham feedback was provided in the screening and calibration runs in which usually no real-time feedback is shown. Selected task combinations and frequency ranges differed between users. The tasks that were included in the 4-class combination most often were (1 motor imagery of the left hand (2, one brain-teaser task (word association or mental subtraction (3, mental rotation task and (4 one more dynamic imagery task (auditory imagery, spatial navigation, imagery of the feet. Participants achieved mean performances over sessions of 44-84% and peak performances in single-sessions of 58-93% in this user-centered 4-class BCI protocol. This protocol is highly adjustable to individual users and thus could increase the percentage of users who can gain and maintain BCI control. A high priority for future work is to examine this protocol with severely

  8. Whatever works: a systematic user-centered training protocol to optimize brain-computer interfacing individually.

    Science.gov (United States)

    Friedrich, Elisabeth V C; Neuper, Christa; Scherer, Reinhold

    2013-01-01

    This study implemented a systematic user-centered training protocol for a 4-class brain-computer interface (BCI). The goal was to optimize the BCI individually in order to achieve high performance within few sessions for all users. Eight able-bodied volunteers, who were initially naïve to the use of a BCI, participated in 10 sessions over a period of about 5 weeks. In an initial screening session, users were asked to perform the following seven mental tasks while multi-channel EEG was recorded: mental rotation, word association, auditory imagery, mental subtraction, spatial navigation, motor imagery of the left hand and motor imagery of both feet. Out of these seven mental tasks, the best 4-class combination as well as most reactive frequency band (between 8-30 Hz) was selected individually for online control. Classification was based on common spatial patterns and Fisher's linear discriminant analysis. The number and time of classifier updates varied individually. Selection speed was increased by reducing trial length. To minimize differences in brain activity between sessions with and without feedback, sham feedback was provided in the screening and calibration runs in which usually no real-time feedback is shown. Selected task combinations and frequency ranges differed between users. The tasks that were included in the 4-class combination most often were (1) motor imagery of the left hand (2), one brain-teaser task (word association or mental subtraction) (3), mental rotation task and (4) one more dynamic imagery task (auditory imagery, spatial navigation, imagery of the feet). Participants achieved mean performances over sessions of 44-84% and peak performances in single-sessions of 58-93% in this user-centered 4-class BCI protocol. This protocol is highly adjustable to individual users and thus could increase the percentage of users who can gain and maintain BCI control. A high priority for future work is to examine this protocol with severely disabled users.

  9. Influence of optimizing protocol choice on the integral dose value in prostate radiotherapy planning by dynamic techniques - Pilot study.

    Science.gov (United States)

    Zaleska, Anna; Bogaczyk, Krzysztof; Piotrowski, Tomasz

    2017-01-01

    The purpose of this study was to compare the values of integral dose, calculated for treatment plans of dynamic radiotherapy techniques prepared with two different optimization protocols. Delivering radiation by IMRT, VMAT and also HT techniques has an influence on the low dose deposition of large areas of the patient body. Delivery of low dose can induce injury of healthy cells. In this situation, a good solution would be to reduce the area, which receives a low dose, but with appropriate dose level for the target volume. To calculate integral dose values of plans structures, we used 90 external beam radiotherapy plans prepared for three techniques (intensity modulated radiotherapy, volumetric modulated arc therapy and helical tomotherapy). One technique includes three different geometry combinations. 45 plans were prepared with classic optimization protocol and 45 with rings optimization protocol which should reduce the low doses in the normal tissue. Differences in values of the integral dose depend on the geometry and technique of irradiation, as well as optimization protocol used in preparing treatment plans. The application of the rings optimization caused the value of normal tissue integral dose (NTID) to decrease. It is possible to limit the area of low dose irradiation and reduce NTID in dynamic techniques with the same clinical constraints for OAR and PTV volumes by using an optimization protocol other than the classic one.

  10. D-MG Tradeoff and Optimal Codes for a Class of AF and DF Cooperative Communication Protocols

    CERN Document Server

    Elia, Petros; Anand, M; Kumar, P Vijay

    2007-01-01

    We consider cooperative relay communication in a fading channel environment under the Orthogonal Amplify and Forward (OAF) and Orthogonal and Non-Orthogonal Selection Decode and Forward (OSDF and NSDF) protocols. For all these protocols, we compute the Diversity-Multiplexing Gain Tradeoff (DMT). We construct DMT optimal codes for the protocols which are sphere decodable and, in certain cases, incur minimum possible delay. Our results establish that the DMT of the OAF protocol is identical to the DMT of the Non-Orthogonal Amplify and Forward (NAF) protocol. Two variants of the NSDF protocol are considered: fixed-NSDF and variable-NSDF protocol. In the variable-NSDF protocol, the fraction of time duration for which the source alone transmits is allowed to vary with the rate of communication. Among the class of static amplify-and-forward and decode-and-forward protocols, the variable-NSDF protocol is shown to have the best known DMT for any number of relays apart from the two-relay case. When there are two relay...

  11. Optimized protocols for cardiac magnetic resonance imaging in patients with thoracic metallic implants

    Energy Technology Data Exchange (ETDEWEB)

    Olivieri, Laura J.; Ratnayaka, Kanishka [Children' s National Health System, Division of Cardiology, Washington, DC (United States); National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD (United States); Cross, Russell R.; O' Brien, Kendall E. [Children' s National Health System, Division of Cardiology, Washington, DC (United States); Hansen, Michael S. [National Institutes of Health, National Heart, Lung and Blood Institute, Bethesda, MD (United States)

    2015-09-15

    Cardiac magnetic resonance (MR) imaging is a valuable tool in congenital heart disease; however patients frequently have metal devices in the chest from the treatment of their disease that complicate imaging. Methods are needed to improve imaging around metal implants near the heart. Basic sequence parameter manipulations have the potential to minimize artifact while limiting effects on image resolution and quality. Our objective was to design cine and static cardiac imaging sequences to minimize metal artifact while maintaining image quality. Using systematic variation of standard imaging parameters on a fluid-filled phantom containing commonly used metal cardiac devices, we developed optimized sequences for steady-state free precession (SSFP), gradient recalled echo (GRE) cine imaging, and turbo spin-echo (TSE) black-blood imaging. We imaged 17 consecutive patients undergoing routine cardiac MR with 25 metal implants of various origins using both standard and optimized imaging protocols for a given slice position. We rated images for quality and metal artifact size by measuring metal artifact in two orthogonal planes within the image. All metal artifacts were reduced with optimized imaging. The average metal artifact reduction for the optimized SSFP cine was 1.5+/-1.8 mm, and for the optimized GRE cine the reduction was 4.6+/-4.5 mm (P < 0.05). Quality ratings favored the optimized GRE cine. Similarly, the average metal artifact reduction for the optimized TSE images was 1.6+/-1.7 mm (P < 0.05), and quality ratings favored the optimized TSE imaging. Imaging sequences tailored to minimize metal artifact are easily created by modifying basic sequence parameters, and images are superior to standard imaging sequences in both quality and artifact size. Specifically, for optimized cine imaging a GRE sequence should be used with settings that favor short echo time, i.e. flow compensation off, weak asymmetrical echo and a relatively high receiver bandwidth. For static

  12. New developments in the application of optimal control theory to therapeutic protocols.

    Science.gov (United States)

    Bayón, L; Otero, J A; Suárez, P M; Tasis, C

    2016-02-01

    Optimal control theory is one of the most important tools in the development of new therapeutic protocols for treating infections. In this work, we present an algorithm able to deal with high-dimensional problems with bounded controls. The optimal solution is obtained by minimizing a positive-definite treatment cost function. Our method, based on Pontryagin's Minimum Principle and the coordinate cyclic descent method, allows solving problems of varied nature. In this paper, and by way of example, therapeutic enhancement of the immune response to invasion by pathogenic attack is addressed as an optimal control problem. The generic mathematical model used describes the evolution of the disease by means of four non-linear, ordinary differential equations. The model is characterized by the concentration of pathogens, plasma cells, antibodies and a numerical value that indicates the relative characteristic of an organ damaged by disease. From a system theory point of view, drugs can be interpreted as control inputs. Therapies based on separate application of the agents are presented in previous studies. We shall present the more general problem in this paper, considering combined therapies and bounded controls. Finally, we present several numerical simulations.

  13. Optimization of a filter-lysis protocol to purify rat testicular homogenates for automated spermatid counting.

    Science.gov (United States)

    Pacheco, Sara E; Anderson, Linnea M; Boekelheide, Kim

    2012-01-01

    Quantifying testicular homogenization-resistant spermatid heads (HRSH) is a powerful indicator of spermatogenesis. These counts have traditionally been performed manually using a hemocytometer, but this method can be time consuming and biased. We aimed to develop a protocol to reduce debris for the application of automated counting, which would allow for efficient and unbiased quantification of rat HRSH. We developed a filter-lysis protocol that effectively removes debris from rat testicular homogenates. After filtering and lysing the homogenates, we found no statistical differences between manual (classic and filter-lysis) and automated (filter-lysis) counts using 1-way analysis of variance with Bonferroni's multiple comparison test. In addition, Pearson's correlation coefficients were calculated to compare the counting methods, and there was a strong correlation between the classic manual counts and the filter-lysis manual (r = 0.85, P = .002) and the filter-lysis automated (r = 0.89, P = .0005) counts. We also tested the utility of the automated method in a low-dose exposure model known to decrease HRSH. Adult Fischer 344 rats exposed to 0.33% 2,5-hexanedione in the drinking water for 12 weeks demonstrated decreased body (P = .02) and testes (P = .002) weights. In addition, there was a significant reduction in the number of HRSH per testis (P = .002) when compared to controls. A filterlysis protocol was optimized to purify rat testicular homogenates for automated HRSH counts. Automated counting systems yield unbiased data and can be applied to detect changes in the testis after low-dose toxicant exposure.

  14. Optimization of Protein Extraction and Two-Dimensional Electrophoresis Protocols for Oil Palm Leaf.

    Science.gov (United States)

    Daim, Leona Daniela Jeffery; Ooi, Tony Eng Keong; Yusof, Hirzun Mohd; Majid, Nazia Abdul; Karsani, Saiful Anuar Bin

    2015-08-01

    Oil palm (Elaeis guineensis) is an important economic crop cultivated for its nutritional palm oil. A significant amount of effort has been undertaken to understand oil palm growth and physiology at the molecular level, particularly in genomics and transcriptomics. Recently, proteomics studies have begun to garner interest. However, this effort is impeded by technical challenges. Plant sample preparation for proteomics analysis is plagued with technical challenges due to the presence of polysaccharides, secondary metabolites and other interfering compounds. Although protein extraction methods for plant tissues exist, none work universally on all sample types. Therefore, this study aims to compare and optimize different protein extraction protocols for use with two-dimensional gel electrophoresis of young and mature leaves from the oil palm. Four protein extraction methods were evaluated: phenol-guanidine isothiocyanate, trichloroacetic acid-acetone precipitation, sucrose and trichloroacetic acid-acetone-phenol. Of these four protocols, the trichloroacetic acid-acetone-phenol method was found to give the highest resolution and most reproducible gel. The results from this study can be used in sample preparations of oil palm tissue for proteomics work.

  15. APPLICATION OF NEWTON RAPHSON ALGORITHM FOR OPTIMIZING TRANSMISSION CONTROL PROTOCOL PERFORMANCE

    Directory of Open Access Journals (Sweden)

    J. Viji Priya

    2013-01-01

    Full Text Available Wireless networks are growing rapidly. TCP is the most widely-used protocol on Internet and so optimizing TCP performance is very important for fast efficient data transfer. The different existing TCP variants and solutions they have not been analyzed together to identify the bottlenecks in wireless networks. TCP has a major problem in its congestion control algorithm which does not allow the flow to achieve the full available bandwidth on fast long-distance links. This problem has been studied in this study using a new high speed congestion control TCP protocol based on the Newton Raphson algorithm This study further analyses involving six TCP performance evaluation constraints namely, TCP full bandwidth utilization, throughput, packet loss rate, fairness in sharing bandwidth, friendliness in short-RTT and long-RTT and these constraints are used to evaluate the proposed Newton Raphson Congestion Control (NRC-TCP performance. This study shows that the proposed algorithm performs better compared with the other methods of application.

  16. Tractographic reconstruction protocol optimization in the rat brain in-vivo: towards a normal atlas.

    Science.gov (United States)

    Preti, Maria Giulia; Di Marzio, Alessandro; Mastropietro, Alfonso; Aquino, Domenico; Baselli, Giuseppe; Laganà, Maria Marcella; Zucca, Ileana; Frassoni, Carolina; Spreafico, Roberto

    2011-01-01

    The tractographic reconstruction of anatomical and microstructural features provided by Magnetic Resonance (MR) Diffusion Tensor Imaging (DTI) gives essential information of brain damage in several pathological animal models. The optimization of a tractographic protocol is undertaken in normal rats for the future construction of a reference atlas, as prerequisite for preclinical pathological in-vivo studies. High field, preclinical in-vivo DTI faces important difficulties relevant to Signal-to-Noise Ratio (SNR), distortion, high required resolution, movement sensitivity. Given a pixel-size of 0.17 mm and TE/TR = 29/6500 ms, b value and slice thickness were fixed at 700 s/mm(2) and 0.58 mm, respectively, on preventive ex-vivo studies. In-vivo studies led to the choice of 30 diffusion directions, averaged on 16 runs. The final protocol required 51 min scanning and permitted a reliable reconstruction of main rat brain bundles. Tract reconstruction stopping rules required proper setting. In conclusion, the viability of DTI tractography on in-vivo rat studies was shown, towards the construction of a normal reference atlas.

  17. Optimization of the protocols for the use of contrast agents in PET/CT studies.

    Science.gov (United States)

    Pelegrí Martínez, L; Kohan, A A; Vercher Conejero, J L

    The introduction of PET/CT scanners in clinical practice in 1998 has improved care for oncologic patients throughout the clinical pathway, from the initial diagnosis of disease through the evaluation of the response to treatment to screening for possible recurrence. The CT component of a PET/CT study is used to correct the attenuation of PET studies; CT also provides anatomic information about the distribution of the radiotracer. CT is especially useful in situations where PET alone can lead to false positives and false negatives, and CT thereby improves the diagnostic performance of PET. The use of intravenous or oral contrast agents and optimal CT protocols have improved the detection and characterization of lesions. However, there are circumstances in which the systematic use of contrast agents is not justified. The standard acquisition in PET/CT scanners is the whole body protocol, but this can lead to artifacts due to the position of patients and respiratory movements between the CT and PET acquisitions. This article discusses these aspects from a constructive perspective with the aim of maximizing the diagnostic potential of PET/CT and providing better care for patients.

  18. [Optimized protocols for interphase FISH analysis of imprints and sections using split signal probes].

    Science.gov (United States)

    Pelluard-Nehme, F; Dupont, T; Turmo, M; Merlio, J-P; Belaud-Rotureau, M-A

    2007-03-01

    Fluorescent in situ hybridization (FISH) analysis is a molecular technique allowing the detection of recurrent translocations in cancer. Several hybridization protocols were assayed in order to evaluate their performances for interphase FISH analysis of histological sections and imprints using split probes. Adult and foetal lymphoid tissues were selected. Touch imprints of fresh (EF) or frozen (EC) tissues, sections (CF) and isolated nuclei (NI) of formol-fixed paraffin-embedded tissues were performed. The cut-off values of the IGH, IGlambda, BCL-2, BCL-6, CCND1 and MYC DNA FISH split signal probes were calculated for adult reactive lymph nodes on the different histological preparations (EC, CF, CC, NI) and on several tissues for the IGH and BCL-6 probes. In reactive lymph nodes, the cut-off values of the probes were between 3 and 13% and found independent of the preparation type. Conversely, slight but significant variations of the cut-off level were observed when different foetal control tissues were assayed with the same probe set. Finally, this study provided optimized-protocols for FISH analysis of either fresh/frozen imprints or formalin-fixed paraffin-embedded sections using split signal DNA probes.

  19. An Efficient Searching and an Optimized Cache Coherence handling Scheme on DSR Routing Protocol for MANETS

    Directory of Open Access Journals (Sweden)

    Rajneesh Kumar Gujral

    2011-01-01

    Full Text Available Mobile ad hoc networks (MANETS are self-created and self organized by a collection of mobile nodes, interconnected by multi-hop wireless paths in a strictly peer to peer fashion. DSR (Dynamic Source Routing is an on-demand routing protocol for wireless ad hoc networks that floods route requests when the route is needed. Route caches in intermediate mobile node on DSR are used to reduce flooding of route requests. But with the increase in network size, node mobility and local cache of every mobile node cached route quickly become stale or inefficient. In this paper, for efficient searching, we have proposed a generic searching algorithm on associative cache memory organization to faster searching single/multiple paths for destination if exist in intermediate mobile node cache with a complexity O(n (Where n is number of bits required to represent the searched field.The other major problem of DSR is that the route maintenance mechanism does not locally repair a broken link and Stale cache information could also result in inconsistencies during the route discovery /reconstruction phase. So to deal this, we have proposed an optimized cache coherence handling scheme for on -demand routing protocol (DSR.

  20. Optimal protocol for teleconsultation with a cellular phone for dentoalveolar trauma: an in-vitro study.

    Science.gov (United States)

    Park, Wonse; Lee, Hae-Na; Jeong, Jin-Sun; Kwon, Jung-Hoon; Lee, Grace H; Kim, Kee-Deog

    2012-06-01

    Dental trauma is frequently unpredictable. The initial assessment and urgent treatment are essential for dentists to save the patient's teeth. Mobile-phone-assisted teleconsultation and telediagnosis for dental trauma could be an aid when a dentist is not available. In the present in-vitro study, we evaluated the success rate and time to transfer images under various conditions. We analyzed the image quality of cameras built into mobile phones based on their resolution, autofocus, white-balance, and anti-movement functions. The image quality of most built-in cameras was acceptable to perform the initial assessment, with the autofocus function being essential to obtain high-quality images. The transmission failure rate increased markedly when the image size exceeded 500 κB and the additional text messaging did not improve the success rate or the transmission time. Our optimal protocol could be useful for emergency programs running on the mobile phones.

  1. Optimal protocol for teleconsultation with a cellular phone for dentoalveolar trauma: an in-vitro study

    Energy Technology Data Exchange (ETDEWEB)

    Park, Won Se; Lee, Hae Na; Jeong, Jin Sun; Kwon, Jung Hoon; Lee, Grace H; Kim, Kee Dong [College of Dentistry, Yonsei University, Seoul (Korea, Republic of)

    2012-06-15

    Dental trauma is frequently unpredictable. The initial assessment and urgent treatment are essential for dentists to save the patient's teeth. Mobile-phone-assisted teleconsultation and telediagnosis for dental trauma could be an aid when a dentist is not available. In the present in-vitro study, we evaluated the success rate and time to transfer images under various conditions. We analyzed the image quality of cameras built into mobile phones based on their resolution, autofocus, white-balance, and anti-movement functions. The image quality of most built-in cameras was acceptable to perform the initial assessment, with the autofocus function being essential to obtain high-quality images. The transmission failure rate increased markedly when the image size exceeded 500 kB and the additional text messaging did not improve the success rate or the transmission time. Our optimal protocol could be useful for emergency programs running on the mobile phones.

  2. Promoting teamwork and surgical optimization: combining TeamSTEPPS with a specialty team protocol.

    Science.gov (United States)

    Tibbs, Sheila Marie; Moss, Jacqueline

    2014-11-01

    This quality improvement project was a 300-day descriptive preintervention and postintervention comparison consisting of a convenience sample of 18 gynecology surgical team members. We administered the Team Strategies & Tools to Enhance Performance and Patient Safety (TeamSTEPPS®) Teamwork Perception Questionnaire to measure the perception of teamwork. In addition, we collected data regarding rates of compliance (ie, huddle, time out) and measurable surgical procedure times. Results showed a statistically significant increase in the number of team members present for each procedure, 2.34 μ before compared with 2.61 μ after (P = .038), and in the final time-out (FTO) compliance as a result of a clarification of the definition of FTO, 1.05 μ before compared with 1.18 μ after (P = .004). Additionally, there was improvement in staff members' perception of teamwork. The implementation of team training, protocols, and algorithms can enhance surgical optimization, communication, and work relationships.

  3. A Structure-Based Design Protocol for Optimizing Combinatorial Protein Libraries.

    Science.gov (United States)

    Lunt, Mark W; Snow, Christopher D

    2016-01-01

    Protein variant libraries created via site-directed mutagenesis are a powerful approach to engineer improved proteins for numerous applications such as altering enzyme substrate specificity. Conventional libraries commonly use a brute force approach: saturation mutagenesis via degenerate codons that encode all 20 natural amino acids. In contrast, this chapter describes a protocol for designing "smarter" degenerate codon libraries via direct combinatorial optimization in "library space." Several case studies illustrate how it is possible to design degenerate codon libraries that are highly enriched for favorable, low-energy sequences as assessed using a standard all-atom scoring function. There is much to gain for experimental protein engineering laboratories willing to think beyond site saturation mutagenesis. In the common case that the exact experimental screening budget is not fixed, it is particularly helpful to perform a Pareto analysis to inspect favorable libraries at a range of possible library sizes.

  4. Hindlimb Suspension as a Model to Study Ophthalmic Complications in Microgravity Status Report: Optimization of Rat Retina Flat Mounts Staining to Study Vascular Remodeling

    Science.gov (United States)

    Theriot, Corey A.; Zanello, Susana B.

    2014-01-01

    Preliminary data from a prior tissue-sharing experiment has suggested that early growth response protein-1 (Egr1), a transcription factor involved in various stress responses in the vasculature, is induced in the rat retina after 14 days of hindlimb suspension (HS) and may be evidence that mechanical stress is occurring secondary to the cephalad fluid shift. This mechanical stress could cause changes in oxygenation of the retina, and the subsequent ischemia- or inflammation-driven hypoxia may lead to microvascular remodeling. This microvascular remodeling process can be studied using image analysis of retinal vessels and can be then be quantified by the VESsel GENeration Analysis (VESGEN) software, a computational tool that quantifies remodeling patterns of branching vascular trees and capillary or vasculogenic networks. Our project investigates whether rodent HS is a valid model to study the effects of simulated-weightlessness on ocular structures and their relationship with intracranial pressure (ICP). One of the hypotheses to be tested is that HS-induced cephalad fluid shift is accompanied by vascular engorgement that produces changes in retinal oxygenation, leading to oxidative stress, hypoxia, microvascular remodeling, and cellular degeneration. We have optimized the procedure to obtain flat mounts of rat retina, staining of the endothelial lining in vasculature and acquisition of high quality images suitable for VESGEN analysis. Briefly, eyes were fixed in 4% paraformaldehyde for 24 hours and retinas were detached and then mounted flat on microscope slides. The microvascular staining was done with endothelial cell-specific isolectin binding, coupled to Alexa-488 fluorophore. Image acquisition at low magnification and high resolution was performed using a new Leica SP8 confocal microscope in a tile pattern across the X,Y plane and multiple sections along the Z-axis. This new confocal microscope has the added capability of dye separation using the Linear

  5. Use of C-Arm Cone Beam CT During Hepatic Radioembolization: Protocol Optimization for Extrahepatic Shunting and Parenchymal Enhancement

    Energy Technology Data Exchange (ETDEWEB)

    Hoven, Andor F. van den, E-mail: a.f.vandenhoven@umcutrecht.nl; Prince, Jip F.; Keizer, Bart de; Vonken, Evert-Jan P. A.; Bruijnen, Rutger C. G.; Verkooijen, Helena M.; Lam, Marnix G. E. H.; Bosch, Maurice A. A. J. van den [University Medical Center Utrecht, Department of Radiology and Nuclear Medicine (Netherlands)

    2016-01-15

    PurposeTo optimize a C-arm computed tomography (CT) protocol for radioembolization (RE), specifically for extrahepatic shunting and parenchymal enhancement.Materials and MethodsA prospective development study was performed per IDEAL recommendations. A literature-based protocol was applied in patients with unresectable and chemorefractory liver malignancies undergoing an angiography before radioembolization. Contrast and scan settings were adjusted stepwise and repeatedly reviewed in a consensus meeting. Afterwards, two independent raters analyzed all scans. A third rater evaluated the SPECT/CT scans as a reference standard for extrahepatic shunting and lack of target segment perfusion.ResultsFifty scans were obtained in 29 procedures. The first protocol, using a 6 s delay and 10 s scan, showed insufficient parenchymal enhancement. In the second protocol, the delay was determined by timing parenchymal enhancement on DSA power injection (median 8 s, range 4–10 s): enhancement improved, but breathing artifacts increased (from 0 to 27 %). Since the third protocol with a 5 s scan decremented subjective image quality, the second protocol was deemed optimal. Median CNR (range) was 1.7 (0.6–3.2), 2.2 (−1.4–4.0), and 2.1 (−0.3–3.0) for protocol 1, 2, and 3 (p = 0.80). Delineation of perfused segments was possible in 57, 73, and 44 % of scans (p = 0.13). In all C-arm CTs combined, the negative predictive value was 95 % for extrahepatic shunting and 83 % for lack of target segment perfusion.ConclusionAn optimized C-arm CT protocol was developed that can be used to detect extrahepatic shunts and non-perfusion of target segments during RE.

  6. Optimization of a protocol for myocardial perfusion scintigraphy by using an anthropomorphic phantom

    Energy Technology Data Exchange (ETDEWEB)

    Ramos, Susie Medeiros Oliveira; Sa, Lidia Vasconcellos de, E-mail: susie@ird.gov.br [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Glavam, Adriana Pereira; Kubo, Tadeu Takao Almodovar [Clinica de Diagnostico Por Imagem (CDPI/DASA), Rio de Janeiro, RJ (Brazil)

    2014-07-15

    Objective: to develop a study aiming at optimizing myocardial perfusion imaging. Materials and Methods: imaging of an anthropomorphic thorax phantom with a GE SPECT Ventri gamma camera, with varied activities and acquisition times, in order to evaluate the influence of these parameters on the quality of the reconstructed medical images. The {sup 99m}Tc-sestamibi radiotracer was utilized, and then the images were clinically evaluated on the basis of data such as summed stress score, and on the technical image quality and perfusion. The software ImageJ was utilized in the data quantification. Results: the results demonstrated that for the standard acquisition time utilized in the procedure (15 seconds per angle), the injected activity could be reduced by 33.34%. Additionally, even if the standard scan time is reduced by 53.34% (7 seconds per angle), the standard injected activity could still be reduced by 16.67%, without impairing the image quality and the diagnostic reliability. Conclusion: the described method and respective results provide a basis for the development of a clinical trial of patients in an optimized protocol. (author)

  7. Optimization of the transcranial magnetic stimulation protocol by defining a reliable estimate for corticospinal excitability.

    Directory of Open Access Journals (Sweden)

    Koen Cuypers

    Full Text Available The goal of this study was to optimize the transcranial magnetic stimulation (TMS protocol for acquiring a reliable estimate of corticospinal excitability (CSE using single-pulse TMS. Moreover, the minimal number of stimuli required to obtain a reliable estimate of CSE was investigated. In addition, the effect of two frequently used stimulation intensities [110% relative to the resting motor threshold (rMT and 120% rMT] and gender was evaluated. Thirty-six healthy young subjects (18 males and 18 females participated in a double-blind crossover procedure. They received 2 blocks of 40 consecutive TMS stimuli at either 110% rMT or 120% rMT in a randomized order. Based upon our data, we advise that at least 30 consecutive stimuli are required to obtain the most reliable estimate for CSE. Stimulation intensity and gender had no significant influence on CSE estimation. In addition, our results revealed that for subjects with a higher rMT, fewer consecutive stimuli were required to reach a stable estimate of CSE. The current findings can be used to optimize the design of similar TMS experiments.

  8. Optimization of the transcranial magnetic stimulation protocol by defining a reliable estimate for corticospinal excitability.

    Science.gov (United States)

    Cuypers, Koen; Thijs, Herbert; Meesen, Raf L J

    2014-01-01

    The goal of this study was to optimize the transcranial magnetic stimulation (TMS) protocol for acquiring a reliable estimate of corticospinal excitability (CSE) using single-pulse TMS. Moreover, the minimal number of stimuli required to obtain a reliable estimate of CSE was investigated. In addition, the effect of two frequently used stimulation intensities [110% relative to the resting motor threshold (rMT) and 120% rMT] and gender was evaluated. Thirty-six healthy young subjects (18 males and 18 females) participated in a double-blind crossover procedure. They received 2 blocks of 40 consecutive TMS stimuli at either 110% rMT or 120% rMT in a randomized order. Based upon our data, we advise that at least 30 consecutive stimuli are required to obtain the most reliable estimate for CSE. Stimulation intensity and gender had no significant influence on CSE estimation. In addition, our results revealed that for subjects with a higher rMT, fewer consecutive stimuli were required to reach a stable estimate of CSE. The current findings can be used to optimize the design of similar TMS experiments.

  9. Optimization of a protocol for myocardial perfusion scintigraphy by using an anthropomorphic phantom*

    Science.gov (United States)

    Ramos, Susie Medeiros Oliveira; Glavam, Adriana Pereira; Kubo, Tadeu Takao Almodovar; de Sá, Lidia Vasconcellos

    2014-01-01

    Objective To develop a study aiming at optimizing myocardial perfusion imaging. Materials and Methods Imaging of an anthropomorphic thorax phantom with a GE SPECT Ventri gamma camera, with varied activities and acquisition times, in order to evaluate the influence of these parameters on the quality of the reconstructed medical images. The 99mTc-sestamibi radiotracer was utilized, and then the images were clinically evaluated on the basis of data such as summed stress score, and on the technical image quality and perfusion. The software ImageJ was utilized in the data quantification. Results The results demonstrated that for the standard acquisition time utilized in the procedure (15 seconds per angle), the injected activity could be reduced by 33.34%. Additionally, even if the standard scan time is reduced by 53.34% (7 seconds per angle), the standard injected activity could still be reduced by 16.67%, without impairing the image quality and the diagnostic reliability. Conclusion The described method and respective results provide a basis for the development of a clinical trial of patients in an optimized protocol. PMID:25741088

  10. Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis.

    Science.gov (United States)

    Hammad, Seddik; Hoehme, Stefan; Friebel, Adrian; von Recklinghausen, Iris; Othman, Amnah; Begher-Tibbe, Brigitte; Reif, Raymond; Godoy, Patricio; Johann, Tim; Vartak, Amruta; Golka, Klaus; Bucur, Petru O; Vibert, Eric; Marchan, Rosemarie; Christ, Bruno; Dooley, Steven; Meyer, Christoph; Ilkavets, Iryna; Dahmen, Uta; Dirsch, Olaf; Böttger, Jan; Gebhardt, Rolf; Drasdo, Dirk; Hengstler, Jan G

    2014-05-01

    Histological alterations often constitute a fingerprint of toxicity and diseases. The extent to which these alterations are cause or consequence of compromised organ function, and the underlying mechanisms involved is a matter of intensive research. In particular, liver disease is often associated with altered tissue microarchitecture, which in turn may compromise perfusion and functionality. Research in this field requires the development and orchestration of new techniques into standardized processing pipelines that can be used to reproducibly quantify tissue architecture. Major bottlenecks include the lack of robust staining, and adequate reconstruction and quantification techniques. To bridge this gap, we established protocols employing specific antibody combinations for immunostaining, confocal imaging, three-dimensional reconstruction of approximately 100-μm-thick tissue blocks and quantification of key architectural features. We describe a standard procedure termed 'liver architectural staining' for the simultaneous visualization of bile canaliculi, sinusoidal endothelial cells, glutamine synthetase (GS) for the identification of central veins, and DAPI as a nuclear marker. Additionally, we present a second standard procedure entitled 'S-phase staining', where S-phase-positive and S-phase-negative nuclei (stained with BrdU and DAPI, respectively), sinusoidal endothelial cells and GS are stained. The techniques include three-dimensional reconstruction of the sinusoidal and bile canalicular networks from the same tissue block, and robust capture of position, size and shape of individual hepatocytes, as well as entire lobules from the same tissue specimen. In addition to the protocols, we have also established image analysis software that allows relational and hierarchical quantifications of different liver substructures (e.g. cells and vascular branches) and events (e.g. cell proliferation and death). Typical results acquired for routinely quantified

  11. Optimization of a vitrification protocol for hatched blastocysts from the dromedary camel (Camelus dromedarius).

    Science.gov (United States)

    Herrid, M; Billah, M; Malo, C; Skidmore, J A

    2016-03-01

    The objective of this study was to modify and optimize a vitrification protocol (open pulled straw) that was originally designed for human oocytes and embryos, to make it suitable for the cryopreservation of camel hatched blastocysts. The original open pulled straw protocol was a complex process with 15-minute exposure of oocytes/embryos in 7.5% ethylene glycol (EG) and 7.5% dimethyl sulfoxide (Me2SO) for equilibration, and cooling in 16% EG + 16% Me2SO + 1 M sucrose. Recognizing a need to better control the cryoprotectant (CPA) concentrations, while avoiding toxicity to the embryos, the effects on the survival rate and developmental potential of camel embryos in vitro were investigated using two different methods of loading the CPAs into the embryos (stepwise and semicontinuous increase in concentration), two different loading temperature/time (room temperature ∼24 °C/15 min and body 37 °C/3 min), and the replacement of Me2SO with EG alone or in combination with glycerol (Gly). A total of 145 in vivo-derived embryos were subjected to these processes, and after warming their morphological quality and integrity, and re-expansion was assessed after 0, 2, 24, 48, 72, and 96 hours of culture. Exposure of embryos in a stepwise method was more beneficial to the survival of embryos than was the semicontinuous process, and loading of CPAs at 37 °C with a short exposure time (3 minutes) resulted in an outcome comparable to the original processing at room temperature with a longer exposure time (15 minutes). The replacement of the Me2SO + EG mixture with EG only or a combination of EG + Gly in the vitrification medium significantly improved the outcome of all these evaluation criteria (P dromedary camel.

  12. Dynamic whole-body PET parametric imaging: I. Concept, acquisition protocol optimization and clinical application.

    Science.gov (United States)

    Karakatsanis, Nicolas A; Lodge, Martin A; Tahari, Abdel K; Zhou, Y; Wahl, Richard L; Rahmim, Arman

    2013-10-21

    Static whole-body PET/CT, employing the standardized uptake value (SUV), is considered the standard clinical approach to diagnosis and treatment response monitoring for a wide range of oncologic malignancies. Alternative PET protocols involving dynamic acquisition of temporal images have been implemented in the research setting, allowing quantification of tracer dynamics, an important capability for tumor characterization and treatment response monitoring. Nonetheless, dynamic protocols have been confined to single-bed-coverage limiting the axial field-of-view to ~15-20 cm, and have not been translated to the routine clinical context of whole-body PET imaging for the inspection of disseminated disease. Here, we pursue a transition to dynamic whole-body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. We investigate solutions to address the challenges of: (i) long acquisitions, (ii) small number of dynamic frames per bed, and (iii) non-invasive quantification of kinetics in the plasma. In the present study, a novel dynamic (4D) whole-body PET acquisition protocol of ~45 min total length is presented, composed of (i) an initial 6 min dynamic PET scan (24 frames) over the heart, followed by (ii) a sequence of multi-pass multi-bed PET scans (six passes × seven bed positions, each scanned for 45 s). Standard Patlak linear graphical analysis modeling was employed, coupled with image-derived plasma input function measurements. Ordinary least squares Patlak estimation was used as the baseline regression method to quantify the physiological parameters of tracer uptake rate Ki and total blood distribution volume V on an individual voxel basis. Extensive Monte Carlo simulation studies, using a wide set of published kinetic FDG parameters and GATE and XCAT platforms, were conducted to optimize the acquisition protocol from a range of ten different clinically

  13. Potential Projective Material on the Rorschach: Comparing Comprehensive System Protocols to Their Modeled R-Optimized Administration Counterparts.

    Science.gov (United States)

    Pianowski, Giselle; Meyer, Gregory J; Villemor-Amaral, Anna Elisa de

    2016-01-01

    Exner ( 1989 ) and Weiner ( 2003 ) identified 3 types of Rorschach codes that are most likely to contain personally relevant projective material: Distortions, Movement, and Embellishments. We examine how often these types of codes occur in normative data and whether their frequency changes for the 1st, 2nd, 3rd, 4th, or last response to a card. We also examine the impact on these variables of the Rorschach Performance Assessment System's (R-PAS) statistical modeling procedures that convert the distribution of responses (R) from Comprehensive System (CS) administered protocols to match the distribution of R found in protocols obtained using R-optimized administration guidelines. In 2 normative reference databases, the results indicated that about 40% of responses (M = 39.25) have 1 type of code, 15% have 2 types, and 1.5% have all 3 types, with frequencies not changing by response number. In addition, there were no mean differences in the original CS and R-optimized modeled records (M Cohen's d = -0.04 in both databases). When considered alongside findings showing minimal differences between the protocols of people randomly assigned to CS or R-optimized administration, the data suggest R-optimized administration should not alter the extent to which potential projective material is present in a Rorschach protocol.

  14. Optimization of Rb-82 PET acquisition and reconstruction protocols for myocardial perfusion defect detection

    Science.gov (United States)

    Tang, Jing; Rahmim, Arman; Lautamäki, Riikka; Lodge, Martin A.; Bengel, Frank M.; Tsui, Benjamin M. W.

    2009-05-01

    The purpose of this study is to optimize the dynamic Rb-82 cardiac PET acquisition and reconstruction protocols for maximum myocardial perfusion defect detection using realistic simulation data and task-based evaluation. Time activity curves (TACs) of different organs under both rest and stress conditions were extracted from dynamic Rb-82 PET images of five normal patients. Combined SimSET-GATE Monte Carlo simulation was used to generate nearly noise-free cardiac PET data from a time series of 3D NCAT phantoms with organ activities modeling different pre-scan delay times (PDTs) and total acquisition times (TATs). Poisson noise was added to the nearly noise-free projections and the OS-EM algorithm was applied to generate noisy reconstructed images. The channelized Hotelling observer (CHO) with 32× 32 spatial templates corresponding to four octave-wide frequency channels was used to evaluate the images. The area under the ROC curve (AUC) was calculated from the CHO rating data as an index for image quality in terms of myocardial perfusion defect detection. The 0.5 cycle cm-1 Butterworth post-filtering on OS-EM (with 21 subsets) reconstructed images generates the highest AUC values while those from iteration numbers 1 to 4 do not show different AUC values. The optimized PDTs for both rest and stress conditions are found to be close to the cross points of the left ventricular chamber and myocardium TACs, which may promote an individualized PDT for patient data processing and image reconstruction. Shortening the TATs for <~3 min from the clinically employed acquisition time does not affect the myocardial perfusion defect detection significantly for both rest and stress studies.

  15. Comparison of two stretching methods and optimization of stretching protocol for the piriformis muscle.

    Science.gov (United States)

    Gulledge, Brett M; Marcellin-Little, Denis J; Levine, David; Tillman, Larry; Harrysson, Ola L A; Osborne, Jason A; Baxter, Blaise

    2014-02-01

    Piriformis syndrome is an uncommon diagnosis for a non-discogenic form of sciatica whose treatment has traditionally focused on stretching the piriformis muscle (PiM). Conventional stretches include hip flexion, adduction, and external rotation. Using three-dimensional modeling, we quantified the amount of (PiM) elongation resulting from two conventional stretches and we investigated by use of a computational model alternate stretching protocols that would optimize PiM stretching. Seven subjects underwent three CT scans: one supine, one with hip flexion, adduction, then external rotation (ADD stretch), and one with hip flexion, external rotation, then adduction (ExR stretch). Three-dimensional bone models were constructed from the CT scans. PiM elongation during these stretches, femoral neck inclination, femoral head anteversion, and trochanteric anteversion were measured. A computer program was developed to map PiM length over a range of hip joint positions and was validated against the measured scans. ExR and ADD stretches elongated the PiM similarly by approximately 12%. Femoral head and greater trochanter anteversion influenced PiM elongation. Placing the hip joints in 115° of hip flexion, 40° of external rotation and 25° of adduction or 120° of hip flexion, 50° of external rotation and 30° of adduction increased PiM elongation by 30-40% compared to conventional stretches (15.1 and 15.3% increases in PiM muscle length, respectively). ExR and ADD stretches elongate the PiM similarly and therefore may have similar clinical effectiveness. The optimized stretches led to larger increases in PiM length and may be more easily performed by some patients due to increased hip flexion.

  16. Electrostatically Stabilized Magnetic Nanoparticles - An Optimized Protocol to Label Murine T Cells for in vivo MRI.

    Science.gov (United States)

    Wuerfel, Eva; Smyth, Maureen; Millward, Jason M; Schellenberger, Eyk; Glumm, Jana; Prozorovski, Timour; Aktas, Orhan; Schulze-Topphoff, Ulf; Schnorr, Jörg; Wagner, Susanne; Taupitz, Matthias; Infante-Duarte, Carmen; Wuerfel, Jens

    2011-01-01

    We present a novel highly efficient protocol to magnetically label T cells applying electrostatically stabilized very small superparamagnetic iron oxide particles (VSOP). Our long-term aim is to use magnetic resonance imaging (MRI) to investigate T cell dynamics in vivo during the course of neuroinflammatory disorders such as experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. Encephalitogenic T cells were co-incubated with VSOP, or with protamine-complexed VSOP (VProt), respectively, at different conditions, optimizing concentrations and incubation times. Labeling efficacy was determined by atomic absorption spectrometry as well as histologically, and evaluated on a 7 T MR system. Furthermore, we investigated possible alterations of T cell physiology caused by the labeling procedure. T cell co-incubation with VSOP resulted in an efficient cellular iron uptake. T2 times of labeled cells dropped significantly, resulting in prominent hypointensity on T2*-weighted scans. Optimal labeling efficacy was achieved by VProt (1 mM Fe/ml, 8 h incubation; T2 time shortening of ∼80% compared to untreated cells). Although VSOP promoted T cell proliferation and altered the ratio of T cell subpopulations toward a CD4(+) phenotype, no effects on CD4 T cell proliferation or phenotypic stability were observed by labeling in vitro differentiated Th17 cells with VProt. Yet, high concentrations of intracellular iron oxide might induce alterations in T cell function, which should be considered in cell tagging studies. Moreover, we demonstrated that labeling of encephalitogenic T cells did not affect pathogenicity; labeled T cells were still capable of inducing EAE in susceptible recipient mice.

  17. Chemical activation of in vitro matured dromedary camel (Camelus dromedarius) oocytes: optimization of protocols.

    Science.gov (United States)

    Wani, N A

    2008-03-15

    Experiments were conducted to study the efficiency of sequential treatments of ionomycine and ethanol combined with phosphorylation inhibitor (6-dimethylaminopurine) or the specific maturation promoting factor inhibitor (roscovitine) in inducing artificial activation in dromedary M-II oocytes. Cumulus oocyte complexes (COCs), collected from slaughterhouse ovaries were cultured at 38.5 degrees C in an atmosphere of 5% CO2 in air for 24-48 h. In experiment 1, the COCs were either fertilized in vitro or activated with 5 microM ionomycine for 5 min or 7% ethanol for 7 min, both followed by exposure to 6-diethylaminopurine or roscovitine for 4h. After 14-15 h of in vitro culture, the oocytes were fixed and stained with 1% aceto-orcein to evaluate their nuclear status. In experiment 2, the oocytes were activated in the same manner as in experiment 1 but were cultured for 7 days to evaluate their post-parthenogenetic development. In experiment 3, oocytes were exposed to the ionomycine for 2, 3, 4 or 5 min to evaluate the better exposure time while as in experiment 4, the oocytes matured for 28-48 h were activated to see the effect of aging on post-parthenogenetic development. Higher proportion (P0.05) in the proportion of oocytes activated with ethanol when compared with in vitro fertilized group. No significant difference was seen on the proportion of morula on day 7 of culture, however the development to blastocyst stage was higher (P0.05). The proportion of blastocysts obtained was higher (Pdromedary camel oocytes with ionomycine/6-DMAP is demonstrated and optimized in the present study for further use in the development of assisted reproductive techniques in this species.

  18. Determination of endocrine disrupting compounds using temperature-dependent inclusion chromatography: I. Optimization of separation protocol.

    Science.gov (United States)

    Zarzycki, Paweł K; Włodarczyk, Elzbieta; Baran, Michał J

    2009-10-30

    In the present work we optimised the separation of battery of key UV non-transparent low-molecular-mass compounds having possible endocrine disrupting compounds (EDCs) activity or which may be used as the endocrine effect biomarkers. Simple optimization strategy was based on strong temperature effect that is driven by electrostatic interactions between macrocyclic mobile phase additives like cyclodextrins and eluted components of interest under C18 stationary phase and acetonitrile/water mobile phase conditions. Particularly, the effect of temperature involving native beta-cyclodextrin and its hydroxypropyl derivative to improve separation of number of natural (d-equilenin, equilin, estetrol, estriol, estrone, 17beta-estradiol, 17alpha-hydroxyprogesterone, 20alpha-hydroxyprogesterone, cortisol, cortisone, progesterone, testosterone, tetrahydrocortisol and tetrahydrocortisone) and artificial steroids (ethynylestradiol, norgestrel isomers, medroxyprogesterone, mestranol, methyltestosterone, norethindrone, 17alpha-estradiol) as well as non-steroidal compounds (diethylstilbesterol, bisphenol A, 4-tert-butylphenol, dimethyl phthalate, dibutyl phthalate and dioctyl phthalate) was investigated. It has been found that successful isocratic separation of 27 chemicals can be achieved using acetonitrile/water eluents modified with beta-cyclodextrin or hydroxypropyl-beta-cyclodextrin at concentration of 10 mM and temperature of 47 degrees C. Separation protocol is simple, reliable, direct and non-radioactive and may be easily adapted for rapid separation and quantification of wide range of given steroids and related EDCs in environmental samples, particularly those that are characterised by unstable biological matrix and components of interest load.

  19. Determination of an optimal priming duration and concentration protocol for pepper seeds (Capsicum annuum L.

    Directory of Open Access Journals (Sweden)

    Hassen ALOUI

    2015-12-01

    Full Text Available Seed priming is a simple pre-germination method to improve seed performance and to attenuate the effects of stress exposure. The objective of this study was to determinate an optimal priming protocol for three pepper cultivars (Capsicum annuum L.: ‘Beldi’, ‘Baklouti’ and ‘Anaheim Chili’. Seeds were primed with three solutions of NaCl, KCl and CaCl2 (0, 10, 20 and 50 mM for three different durations (12, 24 and 36h. Control seeds were soaked in distilled water for the same durations. After that, all seeds were kept to germinate in laboratory under normal light and controlled temperature. Results indicated that priming depends on concentration, duration and cultivar. The best combinations that we obtained were: KCl priming (10 mM, 36h for ‘Beldi’ cultivar, CaCl2 priming (10 mM, 36h for ‘Baklouti’ cultivar and finally NaCl priming (50 mM, 24h for ‘Anaheim Chili’ cultivar. Generally, priming had an effect on total germination percentage, mean germination time, germination index and the coefficient of velocity compared to control seeds. The beneficial effect of seed priming could be used for improving salt tolerance on germination and early seedling growth for pepper cultivar.

  20. Optimal Save-Then-Transmit Protocol for Energy Harvesting Wireless Transmitters

    CERN Document Server

    Luo, Shixin; Lim, Teng Joon

    2012-01-01

    In this paper, the design of a wireless communication device relying exclusively on energy harvesting is considered. Due to the inability of rechargeable energy sources to charge and discharge at the same time, a constraint we term the energy half-duplex constraint, two rechargeable energy storage devices (ESDs) are assumed so that at any given time, there is always one ESD being recharged. The energy harvesting rate is assumed to be a random variable that is constant over the time interval of interest. A save-then-transmit (ST) protocol is introduced, in which a fraction of time {\\rho} (dubbed the save-ratio) is devoted exclusively to energy harvesting, with the remaining fraction 1 - {\\rho} used for data transmission. The ratio of the energy obtainable from an ESD to the energy harvested is termed the energy storage efficiency, {\\eta}. We address the practical case of the secondary ESD being a battery with {\\eta} < 1, and the main ESD being a super-capacitor with {\\eta} = 1. The optimal save-ratio that m...

  1. Blood cell mRNAs and microRNAs: optimized protocols for extraction and preservation.

    Science.gov (United States)

    Eikmans, Michael; Rekers, Niels V; Anholts, Jacqueline D H; Heidt, Sebastiaan; Claas, Frans H J

    2013-03-14

    Assessing messenger RNA (mRNA) and microRNA levels in peripheral blood cells may complement conventional parameters in clinical practice. Working with small, precious samples requires optimal RNA yields and minimal RNA degradation. Several procedures for RNA extraction and complementary DNA (cDNA) synthesis were compared for their efficiency. The effect on RNA quality of freeze-thawing peripheral blood cells and storage in preserving reagents was investigated. In terms of RNA yield and convenience, quality quantitative polymerase chain reaction signals per nanogram of total RNA and using NucleoSpin and mirVana columns is preferable. The SuperScript III protocol results in the highest cDNA yields. During conventional procedures of storing peripheral blood cells at -180°C and thawing them thereafter, RNA integrity is maintained. TRIzol preserves RNA in cells stored at -20°C. Detection of mRNA levels significantly decreases in degraded RNA samples, whereas microRNA molecules remain relatively stable. When standardized to reference targets, mRNA transcripts and microRNAs can be reliably quantified in moderately degraded (quality index 4-7) and severely degraded (quality index blood. The results serve as a guideline for sensitive mRNA and microRNA expression assessment in clinical material.

  2. Standardization and Optimization of Computed Tomography Protocols to Achieve Low-Dose

    Science.gov (United States)

    Chin, Cynthia; Cody, Dianna D.; Gupta, Rajiv; Hess, Christopher P.; Kalra, Mannudeep K.; Kofler, James M.; Krishnam, Mayil S.; Einstein, Andrew J.

    2014-01-01

    The increase in radiation exposure due to CT scans has been of growing concern in recent years. CT scanners differ in their capabilities and various indications require unique protocols, but there remains room for standardization and optimization. In this paper we summarize approaches to reduce dose, as discussed in lectures comprising the first session of the 2013 UCSF Virtual Symposium on Radiation Safety in Computed Tomography. The experience of scanning at low dose in different body regions, for both diagnostic and interventional CT procedures, is addressed. An essential primary step is justifying the medical need for each scan. General guiding principles for reducing dose include tailoring a scan to a patient, minimizing scan length, use of tube current modulation and minimizing tube current, minimizing-tube potential, iterative reconstruction, and periodic review of CT studies. Organized efforts for standardization have been spearheaded by professional societies such as the American Association of Physicists in Medicine. Finally, all team members should demonstrate an awareness of the importance of minimizing dose. PMID:24589403

  3. A Multipath Routing Protocol Based on Clustering and Ant Colony Optimization for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Jing Yang

    2010-05-01

    Full Text Available For monitoring burst events in a kind of reactive wireless sensor networks (WSNs, a multipath routing protocol (MRP based on dynamic clustering and ant colony optimization (ACO is proposed.. Such an approach can maximize the network lifetime and reduce the energy consumption. An important attribute of WSNs is their limited power supply, and therefore some metrics (such as energy consumption of communication among nodes, residual energy, path length were considered as very important criteria while designing routing in the MRP. Firstly, a cluster head (CH is selected among nodes located in the event area according to some parameters, such as residual energy. Secondly, an improved ACO algorithm is applied in the search for multiple paths between the CH and sink node. Finally, the CH dynamically chooses a route to transmit data with a probability that depends on many path metrics, such as energy consumption. The simulation results show that MRP can prolong the network lifetime, as well as balance of energy consumption among nodes and reduce the average energy consumption effectively.

  4. An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides.

    Science.gov (United States)

    Hsieh, Yi-Wen; Alqadah, Amel; Chuang, Chiou-Fen

    2016-11-29

    Electrophoretic Mobility Shift Assays (EMSA) are an instrumental tool to characterize the interactions between proteins and their target DNA sequences. Radioactivity has been the predominant method of DNA labeling in EMSAs. However, recent advances in fluorescent dyes and scanning methods have prompted the use of fluorescent tagging of DNA as an alternative to radioactivity for the advantages of easy handling, saving time, reducing cost, and improving safety. We have recently used fluorescent EMSA (fEMSA) to successfully address an important biological question. Our fEMSA analysis provides mechanistic insight into the effect of a missense mutation, G73E, in the highly conserved HMG transcription factor SOX-2 on olfactory neuron type diversification. We found that mutant SOX-2(G73E) protein alters specific DNA binding activity, thereby causing olfactory neuron identity transformation. Here, we present an optimized and cost-effective step-by-step protocol for fEMSA using infrared fluorescent dye-labeled oligonucleotides containing the LIM-4/SOX-2 adjacent target sites and purified SOX-2 proteins (WT and mutant SOX-2(G73E) proteins) as a biological example.

  5. A Multipath Routing Protocol Based on Clustering and Ant Colony Optimization for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Jing Yang

    2009-10-01

    Full Text Available For monitoring burst events in a kind of reactive wireless sensor networks (WSNs, a multipath routing protocol (MRP based on dynamic clustering and ant colony optimization (ACO is proposed.. Such an approach can maximize the network lifetime and reduce the energy consumption. An important attribute of WSNs is its limited power supply, and therefore in MRP, some metrics (such as energy consumption of communication among nodes, residual energy, path length are considered as very important criteria while designing routing. Firstly, a cluster head (CH is selected among nodes located in the event area according to some parameters, such as residual energy. Secondly, an improved ACO algorithm is applied in search for multiple paths between the CH and sink node. Finally, the CH dynamically chooses a route to transmit data with a probability that depends on many path metrics, such as energy consumption. The simulation results show that MRP can prolong the network lifetime, as well as balance energy consumption among nodes and reduce the average energy consumption effectively.

  6. Optimal Scanning Protocols for Dual-Energy CT Angiography in Peripheral Arterial Stents: An in Vitro Phantom Study

    Directory of Open Access Journals (Sweden)

    Abdulrahman Almutairi

    2015-05-01

    Full Text Available Objective: To identify the optimal dual-energy computed tomography (DECT scanning protocol for peripheral arterial stents while achieving a low radiation dose, while still maintaining diagnostic image quality, as determined by an in vitro phantom study. Methods: Dual-energy scans in monochromatic spectral imaging mode were performed on a peripheral arterial phantom with use of three gemstone spectral imaging (GSI protocols, three pitch values, and four kiloelectron volts (keV ranges. A total of 15 stents of different sizes, materials, and designs were deployed in the phantom. Image noise, the signal-to-noise ratio (SNR, different levels of adaptive statistical iterative reconstruction (ASIR, and the four levels of monochromatic energy for DECT imaging of peripheral arterial stents were measured and compared to determine the optimal protocols. Results: A total of 36 scans with 180 datasets were reconstructed from a combination of different protocols. There was a significant reduction of image noise with a higher SNR from monochromatic energy images between 65 and 70 keV in all investigated preset GSI protocols (p < 0.05. In addition, significant effects were found from the main effect analysis for these factors: GSI, pitch, and keV (p = 0.001. In contrast, there was significant interaction on the unstented area between GSI and ASIR (p = 0.015 and a very high significant difference between keV and ASIR (p < 0.001. A radiation dose reduction of 50% was achieved. Conclusions: The optimal scanning protocol and energy level in the phantom study were GSI-48, pitch value 0.984, and 65 keV, which resulted in lower image noise and a lower radiation dose, but with acceptable diagnostic images.

  7. Optimal Scanning Protocols for Dual-Energy CT Angiography in Peripheral Arterial Stents: An in Vitro Phantom Study

    Science.gov (United States)

    Almutairi, Abdulrahman; Sun, Zhonghua; Al Safran, Zakariya; Poovathumkadavi, Abduljaleel; Albader, Suha; Ifdailat, Husam

    2015-01-01

    Objective: To identify the optimal dual-energy computed tomography (DECT) scanning protocol for peripheral arterial stents while achieving a low radiation dose, while still maintaining diagnostic image quality, as determined by an in vitro phantom study. Methods: Dual-energy scans in monochromatic spectral imaging mode were performed on a peripheral arterial phantom with use of three gemstone spectral imaging (GSI) protocols, three pitch values, and four kiloelectron volts (keV) ranges. A total of 15 stents of different sizes, materials, and designs were deployed in the phantom. Image noise, the signal-to-noise ratio (SNR), different levels of adaptive statistical iterative reconstruction (ASIR), and the four levels of monochromatic energy for DECT imaging of peripheral arterial stents were measured and compared to determine the optimal protocols. Results: A total of 36 scans with 180 datasets were reconstructed from a combination of different protocols. There was a significant reduction of image noise with a higher SNR from monochromatic energy images between 65 and 70 keV in all investigated preset GSI protocols (p < 0.05). In addition, significant effects were found from the main effect analysis for these factors: GSI, pitch, and keV (p = 0.001). In contrast, there was significant interaction on the unstented area between GSI and ASIR (p = 0.015) and a very high significant difference between keV and ASIR (p < 0.001). A radiation dose reduction of 50% was achieved. Conclusions: The optimal scanning protocol and energy level in the phantom study were GSI-48, pitch value 0.984, and 65 keV, which resulted in lower image noise and a lower radiation dose, but with acceptable diagnostic images. PMID:26006234

  8. Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues.

    Science.gov (United States)

    Kennedy, Jacob J; Whiteaker, Jeffrey R; Schoenherr, Regine M; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N; Baird, Geoffrey Stuart; Paulovich, Amanda G

    2016-08-01

    Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues. Although the feasibility of using targeted, multiple reaction monitoring mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope-labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e., nine processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R(2) = 0.94) and immuno-MRM (R(2) = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens.

  9. Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol

    Science.gov (United States)

    Foroni, Elena; Duranti, Sabrina; Turroni, Francesca; Lugli, Gabriele Andrea; Sanchez, Borja; Martín, Rebeca; Gueimonde, Miguel; van Sinderen, Douwe; Margolles, Abelardo; Ventura, Marco

    2013-01-01

    Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota. PMID:23869230

  10. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol.

    Directory of Open Access Journals (Sweden)

    Christian Milani

    Full Text Available Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.

  11. Analytical Models of Cross-Layer Protocol Optimization in Real-Time Wireless Sensor Ad Hoc Networks

    Science.gov (United States)

    Hortos, William S.

    The real-time interactions among the nodes of a wireless sensor network (WSN) to cooperatively process data from multiple sensors are modeled. Quality-of-service (QoS) metrics are associated with the quality of fused information: throughput, delay, packet error rate, etc. Multivariate point process (MVPP) models of discrete random events in WSNs establish stochastic characteristics of optimal cross-layer protocols. Discrete-event, cross-layer interactions in mobile ad hoc network (MANET) protocols have been modeled using a set of concatenated design parameters and associated resource levels by the MVPPs. Characterization of the "best" cross-layer designs for a MANET is formulated by applying the general theory of martingale representations to controlled MVPPs. Performance is described in terms of concatenated protocol parameters and controlled through conditional rates of the MVPPs. Modeling limitations to determination of closed-form solutions versus explicit iterative solutions for ad hoc WSN controls are examined.

  12. Optimal experimental scheme for practical BB84 quantum key distribution protocol with weak coherent sources, noises, and high losses

    CERN Document Server

    Cai, Q

    2005-01-01

    It is the first scheme which allows the detection apparatus to achieve the photon number of arriving signals. Moreover, quantum bit error rates (QBERs) of multiphoton pulses can also be achieved precisely. Thus, our method is sensitive to the photon number splitting and resending (PNSR) attack, i.e., the eavesdropper (Eve) replaces one photon of the multiphoton pulse by a false one and forwards the pulse to the receiver, while the decoy-state protocols are not. In our scheme, Eve's whatever attacks will be limited by using the $improved$ decoy-state protocols and by checking the QBERs. Based on our multiphoton pulses detection apparatus, a quasi-single-photon protocol is presented to improve the security of the communication and the rate of the final key. We analyze that our scheme is optimal under today's technology. PACS: 03.67.Dd

  13. Optimization protocol for the extraction of antioxidant components from Origanum vulgare leaves using response surface methodology.

    Science.gov (United States)

    Majeed, Mudasir; Hussain, Abdullah I; Chatha, Shahzad A S; Khosa, Muhammad K K; Kamal, Ghulam Mustafa; Kamal, Mohammad A; Zhang, Xu; Liu, Maili

    2016-05-01

    In the present work, the response surface methodology (RSM) based on a central composite rotatable design (CCRD), was used to determine optimum conditions for the extraction of antioxidant compounds from Origanum vulgare leaves. Four process variables were evaluated at three levels (31 experimental designs): methanol (70%, 80%, and 90%), the solute:solvent ratio (1:5, 1:12.5, 1:20), the extraction time (4, 10, 16 h), and the solute particle size (20, 65, 110 micron). Using RSM, a quadratic polynomial equation was obtained by multiple regression analysis for predicting optimization of the extraction protocol. Analysis of variance (ANOVA) was applied and the significant effect of the factors and their interactions were tested at 95% confidence interval. The antioxidant extract (AE) yield was significantly influenced by solvent composition, solute to solvent ratio, and time. The maximum AE was obtained at methanol (70%), liquid solid ratio (20), time (16 h), and particle size (20 micron). Predicted values thus obtained were closer to the experimental value indicating suitability of the model. Run 25 (methanol:water 70:30; solute:solvent 1:20; extraction time 16 h and solute particle size 20) showed highest TP contents (18.75 mg/g of dry material, measured as gallic acid equivalents) and DPPH radical scavenging activity (IC50 5.04 μg/mL). Results of the present study indicated good correlation between TP contents and DPPH radical scavenging activity. Results of the study indicated that phenolic compounds are powerful scavengers of free radical as demonstrated by a good correlation between TP contents and DPPH radical scavenging activity.

  14. Optimization and verification of the TR-MAC protocol for wireless sensor networks

    NARCIS (Netherlands)

    Morshed, Sarwar; Heijenk, Geert

    2015-01-01

    Energy-efficiency is an important requirement in the design of communication protocols for wireless sensor networks (WSN). TR-MAC is an energy-efficient medium access control (MAC) layer protocol for low power WSN that exploits transmitted-reference (TR) modulation in the physical layer. The underly

  15. Using Green Star Metrics to Optimize the Greenness of Literature Protocols for Syntheses

    Science.gov (United States)

    Duarte, Rita C. C.; Ribeiro, M. Gabriela T. C.; Machado, Adélio A. S. C.

    2015-01-01

    A procedure to improve the greenness of a synthesis, without performing laboratory work, using alternative protocols available in the literature is presented. The greenness evaluation involves the separate assessment of the different steps described in the available protocols--reaction, isolation, and purification--as well as the global process,…

  16. Computer simulation on reliability of retention index with FDG-PET and optimization of dual-time-point imaging protocol

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The inherent noise in positron emission tomography (PET) leads to the instability of quantitative indicators, which may affect the diagnostic accuracy for differentiating malignant and benign lesions in the management of lung cancer. In this paper, the reliability of retention index (RI) is systematically investigated by using computer simulation for the dual-time-point imaging protocol. The area under the receiver operating characteristic (ROC) curve is used to evaluate the optimal protocol. Results demonstrate that the reliability of RI is affected by several factors including noise level, lesion type, and imaging schedule. The Ris with small absolute values suffer from worse reliability than those larger ones. The results of ROC curves show that over delayed second scan cannot help to improve the diag- nostic performance further, while an early first scan is expected. The method of optimization based on ROC analysis can be easily extended to comprise as many lesions as possible.

  17. WIRELESS ADHOC MULTI ACCESS NETWORKS OPTIMIZATION USING OSPF ROUTING PROTOCOL BASED ON CISCO DEVICES

    Directory of Open Access Journals (Sweden)

    Mohamed E. Khedr

    2015-03-01

    Full Text Available One of the most attractive field for research for researchers and authors so the Wireless adhoc networks. So, this paper will describe the background and basic features of Open Short Path First (OSPF routing protocol due to multi-access networks. Explaining and practice on the OSPF configuration commands. Describe, modify and calculate the metric (Cost used by OSPF due to adhoc networks. Illustrating the Election parameters made by DR/BDR (Designated and Back Designated Routers used in multi-access wireless networks. This paper will use OSPF routing protocol because of its average administrative distance with all routing protocols.

  18. Optimal scanning protocols of 64-slice CT angiography in coronary artery stents: An in vitro phantom study

    Energy Technology Data Exchange (ETDEWEB)

    Almutairi, Abdulrahman Marzouq [Discipline of Medical Imaging, Department of Imaging and Applied Physics, Curtin University of Technology, Perth, Western Australia (Australia); Sun Zhonghua [Discipline of Medical Imaging, Department of Imaging and Applied Physics, Curtin University of Technology, Perth, Western Australia (Australia)], E-mail: z.sun@curtin.edu.au; Ng, Curtise [Discipline of Medical Imaging, Department of Imaging and Applied Physics, Curtin University of Technology, Perth, Western Australia (Australia); Al-Safran, Zakariya A.; Al-Mulla, Abeer A.; Al-Jamaan, Abdulaziz I. [Department of Medical Imaging, King Fahad Specialist Hospital, Dammam (Saudi Arabia)

    2010-04-15

    Purpose: The purpose of the study was to investigate the optimal scanning protocol of 64-slice CT angiography for assessment of coronary artery stents based on a phantom study. Materials and methods: Coronary stents with a diameter of 2.5 mm was implanted in thin plastic tubes with an inner diameter of 3.0 mm to simulate a coronary artery. The tubes were filled with iodinated contrast medium diluted to 178 HU, closed at both ends and positioned in a plastic container filled with vegetable oil (-70 to -100 HU). A series of scans were performed with a 64-slice CT scanner with the following protocols: section thickness: 0.67 mm, 1.0 mm, 1.5 mm, 2.0 mm, pitch value: 0.2, 0.3, 0.5 and reconstruction interval of 50% overlap of the section thickness. 2D axial and multiplanar reformatted images were generated to assess the visibility of stent lumen, while virtual intravascular endoscopy (VIE) was reconstructed to evaluate the artery wall and stent surface. Results: Our results showed that a scanning protocol of 1.0 mm slice thickness with a pitch of 0.3 produced acceptable images with best demonstration of the intrastent lumen and stent surface with minimal image noise or artifacts. In contrast, submillimeter scans with 0.67 mm resulted in moderate artifacts which affected visualization of the coronary lumen, in addition to the increased noise. When the section thickness increased to 1.5 mm and 2.0 mm, visualization of the artery wall and stent surface was compromised, although the intrastent lumen was still visible. Conclusion: Our in vitro study suggested that a scanning protocol of 1.0 mm section thickness with pitch of 0.3 is the optimal protocol for evaluation of coronary artery stents as it allows generation of acceptable images with better visualization of stent lumen, stent surface and coronary artery wall.

  19. An Optimized Energy-aware Routing Protocol for Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    Basma M. Mohammad El-Basioni

    2011-07-01

    Full Text Available Because sensor nodes typically are battery-powered and in most cases it may not be possible to change or recharge batteries, the key challenge in Wireless Sensor Networks (WSNs design is the energy-efficiency and how to deal with the trade-off between it and the QoS parameters required by some applications. This paper studies the QoS of an energy-efficient cluster-based routing protocol called Energy-Aware routing Protocol (EAP in terms of lifetime, delay, loss percentage, and throughput, and proposes some modifications on it to enhance its performance. The modified protocol offers better characteristics in terms of packets loss, delay, and throughput, but slightly affects lifetime negatively. Simulation results showed that the modified protocol significantly outperforms EAP in terms of packet loss percentage by on average 93.4%.

  20. Cross-layer protocol design for QoS optimization in real-time wireless sensor networks

    Science.gov (United States)

    Hortos, William S.

    2010-04-01

    The metrics of quality of service (QoS) for each sensor type in a wireless sensor network can be associated with metrics for multimedia that describe the quality of fused information, e.g., throughput, delay, jitter, packet error rate, information correlation, etc. These QoS metrics are typically set at the highest, or application, layer of the protocol stack to ensure that performance requirements for each type of sensor data are satisfied. Application-layer metrics, in turn, depend on the support of the lower protocol layers: session, transport, network, data link (MAC), and physical. The dependencies of the QoS metrics on the performance of the higher layers of the Open System Interconnection (OSI) reference model of the WSN protocol, together with that of the lower three layers, are the basis for a comprehensive approach to QoS optimization for multiple sensor types in a general WSN model. The cross-layer design accounts for the distributed power consumption along energy-constrained routes and their constituent nodes. Following the author's previous work, the cross-layer interactions in the WSN protocol are represented by a set of concatenated protocol parameters and enabling resource levels. The "best" cross-layer designs to achieve optimal QoS are established by applying the general theory of martingale representations to the parameterized multivariate point processes (MVPPs) for discrete random events occurring in the WSN. Adaptive control of network behavior through the cross-layer design is realized through the parametric factorization of the stochastic conditional rates of the MVPPs. The cross-layer protocol parameters for optimal QoS are determined in terms of solutions to stochastic dynamic programming conditions derived from models of transient flows for heterogeneous sensor data and aggregate information over a finite time horizon. Markov state processes, embedded within the complex combinatorial history of WSN events, are more computationally

  1. Automata-based Optimization of Interaction Protocols for Scalable Multicore Platforms (Technical Report)

    NARCIS (Netherlands)

    Jongmans, S.-S.T.Q.; Halle, S.; Arbab, F.

    2014-01-01

    Multicore platforms offer the opportunity for utilizing massively parallel resources. However, programming them is challenging. We need good compilers that optimize commonly occurring synchronization/interaction patterns. To facilitate optimization, a programming language must convey what needs to b

  2. An optimized chloroplast DNA extraction protocol for grasses (Poaceae proves suitable for whole plastid genome sequencing and SNP detection.

    Directory of Open Access Journals (Sweden)

    Kerstin Diekmann

    Full Text Available BACKGROUND: Obtaining chloroplast genome sequences is important to increase the knowledge about the fundamental biology of plastids, to understand evolutionary and ecological processes in the evolution of plants, to develop biotechnological applications (e.g. plastid engineering and to improve the efficiency of breeding schemes. Extraction of pure chloroplast DNA is required for efficient sequencing of chloroplast genomes. Unfortunately, most protocols for extracting chloroplast DNA were developed for eudicots and do not produce sufficiently pure yields for a shotgun sequencing approach of whole plastid genomes from the monocot grasses. METHODOLOGY/PRINCIPAL FINDINGS: We have developed a simple and inexpensive method to obtain chloroplast DNA from grass species by modifying and extending protocols optimized for the use in eudicots. Many protocols for extracting chloroplast DNA require an ultracentrifugation step to efficiently separate chloroplast DNA from nuclear DNA. The developed method uses two more centrifugation steps than previously reported protocols and does not require an ultracentrifuge. CONCLUSIONS/SIGNIFICANCE: The described method delivered chloroplast DNA of very high quality from two grass species belonging to highly different taxonomic subfamilies within the grass family (Lolium perenne, Pooideae; Miscanthus x giganteus, Panicoideae. The DNA from Lolium perenne was used for whole chloroplast genome sequencing and detection of SNPs. The sequence is publicly available on EMBL/GenBank.

  3. Dye purity and dye standardization for biological staining

    DEFF Research Database (Denmark)

    Lyon, H O

    2002-01-01

    for separating, identifying and assaying dye components. In the second part of the review, descriptions are given of the standardized staining method approach using standard staining methods for assessing stains, and practical responses to stain impurity including commercial quality control, third-party quality...... control and standardization of reagents, protocols and documentation. Finally, reference is made to the current state of affairs in the dye field....

  4. Time-saving design of experiment protocol for optimization of LC-MS data processing in metabolomic approaches.

    Science.gov (United States)

    Zheng, Hong; Clausen, Morten Rahr; Dalsgaard, Trine Kastrup; Mortensen, Grith; Bertram, Hanne Christine

    2013-08-06

    We describe a time-saving protocol for the processing of LC-MS-based metabolomics data by optimizing parameter settings in XCMS and threshold settings for removing noisy and low-intensity peaks using design of experiment (DoE) approaches including Plackett-Burman design (PBD) for screening and central composite design (CCD) for optimization. A reliability index, which is based on evaluation of the linear response to a dilution series, was used as a parameter for the assessment of data quality. After identifying the significant parameters in the XCMS software by PBD, CCD was applied to determine their values by maximizing the reliability and group indexes. Optimal settings by DoE resulted in improvements of 19.4% and 54.7% in the reliability index for a standard mixture and human urine, respectively, as compared with the default setting, and a total of 38 h was required to complete the optimization. Moreover, threshold settings were optimized by using CCD for further improvement. The approach combining optimal parameter setting and the threshold method improved the reliability index about 9.5 times for a standards mixture and 14.5 times for human urine data, which required a total of 41 h. Validation results also showed improvements in the reliability index of about 5-7 times even for urine samples from different subjects. It is concluded that the proposed methodology can be used as a time-saving approach for improving the processing of LC-MS-based metabolomics data.

  5. CANopen协议总线负载优化的研究%Research on Bus Load Optimization of CANopen protocol

    Institute of Scientific and Technical Information of China (English)

    冯化

    2016-01-01

    The paper introduces CAN and CANopen protocol, and describes the bus load of CANopen protocol in detail. A method is pro-posed to optimize the bus load through the setting of bus communication rate and PDO communication type. The actual results prove that this method can effectively control the bus load.%介绍了CAN和CANopen协议,并对CANopen协议的总线负载进行了详细的描述,提出了通过总线通信速率和PDO通信类型的设置对总线负载进行优化的方法,实际证明该方法可以有效的控制总线负载。

  6. Economic comparison of common treatment protocols and J5 vaccination for clinical mastitis in dairy herds using optimized culling decisions.

    Science.gov (United States)

    Kessels, J A; Cha, E; Johnson, S K; Welcome, F L; Kristensen, A R; Gröhn, Y T

    2016-05-01

    This study used an existing dynamic optimization model to compare costs of common treatment protocols and J5 vaccination for clinical mastitis in US dairy herds. Clinical mastitis is an infection of the mammary gland causing major economic losses in dairy herds due to reduced milk production, reduced conception, and increased risk of mortality and culling for infected cows. Treatment protocols were developed to reflect common practices in dairy herds. These included targeted therapy following pathogen identification, and therapy without pathogen identification using a broad-spectrum antimicrobial or treating with the cheapest treatment option. The cost-benefit of J5 vaccination was also estimated. Effects of treatment were accounted for as changes in treatment costs, milk loss due to mastitis, milk discarded due to treatment, and mortality. Following ineffective treatments, secondary decisions included extending the current treatment, alternative treatment, discontinuing treatment, and pathogen identification followed by recommended treatment. Average net returns for treatment protocols and vaccination were generated using an existing dynamic programming model. This model incorporates cow and pathogen characteristics to optimize management decisions to treat, inseminate, or cull cows. Of the treatment protocols where 100% of cows received recommended treatment, pathogen-specific identification followed by recommended therapy yielded the highest average net returns per cow per year. Out of all treatment scenarios, the highest net returns were achieved with selecting the cheapest treatment option and discontinuing treatment, or alternate treatment with a similar spectrum therapy; however, this may not account for the full consequences of giving nonrecommended therapies to cows with clinical mastitis. Vaccination increased average net returns in all scenarios. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  7. Optimized QKD BB84 protocol using quantum dense coding and CNOT gates: feasibility based on probabilistic optical devices

    Science.gov (United States)

    Gueddana, Amor; Attia, Moez; Chatta, Rihab

    2014-05-01

    In this work, we simulate a fiber-based Quantum Key Distribution Protocol (QKDP) BB84 working at the telecoms wavelength 1550 nm with taking into consideration an optimized attack strategy. We consider in our work a quantum channel composed by probabilistic Single Photon Source (SPS), single mode optical Fiber and quantum detector with high efficiency. We show the advantages of using the Quantum Dots (QD) embedded in micro-cavity compared to the Heralded Single Photon Sources (HSPS). Second, we show that Eve is always getting some information depending on the mean photon number per pulse of the used SPS and therefore, we propose an optimized version of the QKDP BB84 based on Quantum Dense Coding (QDC) that could be implemented by quantum CNOT gates. We evaluate the success probability of implementing the optimized QKDP BB84 when using nowadays probabilistic quantum optical devices for circuit realization. We use for our modeling an abstract probabilistic model of a CNOT gate based on linear optical components and having a success probability of sqrt (4/27), we take into consideration the best SPSs realizations, namely the QD and the HSPS, generating a single photon per pulse with a success probability of 0.73 and 0.37, respectively. We show that the protocol is totally secure against attacks but could be correctly implemented only with a success probability of few percent.

  8. Port-wine stain

    Science.gov (United States)

    Many treatments have been tried for port-wine stains, including freezing, surgery, radiation, and tattooing. Laser therapy is most successful in eliminating port-wine stains. It is the only method that can destroy the tiny blood vessels in the skin ...

  9. Two-phase helical hepatic CT. Contrast-injection protocol, optimal timing and its usefulness in clinical cases

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Rie [Univ. of Occupational and Environmental Health, Kitakyushu, Fukuoka (Japan)

    1998-03-01

    The usefulness of two-phase helical computed tomography (CT) of the liver was evaluated in clinical cases. First, an optimal scanning protocol was determined using time-attenuation analysis. Monophasic dynamic CT was performed with 100 ml of contrast media (iodine 300 mg/ml) injected either at 3 ml/s or at 2 ml/s. Aortic, hepatic and portal time-attenuation curves were made for each protocol. The results showed that these two different injection protocols produce equivalent enhancements and that the injection rate of 2 ml/s is satisfactorily applicable to clinical cases. The first scanning (arterial phase) must be started 40-45 s after the beginning of the injection of contrast media and the second scanning (delayed phase) 80-120 s after the beginning of injection. Using these CT protocols, 327 cases were examined. In this study 83 hepatic lesions (hepatocellular carcinoma; HCC, n=29; suspected HCC, n=30; hemangioma, n=24) were evaluated. There were 15 HCCs smaller than 30 mm in diameter (71.4%) detected by either arterial phase or delayed phase alone. This result indicates that two-phase helical hepatic CT is very useful in the detection of small HCC. Particularly, four or 5 HCCs of less than 10 mm in size (80%) showed a hyperattenuation area in the arterial phase alone. HCCs which have sufficient vascularity were also easily demonstrated. However, this two-phase helical hepatic CT could not demonstrate 11 lesions (13.3%) with almost normal blood supply. In such cases the complementary role of ultrasound (US) seems to be important. Hence as a screening of hepatic mass lesions both CT and US are necessary. Most HCC could be differentiated from hemangioma by an enhancement pattern using this protocol. But the small liver lesions of less than 15 mm in size with homogeneous hyperattenuation in the arterial phase and isoattenuation in the delayed phase included HCC, hemangioma and metastatic tumors. (author)

  10. Comparison and optimization of hiPSC forebrain cortical differentiation protocols.

    Science.gov (United States)

    Muratore, Christina R; Srikanth, Priya; Callahan, Dana G; Young-Pearse, Tracy L

    2014-01-01

    Several protocols have been developed for human induced pluripotent stem cell neuronal differentiation. We compare several methods for forebrain cortical neuronal differentiation by assessing cell morphology, immunostaining and gene expression. We evaluate embryoid aggregate vs. monolayer with dual SMAD inhibition differentiation protocols, manual vs. AggreWell aggregate formation, plating substrates, neural progenitor cell (NPC) isolation methods, NPC maintenance and expansion, and astrocyte co-culture. The embryoid aggregate protocol, using a Matrigel substrate, consistently generates a high yield and purity of neurons. NPC isolation by manual selection, enzymatic rosette selection, or FACS all are efficient, but exhibit some differences in resulting cell populations. Expansion of NPCs as neural aggregates yields higher cell purity than expansion in a monolayer. Finally, co-culture of iPSC-derived neurons with astrocytes increases neuronal maturity by day 40. This study directly compares commonly employed methods for neuronal differentiation of iPSCs, and can be used as a resource for choosing between various differentiation protocols.

  11. Comparison and optimization of hiPSC forebrain cortical differentiation protocols.

    Directory of Open Access Journals (Sweden)

    Christina R Muratore

    Full Text Available Several protocols have been developed for human induced pluripotent stem cell neuronal differentiation. We compare several methods for forebrain cortical neuronal differentiation by assessing cell morphology, immunostaining and gene expression. We evaluate embryoid aggregate vs. monolayer with dual SMAD inhibition differentiation protocols, manual vs. AggreWell aggregate formation, plating substrates, neural progenitor cell (NPC isolation methods, NPC maintenance and expansion, and astrocyte co-culture. The embryoid aggregate protocol, using a Matrigel substrate, consistently generates a high yield and purity of neurons. NPC isolation by manual selection, enzymatic rosette selection, or FACS all are efficient, but exhibit some differences in resulting cell populations. Expansion of NPCs as neural aggregates yields higher cell purity than expansion in a monolayer. Finally, co-culture of iPSC-derived neurons with astrocytes increases neuronal maturity by day 40. This study directly compares commonly employed methods for neuronal differentiation of iPSCs, and can be used as a resource for choosing between various differentiation protocols.

  12. Energy Optimization for Wireless Sensor Networks using a Novel Dynamic Multicast Routing Protocol

    Directory of Open Access Journals (Sweden)

    S. Sundar Raj

    2014-07-01

    Full Text Available Minimization of energy consumption has always been the predominant factor deciding the acceptability of a routing protocol for wireless ad-hoc networks. In this study we have proposed a novel efficient multicast routing protocols in wireless mobile ad hoc networks is proposed. Due to the high mobility of nodes and highly dynamic topology, performing efficient and robust multicast in a Mobile Ad hoc Network (MANET is a challenging task. Most of existing multicast protocols in MANETs discover the routing path by flooding message over the whole network, which result in considerable cost for routing discovery and maintenance. Moreover, the reliability of the discovered path cannot be guaranteed, since the stabilities of nodes along such path are unpredictable. Here an attempt is made to devise an algorithm combining the features of both energy efficient and low latency algorithms. The new algorithm is intended to do well in real-world scenarios where the energy capacities of the nodes are not uniform. It employs a mobility prediction based election process to construct a reliable backbone structure performing packet transmission, message flooding, routing discovery and maintenance. Several virtual architectures are used in the protocol without need of maintaining state information for more robust and scalable membership management and packet forwarding in the presence of high network dynamics due to unstable wireless channels and node movements.

  13. Acute beneficial hemodynamic effects of a novel 3D-echocardiographic optimization protocol in cardiac resynchronization therapy.

    Directory of Open Access Journals (Sweden)

    Carolin Sonne

    , individualized echocardiographic optimization with the integration of 3-dimensional indices into the optimization protocol acutely improved LV systolic function and decreased ESV and can be used to select the optimal AV delay and VV interval in CRT.

  14. Active SAmpling Protocol (ASAP) to Optimize Individual Neurocognitive Hypothesis Testing: A BCI-Inspired Dynamic Experimental Design.

    Science.gov (United States)

    Sanchez, Gaëtan; Lecaignard, Françoise; Otman, Anatole; Maby, Emmanuel; Mattout, Jérémie

    2016-01-01

    The relatively young field of Brain-Computer Interfaces has promoted the use of electrophysiology and neuroimaging in real-time. In the meantime, cognitive neuroscience studies, which make extensive use of functional exploration techniques, have evolved toward model-based experiments and fine hypothesis testing protocols. Although these two developments are mostly unrelated, we argue that, brought together, they may trigger an important shift in the way experimental paradigms are being designed, which should prove fruitful to both endeavors. This change simply consists in using real-time neuroimaging in order to optimize advanced neurocognitive hypothesis testing. We refer to this new approach as the instantiation of an Active SAmpling Protocol (ASAP). As opposed to classical (static) experimental protocols, ASAP implements online model comparison, enabling the optimization of design parameters (e.g., stimuli) during the course of data acquisition. This follows the well-known principle of sequential hypothesis testing. What is radically new, however, is our ability to perform online processing of the huge amount of complex data that brain imaging techniques provide. This is all the more relevant at a time when physiological and psychological processes are beginning to be approached using more realistic, generative models which may be difficult to tease apart empirically. Based upon Bayesian inference, ASAP proposes a generic and principled way to optimize experimental design adaptively. In this perspective paper, we summarize the main steps in ASAP. Using synthetic data we illustrate its superiority in selecting the right perceptual model compared to a classical design. Finally, we briefly discuss its future potential for basic and clinical neuroscience as well as some remaining challenges.

  15. Optimizing the MAC Protocol in Localization Systems Based on IEEE 802.15.4 Networks

    Directory of Open Access Journals (Sweden)

    Juan J. Pérez-Solano

    2017-07-01

    Full Text Available Radio frequency signals are commonly used in the development of indoor localization systems. The infrastructure of these systems includes some beacons placed at known positions that exchange radio packets with users to be located. When the system is implemented using wireless sensor networks, the wireless transceivers integrated in the network motes are usually based on the IEEE 802.15.4 standard. But, the CSMA-CA, which is the basis for the medium access protocols in this category of communication systems, is not suitable when several users want to exchange bursts of radio packets with the same beacon to acquire the radio signal strength indicator (RSSI values needed in the location process. Therefore, new protocols are necessary to avoid the packet collisions that appear when multiple users try to communicate with the same beacons. On the other hand, the RSSI sampling process should be carried out very quickly because some systems cannot tolerate a large delay in the location process. This is even more important when the RSSI sampling process includes measures with different signal power levels or frequency channels. The principal objective of this work is to speed up the RSSI sampling process in indoor localization systems. To achieve this objective, the main contribution is the proposal of a new MAC protocol that eliminates the medium access contention periods and decreases the number of packet collisions to accelerate the RSSI collection process. Moreover, the protocol increases the overall network throughput taking advantage of the frequency channel diversity. The presented results show the suitability of this protocol for reducing the RSSI gathering delay and increasing the network throughput in simulated and real environments.

  16. Optimizing the MAC Protocol in Localization Systems Based on IEEE 802.15.4 Networks.

    Science.gov (United States)

    Pérez-Solano, Juan J; Claver, Jose M; Ezpeleta, Santiago

    2017-07-06

    Radio frequency signals are commonly used in the development of indoor localization systems. The infrastructure of these systems includes some beacons placed at known positions that exchange radio packets with users to be located. When the system is implemented using wireless sensor networks, the wireless transceivers integrated in the network motes are usually based on the IEEE 802.15.4 standard. But, the CSMA-CA, which is the basis for the medium access protocols in this category of communication systems, is not suitable when several users want to exchange bursts of radio packets with the same beacon to acquire the radio signal strength indicator (RSSI) values needed in the location process. Therefore, new protocols are necessary to avoid the packet collisions that appear when multiple users try to communicate with the same beacons. On the other hand, the RSSI sampling process should be carried out very quickly because some systems cannot tolerate a large delay in the location process. This is even more important when the RSSI sampling process includes measures with different signal power levels or frequency channels. The principal objective of this work is to speed up the RSSI sampling process in indoor localization systems. To achieve this objective, the main contribution is the proposal of a new MAC protocol that eliminates the medium access contention periods and decreases the number of packet collisions to accelerate the RSSI collection process. Moreover, the protocol increases the overall network throughput taking advantage of the frequency channel diversity. The presented results show the suitability of this protocol for reducing the RSSI gathering delay and increasing the network throughput in simulated and real environments.

  17. Optimization of an amplification protocol for misfolded proteins by using relaxed control.

    Science.gov (United States)

    Coron, Jean-Michel; Gabriel, Pierre; Shang, Peipei

    2015-01-01

    We investigate an optimal control problem which arises in the optimization of an amplification technique for misfolded proteins. The improvement of this technique may play a role in the detection of prion diseases. The model consists in a linear system of differential equations with a nonlinear control. The appearance of oscillations in the numerical simulations is understood by using the Perron and Floquet eigenvalue theory for nonnegative irreducible matrices. Then to overcome the unsolvability of the optimal control, we relax the problem. In the two dimensional case, we solve explicitly the optimal relaxed control problem when the final time is large enough.

  18. Optimization of Protocol CT, PET-CT, whole body; Optimizacion de protocolo CT, en PET-CT, de cuerpo entero

    Energy Technology Data Exchange (ETDEWEB)

    Gutierrez, Fredys Santos, E-mail: fsantos@ccss.sa.cr [Caja Costarricense de Seguro Social (ACCPR/CCSS), San Jose (Costa Rica). Area Control de Calidade Y Proteccion Radiologica; Namias, Mauro, E-mail: mnamias@gmail.com [Comision Nacional de Energia Atomica (FCDN/CNEA), Buenos Aires (Argentina). Fundacion Centro Diagnostico Nuclear

    2013-11-01

    The objective of this study was to optimize the acquisition protocols and processing existing of the CT PET/CT scanner for clinical use of Nuclear Diagnostic Center Foundation, a way to minimize the radiation dose while maintaining diagnostic image quality properly. Dosimetric data of PET / CT service were surveyed and obtained the baseline against which we compare and define strategies and modifications to develop online. We selected transaxial up to the pulmonary hilum and liver slices as the anatomical regions of interest that led to the standardization of the study.

  19. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology1

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    • Premise of the study: We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • Methods and Results: We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • Conclusions: The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes. PMID:25202476

  20. Optimizing Libraries’ Content Findability Using Simple Object Access Protocol (SOAP) With Multi-Tier Architecture

    Science.gov (United States)

    Lahinta, A.; Haris, I.; Abdillah, T.

    2017-03-01

    The aim of this paper is to describe a developed application of Simple Object Access Protocol (SOAP) as a model for improving libraries’ digital content findability on the library web. The study applies XML text-based protocol tools in the collection of data about libraries’ visibility performance in the search results of the book. Model from the integrated Web Service Document Language (WSDL) and Universal Description, Discovery and Integration (UDDI) are applied to analyse SOAP as element within the system. The results showed that the developed application of SOAP with multi-tier architecture can help people simply access the website in the library server Gorontalo Province and support access to digital collections, subscription databases, and library catalogs in each library in Regency or City in Gorontalo Province.

  1. An algorithm for optimal fusion of atlases with different labeling protocols

    DEFF Research Database (Denmark)

    Eugenio Iglesias, Juan; Sabuncu, Mert Rory; Aganj, Iman

    2015-01-01

    the generalizations of majority voting, semi-locally weighted voting and STAPLE (mean Dice score 83%, vs. 77%, 80% and 79%, respectively). We also evaluated the proposed algorithm in an aging study, successfully reproducing some well-known results in cortical and subcortical structures. (C) 2014 The Authors......In this paper we present a novel label fusion algorithm suited for scenarios in which different manual delineation protocols with potentially disparate structures have been used to annotate the training scans (hereafter referred to as "atlases"). Such scenarios arise when atlases have missing...... structures, when they have been labeled with different levels of detail, or when they have been taken from different heterogeneous databases. The proposed algorithm can be used to automatically label a novel scan with any of the protocols from the training data. Further, it enables us to generate new labels...

  2. Size-based protocol optimization using automatic tube current modulation and automatic kV selection in computed tomography.

    Science.gov (United States)

    MacDougall, Robert D; Kleinman, Patricia L; Callahan, Michael J

    2016-01-08

    Size-based diagnostic reference ranges (DRRs) for contrast-enhanced pediatric abdominal computed tomography (CT) have been published in order to establish practical upper and lower limits of CTDI, DLP, and SSDE. Based on these DRRs, guidelines for establishing size-based SSDE target levels from the SSDE of a standard adult by applying a linear correction factor have been published and provide a great reference for dose optimization initiatives. The necessary step of designing manufacturer-specific CT protocols to achieve established SSDE targets is the responsibility of the Qualified Medical Physicist. The task is straightforward if fixed-mA protocols are used, however, more difficult when automatic exposure control (AEC) and automatic kV selection are considered. In such cases, the physicist must deduce the operation of AEC algorithms from technical documentation or through testing, using a wide range of phantom sizes. Our study presents the results of such testing using anthropomorphic phantoms ranging in size from the newborn to the obese adult. The effect of each user-controlled parameter was modeled for a single-manufacturer AEC algorithm (Siemens CARE Dose4D) and automatic kV selection algorithm (Siemens CARE kV). Based on the results presented in this study, a process for designing mA-modulated, pediatric abdominal CT protocols that achieve user-defined SSDE and kV targets is described.

  3. Mesenchymal Stem Cells for Regenerative Therapy: Optimization of Cell Preparation Protocols

    Directory of Open Access Journals (Sweden)

    Chiho Ikebe

    2014-01-01

    Full Text Available Administration of bone marrow-derived mesenchymal stem cells (MSCs is an innovative approach for the treatment of a range of diseases that are not curable by current therapies including heart failure. A number of clinical trials have been completed and many others are ongoing; more than 2,000 patients worldwide have been administered with culture-expanded allogeneic or autologous MSCs for the treatment of various diseases, showing feasibility and safety (and some efficacy of this approach. However, protocols for isolation and expansion of donor MSCs vary widely between these trials, which could affect the efficacy of the therapy. It is therefore important to develop international standards of MSC production, which should be evidence-based, regulatory authority-compliant, of good medical practice grade, cost-effective, and clinically practical, so that this innovative approach becomes an established widely adopted treatment. This review article summarizes protocols to isolate and expand bone marrow-derived MSCs in 47 recent clinical trials of MSC-based therapy, which were published after 2007 onwards and provided sufficient methodological information. Identified issues and possible solutions associated with the MSC production methods, including materials and protocols for isolation and expansion, are discussed with reference to relevant experimental evidence with aim of future clinical success of MSC-based therapy.

  4. Lead optimization through VLAK protocol: new annelated pyrrolo-pyrimidine derivatives as antitumor agents.

    Science.gov (United States)

    Lauria, Antonino; Patella, Chiara; Abbate, Ilenia; Martorana, Annamaria; Almerico, Anna Maria

    2012-09-01

    The chemometric protocol VLAK was applied to predict improvement of the biological activity of pyrrolo-pyrimidine derivatives as anticancer agents, by using the NCI ACAM Database as depository of antitumor drugs with a known mechanism of action. Among the selected compounds two of these showed a good increase in the antitumor activity. These new pyrrolo-pyrimidine compounds were demonstrated effective against the full panels of NCI DTP tumour human cell lines. The derivative 8-[3-(piperidino)propyl]-4,10-dimethyl-9-phenyl-6-(methylsulfanyl)-3,4-dihydropyrimido[1,2-c]pyrrolo[3,2-e]pyrimidin-2(8H)-one reveled efficacious against the leukemia subpanel, in particular the RPMI cell line resulted the most sensitive (pGI(50) = 6.68). Moreover the derivative 7-(3-Chloropropyl)-9-methyl-5-(methylsulfanyl)-8-phenyl-3H-imidazo[1,2-c]pyrrolo[3,2-e]pyrimidin-2(7H)-one showed a good antitumor activity against the leukemia subpanel with a low cytotoxic activity, above all against the HCT11 human tumour cell line. The VLAK protocol revealed a good method to design new molecules with good antitumor activity, starting from low active compounds. Moreover this protocol focused on the pyrrolo-pyrimidine derivatives as useful starting point for further development to obtain more potent antitumor agents.

  5. Low-radiation-dose dual-phase MDCT protocol with split contrast media dose and time optimization: protocol design for renal donors evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Bazeed, Mohamed Fayez (Dept. of Diagnostic Radiology, Faculty of Medicine, Mansoura Univ. (Egypt)), email: bazeed@mans.eun.eg; Fooshang, Fawzy F (National Inst. of Urology and Nephrology (Egypt)); Ahmed, Magdy Aly (Nephrology Dept., Armed Forces Hospitals Southern Region (Saudi Arabia))

    2011-10-15

    Background A routine, multiphase, computed tomography (CT) protocol is associated with high radiation exposure to potential kidney donors. To reduce radiation exposure, several authors have suggested a reduction in the number of phases. Purpose To evaluate a low-radiation-dose, dual-phase protocol (i.e. a protocol with an unenhanced phase and combined vascular and excretory phase) for the preoperative evaluation of potential renal donors. Material and Methods Sixty-five potential renal donors were divided into two groups. The first group was scanned with a routine quadric-phase protocol (non-contrast, arterial, venous, and delayed), and the second group was scanned with a triple-phase protocol (dual phase protocol + venous phase). In the second group, we replaced CT angiography with a routine abdominal CT technique. In addition to the evaluation of renal arteries, veins, and excretory systems, the radiation dose of the suggested protocol was compared to that of the routine quadric-phase protocol. Results The suggested protocol was efficient in the evaluation of renal arteries, veins, and excretory systems in all studied potential renal donors. Renal arteries were well visualized in the combined vascular excretory phase using the routine abdominal CT technique; no significant difference was noted when these results were compared to those obtained from the CT angiography used in the quadric-phase protocol. The mean effective radiation dose of our suggested dual-phase protocol was only 34% of the dose resulting from the routine quadric-phase protocol. Conclusion Use of a low-radiation, dual-phase, CT protocol, which relied on both an unenhanced phase and a combined vascular and excretory phase, significantly reduced radiation dose. Furthermore, the proposed protocol provides adequate visualization of renal arteries and veins, and affords sufficient opacification of the urinary tract using improved acquisition triggering

  6. Optimization of the imaging quality of 64-slice CT acquisition protocol using Taguchi analysis: A phantom study.

    Science.gov (United States)

    Pan, Lung Fa; Erdene, Erdenetsetseg; Chen, Chun Chi; Pan, Lung Kwang

    2015-01-01

    In this study, the phantom imaging quality of 64-slice CT acquisition protocol was quantitatively evaluated using Taguchi. The phantom acrylic line group was designed and assembled with multiple layers of solid water plate in order to imitate the adult abdomen, and scanned with Philips brilliance CT in order to simulate a clinical examination. According to the Taguchi L8(2(7)) orthogonal array, four major factors of the acquisition protocol were optimized, including (A) CT slice thickness, (B) the image reconstruction filter type, (C) the spiral CT pitch, and (D) the matrix size. The reconstructed line group phantom image was counted by four radiologists for three discrete rounds in order to obtain the averages and standard deviations of the line counts and the corresponding signal to noise ratios (S/N). The quantified S/N values were analyzed and the optimal combination of the four factor settings was determined to be comprised of (A) a 1-mm thickness, (B) a sharp filter type, (C) a 1.172 spiral CT pitch, and (D) a 1024×1024 matrix size. The dominant factors included the (A) filter type and the cross interaction between the filter type and CT slice thickness (A×B). The minor factors were determined to be (C) the spiral CT pitch and (D) the matrix size since neither was capable of yielding a 95% confidence level in the ANOVA test.

  7. Pericardial fluid Gram stain

    Science.gov (United States)

    ... staining a sample of fluid taken from the pericardium. This is the sac surrounding the heart to ... sample of fluid will be taken from the pericardium. This is done through a procedure called pericardiocentesis . ...

  8. Proposal of a quantitative PCR-based protocol for an optimal Pseudomonas aeruginosa detection in patients with cystic fibrosis.

    Science.gov (United States)

    Le Gall, Florence; Le Berre, Rozenn; Rosec, Sylvain; Hardy, Jeanne; Gouriou, Stéphanie; Boisramé-Gastrin, Sylvie; Vallet, Sophie; Rault, Gilles; Payan, Christopher; Héry-Arnaud, Geneviève

    2013-06-21

    The lung of patients with cystic fibrosis (CF) is particularly sensitive to Pseudomonas aeruginosa. This bacterium plays an important role in the poor outcome of CF patients. During the disease progress, first acquisition of P. aeruginosa is the key-step in the management of CF patients. Quantitative PCR (qPCR) offers an opportunity to detect earlier the first acquisition of P. aeruginosa by CF patients. Given the lack of a validated protocol, our goal was to find an optimal molecular protocol for detection of P. aeruginosa in CF patients. We compared two formerly described qPCR formats in early detection of P. aeruginosa in CF sputum samples: a qPCR targeting oprL gene, and a multiplex PCR targeting gyrB and ecfX genes. Tested in vitro on a large panel of P. aeruginosa isolates and others gram-negative bacilli, oprL qPCR exhibited a better sensitivity (threshold of 10 CFU/mL versus 730 CFU/mL), whereas the gyrB/ecfX qPCR exhibited a better specificity (90% versus 73%). These results were validated ex vivo on 46 CF sputum samples positive for P. aeruginosa in culture. Ex vivo assays revealed that qPCR detected 100 times more bacterial cells than culture-based method did. Based on these results, we proposed a reference molecular protocol combining the two qPCRs, which offers a sensitivity of 100% with a threshold of 10 CFU/mL and a specificity of 100%. This combined qPCR-based protocol can be adapted and used for other future prospective studies.

  9. Flow cytometric 96-well microplate-based in vitro micronucleus assay with human TK6 cells: protocol optimization and transferability assessment.

    Science.gov (United States)

    Bryce, Steven M; Avlasevich, Svetlana L; Bemis, Jeffrey C; Tate, Matthew; Walmsley, Richard M; Saad, Frédéric; Van Dijck, Kris; De Boeck, Marlies; Van Goethem, Freddy; Lukamowicz-Rajska, Magdalena; Elhajouji, Azeddine; Dertinger, Stephen D

    2013-04-01

    An automated approach for scoring in vitro micronuclei (MN) has been described in which flow cytometric analysis is combined with compound exposure, processing, and sampling in a single 96-well plate (Bryce SM et al. [2010]: Mutat Res 703:191-199). The current report describes protocol optimization and an interlaboratory assessment of the assay's transferability and reproducibility. In a training phase, the methodology was refined and collaborating laboratories were qualified by repeatedly testing three compounds. Second, a set of 32 chemicals comprised of reference genotoxicants and presumed non-genotoxicants was tested at each of four sites. TK6 cells were exposed to 10 closely spaced compound concentrations for 1.5- to 2-cell population doublings, and were then stained and lysed for flow cytometric analysis. MN frequencies were determined by evaluating ≥ 5,000 cells per replicate well, and several indices of cytotoxicity were acquired. The prevalence of positive results varied according to the MN-fold increase used to signify a genotoxic result, as well as the endpoint used to define a cytotoxicity limit. By varying these parameters, assay sensitivity and specificity values ranged from 82 to 98%, and 86 to 97%, respectively. In a third phase, one laboratory tested a further six genotoxicants and five non-genotoxic apoptosis inducers. In these experiments assay specificity was markedly improved when top concentration selection was based on two cytotoxicity endpoints-relative survival and quantification of ethidium monoazide-positive events. Collectively, the results indicate that the miniaturized assay is transferable across laboratories. The 96-well format consumes considerably less compound than conventional in vitro MN test methods, and the high information content provided by flow cytometry helps guard against irrelevant positive results arising from overt toxicity.

  10. Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues.

    Science.gov (United States)

    Belder, Nevin; Coşkun, Öznur; Erdoğan, Beyza Doğanay; Savaş, Berna; Ensari, Arzu; Özdağ, Hilal

    2016-03-01

    Formalin-fixed paraffin-embedded (FFPE) tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013) [1]; Scicchitano et al., Scicchitano et al. (2006) [2]; Frank et al., Frank et al. (2007) [3]; Fedorowicz et al., Fedorowicz et al. (2009) [4]). However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO) database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples.

  11. Secured Communication for Business Process Outsourcing Using Optimized Arithmetic Cryptography Protocol Based on Virtual Parties

    Science.gov (United States)

    Pathak, Rohit; Joshi, Satyadhar

    Within a span of over a decade, India has become one of the most favored destinations across the world for Business Process Outsourcing (BPO) operations. India has rapidly achieved the status of being the most preferred destination for BPO for companies located in the US and Europe. Security and privacy are the two major issues needed to be addressed by the Indian software industry to have an increased and long-term outsourcing contract from the US. Another important issue is about sharing employee’s information to ensure that data and vital information of an outsourcing company is secured and protected. To ensure that the confidentiality of a client’s information is maintained, BPOs need to implement some data security measures. In this paper, we propose a new protocol for specifically for BPO Secure Multi-Party Computation (SMC). As there are many computations and surveys which involve confidential data from many parties or organizations and the concerned data is property of the organization, preservation and security of this data is of prime importance for such type of computations. Although the computation requires data from all the parties, but none of the associated parties would want to reveal their data to the other parties. We have proposed a new efficient and scalable protocol to perform computation on encrypted information. The information is encrypted in a manner that it does not affect the result of the computation. It uses modifier tokens which are distributed among virtual parties, and finally used in the computation. The computation function uses the acquired data and modifier tokens to compute right result from the encrypted data. Thus without revealing the data, right result can be computed and privacy of the parties is maintained. We have given a probabilistic security analysis of hacking the protocol and shown how zero hacking security can be achieved. Also we have analyzed the specific case of Indian BPO.

  12. Optimization of gene expression microarray protocol for formalin-fixed paraffin-embedded tissues

    Directory of Open Access Journals (Sweden)

    Nevin Belder

    2016-03-01

    Full Text Available Formalin-fixed paraffin-embedded (FFPE tissue is a widely available clinical specimen for retrospective studies. The possibility of long-term clinical follow-up of FFPE samples makes them a valuable source to evaluate links between molecular and clinical information. Working with FFPE samples in the molecular research area, especially using high-throughput molecular techniques such as microarray gene expression profiling, has come into prominence. Because of the harmful effects of formalin fixation process such as degradation of nucleic acids, cross-linking with proteins, and chemical modifications on DNA and RNA, there are some limitations in gene expression profiling studies using FFPE samples. To date many studies have been conducted to evaluate gene expression profiling using microarrays (Thomas et al., Thomas et al. (2013 [1]; Scicchitano et al., Scicchitano et al. (2006 [2]; Frank et al., Frank et al. (2007 [3]; Fedorowicz et al., Fedorowicz et al. (2009 [4]. However, there is still no generally accepted, efficient and standardized procedure for microarray analysis of FFPE samples. This paper describes the microarray data presented in our recently accepted to be published article showing a standard protocol from deparaffinization of FFPE tissue sections and RNA extraction to microarray gene expression analysis. Here we represent our data in detail, deposited in the gene expression omnibus (GEO database with the accession number GSE73883. Four combinations of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P were evaluated to determine which combination gives the best percentage of present call. The study presents a dataset for comparative analysis which has a potential in terms of providing a robust protocol for gene expression profiling with FFPE tissue samples.

  13. Optimizing the ASC WAN: evaluating network performance tools for comparing transport protocols.

    Energy Technology Data Exchange (ETDEWEB)

    Lydick, Christopher L.

    2007-07-01

    The Advanced Simulation & Computing Wide Area Network (ASC WAN), which is a high delay-bandwidth network connection between US Department of Energy National Laboratories, is constantly being examined and evaluated for efficiency. One of the current transport-layer protocols which is used, TCP, was developed for traffic demands which are different from that on the ASC WAN. The Stream Control Transport Protocol (SCTP), on the other hand, has shown characteristics which make it more appealing to networks such as these. Most important, before considering a replacement for TCP on any network, a testing tool that performs well against certain criteria needs to be found. In order to try to find such a tool, two popular networking tools (Netperf v.2.4.3 & v.2.4.6 (OpenSS7 STREAMS), and Iperf v.2.0.6) were tested. These tools implement both TCP and SCTP and were evaluated using four metrics: (1) How effectively can the tool reach a throughput near the bandwidth? (2) How much of the CPU does the tool utilize during operation? (3) Is the tool freely and widely available? And, (4) Is the tool actively developed? Following the analysis of those tools, this paper goes further into explaining some recommendations and ideas for future work.

  14. Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut.

    Science.gov (United States)

    Castro-Mejía, Josué L; Muhammed, Musemma K; Kot, Witold; Neve, Horst; Franz, Charles M A P; Hansen, Lars H; Vogensen, Finn K; Nielsen, Dennis S

    2015-11-17

    The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset. We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery, samples were spiked with low numbers of c2, ϕ29, and T4 phages (representatives of the Siphoviridae, Podoviridae, and Myoviridae families, respectively) and their concentration (plaque-forming units) followed at every step during the extraction procedure. Compared with LIT, TFF and PEG had higher recovery of all spiked phages, yielding up to 16 times more phage particles (PPs) and up to 68 times more phage DNA per volume, increasing thus the chances of extracting low abundant phages. TFF- and PEG-derived metaviromes showed 10% increase in relative abundance of Caudovirales and unclassified phages infecting gut-associated bacteria (>92% for TFF and PEG, 82.4% for LIT). Our methods obtained lower relative abundance of the Myoviridae family (32.5%, LIT 22.6%), which was achieved with the enhanced conditions of our procedures (e.g., reduced filter clogging). A high degree of phage diversity in samples extracted using TFF and PEG was documented by transmission electron microscopy. Two procedures (TFF and PEG) for extraction of bacteriophages from fecal samples were optimized using a set of spiked bacteriophages as process control. These protocols are highly efficient tools for extraction and purification of PPs prior

  15. SU-E-J-113: The Influence of Optimizing Pediatric CT Simulator Protocols On the Treatment Dose Calculation in Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y; Zhang, J; Hu, Q; Tie, J; Wu, H [Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Radiotherapy, Peking University Cancer Hospital ' Institute, Beijing (China); Deng, J [Department of Therapeutic Radiology, Yale University, New Haven, CT (United States)

    2014-06-01

    Purpose: To investigate the possibility of applying optimized scanning protocols for pediatric CT simulation by quantifying the dosimetric inaccuracy introduced by using a fixed HU to density conversion. Methods: The images of a CIRS electron density reference phantom (Model 062) were acquired by a Siemens CT simulator (Sensation Open) using the following settings of tube voltage and beam current: 120 kV/190mA (the reference protocol used to calibrate CT for our treatment planning system (TPS)); Fixed 190mA combined with all available kV: 80, 100, and 140; fixed 120 kV and various current from 37 to 444 mA (scanner extremes) with interval of 30 mA. To avoid the HU uncertainty of point sampling in the various inserts of known electron densities, the mean CT numbers of the central cylindrical volume were calculated using DICOMan software. The doses per 100 MU to the reference point (SAD=100cm, Depth=10cm, Field=10X10cm, 6MV photon beam) in a virtual cubic phantom (30X30X30cm) were calculated using Eclipse TPS (calculation model: AcurosXB-11031) by assigning the CT numbers to HU of typical materials acquired by various protocols. Results: For the inserts of densities less than muscle, CT number fluctuations of all protocols were within the tolerance of 10 HU as accepted by AAPM-TG66. For more condensed materials, fixed kV yielded stable HU with any mA combination where largest disparities were found in 1750mg/cc insert: HU{sub reference}=1801(106.6cGy), HU{sub minimum}=1799 (106.6cGy, error{sub dose}=0.00%), HU{sub maximum}=1815 (106.8cGy, error{sub dose}=0.19%). Yet greater disagreements were observed with increasing density when kV was modified: HU{sub minimum}=1646 (104.5cGy, error{sub dose}=- 1.97%), HU{sub maximum}=2487 (116.4cGy, error{sub dose}=9.19%) in 1750mg/cc insert. Conclusion: Without affecting treatment dose calculation, personalized mA optimization of CT simulator can be conducted by fixing kV for a better cost-effectiveness of imaging dose and quality

  16. leaves extracts as counter stain in gram staining reaction 56

    African Journals Online (AJOL)

    DR. AMINU

    Keywords: Aqueous Extract, Dyes, Henna, Counter-Staining. INTRODUCTION ... is a stain with color contrasting to the principal stain, making the .... different solutions of ethanol extracts were prepared .... this plant a true natural dye. Saponins ...

  17. O-DSR: OPTIMIZED DSR ROUTING PROTOCOL FOR MOBILE AD HOC NETWORK

    Directory of Open Access Journals (Sweden)

    Rjab Hajlaoui

    2015-08-01

    Full Text Available A MANET is an autonomous collection of mobile users that communicate over relatively bandwidth constrained wireless links. When designing mobile ad hoc networks, several interesting and difficult problems arise because of the shared nature of the wireless medium, limited transmission power (range of wireless devices, node mobility, and battery limitations. This paper aims at providing a new schema to improve Dynamic Source Routing (DSR Protocol. The aim behind the proposed enhancement is to find the best route in acceptable time limit without having broadcast storm. Moreover, O-DSR enables network not only to overcome congestion but also maximize the lifetime of mobile nodes. Some simulations results show that the Route Request (RREQ and the Control Packet Overhead decrease by 15% when O-DSR is used, consequently. Also the global energy consumption in O-DSR is lower until to 60 % , which leads to a long lifetime of the network.

  18. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis

    DEFF Research Database (Denmark)

    Leon, Ileana R; Schwämmle, Veit; Jensen, Ole N;

    2013-01-01

    a combination of qualitative and quantitative LC-MS/MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein...... conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents prior to analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative LC-MS/MS workflow quantified over 3700 distinct peptides with 96% completeness between all...... protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows...

  19. Optimization of PMA-PCR Protocol for Viability Detection of Pathogens

    Science.gov (United States)

    Mikkelson, Brian J.; Lee, Christine M.; Ponce, Adrian

    2011-01-01

    This presented study demonstrates the need that PMA-PCR can be used to capture the loss of viability of a sample that is much more specific and time-efficient than alternative methods. This protocol is particularly useful in scenarios in which sterilization treatments may inactivate organisms but not degrade their DNA. The use of a PCR-based method of pathogen detection without first inactivating the DNA of nonviable cells will potentially lead to false positives. The loss of culturability, by heat-killing, did not prevent amplified PCR products, which supports the use of PMA to prevent amplification and differentiate between viable and dead cells. PMA was shown to inhibit the amplification of DNA by PCR in vegetative cells that had been heat-killed.

  20. Performance Analysis and Optimization of Hmipv6 and Fmipv6 Handoff Management Protocols

    Directory of Open Access Journals (Sweden)

    Ambar Yadav, Arti Singh

    2014-05-01

    Full Text Available Seamless communication is becoming the main aspect for the next generation of the mobile and wireless networks. Roaming among multiple wireless access networks connected together through one IP core makes the mobility support for the internet is very critical and more important research topics nowadays. Mobile IP is one of the most successful solutions for the mobility support in the IP based networks, but it has poor performance in term of handover delay. Many improvements have been done to reduce the handover delay, which result in two new standards: the Hierarchical MIP (HMIPv6 and the Fast MIP (FMIPv6. In this paper we present an analysis of handoff management protocols HMIPv6 and FMIPv6 in supporting mobility and latency reduction.

  1. Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for next-generation sequencing.

    Science.gov (United States)

    Pérez-Portela, Rocío; Riesgo, Ana

    2013-09-01

    Transcriptomic information provides fundamental insights into biological processes. Extraction of quality RNA is a challenging step, and preservation and extraction protocols need to be adjusted in many cases. Our objectives were to optimize preservation protocols for isolation of high-quality RNA from diverse echinoderm tissues and to compare the utility of parameters as absorbance ratios and RIN values to assess RNA quality. Three different tissues (gonad, oesophagus and coelomocytes) were selected from the sea urchin Arbacia lixula. Solid tissues were flash-frozen and stored at -80 °C until processed. Four preservation treatments were applied to coelomocytes: flash freezing and storage at -80 °C, RNAlater and storage at -20 °C, preservation in TRIzol reagent and storage at -80 °C and direct extraction with TRIzol from fresh cells. Extractions of total RNA were performed with a modified TRIzol protocol for all tissues. Our results showed high values of RNA quantity and quality for all tissues, showing nonsignificant differences among them. However, while flash freezing was effective for solid tissues, it was inadequate for coelomocytes because of the low quality of the RNA extractions. Coelomocytes preserved in RNAlater displayed large variability in RNA integrity and insufficient RNA amount for further isolation of mRNA. TRIzol was the most efficient system for stabilizing RNA which resulted on high RNA quality and quantity. We did not detect correlation between absorbance ratios and RNA integrity. The best strategies for assessing RNA integrity was the visualization of 18S rRNA and 28S rRNA bands in agarose gels and estimation of RIN values with Agilent Bioanalyzer chips. © 2013 John Wiley & Sons Ltd.

  2. Optimal Design for Informative Protocols in Xenograft Tumor Growth Inhibition Experiments in Mice.

    Science.gov (United States)

    Lestini, Giulia; Mentré, France; Magni, Paolo

    2016-09-01

    Tumor growth inhibition (TGI) models are increasingly used during preclinical drug development in oncology for the in vivo evaluation of antitumor effect. Tumor sizes are measured in xenografted mice, often only during and shortly after treatment, thus preventing correct identification of some TGI model parameters. Our aims were (i) to evaluate the importance of including measurements during tumor regrowth and (ii) to investigate the proportions of mice included in each arm. For these purposes, optimal design theory based on the Fisher information matrix implemented in PFIM4.0 was applied. Published xenograft experiments, involving different drugs, schedules, and cell lines, were used to help optimize experimental settings and parameters using the Simeoni TGI model. For each experiment, a two-arm design, i.e., control versus treatment, was optimized with or without the constraint of not sampling during tumor regrowth, i.e., "short" and "long" studies, respectively. In long studies, measurements could be taken up to 6 g of tumor weight, whereas in short studies the experiment was stopped 3 days after the end of treatment. Predicted relative standard errors were smaller in long studies than in corresponding short studies. Some optimal measurement times were located in the regrowth phase, highlighting the importance of continuing the experiment after the end of treatment. In the four-arm designs, the results showed that the proportions of control and treated mice can differ. To conclude, making measurements during tumor regrowth should become a general rule for informative preclinical studies in oncology, especially when a delayed drug effect is suspected.

  3. Optimal duration of dual antiplatelet therapy following percutaneous coronary intervention: protocol for an umbrella review

    Science.gov (United States)

    Kelly, Shannon E; Bai, Zemin; Liu, Wenfei; Skidmore, Becky; Boucher, Michel; So, Derek Y F; Wells, George A

    2017-01-01

    Introduction Although dual antiplatelet therapy (DAPT) is routinely given to patients after percutaneous coronary intervention (PCI) with stenting, the optimal duration is unknown. Recent evidence indicates there may be benefits in extending the duration beyond 12 months but such decisions may increase the risk of bleeding. Our objective is to provide a comprehensive overview of the literature for clinicians and policymakers via an umbrella review assessing the optimal duration of DAPT. Methods and analysis We will perform a comprehensive search of the published and grey literature for systematic reviews involving randomised controlled trials (RCTs) assessing the optimal duration of DAPT following PCI with stenting. The intervention of interest is extended DAPT (beyond 12 months) compared with short-term DAPT (6–12 months). Studies will be selected for inclusion by two reviewers, and the quality will be assessed. The primary outcomes of interest are all-cause mortality and cardiovascular mortality. Secondary outcomes will be bleeding (major, minor and gastrointestinal), urgent target vessel revascularisation, major adverse cardiovascular events, myocardial infarction, stroke and stent thrombosis. Outcomes will be assessed while on DAPT and after withdrawal of DAPT. Data will be summarised with respect to the number of included RCTs, number of participants, effect estimates and heterogeneity. Data will be reported separately based on patient demographics, procedural parameters (eg, stent types, lesion complexity and concurrent disease) and clinical presentation (eg, acute coronary syndromes, infarct type). Ethics and dissemination Our umbrella review aims to provide a comprehensive overview of the benefits and harms associated with extending DAPT beyond 12 months following PCI with stenting. The results of this review will inform clinical and policy decisions regarding the optimal treatment duration and reimbursement of DAPT following PCI with stenting

  4. Optimizing diffusion of an online computer tailored lifestyle program: a study protocol

    Directory of Open Access Journals (Sweden)

    Schulz Daniela N

    2011-06-01

    Full Text Available Abstract Background Although the Internet is a promising medium to offer lifestyle interventions to large amounts of people at relatively low costs and effort, actual exposure rates of these interventions fail to meet the high expectations. Since public health impact of interventions is determined by intervention efficacy and level of exposure to the intervention, it is imperative to put effort in optimal dissemination. The present project attempts to optimize the dissemination process of a new online computer tailored generic lifestyle program by carefully studying the adoption process and developing a strategy to achieve sustained use of the program. Methods/Design A prospective study will be conducted to yield relevant information concerning the adoption process by studying the level of adoption of the program, determinants involved in adoption and characteristics of adopters and non-adopters as well as satisfied and unsatisfied users. Furthermore, a randomized control trial will be conducted to the test the effectiveness of a proactive strategy using periodic e-mail prompts in optimizing sustained use of the new program. Discussion Closely mapping the adoption process will gain insight in characteristics of adopters and non-adopters and satisfied and unsatisfied users. This insight can be used to further optimize the program by making it more suitable for a wider range of users, or to develop adjusted interventions to attract subgroups of users that are not reached or satisfied with the initial intervention. Furthermore, by studying the effect of a proactive strategy using period prompts compared to a reactive strategy to stimulate sustained use of the intervention and, possibly, behaviour change, specific recommendations on the use and the application of prompts in online lifestyle interventions can be developed. Trial registration Dutch Trial Register NTR1786 and Medical Ethics Committee of Maastricht University and the University Hospital

  5. In vitro detection of contact allergens: development of an optimized protocol using human peripheral blood monocyte-derived dendritic cells.

    Science.gov (United States)

    Reuter, Hendrik; Spieker, Jochem; Gerlach, Silke; Engels, Ursula; Pape, Wolfgang; Kolbe, Ludger; Schmucker, Robert; Wenck, Horst; Diembeck, Walter; Wittern, Klaus-Peter; Reisinger, Kerstin; Schepky, Andreas G

    2011-02-01

    Allergic contact dermatitis is a delayed T-cell mediated allergic response associated with relevant social and economic impacts. Animal experiments (e.g. the local lymph node assay) are still supplying most of the data used to assess the sensitization potential of new chemicals. However, the 7th amendment to the EU Cosmetic Directive will introduce a testing ban for cosmetic ingredients after 2013. In vitro alternative methods are thus being actively developed. Although promising results have been obtained with cell lines, their reduced functionality and inherent genomic instability led us to reinvestigate the use of peripheral blood monocyte-derived dendritic cells (PBMDCs) for the establishment of a reliable in vitro sensitization test. To solve the issues associated with the use of primary cells, the culture and exposure conditions (cytokine concentrations, incubation time, readout, pooled vs. single donors and cytotoxicity) were re-assessed and optimized. Here we propose a stable and reproducible protocol based on PBMDCs. This should allow a wider acceptance of PBMDCs as a reliable test system for the detection of human skin sensitizers and the inclusion of this protocol in an integrated testing strategy.

  6. Optimization of struvite crystallization protocol for pretreating the swine wastewater and its impact on subsequent anaerobic biodegradation of pollutants.

    Science.gov (United States)

    Zhang, Dong-mei; Chen, Ying-xu; Jilani, Ghulam; Wu, Wei-xiang; Liu, Wen-li; Han, Zhi-ying

    2012-07-01

    Higher contents of NH(4)(+) and SS in wastewater hamper the anaerobic digestion; necessitating its pretreatment to reduce them. This study reveals optimization of struvite/MAP precipitation protocol followed by anaerobic digestion of pretreated swine wastewater for pollutants removal. Levels of different treatments: stirring speeds, 400 and 160 rpm; pH values, 9.0, 9.5, 10.0, 10.5, 11.0 and 11.5; and P:Mg:N ratios, 1:1:1.2, 1:1:1.7, 1:1:2.2, 1:1:2.7, 1:1:4.0 and 1:1:5.0 were evaluated for MAP crystallization. Among various combinations, protocol comprising of initial 10 min stirring at 400 rpm followed by 160 rpm for 30 min, pH 10.0, and P:Mg:N ratio 1:1:1.2 rendered the best removal efficiency for NH(4)(+), PO(4)(3-), COD, TC and TOC. Subsequent anaerobic biodegradation revealed superiority of MAP supernatant over raw swine wastewater for methane yield and NH(4)(+)-N, PO(4)(3-)-P, COD, TC and TOC removals. It suggests that struvite precipitation as pretreatment to anaerobic digestion is highly effective and advantageous in wastewater treatment.

  7. Latency-Optimized and Energy-Efficient MAC Protocol for Underwater Acoustic Sensor Networks: A Cross-Layer Approach

    Directory of Open Access Journals (Sweden)

    Qingchun Ren

    2010-01-01

    Full Text Available Considering the energy constraint for fixed sensor nodes and the unacceptable long propagation delay, especially for latency sensitive applications of underwater acoustic sensor networks, we propose a MAC protocol that is latency-optimized and energy-efficient scheme and combines the physical layer and the MAC layer to shorten transmission delay. On physical layer, we apply convolution coding and interleaver for transmitted information. Moreover, dynamic code rate is exploited at the receiver side to accelerate data reception rate. On MAC layer, unfixed frame length scheme is applied to reduce transmission delay, and to ensure the data successful transmission rate at the same time. Furthermore, we propose a network topology: an underwater acoustic sensor network with mobile agent. Through fully utilizing the supper capabilities on computation and mobility of autonomous underwater vehicles, the energy consumption for fixed sensor nodes can be extremely reduced, so that the lifetime of networks is extended.

  8. Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol

    DEFF Research Database (Denmark)

    Spens, Johan; Evans, Alice Ruth; Halfmaerten, David

    2017-01-01

    capture, storage and extraction techniques of eDNA. Previous comparative studies for eDNA capture/storage have tested precipitation and ‘open’ filters. However, practical ‘enclosed’ filters which reduce unnecessary handling have not been included. Here, we fill this gap by comparing a filter capsule......-free control pond). We selected documented capture methods that have successfully targeted a wide range of fauna. The eDNA was extracted using an optimized protocol modified from the DNeasy® Blood & Tissue kit (Qiagen). We measured total eDNA concentrations and Cq-values (cycles used for DNA quantification......-values than cellulose nitrate filters (CN) for one of the target species. DNA integrity of SX samples did not decrease significantly after 2 weeks of storage in contrast to GF and PCTE. Adding preservative before storage improved SX results. In conclusion, we recommend SX filters (originally designed...

  9. Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

    Directory of Open Access Journals (Sweden)

    Børresen-Dale Anne-Lise

    2002-10-01

    Full Text Available Abstract Background T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. Results Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation. Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A+ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3–3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification. Conclusion T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays.

  10. Stained Glass and Flu

    Centers for Disease Control (CDC) Podcasts

    2017-02-01

    Dr. Robert Webster, an Emeritus member of the Department of Infectious Diseases at St. Jude Children's Research Hospital, discusses his cover art story on stained glass and influenza.  Created: 2/1/2017 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 2/1/2017.

  11. Stained-Glass Pastels

    Science.gov (United States)

    Laird, Shirley

    2009-01-01

    The author has always liked the look of stained-glass windows. Usually the designs are simplified and the shapes are easier for younger students to draw. This technique seemed to be the perfect place for her fifth-graders to try their hand at color mixing. The smaller spaces and simple shapes were just what she needed for this group. Her students…

  12. Stained Glass and Flu

    Centers for Disease Control (CDC) Podcasts

    2016-02-01

    Dr. Robert Webster, an Emeritus member of the Department of Infectious Diseases at St. Jude Children's Research Hospital, discusses his cover art story on stained glass and influenza.  Created: 2/1/2016 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 2/1/2016.

  13. "Stained Glass" Landscape Windows

    Science.gov (United States)

    Vannata, Janine

    2008-01-01

    Both adults and children alike marvel at the grand vivid stained-glass windows created by American artist Louis Comfort Tiffany. Today he is commonly recognized as one of America's most influential designers and artists throughout the last nineteenth and early twentieth century. In the lesson described in this article, students created their own…

  14. What is the optimal anesthetic protocol for measurements of cerebral autoregulation in spontaneously breathing mice?

    Science.gov (United States)

    Wang, Zhenghui; Schuler, Beat; Vogel, Olga; Arras, Margarete; Vogel, Johannes

    2010-12-01

    Autoregulation, an important feature of the cerebral circulation, is affected in many diseases. Since genetically modified mice are a fundamental tool in biomedical research, including neuro(bio)logy also in this specie measurements of cerebral autoregulation (CA) are mandatory. However, this requires anesthesia that unfortunately significantly impacts cerebral perfusion and consequently might distort CA measurements directly or by altering arterial pCO(2). The latter can be avoided by artificial ventilation but requires several control measurements of blood gases, each consuming at least 100 μl of blood or 5% of a mouse's blood volume. To avoid such diagnostic hemorrhage, we systematically analyzed the effect of different common anesthetic protocols used for rodents in spontaneously breathing mice on CA measured with Laser speckle perfusion imaging. Halothane, Isoflurane and Pentobarbital abrogated CA and Ketamin/Xylazine as well as Chloralose had a moderate reproducibility. In contrast, the rather rarely used anesthetic Ethomidate applied in low doses combined with local anesthetics had the best reproducibility. Although with this anesthesia the lower CA limit was lower than with Ketamin/Xylazine and Chloralose as reported in the handful of papers so far dealing with CA in mice, we suggest Ethomidate as the anesthetic of choice for CA measurements in spontaneously breathing mice.

  15. Comparative assessment of various lipid extraction protocols and optimization of transesterification process for microalgal biodiesel production.

    Science.gov (United States)

    Mandal, Shovon; Patnaik, Reeza; Singh, Amit Kumar; Mallick, Nirupama

    2013-01-01

    Biodiesel, using microalgae as feedstocks, is being explored as the most potent form of alternative diesel fuel for sustainable economic development. A comparative assessment of various protocols for microalgal lipid extraction was carried out using five green algae, six blue-green algae and two diatom species treated with different single and binary solvents both at room temperature and using a soxhlet. Lipid recovery was maximum with chloroform-methanol in the soxhlet extractor. Pretreatments ofbiomass, such as sonication, homogenization, bead-beating, lyophilization, autoclaving, microwave treatment and osmotic shock did not register any significant rise in lipid recovery. As lipid recovery using chloroform-methanol at room temperature demonstrated a marginally lower value than that obtained under the soxhlet extractor, on economical point of view, the former is recommended for microalgal total lipid extraction. Transesterification process enhances the quality of biodiesel. Experiments were designed to determine the effects of catalyst type and quantity, methanol to oil ratio, reaction temperature and time on the transesterification process using response surface methodology. Fatty acid methyl ester yield reached up to 91% with methanol:HCl:oil molar ratio of 82:4:1 at 65 degrees C for 6.4h reaction time. The biodiesel yield relative to the weight of the oil was found to be 69%.

  16. Optimization of DNA extraction and PCR protocols for phylogenetic analysis in Schinopsis spp. and related Anacardiaceae.

    Science.gov (United States)

    Mogni, Virginia Y; Kahan, Mariano A; de Queiroz, Luciano Paganucci; Vesprini, José L; Ortiz, Juan Pablo A; Prado, Darién E

    2016-01-01

    The Anacardiaceae is an important and worldwide distributed family of ecological and socio-economic relevance. Notwithstanding that, molecular studies in this family are scarce and problematic because of the particularly high concentration of secondary metabolites-i.e. tannins and oleoresins-that are present in almost all tissues of the many members of the group, which complicate the purification and amplification of the DNA. The objective of this work was to improve an available DNA isolation method for Schinopsis spp. and other related Anacardiaceae, as well as the PCR protocols for DNA amplification of the chloroplast trnL-F, rps16 and ndhF and nuclear ITS-ETS fragments. The modifications proposed allowed the extraction of 70-120 µg of non-degraded genomic DNA per gram of dry tissue that resulted useful for PCR amplification. PCR reactions produced the expected fragments that could be directly sequenced. Sequence analyses of amplicons showed similarity with the corresponding Schinopsis accessions available at GenBank. The methodology presented here can be routinely applied for molecular studies of the group aimed to clarify not only aspects on the molecular biology but also the taxonomy and phylogeny of this fascinating group of vascular plants.

  17. Location and Mobility Optimized On-demand Geographical Multipath Routing Protocol for MANET

    Directory of Open Access Journals (Sweden)

    M. Kokilamani

    2016-01-01

    Full Text Available The advancement of science and technology had made mobile ad hoc network an important tool to access network of next generation. Recently, numerous multipath routing protocols for mobile ad hoc network are reported in literature. Each routing methods works based on their salient feature, but failed to control congestion, energy efficiency, overhead packets, signal stability during data transmission which leads to edge effect, signal decay and bottleneck situation of the bandwidth consumption. In this paper a novel approach havely Geographical Distance based Ad Hoc On-demand Distance Vector Routing (GD-AOMDV, which selects the path based on transmission distance value to limit and control the congestion and control overheads has been proposed. The salient feature of the proposed model is that it establishes a relationship between path distance and MANET design parameters including transmission range, consumption of energy and bandwidth. The accuracy of the proposed scheme is analyzed and validated with the experimental results in respect to various flow using NS2 simulations.

  18. Challenges to protocol optimization due to unexpected variation of CT contrast dose amount and flow.

    Science.gov (United States)

    Robinson, Tracy J; Robinson, Jeffrey D; Hippe, Daniel S; Mitsumori, Lee M

    2013-06-01

    High-quality computed tomography (CT) exams are critical to maximizing radiologist's interpretive ability. Exam quality in part depends on proper contrast administration. We examined injector data from consecutive abdominal and pelvic CT exams to analyze variation in contrast administration. Discrepancies between intended IV contrast dose and flow rate with the actual administered contrast dose and measured flow rate were common. In particular, delivered contrast dose discrepancies of at least 10% occurred in 13% of exams while discrepancies in flow rate of at least 10% occurred in 42% of exams. Injector logs are useful for assessing and tracking this type of variability which may confound contrast administration optimization and standardization efforts.

  19. Optimized fabrication protocols of microfluidic devices for X-ray analysis

    KAUST Repository

    Catalano, Rossella

    2014-07-01

    Microfluidics combined with X-ray scattering techniques allows probing conformational changes or assembly processes of biological materials. Our aim was to develop a highly X-ray transparent microfluidic cell for detecting small variations of X-ray scattering involved in such processes. We describe the fabrication of a polyimide microfluidic device based on a simple, reliable and inexpensive lamination process. The implemented microstructured features result in windows with optimized X-ray transmission. The microfluidic device was characterized by X-ray microbeam scattering at the ID13 beamline of the European Synchrotron Radiation Facility. © 2014 Elsevier B.V. All rights reserved.

  20. Protocols for the Fabrication, Characterization, and Optimization of n-Type Thermoelectric Ceramic Oxides

    OpenAIRE

    Boston, R; Schmidt,W.; Lewin, G.D.; Iyasara, A.C.; Lu, Z; Zhang, H; Sinclair, D.C.; Reaney, I.M.

    2017-01-01

    The development of oxides with high figure of merit, ZT, at modest temperatures (∼300–500 °C) is desirable for ceramic-based thermoelectric generator technology. Although ZT is a compound metric with contributions from thermal conductivity (κ), Seebeck coefficient (S), and electrical conductivity (σ), it has been empirically demonstrated that the key to developing thermoelectric n-type oxides is to optimize σ of the ceramic to ∼1000 S/cm at the operating temperature. Titanate-based perovskite...

  1. Engineering Secure Two-Party Computation Protocols Design, Optimization, and Applications of Efficient Secure Function Evaluation

    CERN Document Server

    Schneider, Thomas

    2012-01-01

    Secure two-party computation, called secure function evaluation (SFE), enables two mutually mistrusting parties, the client and server, to evaluate an arbitrary function on their respective private inputs while revealing nothing but the result. Originally the technique was considered to be too inefficient for practical privacy-preserving applications, but in recent years rapid speed-up in computers and communication networks, algorithmic improvements, automatic generation, and optimizations have enabled their application in many scenarios. The author offers an extensive overview of the most pr

  2. Ecophysiological Analysis of Microorganisms in Complex Microbial Systems by Combination of Fluorescence In Situ Hybridization with Extracellular Staining Techniques

    Science.gov (United States)

    Nielsen, Jeppe Lund; Kragelund, Caroline; Nielsen, Per Halkjær

    Ecophysiological analysis and functions of single cells in complex microbial systems can be examined by simple combinations of Fluorescence in situ hybridization (FISH) for identification with various staining techniques targeting functional phenotypes. In this chapter, we describe methods and protocols optimized for the study of extracellular enzymes, surface hydrophobicity and specific surface structures. Although primarily applied to the study of microbes in wastewater treatment (activated sludge and biofilms), the methods may also be used with minor modifications in several other ecosystems.

  3. Optimization of single-cell electroporation protocol for forced gene expression in primary neuronal cultures.

    Science.gov (United States)

    Nishikawa, Shin; Hirashima, Naohide; Tanaka, Masahiko

    2014-09-01

    The development and function of the central nervous system (CNS) are realized through interactions between many neurons. To investigate cellular and molecular mechanisms of the development and function of the CNS, it is thus crucial to be able to manipulate the gene expression of single neurons in a complex cell population. We recently developed a technique for gene silencing by introducing small interfering RNA into single neurons in primary CNS cultures using single-cell electroporation. However, we had not succeeded in forced gene expression by introducing expression plasmids using single-cell electroporation. In the present study, we optimized the experimental conditions to enable the forced expression of green fluorescent protein (GFP) in cultured cerebellar Purkinje neurons using single-cell electroporation. We succeeded in strong GFP expression in Purkinje neurons by increasing the inside diameter of micropipettes or by making the size of the original plasmid smaller by digestion and cyclizing it by ligation. Strong GFP expression in Purkinje neurons electroporated under the optimal conditions continued to be observed for more than 25 days after electroporation. Thus, this technique could be used for forced gene expression in single neurons to investigate cellular and molecular mechanisms of the development, function, and disease of the CNS.

  4. Performance Enhancing Diets and the PRISE Protocol to Optimize Athletic Performance

    Directory of Open Access Journals (Sweden)

    Paul J. Arciero

    2015-01-01

    Full Text Available The training regimens of modern-day athletes have evolved from the sole emphasis on a single fitness component (e.g., endurance athlete or resistance/strength athlete to an integrative, multimode approach encompassing all four of the major fitness components: resistance (R, interval sprints (I, stretching (S, and endurance (E training. Athletes rarely, if ever, focus their training on only one mode of exercise but instead routinely engage in a multimode training program. In addition, timed-daily protein (P intake has become a hallmark for all athletes. Recent studies, including from our laboratory, have validated the effectiveness of this multimode paradigm (RISE and protein-feeding regimen, which we have collectively termed PRISE. Unfortunately, sports nutrition recommendations and guidelines have lagged behind the PRISE integrative nutrition and training model and therefore limit an athletes’ ability to succeed. Thus, it is the purpose of this review to provide a clearly defined roadmap linking specific performance enhancing diets (PEDs with each PRISE component to facilitate optimal nourishment and ultimately optimal athletic performance.

  5. Performance Enhancing Diets and the PRISE Protocol to Optimize Athletic Performance.

    Science.gov (United States)

    Arciero, Paul J; Miller, Vincent J; Ward, Emery

    2015-01-01

    The training regimens of modern-day athletes have evolved from the sole emphasis on a single fitness component (e.g., endurance athlete or resistance/strength athlete) to an integrative, multimode approach encompassing all four of the major fitness components: resistance (R), interval sprints (I), stretching (S), and endurance (E) training. Athletes rarely, if ever, focus their training on only one mode of exercise but instead routinely engage in a multimode training program. In addition, timed-daily protein (P) intake has become a hallmark for all athletes. Recent studies, including from our laboratory, have validated the effectiveness of this multimode paradigm (RISE) and protein-feeding regimen, which we have collectively termed PRISE. Unfortunately, sports nutrition recommendations and guidelines have lagged behind the PRISE integrative nutrition and training model and therefore limit an athletes' ability to succeed. Thus, it is the purpose of this review to provide a clearly defined roadmap linking specific performance enhancing diets (PEDs) with each PRISE component to facilitate optimal nourishment and ultimately optimal athletic performance.

  6. Optimization of intermittent oxygen/air exposure protocols prolongs the safe use of hyperoxia

    Directory of Open Access Journals (Sweden)

    Haim Bitterman

    2012-08-01

    Full Text Available A steadily growing body of data indicates that hyperoxia (the use of oxygen at pressures that are higher than its normal atmospheric partial pressure exerts an extensive profile of physiologic and pharmacologic effects that improve tissue oxygenation, exert anti-inflammatory and anti-bacterial effects, and augment tissue repair mechanisms. Such data establish the rational for the use of normobaric and hyperbaric hyperoxia in a list of clinical conditions characterized by tissue hypoxia, inflammation, infection, and impaired tissue healing. The major limitation confronting the clinical use of hyperoxia is its potential toxicity and the relatively narrow margin of safety that exists between its effective and toxic doses. The most obvious toxic manifestations of oxygen are those exerted on the respiratory and central nervous systems. At pressures higher than 0.6 ATA (atmospheres absolute, (e.g. 60% oxygen at normal atmospheric pressure, and up to 2.8 ATA the most important toxic effect of hyperoxia is a pulmonary inflammatory response that may culminate to a full blown ARDS (Acute Respiratory Distress Syndrome. At pressures higher than 2.8 ATA the most prominent toxic effect of hyperoxia is on the brain, usually manifesting as tonic-clonic grand-mal type convulsions. Currently employed hyperoxic treatment protocols or exposures to oxygen in recreational and military diving are safe because they are restricted to durations that are significantly shorter than the latent period required for development of toxic effects. Another currently employed approach to effective safe use of hyperoxia is... [J Exp Integr Med 2012; 2(4: 283-285

  7. Designing, optimization and validation of tetra-primer ARMS PCR protocol for genotyping mutations in caprine Fec genes.

    Science.gov (United States)

    Ahlawat, Sonika; Sharma, Rekha; Maitra, A; Roy, Manoranjan; Tantia, M S

    2014-12-01

    New, quick, and inexpensive methods for genotyping novel caprine Fec gene polymorphisms through tetra-primer ARMS PCR were developed in the present investigation. Single nucleotide polymorphism (SNP) genotyping needs to be attempted to establish association between the identified mutations and traits of economic importance. In the current study, we have successfully genotyped three new SNPs identified in caprine fecundity genes viz. T(-242)C (BMPR1B), G1189A (GDF9) and G735A (BMP15). Tetra-primer ARMS PCR protocol was optimized and validated for these SNPs with short turn-around time and costs. The optimized techniques were tested on 158 random samples of Black Bengal goat breed. Samples with known genotypes for the described genes, previously tested in duplicate using the sequencing methods, were employed for validation of the assay. Upon validation, complete concordance was observed between the tetra-primer ARMS PCR assays and the sequencing results. These results highlight the ability of tetra-primer ARMS PCR in genotyping of mutations in Fec genes. Any associated SNP could be used to accelerate the improvement of goat reproductive traits by identifying high prolific animals at an early stage of life. Our results provide direct evidence that tetra-primer ARMS-PCR is a rapid, reliable, and cost-effective method for SNP genotyping of mutations in caprine Fec genes.

  8. Electrostatically stabilized magnetic nanoparticles – an optimized protocol to label murine T cells for in vivo MRI

    Directory of Open Access Journals (Sweden)

    Eva eWuerfel

    2011-12-01

    Full Text Available We present a novel highly efficient protocol to magnetically label T cells applying electrostatically stabilized very small superparamagnetic iron oxide particles (VSOP. Our long-term aim is to use magnetic resonance imaging (MRI to investigate T cell dynamics in vivo during the course of neuroinflammatory disorders such as experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis. Encephalitogenic T cells were co-incubated with VSOP, or with protamine-complexed VSOP (VProt, respectively, at different conditions, optimizing concentrations and incubation times. Labeling efficacy was determined by atomic absorption spectrometry as well as histologically, and evaluated on a 7 Tesla MR system. Furthermore, we investigated possible alterations of T cell physiology caused by the labeling procedure. T cell co-incubation with VSOP resulted in an efficient cellular iron uptake. T2 times of labeled cells dropped significantly, resulting in prominent hypointensity on T2*-weighted scans. Optimal labeling efficacy was achieved by VProt (1 mM Fe/ml, 8 h incubation; T2 time shortening of ∼ 80 % compared to untreated cells. VSOP promoted T cell proliferation and altered the ratio of T cell subpopulations towards a CD4+ phenotype. VProt yields a highly efficient T cell labeling, adapted for applications in future in vivo trials. High concentrations of intracellular iron oxide might induce alterations in T cell function, which should be considered in cell tagging studies.

  9. Preliminary pilot fMRI study of neuropostural optimization with a noninvasive asymmetric radioelectric brain stimulation protocol in functional dysmetria

    Directory of Open Access Journals (Sweden)

    Mura M

    2012-04-01

    Full Text Available Marco Mura1, Alessandro Castagna2, Vania Fontani2, Salvatore Rinaldi21Institute of Radiology, University of Cagliari, 2Rinaldi Fontani Institute – Department of Neuro Psycho Physical Optimization, Florence, ItalyPurpose: This study assessed changes in functional dysmetria (FD and in brain activation observable by functional magnetic resonance imaging (fMRI during a leg flexion-extension motor task following brain stimulation with a single radioelectric asymmetric conveyer (REAC pulse, according to the precisely defined neuropostural optimization (NPO protocol.Population and methods: Ten healthy volunteers were assessed using fMRI conducted during a simple motor task before and immediately after delivery of a single REAC-NPO pulse. The motor task consisted of a flexion-extension movement of the legs with the knees bent. FD signs and brain activation patterns were compared before and after REAC-NPO.Results: A single 250-millisecond REAC-NPO treatment alleviated FD, as evidenced by patellar asymmetry during a sit-up motion, and modulated activity patterns in the brain, particularly in the cerebellum, during the performance of the motor task.Conclusion: Activity in brain areas involved in motor control and coordination, including the cerebellum, is altered by administration of a REAC-NPO treatment and this effect is accompanied by an alleviation of FD.Keywords: motor behavior, motor control, cerebellum, dysmetria, functional dysmetria, fluctuating asymmetry

  10. Designing, optimization and validation of tetra-primer ARMS PCR protocol for genotyping mutations in caprine Fec genes

    Directory of Open Access Journals (Sweden)

    Sonika Ahlawat

    2014-12-01

    Full Text Available New, quick, and inexpensive methods for genotyping novel caprine Fec gene polymorphisms through tetra-primer ARMS PCR were developed in the present investigation. Single nucleotide polymorphism (SNP genotyping needs to be attempted to establish association between the identified mutations and traits of economic importance. In the current study, we have successfully genotyped three new SNPs identified in caprine fecundity genes viz. T(-242C (BMPR1B, G1189A (GDF9 and G735A (BMP15. Tetra-primer ARMS PCR protocol was optimized and validated for these SNPs with short turn-around time and costs. The optimized techniques were tested on 158 random samples of Black Bengal goat breed. Samples with known genotypes for the described genes, previously tested in duplicate using the sequencing methods, were employed for validation of the assay. Upon validation, complete concordance was observed between the tetra-primer ARMS PCR assays and the sequencing results. These results highlight the ability of tetra-primer ARMS PCR in genotyping of mutations in Fec genes. Any associated SNP could be used to accelerate the improvement of goat reproductive traits by identifying high prolific animals at an early stage of life. Our results provide direct evidence that tetra-primer ARMS-PCR is a rapid, reliable, and cost-effective method for SNP genotyping of mutations in caprine Fec genes.

  11. Technical advancements and protocol optimization of diffusion-weighted imaging (DWI) in liver.

    Science.gov (United States)

    Ni, Ping; Lin, Yuning; Zhong, Qun; Chen, Ziqian; Sandrasegaran, Kumar; Lin, Chen

    2016-01-01

    An area of rapid advancement in abdominal MRI is diffusion-weighted imaging (DWI). By measuring diffusion properties of water molecules, DWI is capable of non-invasively probing tissue properties and physiology at cellular and macromolecular level. The integration of DWI as part of abdominal MRI exam allows better lesion characterization and therefore more accurate initial diagnosis and treatment monitoring. One of the most technical challenging, but also most useful abdominal DWI applications is in liver and therefore requires special attention and careful optimization. In this article, the latest technical developments of DWI and its liver applications are reviewed with the explanations of the technical principles, recommendations of the imaging parameters, and examples of clinical applications. More advanced DWI techniques, including Intra-Voxel Incoherent Motion (IVIM) diffusion imaging, anomalous diffusion imaging, and Diffusion Kurtosis Imaging (DKI) are discussed.

  12. Optimized formulation and processing protocol for a supplementary bean-based composite flour.

    Science.gov (United States)

    Ndagire, Catherine T; Muyonga, John H; Manju, Reddy; Nakimbugwe, Dorothy

    2015-11-01

    Protein-energy malnutrition is the most serious nutritional body depletion disorder among infants and young children in developing countries, attributable to inadequate energy and nutrient intake, partly due to high dietary bulk of weaning and infant foods. The gruels fed to children are typically of low nutrient and energy density due to the low flour incorporation rate required for drinking viscosity. The aim of this study was to develop a nutritious product, based on common dry beans and other grains, suitable for supplementary feeding. The optimal processing conditions for desired nutritional and sensory attributes were determined using Response Surface Methodology. For bean processing, soaking for 6, 15, or 24 h, germination for 24 or 48 h, and cooking under pressure for either 10 or 20 min were the independent variables. The processed bean flour's total polyphenol, phytic acid and protein content, the sensory acceptability of the bean-based composite porridge and its protein and starch digestibility were dependent variables. Based on product acceptability, antinutrients and protein content, as well as on protein and starch digestibility, the optimum processing conditions for the bean flour for infant and young child feeding were 24 h of soaking, 48 h of malting, and 19 min of steaming under pressure. These conditions resulted in a product with the highest desirability. The model equations developed can be used for predicting the quality of the bean flour and the bean-based composite porridge. Bean optimally processed and incorporated with grain amaranth and rice flours of a ratio of 40: 30: 30, respectively, resulted into flour with high energy, mineral, and nutrient density of the final porridge. The composite is well adaptable to preparation at rural community level. The use of these locally available grains and feasible processes could make a great contribution to nutrition security in sub-Saharan Africa and other developing countries.

  13. The optimization of a rapid pulsed-field gel electrophoresis protocol for the typing of Acinetobacter baumannii, Escherichia coli and Klebsiella spp.

    Science.gov (United States)

    Durmaz, Riza; Otlu, Baris; Koksal, Fatih; Hosoglu, Salih; Ozturk, Recep; Ersoy, Yasemin; Aktas, Elif; Gursoy, Nafia Canan; Caliskan, Ahmet

    2009-09-01

    Pulsed-field gel electrophoresis (PFGE) is the most common genotyping method used for the typing of a number of bacterial species. Generally, investigators use their own custom-developed protocol, but a standardized PFGE protocol would allow the comparison of typing results between laboratories and the tracing of strains around the country. In the present study, we optimized a PFGE protocol for subtyping of Acinetobacter baumannii, Escherichia coli and Klebsiella spp., which are commonly isolated from nosocomial infections in many hospitals. Reproducibility of our PFGE procedure was studied three times at 2- to 3-week intervals. Epidemiological concordance of the optimized PFGE procedure was tested on seven isolates of A. baumannii from a previous outbreak and seven A. baumannii isolates randomly selected among the clinical isolates. The optimized PFGE procedure was evaluated on a total of 174 clinical isolates including 62 A. baumannii, 50 E. coli, and 62 Klebsiella spp. The inter-laboratory reproducibility of the optimized protocol was tested at four laboratories. The optimized procedure is completed in 28 h after culturing. It is likely to be cost-effective, due to the reduction in the time, reagent volume and enzyme concentration needed. The procedure showed high concordance with epidemiological data. There were no non-typeable isolates among the tested bacteria. It is reproducible and versatile. This protocol can be used to identify outbreaks and monitor the spreading rate of nosocomial infections caused by the tested bacterial isolates. Furthermore, due to its high intra- and inter-laboratory reproducibility, the protocol has the potential to be useful for comparing PFGE fingerprinting profiles of the isolates from different settings.

  14. Clarifying CLARITY: Quantitative Optimization of the Diffusion Based Delipidation Protocol for Genetically Labeled Tissue.

    Science.gov (United States)

    Magliaro, Chiara; Callara, Alejandro L; Mattei, Giorgio; Morcinelli, Marco; Viaggi, Cristina; Vaglini, Francesca; Ahluwalia, Arti

    2016-01-01

    Tissue clarification has been recently proposed to allow deep tissue imaging without light scattering. The clarification parameters are somewhat arbitrary and dependent on tissue type, source and dimension: every laboratory has its own protocol, but a quantitative approach to determine the optimum clearing time is still lacking. Since the use of transgenic mouse lines that express fluorescent proteins to visualize specific cell populations is widespread, a quantitative approach to determine the optimum clearing time for genetically labeled neurons from thick murine brain slices using CLARITY2 is described. In particular, as the main objective of the delipidation treatment is to clarify tissues, while limiting loss of fluorescent signal, the "goodness" of clarification was evaluated by considering the bulk tissue clarification index (BTCi) and the fraction of the fluorescent marker retained in the slice as easily quantifiable macroscale parameters. Here we describe the approach, illustrating an example of how it can be used to determine the optimum clearing time for 1 mm-thick cerebellar slice from transgenic L7GFP mice, in which Purkinje neurons express the GFP (green fluorescent protein) tag. To validate the method, we evaluated confocal stacks of our samples using standard image processing indices (i.e., the mean pixel intensity of neurons and the contrast-to-noise ratio) as figures of merit for image quality. The results show that detergent-based delipidation for more than 5 days does not increase tissue clarity but the fraction of GFP in the tissue continues to diminish. The optimum clearing time for 1 mm-thick slices was thus identified as 5 days, which is the best compromise between the increase in light penetration depth due to removal of lipids and a decrease in fluorescent signal as a consequence of protein loss: further clearing does not improve tissue transparency, but only leads to more protein removal or degradation. The rigorous quantitative approach

  15. Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination

    Directory of Open Access Journals (Sweden)

    Dorota Tataruch-Weinert

    2016-06-01

    Full Text Available Background: Urinary extracellular vesicles (UEVs represent an ideal platform for biomarker discovery. They carry different types of RNA species, and reported profile discrepancies related to the presence/absence of 18s and 28s rRNA remain controversial. Moreover, sufficient urinary RNA yields and respective quality RNA profiles are still to be fully established. Methods: UEVs were enriched by hydrostatic filtration dialysis, and RNA content was extracted using 7 different commercially available techniques. RNA quantity was assessed using spectrophotometry and fluorometry, whilst RNA quality was determined by capillary electrophoresis. Results: The presence of prokaryotic transcriptome was stressed when cellular RNA, as a control, was spiked into the UEVs samples before RNA extraction. The presence of bacteria in hydrostatic filtration dialysis above 1,000 kDa molecular weight cut-off and in crude urine was confirmed with growth media plates. The efficiency in removing urinary bacteria was evaluated by differential centrifugation, filtration (0.22 µm filters and chemical pretreatment (water purification tablet. For volumes of urine >200 ml, the chemical treatment provides ease of handling without affecting vesicle integrity, protein and RNA profiles. This protocol was selected to enrich RNA with 7 methods, and its respective quality and quantity were assessed. The results were given as follows: (a Fluorometry gave more repeatability and reproducibility than spectrophotometry to assess the RNA yields, (b UEVs were enriched with small RNA, (c Ribosomal RNA peaks were not observed for any RNA extraction method used and (d RNA yield was higher for column-based method designed for urinary exosome, whilst the highest relative microRNA presence was obtained using TRIzol method. Conclusion: Our results show that the presence of bacteria can lead to misidentification in the electrophoresis peaks. Fluorometry is more reliable than spectrophotometry. RNA

  16. Optimization and validation of a fast amplification protocol for AmpFlSTR® Profiler Plus® for rapid forensic human identification.

    Science.gov (United States)

    Laurin, Nancy; Frégeau, Chantal

    2012-01-01

    The goal of this work was to optimize and validate a fast amplification protocol for the multiplex amplification of the STR loci included in AmpFlSTR(®) Profiler Plus(®) to expedite human DNA identification. By modifying the cycling conditions and by combining the use of a DNA polymerase optimized for high speed PCR (SpeedSTAR™ HS) and a more efficient thermal cycler instrument (Bio-RAD C1000™), we were able to reduce the amplification process from 4h to 26 min. No modification to the commercial AmpFlSTR(®) Profiler Plus(®) primer mix was required. When compared to the current Royal Canadian Mounted Police (RCMP) amplification protocol, no differences with regards to specificity, sensitivity, heterozygote peak height ratios and overall profile balance were noted. Moreover, complete concordance was obtained with profiles previously generated with the standard amplification protocol and minor alleles in mixture samples were reliably typed. An increase in n-4 stutter ratios (2.2% on average for all loci) was observed for profiles amplified with the fast protocol compared to the current procedure. Our results document the robustness of this rapid amplification protocol for STR profiling using the AmpFlSTR(®) Profiler Plus(®) primer set and demonstrate that comparable data can be obtained in substantially less time. This new approach could provide an alternative option to current multiplex STR typing amplification protocols in order to increase throughput or expedite time-sensitive cases.

  17. Optimization of a lipitoid-based plasmid DNA transfection protocol for bovine trophectoderm CT-1 cells.

    Science.gov (United States)

    Schiffmacher, Andrew T; Keefer, Carol L

    2012-08-01

    Embryo-derived cell lines are important in vitro models for investigating the molecular mechanisms directing embryonic tissue lineage segregation and maintenance. The bovine trophectoderm-derived CT-1 cell line has been widely used to identify regulatory mechanisms of interferon tau gene expression, and it possesses potential as a model for characterizing the gene regulatory network controlling trophoblast lineage differentiation and development. This functional potential, however, is severely limited as CT-1 cells are very recalcitrant to standard transfection methods. The focus of this study was to test the cationic lipitoid reagent as an effective transfection reagent for DNA plasmid delivery. Optimization of liptoid-based transfection of plasmid DNA resulted in 9% transfection efficiency averaged across entire CT-1 colonies, with many subregions of CT-1 colonies achieving transfection rates of 15%. These rates are a substantial improvement over near-zero efficiencies achieved using other standard transfection techniques. CT-1 cells were also successfully adapted to substrate-free culture for over 20 passages, eliminating the need to culture CT-1 colonies on feeder cells or matrix-coated cultureware. Together, these results increase the utility of the CT-1 cell line as an in vitro bovine trophoblast model and provide insight into overcoming DNA delivery difficulties in other cell lines not amenable to genetic manipulation.

  18. Optimization of In Vitro Conservation Protocol of Carica pubescens Lenne & K. Koch through Medium Concentration, Temperature and Irradiation Duration Decrease

    Directory of Open Access Journals (Sweden)

    Enni Suwarsi Rahayu

    2016-03-01

    Full Text Available Carica pubescens Lenne & K. Koch, an endemic species in Dieng mountains, must be conserved. The in vitro conservation has been developed, but sub-culture period needs to be extended. This study aimed to obtain a more efficient in vitro conservation protocol of C. pubescens. The research was carried out experimentally by using a completely randomized factorial design with three factors, namely decreasing in storage medium concentration (75% and 50% of MS medium, temperature (4oC and 8°C, and irradiation duration (8 hours/day and 16 hours/day. Shoots were kept in the storage medium for 6, 9 and 12 months, then their viability were tested by growing them in the regeneration medium. Data were analyzed by Analyses of Variance and Least Significant Difference Test. The results showed that medium concentration of 50% of MS, the temperature of 8 °C, and 16 hours/day of irradiation were able to suppress the C. pubescens growth in vitro storage for six months and could maintain its viability in the regeneration medium. Based on these results the medium concentration of 50% of MS, the temperature of 8 °C and 16 hours/day irradiation can be used for in vitro conservation of C. pubescens without sub-culture for six months. How to CiteRahayu, E., & Habibah, N. (2016. Optimization of In Vitro Conservation Protocol of Carica pubescens Lenne & K. Koch through Medium Concentration, Temperature and Irradiation Duration Decrease. Biosaintifika: Journal of Biology & Biology Education, 8(1, 85-93.

  19. Quercetin-imprinted chromatographic sorbents revisited: optimization of synthesis and rebinding protocols for application to natural resources.

    Science.gov (United States)

    Pardo, Antonelle; Mespouille, Laetitia; Blankert, Bertrand; Trouillas, Patrick; Surin, Mathieu; Dubois, Philippe; Duez, Pierre

    2014-10-17

    Molecularly imprinted polymers (MIPs) based on quercetin and synthesized by either bulk, precipitation or suspension polymerization were characterized in terms of size and shape by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). After a study of rebinding protocols, the optimal materials were evaluated as sorbents for solid-phase extraction (SPE) and high-performance liquid chromatography (HPLC) to confirm the presence of imprinted cavities and to assess their selectivity. Besides quercetin, other structurally related natural compounds, naringenin, daidzein and curcumin, were employed for selectivity tests of MIPs. Although rebinding protocols previously described for such MIPs are typically based on binding, washing and eluting methanol-based solutions, we show that this highly polar solvent leads to weak specific interactions (imprinting factor2.4). This calls for reviewing most of previously published data on quercetin-MIPs; in proper binding conditions, published MIPs may prove more performing than initially assessed. As expected, tested MIPs exhibited the highest selective rebinding towards quercetin template (imprinting effect, quercetin, 3.41; naringenin, 1.54; daidzein, 1.38; curcumin, 1.67); the differences in selectivity between quercetin analogues were explained by the ligand geometries and H-bonding patterns obtained from quantum-chemical calculations. The evaluation of MIPs under identical analytical conditions allowed investigating the effect of the production method on chromatographic performances. The MIPs in bead materials (for quercetin, peak width, 0.69; number of theoretical plates, 143; symmetry factor, 2.22) provided a significant improvement in chromatographic efficiency over the bulk materials (for quercetin, peak width, 1.25; number of theoretical plates, 115; symmetry factor, 2.92). Using the quercetin-beaded MIP as SPE sorbent, quercetin was selectively extracted from Allium cepa L. extract. The MIP

  20. Optimizing postoperative care protocols in thoracic surgery: best evidence and new technology

    Science.gov (United States)

    French, Daniel G.; Dilena, Michael; LaPlante, Simon; Shamji, Farid; Sundaresan, Sudhir; Villeneuve, James; Seely, Andrew; Maziak, Donna

    2016-01-01

    Postoperative clinical pathways have been shown to improve postoperative care and decrease length of stay in hospital. In thoracic surgery there is a need to develop chest tube management pathways. This paper considers four aspects of chest tube management: (I) appraising the role of chest X-rays in the management of lung resection patients with chest drains; (II) selecting of a fluid output threshold below which chest tubes can be removed safely; (III) deciding whether suction should be applied to chest tubes; (IV) and selecting the safest method for chest tube removal. There is evidence that routine use of chest X-rays does not influence the management of chest tubes. There is a lack of consensus on the highest fluid output threshold below which chest tubes can be safely removed. The optimal use of negative intra-pleural pressure has not yet been established despite multiple randomized controlled trials and meta-analyses. When attempting to improve efficiency in the management of chest tubes, evidence in support of drain removal without a trial of water seal should be considered. Inconsistencies in the interpretation of air leaks and in chest tube management are likely contributors to the conflicting results found in the literature. New digital pleural drainage systems, which provide a more objective air leak assessment and can record air leak trend over time, will likely contribute to the development of new evidence-based guidelines. Technology should be combined with continued efforts to standardize care, create clinical pathways, and analyze their impact on postoperative outcomes. PMID:26941968

  1. Optimizing postoperative care protocols in thoracic surgery: best evidence and new technology.

    Science.gov (United States)

    French, Daniel G; Dilena, Michael; LaPlante, Simon; Shamji, Farid; Sundaresan, Sudhir; Villeneuve, James; Seely, Andrew; Maziak, Donna; Gilbert, Sebastien

    2016-02-01

    Postoperative clinical pathways have been shown to improve postoperative care and decrease length of stay in hospital. In thoracic surgery there is a need to develop chest tube management pathways. This paper considers four aspects of chest tube management: (I) appraising the role of chest X-rays in the management of lung resection patients with chest drains; (II) selecting of a fluid output threshold below which chest tubes can be removed safely; (III) deciding whether suction should be applied to chest tubes; (IV) and selecting the safest method for chest tube removal. There is evidence that routine use of chest X-rays does not influence the management of chest tubes. There is a lack of consensus on the highest fluid output threshold below which chest tubes can be safely removed. The optimal use of negative intra-pleural pressure has not yet been established despite multiple randomized controlled trials and meta-analyses. When attempting to improve efficiency in the management of chest tubes, evidence in support of drain removal without a trial of water seal should be considered. Inconsistencies in the interpretation of air leaks and in chest tube management are likely contributors to the conflicting results found in the literature. New digital pleural drainage systems, which provide a more objective air leak assessment and can record air leak trend over time, will likely contribute to the development of new evidence-based guidelines. Technology should be combined with continued efforts to standardize care, create clinical pathways, and analyze their impact on postoperative outcomes.

  2. Re-evaluation, optimization, and multilaboratory validation of the PulseNet-standardized pulsed-field gel electrophoresis protocol for Listeria monocytogenes.

    Science.gov (United States)

    Halpin, Jessica L; Garrett, Nancy M; Ribot, Efrain M; Graves, Lewis M; Cooper, Kara L

    2010-03-01

    The PulseNet Methods Development and Validation Laboratory began a re-evaluation of the standardized pulsed-field gel electrophoresis (PFGE) protocols with the goal of optimizing their overall performance and robustness. Herein, we describe a stepwise evaluation of the PulseNet-standardized PFGE protocol for Listeria monocytogenes that led to the modification of several steps which significantly improved the overall appearance and reproducibility of the resulting PFGE data. These improvements included the following: (1) reducing the cell suspension concentration, (2) increasing lysozyme incubation temperature from 37 degrees C to 56 degrees C, and (3) decreasing the number of units of restriction enzymes AscI and ApaI. These changes were incorporated into a proposed protocol that was evaluated by 16 PulseNet participating laboratories, including 2 international participants. Results from the validation study indicated that the updated L. monocytogenes protocol is more robust than the original PulseNet-standardized protocol established in 1998 and this resulted in the official adoption of the new protocol into the PulseNet system in the spring of 2008. The modifications not only represent an improvement to the protocol but also describe procedural improvements that could be potentially applied to the PFGE analysis of other Gram-positive organisms.

  3. 基于遗传算法的Ad hoc路由协议优化%Routing Protocol Optimization for Ad hoc Networks Based on Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    詹思瑜; 李建平

    2012-01-01

    目前存在大量的Ad hoc网络路由协议,但是很少有研究对这些协议的最优性能进行过分析.通过对Ad hoc网络路由协议的分析,结合遗传算法的基本原理,对路由协议参数的全局优化配置提出一种启发式求解算法.该算法采用可变长编码,结合遗传算法的选择、交叉和变异操作,对路由协议的性能进行全局优化.在NS2平台上的仿真试验结果表明,优化后的路由协议性能比未优化之前提高30%.%A huge number of routing protocols have been proposed but few researches of the optimal performance of these protocols have been done. In this paper, the performance of Ad hoc networks routing protocols was studied and a novel algorithm was proposed to do a global optimization for routing protocols parameters setting based on genetic algorithm. The presented algorithm adopted variable-length chromosomes encoding, applied selection, crossover and mutation to optimize the routing protocols performance of Ad hoc networks. As shown in our simulations implemented on ns2, the performance of optimized routing protocols can be improved more than 30%.

  4. Plant or fungal sequences? An alternative optimized PCR protocol to avoid ITS (nrDNA misamplification

    Directory of Open Access Journals (Sweden)

    Vitor Fernandes Oliveira de Miranda

    2010-02-01

    Full Text Available The nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2 from leaves of Drosera (Droseraceae were amplified using "universal" primers. The analysis of the products demonstrated most samples were a molecular mixture as a result of unsuccessful and non-specific amplifications. Among the obtained sequences, two were from Basidiomycota fungi. Homologous sequences of Basidiomycota were obtained from GenBank database and added to a data set with sequences from Drosera leaves. Parsimony analysis demonstrated that one sequence was amplified from an Ustilaginomycetes fungus, and another from a Heterobasidiomycetes. Possibly these fungi were associated to leaves of Drosera, and not because of samples contamination. In order to provide optimization and a better specificity of PCR (polymerase chain reaction, a very successful method was demonstrated using dimethyl sulfoxide (DMSO and bovine serum albumin (BSA in reactions.Os espaçadores internos transcritos do DNA nuclear ribossomal (ITS1 e ITS2 de folhas de Drosera (Droseraceae foram amplificados com o emprego de iniciadores "universais". A análise demonstrou que a maior parte das amostras continha uma mistura resultante de amplificações não-específicas. Dentre as sequências de DNA obtidas, duas delas foram de fungos basidiomicetos. Sequências homólogas foram obtidas do GenBank e analisadas junto às sequências obtidas de folhas de Drosera. Através das análises filogenéticas de máxima parcimônia foi possível identificar uma seqüência como sendo de um Ustilaginomycetes e outra de Heterobasidiomycetes (Basidiomycota. Possivelmente esses organismos estavam associados às folhas de Drosera e assim não sejam resultantes de contaminação. Com o objetivo de otimizar e buscar uma melhor especificidade das reações de PCR, um protocolo bem sucedido foi demonstrado com o uso de dimetilsulfóxido (DMSO e soroalbumina bovina (BSA.

  5. International Study to Predict Optimized Treatment for Depression (iSPOT-D, a randomized clinical trial: rationale and protocol

    Directory of Open Access Journals (Sweden)

    Cooper Nicholas J

    2011-01-01

    Full Text Available Abstract Background Clinically useful treatment moderators of Major Depressive Disorder (MDD have not yet been identified, though some baseline predictors of treatment outcome have been proposed. The aim of iSPOT-D is to identify pretreatment measures that predict or moderate MDD treatment response or remission to escitalopram, sertraline or venlafaxine; and develop a model that incorporates multiple predictors and moderators. Methods/Design The International Study to Predict Optimized Treatment - in Depression (iSPOT-D is a multi-centre, international, randomized, prospective, open-label trial. It is enrolling 2016 MDD outpatients (ages 18-65 from primary or specialty care practices (672 per treatment arm; 672 age-, sex- and education-matched healthy controls. Study-eligible patients are antidepressant medication (ADM naïve or willing to undergo a one-week wash-out of any non-protocol ADM, and cannot have had an inadequate response to protocol ADM. Baseline assessments include symptoms; distress; daily function; cognitive performance; electroencephalogram and event-related potentials; heart rate and genetic measures. A subset of these baseline assessments are repeated after eight weeks of treatment. Outcomes include the 17-item Hamilton Rating Scale for Depression (primary and self-reported depressive symptoms, social functioning, quality of life, emotional regulation, and side-effect burden (secondary. Participants may then enter a naturalistic telephone follow-up at weeks 12, 16, 24 and 52. The first half of the sample will be used to identify potential predictors and moderators, and the second half to replicate and confirm. Discussion First enrolment was in December 2008, and is ongoing. iSPOT-D evaluates clinical and biological predictors of treatment response in the largest known sample of MDD collected worldwide. Trial registration International Study to Predict Optimised Treatment - in Depression (iSPOT-D ClinicalTrials.gov Identifier

  6. Photoacoustic imaging of port-wine stains

    NARCIS (Netherlands)

    Kolkman, Roy G.M.; Mulder, Miranda J.; Glade, Conrad P.; Steenbergen, Wiendelt; Leeuwen, van Ton G.

    2008-01-01

    Background and Objective: To optimize laser therapy of port-wine stains (PWSs), information about the vasculature as well as lesion depth is valuable. In this study we investigated the use of photoacoustic imaging (PAI) to obtain this information. - Study Design/Materials and Methods: PAI uses puls

  7. Dose versus image quality in multidetector CT scanning: a methodology for acquisition protocols optimization;Dose versus qualite image en TDM multidetecteur: une methodologie pour l'optimisation des protocoles d'acquisition

    Energy Technology Data Exchange (ETDEWEB)

    Bonniaud, G.; Tran Dinh, V.; Texier, N.; Touati, R.; Simon, J.; Roger, P.

    2009-10-15

    Objective: to determine the influence of acquisition and reconstruction parameters on the dose and the image quality in multi detectors CT scanning to optimize the protocols. As conclusion: The optimization allowed to reduce, in average, the weighted computed tomography dose index-vol (wC.T.D.I.vol) of 20% through the pitch increase, the use of the broadest collimation and/or the use of a retrospectively reconstruction (zoom factor and/or increase matrix size) without deteriorating the noise and/or resolution performances more than 10%. (N.C.)

  8. Dose versus image quality in multidetector CT scanning: a methodology for the optimization of acquisition protocols;Dose versus qualite image en TDM multidetecteur: une methodologie pour l'optimisation des protocoles d'acquisition

    Energy Technology Data Exchange (ETDEWEB)

    Bonniaud, G.; Tran Dinh, V.; Texier, N.; Touati, R.; Simon, J.; Roger, P. [Centre Saint Yves, 56 - Vannes (France)

    2009-10-15

    Objective: to determine the influence of acquisition parameters and reconstruction of dose and the image quality in multi detectors T.D.M. for protocols optimization. conclusion: the optimization allowed to reduce in average, the C.T.D.I.vol (weighted computed tomography dose index) of 20% via the pitch increase, the use of a collimation as broad as possible and/or the use of a retrospectively construction (factor zoom and/or increased size of matrix) without degrading the performances of noise and:or resolution of more than 10%. (N.C.)

  9. 基于参数优化批处理的TLS协议%Parameter Optimization-Based Batching TLS Protocol

    Institute of Scientific and Technical Information of China (English)

    齐芳; 贾维嘉; 鲍丰; 吴永东; 王国军

    2007-01-01

    TLS(transport layer security)协议的基本设计目标是为两个通信实体之间提供数据的保密性和完整性.由于在传输层安全握手协议中最耗费计算资源的步骤是服务器RSA解密运算,优化的批处理的RSA方法提出可以用于加速TLS会话的初始化.首先指出了以前的批处理方法由于要求多证书实现而实用性不强.然后提出了单一证书策略的方法,从而克服了这一问题.还提出结合用户对于因特网服务质量的要求优化了批处理参数.为了选择优化的批处理的参数,不仅考虑了服务器的性能,而且还考虑了客户可容忍的等待时间.通过分析并在阐述平均排队时间、批处理服务时间和系统稳定性的基础上提出了一种新颖的优化批处理调度算法,已部署在服务器上.最后通过分析和模拟两种方法验证了所提出方案的实用性和有效性.%The primary goal of the Transport Layer Security (TLS) protocol is to provide confidentiality and data integrity between two communicating entities. Since the most computationally expensive step in the TLS handshake protocol is the server's RSA decryption, it is introduced that optimal batch RSA can be used to speedup TLS session initialization. This paper first indicates that the previous batch method is impractical since it requires a multiple of certificates, then it proposes the unique certificate scheme to overcome the problem. It is also introduced that the batching parameter is optimized when integrating users' requirements for Internet Quality of Service (QoS). To select the optimal batching parameters, not only the server's performance but also the client's tolerable waiting time is considered. Based on the analysis of the mean queue time, batching service time and the stability of the system, a novel batch optimal scheduling algorithm which is deployed in a batching Web server is proposed. Finally, the proposed algorithm is evaluated to be practical and

  10. Electrostatically Stabilized Magnetic Nanoparticles – An Optimized Protocol to Label Murine T Cells for in vivo MRI

    Science.gov (United States)

    Wuerfel, Eva; Smyth, Maureen; Millward, Jason M.; Schellenberger, Eyk; Glumm, Jana; Prozorovski, Timour; Aktas, Orhan; Schulze-Topphoff, Ulf; Schnorr, Jörg; Wagner, Susanne; Taupitz, Matthias; Infante-Duarte, Carmen; Wuerfel, Jens

    2011-01-01

    We present a novel highly efficient protocol to magnetically label T cells applying electrostatically stabilized very small superparamagnetic iron oxide particles (VSOP). Our long-term aim is to use magnetic resonance imaging (MRI) to investigate T cell dynamics in vivo during the course of neuroinflammatory disorders such as experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. Encephalitogenic T cells were co-incubated with VSOP, or with protamine-complexed VSOP (VProt), respectively, at different conditions, optimizing concentrations and incubation times. Labeling efficacy was determined by atomic absorption spectrometry as well as histologically, and evaluated on a 7 T MR system. Furthermore, we investigated possible alterations of T cell physiology caused by the labeling procedure. T cell co-incubation with VSOP resulted in an efficient cellular iron uptake. T2 times of labeled cells dropped significantly, resulting in prominent hypointensity on T2*-weighted scans. Optimal labeling efficacy was achieved by VProt (1 mM Fe/ml, 8 h incubation; T2 time shortening of ∼80% compared to untreated cells). Although VSOP promoted T cell proliferation and altered the ratio of T cell subpopulations toward a CD4+ phenotype, no effects on CD4 T cell proliferation or phenotypic stability were observed by labeling in vitro differentiated Th17 cells with VProt. Yet, high concentrations of intracellular iron oxide might induce alterations in T cell function, which should be considered in cell tagging studies. Moreover, we demonstrated that labeling of encephalitogenic T cells did not affect pathogenicity; labeled T cells were still capable of inducing EAE in susceptible recipient mice. PMID:22203815

  11. Blood stain pattern analysis.

    Science.gov (United States)

    Peschel, O; Kunz, S N; Rothschild, M A; Mützel, E

    2011-09-01

    Bloodstain pattern analysis (BPA) refers to the collection, categorization and interpretation of the shape and distribution of bloodstains connected with a crime. These kinds of stains occur in a considerable proportion of homicide cases. They offer extensive information and are an important part of a functional, medically and scientifically based reconstruction of a crime. The following groups of patterns can essentially be distinguished: dripped and splashed blood, projected blood, impact patterns, cast-off stains, expirated and transferred bloodstains. A highly qualified analysis can help to estimate facts concerning the location, quality and intensity of an external force. A sequence of events may be recognized, and detailed questions connected with the reconstruction of the crime might be answered. In some cases, BPA helps to distinguish between accident, homicide and suicide or to identify bloodstains originating from a perpetrator. BPA is based on systematic training, a visit to the crime scene or alternatively good photographic documentation, and an understanding and knowledge of autopsy findings or statements made by the perpetrator and/or victim. A BPA working group has been established within the German Society of Legal Medicine aiming to put the knowledge and practical applications of this subdiscipline of forensic science on a wider basis.

  12. Cost-Optimizing Adaptive Location Service Protocol in MANET%开销优化的MANET按需位置服务协议

    Institute of Scientific and Technical Information of China (English)

    宗明; 王晓东; 周兴铭

    2012-01-01

    Location service protocols in mobile ad hoc network maintain nodes' positions. The performance of upper layer protocols depends on the performance of location service. Protocol cost is defined as the number of one-hop location querying packages and location updating packages. It is one of the most important performance indices of location service protocol and determines the scalability and other performance of the protocol. Without considering location reguest, existing location service protocols optimize protocol cost for networks with specific communication features. For optimizing the location service protocol cost in networks with different communication features, this paper proposes a minimum cost location updating tree. It is used to optimize protocol cost of multi-home region location service protocol according to the number of location querying to each home region and the protocol package transmission costs. Then, it is proved that the minimum cost location updating tree problem is an NP-hard problem. Based on these works, this paper then proposes a demand-driven multi-home region location service protocol. This protocol uses a kind of real time algorithm to get the minimum cost location updating tree just before location updating, and then forwards location updating packages according to the tree. The experimental results show that the proposed protocol can decrease the protocol cost and is more scalable.%在移动自组网中,位置服务协议的开销是指更新和查询所发送的一跳报文数量,决定协议的可扩展性及其各方面性能.现有的位置服务协议只针对特定的通信场景,并且绝大部分不能根据位置需求的变化进一步优化开销.提出在基于多家乡区域的位置服务结构基础上,根据位置服务协议的报文传输开销以及位置信息请求在家乡区域中的分布情况,采用最小更新树来优化协议开销,并证明求解最小更新树的问题是NP难问题.在此基础上,

  13. Optimization and clinical validation of a Real-Time PCR protocol for direct detection of Trichomonas vaginalis in pooled urine samples

    Directory of Open Access Journals (Sweden)

    WHA Zandijk

    2009-12-01

    Full Text Available Background and Objectives: A new Real- Time PCR protocol for the detection of Trichomonas vaginalis in pooled urine"nsamples has been optimized and validated."nMaterials and Methods: The amplification protocol, targeting a 2kb repeated gene in the T. vaginalis genome, was optimized"nby varying PCR parameters. As a reference method, a Real-Time PCR protocol targeting the beta-tubulin gene (Y. Versluis"net al, 2006, Int J STD AIDS 17:642 was used. Clinical validation was performed with pooled urine samples obtained from"npatients of the sexually transmitted diseases clinic of a university hospital (n=963; from February – June 2007."nResults: Positive samples with the new optimized technique is 1.1% (n=10, while the beta-tubulin real-time PCR method"ngenerated four positives (0.3%."nConclusion: The new RT- PCR protocol is a sensitive (1.000 and specific (0.993 procedure to detect and to identify T."nvaginalis in urine samples.

  14. Development of an in vitro skin sensitization test using human cell lines: the human Cell Line Activation Test (h-CLAT). I. Optimization of the h-CLAT protocol.

    Science.gov (United States)

    Ashikaga, T; Yoshida, Y; Hirota, M; Yoneyama, K; Itagaki, H; Sakaguchi, H; Miyazawa, M; Ito, Y; Suzuki, H; Toyoda, H

    2006-08-01

    The aim of this study is to optimize the experimental conditions for an in vitro skin sensitization test using the human cell lines THP-1 and U-937. As regards pre-culturing time, the expression of CD86 on DNCB-treated THP-1 cells tended to be higher after 48h and 72h pre-culture compared with other time points evaluated. Next, we investigated the effect of chemical treatment time, and found that induction of CD86 expression on THP-1 cells by DNCB reached a plateau after 24h. Augmentation of CD86 expression is often observed when cells are treated with a subtoxic dose of allergens. To determine the appropriate dose of test samples, the cytotoxicity of test samples to THP-1 and U-937 cells was assessed with MTT assay, and the 50% inhibitory concentration (IC50) of each test sample was calculated. Based on the cytotoxicity assay data, four concentrations in the range between toxic and non-toxic were selected (0.1x, 0.5x, 1x and 2x IC50). Several kinds of antibodies were tested for staining THP-1 and U-937 cells treated with allergens/non-allergens (e.g., DNCB, Ni/SLS), and suitable antibodies for staining CD86 and CD54 were selected. We confirmed that the working dilutions of the selected CD86 and CD54 antibodies were appropriate for use in our method. The effect of an FcR blocking procedure was also evaluated. The mean fluorescence intensity (MFI value) was decreased by the FcR blocking procedure, which indicated that non-specific staining was blocked. Therefore, this procedure should be included in the method. Based on our findings, the protocol for this assay was optimized and the experimental conditions to be used in a future validation study were identified. We propose to call this kind of in vitro skin sensitization test h-CLAT, which is short for human Cell Line Activation Test.

  15. Optimization of Parameters in 16-slice CT-‌‌scan Protocols for Reduction of the Absorbed Dose

    Directory of Open Access Journals (Sweden)

    Shahrokh Naseri

    2014-08-01

    Full Text Available Introduction In computed tomography (CT technology, an optimal radiation dose can be achieved via changing radiation parameters such as mA, pitch factor, rotation time and tube voltage (kVp for diagnostic images. Materials and Methods In this study, the brain, abdomen, and thorax scaning was performed using Toshiba 16-slice scannerand standard AAPM and CTDI phantoms. AAPM phantom was used for the measurement of image-related parameters and CTDI phantom was utilized for the calculation of absorbed dose to patients. Imaging parameters including mA (50-400 mA, pitch factor (1 and 1.5 and rotation time (range of 0.5, 0.75, 1, 1.5 and 2 seconds were considered as independent variables. The brain, abdomen and chest imaging was performed multi-slice and spiral modes. Changes in image quality parameters including contrast resolution (CR and spatial resolution (SR in each condition were measured and determined by MATLAB software. Results After normalizing data by plotting the full width at half maximum (FWHM of point spread function (PSF in each condition, it was observed that image quality was not noticeably affected by each cases. Therefore, in brain scan, the lowest patient dose was in 150 mA and rotation time of 1.5 seconds. Based on results of scanning of the abdomen and chest, the lowest patient dose was obtained by 100 mA and pitch factors of 1 and 1.5. Conclusion It was found that images with acceptable quality and reliable detection ability could be obtained using smaller doses of radiation, compared to protocols commonly used by operators.

  16. The optimized acupuncture treatment for neck pain caused by cervical spondylosis: a study protocol of a multicentre randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Liang Zhao-Hui

    2012-07-01

    Full Text Available Abstract Background Neck pain is one of the chief symptoms of cervical spondylosis (CS. Acupuncture is a well-accepted and widely used complementary therapy for the management of neck pain caused by CS. In this paper, we present a randomized controlled trial protocol evaluating the use of acupuncture for CS neck pain, comparing the effects of the optimized acupuncture therapy in real practice compared with sham and shallow acupuncture. Methods/Design This trial uses a multicentre, parallel-group, randomized, sham acupuncture and shallow acupuncture, controlled single-blind design. Nine hospitals are involved as trial centres. 945 patients who meet inclusion criteria are randomly assigned to receive optimized acupuncture therapy, sham acupuncture or shallow acupuncture by a computerized central randomization system. The interventions past for 4 weeks with eight to ten treatments in total. The group allocations and interventions are concealed to patients and statisticians. The Northwick Park Neck Pain Questionnaire (NPQ is used as the primary outcome measure, and the McGill Pain Questionnaire (MPQ and The Short Form (36 Health Survey (SF-36 are applied as secondary outcome measures. The evaluation is performed at baseline, at the end of the intervention, and at the end of the first month and the third month during follow-up. The statistical analyses will include baseline data comparison and repeated measures of analysis of variance (ANOVA for primary and secondary outcomes of group and time differences. Adverse events (AEs will be reported if they occur. Discussion This trial is a multicentre randomized control trial (RCT on the efficacy of acupuncture for CS neck pain and has a large sample size and central randomization in China. It will strictly follow the CONSORT statement and STRICTA extension guideline to report high-quality study results. By setting the control groups as sham and shallow acupuncture, this study attempts to reveal the

  17. 一种基于分簇的优化定向扩散路由协议%A Cluster- based Optimizing Directed Diffusion Routing Protocol

    Institute of Scientific and Technical Information of China (English)

    梁小宇; 刘泉; 刘新华

    2011-01-01

    提出了一种优化的路由协议CBODD( cluster- based optimizing directed diffusion).该协议是一种利用被动分簇来简化网络拓扑、抑制泛洪传播产生的冗余消息,从而节约能量,实现能源有效性的定向扩散路由协议.详细描述了CBODD协议及其实现算法,并在NS2上进行了仿真,实验结果表明,该协议相比传统的定向扩散路由协议具有更好的能源有效性和更小的网络延迟.当节点大规模增加时,仍然具有良好的性能.%An optimized routing protocol CBODD (cluster - based optimizing directed diffusion) that was used for directed diffusion was presented to fully utilize the benefits of clustering in the wireless sensor network. CBODD is an energy - efficient routing protocol based on passive clustering, which predigests network topology and saves energy by suppressing the redundant message in plain flooding. The CBODD protocol and its implementation algorithm were described in detail. The routing protocol was simulated in NS2. The results show that CBODD is more energy - efficient and has a good performance even when the number of nodes increased in large scale than traditional directed diffusion routing protocol.

  18. An improved silver staining procedure for schizodeme analysis in polyacrylamide gradient gels

    Directory of Open Access Journals (Sweden)

    Antonio M. Gonçalves

    1990-03-01

    Full Text Available A simple protocol is described for the silver staining of polyacrylamide gradient gels used for the separation of restriction fragments of kinetoplast DNA [schizodeme analysis of trypanosomatids (Morel et al., 1980]. The method overcomes the problems of non-uniform staining and strong background color which are frequently encountered when conventional protocols for silver staining of linear gels. The method described has proven to be of general applicability for DNA, RNA and protein separations in gradient gels.

  19. Isolation, Culture, and Staining of Single Myofibers

    Science.gov (United States)

    Gallot, Yann Simon; Hindi, Sajedah M.; Mann, Aman K.; Kumar, Ashok

    2016-01-01

    Adult skeletal muscle regeneration is orchestrated by a specialized population of adult stem cells called satellite cells, which are localized between the basal lamina and the plasma membrane of myofibers. The process of satellite cell-activation, proliferation, and subsequent differentiation that occurs during muscle regeneration can be recapitulated ex vivo by isolation of single myofibers from skeletal muscles and culturing them under suspension conditions. Here, we describe an improved protocol to evaluate ex vivo satellite cells activation through isolation of single myofibers from extensor digitorum longus (EDL) muscle of mice and culturing and staining of myofiber-associated satellite cells with the markers of self-renewal, proliferation, and differentiation.

  20. SU-F-I-46: Optimizing Dose Reduction in Adult Head CT Protocols While Maintaining Image Quality in Postmortem Head Scans

    Energy Technology Data Exchange (ETDEWEB)

    Lipnharski, I; Carranza, C; Quails, N; Correa, N; Rajderkar, D; Bennett, J; Rill, L; Arreola, M [University of Florida, Gainesville, FL (United States)

    2016-06-15

    Purpose: To optimize adult head CT protocol by reducing dose to an appropriate level while providing CT images of diagnostic quality. Methods: Five cadavers were scanned from the skull base to the vertex using a routine adult head CT protocol (120 kVp, 270 mA, 0.75 s rotation, 0.5 mm × 32 detectors, 70.8 mGy CTDIvol) followed by seven reduced-dose protocols with varying combinations of reduced tube current, reduced rotation time, and increased detectors with CTDIvol ranging from 38.2 to 65.6 mGy. Organ doses were directly measured with 21 OSL dosimeters placed on the surface and implanted in the head by a neurosurgeon. Two neuroradiologists assessed grey-white matter differentiation, fluid space, ventricular size, midline shift, brain mass, edema, ischemia, and skull fractures on a three point scale: (1) Unacceptable, (2) Borderline Acceptable, and (3) Acceptable. Results: For the standard scan, doses to the skin, lens of the eye, salivary glands, thyroid, and brain were 37.55 mGy, 49.65 mGy, 40.67 mGy, 4.63 mGy, and 27.33 mGy, respectively. Two cadavers had cerebral edema due to changing dynamics of postmortem effects, causing the grey-white matter differentiation to appear less distinct. Two cadavers with preserved grey-white matter received acceptable scores for all image quality features for the protocol with a CTDIvol of 57.3 mGy, allowing organ dose savings ranging from 34% to 45%. One cadaver allowed for greater dose reduction for the protocol with a CTDIvol of 42 mGy. Conclusion: Efforts to optimize scan protocol should consider both dose and clinical image quality. This is made possible with postmortem subjects, whose brains are similar to patients, allowing for an investigation of ideal scan parameters. Radiologists at our institution accepted scan protocols acquired with lower scan parameters, with CTDIvol values closer to the American College of Radiology’s (ACR) Achievable Dose level of 57 mGy.

  1. Tips and step-by-step protocol for the optimization of important factors affecting cellular enzyme-linked immunosorbent assay (CELISA).

    Science.gov (United States)

    Morandini, R; Boeynaems, J M; Wérenne, J; Ghanem, G

    2001-01-01

    CELISA, or cellular enzyme-linked immunosorbent assay, is a powerful and easy to use technique to study cell surface antigens under different stimulations. Nevertheless, some factors must be discussed and optimized prior to reaching a reproducible CELISA. These include the choice of cell density, fixative agent, blocking agent, culture medium, optimal antibody dilutions, and incubation time. In this paper, we first present a short review of some references devoted to CELISA by means of a comparison of these parameters, followed by their description. Then, we describe and study these different parameters using practical examples comparing TNF-induced ICAM-1 expression as an end point, on HBL melanoma and HUVEC. These cell lines were also chosen because they differ in their ability to grow as discontinuous and continuous layers, respectively. Furthermore, we designed a comprehensive flow chart, as well as a complete step-by-step protocol for CELISA optimization.

  2. A cross-layer design and ant-colony optimization based load-balancing routing protocol for ad-hoc networks

    Institute of Scientific and Technical Information of China (English)

    ZHENG Xiangquan; GUO Wei; GE Lijia; LIU Renting

    2007-01-01

    In order to periodically reassess the status of the alternate path route (APR) set and to improve the efficiency of alternate path construction existing in most current alternate path routing protocols,we present a cross-layer design and ant-colony optimization based load-balancing routing protocol for ad-hoc networks (CALRA) in this paper.In CALRA,the APR set maintained in nodes is aged and reassessed by the inherent mechanism of pheromone evaporation of ant-colony optimization algorithm,and load balance of network is achieved by ant-colony optimization combining with cross-layer synthetic optimization.The efficiency of APR set construction is improved by bidirectional and hop-by-hop routing update during routing discovery and routing maintenance process.Moreover,ants in CALRA deposit simulated pheromones as a function of multiple parameters corresponding to the information collected by each layer of each node visited,such as the distance from their source node,the congestion degree of the visited nodes,the current pheromones the nodes possess,the velocity of the nodes,and so on,and provide the information to the visiting nodes to update their pheromone tables by endowing the different parameters corresponding to different information and different weight values,which provides a new method to improve the congestion problem,the shortcut problem,the convergence rate and the heavy overheads commonly existed in existing ant-based routing protocols for ad-hoc networks.The performance of the algorithm is measured by the packet delivery rate,good-put ratio (routing overhead),and end-to-end delay.Simulation results show that CALRA performs well in decreasing the route overheads,balancing traffic load,as well as increasing the packet delivery rate,etc.

  3. Optimization of DNA isolation and PCR protocol for analysis and evaluation of genetic diversity of the medicinal plant, Anemopsis californica using RAPD.

    Science.gov (United States)

    Lizette Del-Toro-Sánchez, C; Villaseñor-Alvarado, S; Zurita-Martínez, Florentina; Castellanos-Hernández, O A; Rodríguez-Sahagún, Araceli; Isabel Torres-Morán, M; Rojas-Bravo, D; Gutiérrez-Lomelí, M

    2013-06-01

    Anemopsis californica is a perennial herbaceous plant that has been utilized as a medicinal plant for the treatment of various diseases. The present work was carried out with the objective of optimizing a method of extraction of the genomic DNA of A. californica and a PCR protocol and later to evaluate the existing genetic diversity among the genotypes deriving from different origins. For DNA extraction, we tested four procedures: with the CTA B-2 protocol, we obtained the highest yield (61.5±2.2 μg DNA/g of leaf tissues) and the best quality (A260/280 1.83±0.022). To estimate genetic variability, we utilized the randomly amplified polymorphism DNA (RAPD) technique, employing 20 oligonucleotides, of which only 18 generated reproducible banding patterns, producing 123 polymorphic bands generated, thus obtaining a polymorphism rate of 93.93% among the genotypes analyzed. The Jaccard similarity coefficient generated a variation ranging from 0.325-0.921, indicating a high level of genetic variation among the studied genotypes. An Unweighted pair-group method with arithmetic mean (UPGMA) group analysis indicated six distinct groups. The present optimized method for DNA isolation and RAPD protocol may serve as an efficient tool for further molecular studies.

  4. In vitro comparative study of two decellularization protocols in search of an optimal myocardial scaffold for recellularization

    Science.gov (United States)

    Perea-Gil, Isaac; Uriarte, Juan J; Prat-Vidal, Cristina; Gálvez-Montón, Carolina; Roura, Santiago; Llucià-Valldeperas, Aida; Soler-Botija, Carolina; Farré, Ramon; Navajas, Daniel; Bayes-Genis, Antoni

    2015-01-01

    Introduction. Selection of a biomaterial-based scaffold that mimics native myocardial extracellular matrix (ECM) architecture can facilitate functional cell attachment and differentiation. Although decellularized myocardial ECM accomplishes these premises, decellularization processes may variably distort or degrade ECM structure. Materials and methods. Two decellularization protocols (DP) were tested on porcine heart samples (epicardium, mid myocardium and endocardium). One protocol, DP1, was detergent-based (SDS and Triton X-100), followed by DNase I treatment. The other protocol, DP2, was focused in trypsin and acid with Triton X-100 treatments. Decellularized myocardial scaffolds were reseeded by embedding them in RAD16-I peptidic hydrogel with adipose tissue-derived progenitor cells (ATDPCs). Results. Both protocols yielded acellular myocardial scaffolds (~82% and ~94% DNA reduction for DP1 and DP2, respectively). Ultramicroscopic assessment of scaffolds was similar for both protocols and showed filamentous ECM with preserved fiber disposition and structure. DP1 resulted in more biodegradable scaffolds (P = 0.04). Atomic force microscopy revealed no substantial ECM stiffness changes post-decellularization compared to native tissue. The Young’s modulus did not differ between heart layers (P = 0.69) or decellularization protocols (P = 0.15). After one week, recellularized DP1 scaffolds contained higher cell density (236 ± 106 and 98 ± 56 cells/mm2 for recellularized DP1 and DP2 scaffolds, respectively; P = 0.04). ATDPCs in both DP1 and DP2 scaffolds expressed the endothelial marker isolectin B4, but only in the DP1 scaffold ATDPCs expressed the cardiac markers GATA4, connexin43 and cardiac troponin T. Conclusions. In our hands, DP1 produced myocardial scaffolds with higher cell repopulation and promotes ATDPCs expression of endothelial and cardiomyogenic markers. PMID:26045895

  5. Optimization and staining characteristic of immunohistochemical methods in detecting isocitrate dehydrogenase-1 mutations in human gliomas%免疫组化染色检测脑胶质瘤IDH1的优化及染色特点

    Institute of Scientific and Technical Information of China (English)

    黎相照; 薛小磊; 张中满; 张颖芬; 丁彦青; 韩慧霞

    2016-01-01

    Objective To compare the advantages and disadvantages of different immunohistochemical methods in detecting isocitrate dehydrogenase-1 (IDH 1) mutations in gliomas,and to optimize the processes these detection.Methods One hundred and thirty-eighty glioma specimens,collected and conformed by pathology in our hospital from January 2013 to December 2013,were used in our study,including 18 of WHO grade Ⅰ,49 of WHO grade Ⅱ,24 of WHO grade Ⅲ and 47 of WHO grade Ⅳ.Manual immunohistochemical method and automatic immunohistochemical instrument were used to detect the IDH1 mutation.PCR-high resolution melting curve analysis (PCR-HRM) was used to verify the above results.Results There were 65.9% positive specimens those had IDH1 positive tumor cells higher than 75%,and 70.7% positive specimens those were strong staining.Manual immunohistochemical method enjoyed advantages as clean background,clearness and easy reading,and no interpretation difficulty or false-positive result were noted with this method;while automatic immunohistochemical instrument enjoyed dark background,which led to interpretation difficulty or false-positive result;the results of IDH1 staining had significant differences between and automatic immunohistochemical instrument (x2=22.042,P=0.000).The positive detection rate of automatic immunohistochemical instrument was significantly higher than that of manual immunohistochemical method,and the results of IDH1 detection had no significant difference between manual immunohistochemical method and PCR-HRM (x2=0.800,P=0.371).Conclusions The results of IDH1 detection by manual immunohistochemical method are more accurate than that of immunohistochemical instrument.IDH1 gene mutation only has a relationship with the number of positive tumor cells,and not the staining intensity.The specimen can be considered to IDH1 gene mutation when the positive cells are more than 5%.%目的 比较胶质瘤中异柠檬酸脱氢酶-1(IDH1)不同检测方法的优

  6. ENHANCED DAPI STAINING FOR CRYPTOSPORIDIUM IN WATER SAMPLES

    Science.gov (United States)

    The U.S. Environmental Protection Agency's Method 1623 is used to detect and quantify the presence of {ital Cryptosporidium} spp. oocysts in water. The protocol consists of concentrating a sample, staining this concentrate with a fluorescent antibody, and examining the sample mi...

  7. Optimization of an animal test protocol for toxicogenomics studies (ii); a cross-laboratory gene expression analysis.

    Science.gov (United States)

    Sumida, Kayo; Saito, Koichi; Oeda, Kenji; Otsuka, Masanori; Tsujimura, Kazunari; Miyaura, Hideki; Sekijima, Masaru; Nakayama, Koji; Kawano, Yukiko; Kawakami, Yuki; Asamoto, Makoto; Shirai, Tomoyuki

    2007-02-01

    Toxicogenomics is a promising new tool for prediction of chemical toxicities including carcinogenicity in a relatively short period. However, it is important to develop a reliable animal test protocol for toxicogenomics studies. The preparation of RNA and tissues is also crucial, since it greatly influences outcomes of gene expression analysis. We proposed an animal test protocol for toxicogenomics studies. In the present study, we examined an animal test protocol by comparing biological and gene expression data from different laboratories running identical in vivo studies on the same microarray platform. The results gave good correspondence in all three laboratories at the level of biological responses and gene expression, especially for genes whose expression changes were quite large. As the fold change or the signal values become smaller, however, discrepancies occur in gene expression data. For example, one laboratory shows an opposite directional change to the other two or no change. The results of hierarchical clustering and principal component analysis (PCA) demonstrated all samples from the three laboratories being clearly divided between control and treatment. Examination of the reproducibility of gene expression data across laboratories using the proposed animal test protocol thus confirmed only minor differences, which was expected to present no problems for gene expression analysis.

  8. A simple protocol for attenuating the auto-fluorescence of cyanobacteria for optimized fluorescence in situ hybridization (FISH) imaging.

    Science.gov (United States)

    Zeller, Perrine; Ploux, Olivier; Méjean, Annick

    2016-03-01

    Cyanobacteria contain pigments, which generate auto-fluorescence that interferes with fluorescence in situ hybridization (FISH) imaging of cyanobacteria. We describe simple chemical treatments using CuSO4 or H2O2 that significantly reduce the auto-fluorescence of Microcystis strains. These protocols were successfully applied in FISH experiments using 16S rRNA specific probes and filamentous cyanobacteria.

  9. Development of a preparation and staining method for fetal erythroblasts in maternal blood : Simultaneous immunocytochemical staining and FISH analysis

    NARCIS (Netherlands)

    Oosterwijk, JC; Mesker, WE; Ouwerkerk-van Velzen, MCM; Knepfle, CFHM; Wiesmeijer, KC; van den Burg, MJM; Beverstock, GC; Bernini, LF; van Ommen, Gert-Jan B; Kanhai, HHH; Tanke, HJ

    1998-01-01

    In order to detect fetal nucleated red blood cells (NRBCs) in maternal blood, a protocol was developed which aimed at producing a reliable staining method for combined immunocytochemical and FISH analysis. The technique had to be suitable for eventual automated screening of slides. Chorionic villi w

  10. Multispectral Enhancement towards Digital Staining

    Directory of Open Access Journals (Sweden)

    Pinky A. Bautista

    2012-01-01

    Full Text Available Background: Digital staining can be considered as a special form of image enhancement wherein the concern is not only to increase the contrast between the background objects and objects of interest, but to also impart the colors that mark the objects’ unique reactions to a specific stain. In this paper, we extended the previously proposed multispectral enhancement methods such that the colors of the background pixels can also be changed.

  11. DAPI Staining of Drosophila Embryos.

    Science.gov (United States)

    Rothwell, Wendy F; Sullivan, William

    2007-10-01

    INTRODUCTIONDrosophila embryos can be stained with specific fluorescent probes or antibodies through either direct or indirect immunofluorescence. In particular, several effective probes exist for visualizing DNA. 4',6-diamidino-2-phenylindole (DAPI) is a commonly used DNA-binding dye. Because it is specific for double-stranded DNA, no prior RNase treatment is required. While the embryo staining method described here uses DAPI, other fluorescent DNA probes can be processed similarly.

  12. Voice Traffic over Mobile Ad Hoc Networks: A Performance Analysis of the Optimized Link State Routing Protocol

    Science.gov (United States)

    2009-03-26

    Investigating MANETs in a VoIP Context. Prior research has inves- tigated the performance of MANETS carrying VoIP traffic. Thibodeau et al. studied whether...number of hops contained in the repaired route is observed. Thibodeau et al. concludes that node mobility and node density have limited influence on...testbeds. Most studies account for mobile nodes and study the routing protocols AODV and OLSR. For example, Thibodeau et al. study the effects of AODV

  13. As Low Dose as Sufficient Quality: Optimization of Cone-beam Computed Tomographic Scanning Protocol for Tooth Autotransplantation Planning and Follow-up in Children.

    Science.gov (United States)

    EzEldeen, Mostafa; Stratis, Andreas; Coucke, Wim; Codari, Marina; Politis, Constantinus; Jacobs, Reinhilde

    2017-02-01

    Tooth autotransplantation (TAT) offers a viable biological approach to tooth replacement in children. To enhance the outcome predictability of the TAT procedure, a cone-beam computed tomographic (CBCT)-based surgical planning and transfer technique has been developed. The aim of this study was to optimize the CBCT scanning protocol to achieve a dose as low as possible and to maintain sufficient image quality. A sectional head phantom (SK150; The Phantom Laboratory, Salem, NY) was scanned using 18 exposure protocols in 3 different CBCT machines: 3D Accuitomo 170 (Morita, Kyoto, Japan), ProMax 3D MAX (Planmeca, Helsinki, Finland), and NewTom VGI EVO (QR Verona, Verona, Italy). The effective dose (ED) was calculated using Monte Carlo simulation and pediatric voxel phantoms (5- and 8-year-old males and a 12-year-old female). Image quality was assessed by comparing segmented teeth volumes, evaluation of the visibility of the lamina dura, and morphologic surface analysis of 3-dimensional models. A general linear mixed model was fit to combine image quality parameters and radiation effective dose for each protocol in order to rank and compare the protocols examined in the study. The ED for the preoperative scan can be reduced to the range of 74.6-157.9 μSv, with ProMax with ultra-low-dose high-definition reconstruction (Planmeca) 100 × 90 scoring the highest. The ED for the postoperative scan can be reduced to the range of 24.2-41.5 μSv with ProMax with ultra-low-dose normal-dose reconstruction 50 × 55 and NewTom 50 × 50 with the standard mode scoring the highest. A considerable reduction in the pediatric ED can be achieved while maintaining sufficient image quality for tooth autotransplantation planning and follow-up using the dose optimization protocols. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  14. Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Moniya Chatterjee

    2012-01-01

    Full Text Available Two-dimensional electrophoresis and mass spectrometry are undoubtedly two essential tools popularly used in proteomic analyses. Utilization of these techniques however largely depends on efficient and optimized sample preparation, regarded as one of the most crucial steps for recovering maximum amount of reliable information. The present study highlights the optimization of an effective and efficient protocol, capable of extraction of root proteins from recalcitrant phenolic rich tissues of chickpea. The widely applicable TCA-acetone and phenol-based methods have been comparatively evaluated, amongst which the latter appeared to be better suited for the sample. The phenol extraction-based method further complemented with sodium dodecyl sulphate (SDS and pulsatory treatments proved to be the most suitable method represented by greatest spot number, good resolution, and spot intensities. All the randomly selected spots showed successful identification when subjected to further downstream MALDI-TOF and MS/MS analyses. Hence, the information obtained collectively proposes the present protein extraction protocol to be an effective one that could be applicable for recalcitrant leguminous root samples.

  15. Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Chatterjee, Moniya; Gupta, Sumanti; Bhar, Anirban; Das, Sampa

    2012-01-01

    Two-dimensional electrophoresis and mass spectrometry are undoubtedly two essential tools popularly used in proteomic analyses. Utilization of these techniques however largely depends on efficient and optimized sample preparation, regarded as one of the most crucial steps for recovering maximum amount of reliable information. The present study highlights the optimization of an effective and efficient protocol, capable of extraction of root proteins from recalcitrant phenolic rich tissues of chickpea. The widely applicable TCA-acetone and phenol-based methods have been comparatively evaluated, amongst which the latter appeared to be better suited for the sample. The phenol extraction-based method further complemented with sodium dodecyl sulphate (SDS) and pulsatory treatments proved to be the most suitable method represented by greatest spot number, good resolution, and spot intensities. All the randomly selected spots showed successful identification when subjected to further downstream MALDI-TOF and MS/MS analyses. Hence, the information obtained collectively proposes the present protein extraction protocol to be an effective one that could be applicable for recalcitrant leguminous root samples.

  16. Determination of hydrazine in drinking water: Development and multivariate optimization of a rapid and simple solid phase microextraction-gas chromatography-triple quadrupole mass spectrometry protocol.

    Science.gov (United States)

    Gionfriddo, Emanuela; Naccarato, Attilio; Sindona, Giovanni; Tagarelli, Antonio

    2014-07-04

    In this work, the capabilities of solid phase microextraction were exploited in a fully optimized SPME-GC-QqQ-MS analytical approach for hydrazine assay. A rapid and easy method was obtained by a simple derivatization reaction with propyl chloroformate and pyridine carried out directly in water samples, followed by automated SPME analysis in the same vial without further sample handling. The affinity of the different derivatized compounds obtained towards five commercially available SPME coatings was evaluated, in order to achieve the best extraction efficiency. GC analyses were carried out using a GC-QqQ-MS instrument in selected reaction monitoring (SRM) acquisition mode which has allowed the achievement of high specificity by selecting appropriate precursor-product ion couples improving the capability in analyte identification. The multivariate approach of experimental design was crucial in order to optimize derivatization reaction, SPME process and tandem mass spectrometry parameters. Accuracy of the proposed protocol, tested at 60, 200 and 800 ng L(-1), provided satisfactory values (114.2%, 83.6% and 98.6%, respectively), whereas precision (RSD%) at the same concentration levels were of 10.9%, 7.9% and 7.7% respectively. Limit of detection and quantification of 4.4 and 8.3 ng L(-1) were obtained. The reliable application of the proposed protocol to real drinking water samples confirmed its capability to be used as analytical tool for routine analyses.

  17. Western Blot of Stained Proteins from Dried Polyacrylamide Gels

    Science.gov (United States)

    Gruber, Claudia; Stan-Lotter, Helga

    1996-01-01

    Western blotting of proteins is customarily performed following their separation on polyacrylamide gels, either prior to staining (1) or, as recently reported, following staining (2). We describe here Western blotting with stained gels, which had been dried and some of which had been stored for years. This procedure permits immunological analysis of proteins, to which antisera may have become available only later, or where the application of newly developed sensitive detection methods is desired. Once rehydration of the gels is achieved, proteins can be-transferred to blotting membranes by any appropriate protocol. Proteins stained with Coomassie Blue have to be detected with a non-chromogenic method, such as the film-based enhanced chemiluminescence (ECL)2) procedure (3). Silver stained proteins, which transfer in the colorless form, may be visualized by any detection method, although, because of the usually very low amounts of proteins, detection by ECL is preferable. Blotting of stained proteins from rehydrated gels is as rapid and as quantitative as from freshly prepared gels, in contrast to blotting from wet stained gels, which requires extensive washing and results in low transfer efficiency (2). Together with a photographic record of the gel pattern, unambiguous identification of immunoreactive proteins from complex mixtures is possible. Some further applications of this work are discussed.

  18. Identification and quantification of microplastics using Nile Red staining.

    Science.gov (United States)

    Shim, Won Joon; Song, Young Kyoung; Hong, Sang Hee; Jang, Mi

    2016-12-15

    We investigated the applicability of Nile Red (NR), a fluorescent dye, for microplastic analysis, and determined the optimal staining conditions. Five mg/L NR solution in n-hexane effectively stained plastics, and they were easily recognized in green fluorescence. The NR staining method was successfully applied to micro-sized polyethylene, polypropylene, polystyrene, polycarbonate, polyurethane, and poly(ethylene-vinyl acetate), except for polyvinylchloride, polyamide and polyester. The recovery rate of polyethylene (100-300μm) spiked to pretreated natural sand was 98% in the NR stating method, which was not significantly (p<0.05) different with FT-IR identification. The NR staining method was suitable for discriminating fragmented polypropylene particles from large numbers of sand particles in laboratory weathering test samples. The method is straightforward and quick for identifying and quantifying polymer particles in the laboratory controlled samples. Further studies, however, are necessary to investigate the application of NR staining to field samples with organic remnants.

  19. 快速移动环境中上下文感知优化链路状态路由协议%Context-aware Optimized Link State Routing Protocol for Fast Movement Scene

    Institute of Scientific and Technical Information of China (English)

    张可; 张伟; 李炜; 曾家智

    2011-01-01

    提出了一种应用于快速移动环境的上下文感知优化链路状态协议CAOLSR(Context-aware Optimized Link State Routing Protocol).CAOLSR采用了一种上下文信息机制,将节点间相对移动预测、前后访问时间以及节点连接度情况引入MPR(Multi Point Relays)选择,并设计了CAOLSR-MPR算法.此外,CAOLSR通过引入Fisheye减少了移动性对路由精度的影响.模拟实验表明,在节点快速移动与拓扑快速变化环境下与HOLSR(Hierarchical Optimized Link State Routing Protocol),OLSR(Optimized Link State Routing Protocol),DSDV(Destination Sequenced Distance Vector)相比,CAOLSR具有更为良好的性能.%An Context-aware optimized link state routing protocol for networks with fast-moving nodes was proposed CAOLSR (Context-aware Optimized Link State Routing Protocol) adopts a context-aware mechanism,and selects MPR (Multi Point Relays) based on relative movement of nodes, recent access-time and connection number of nodes, and adopts a special flow of MPR selection. In addition, by the introduction of Fisheye, reduces the influence from mobility on the routing accuracy. Experimental results show that CAOLSR can achieve good performance and outperform HOLSR (Hierarchical Optimized Link State Routing Protocol), OLSR (Optimized Link State Routing Protocol) and DSDV (Destination Sequenced Distance Vector) in networks with fast-moving nodes.

  20. Multi-response optimization of the extraction and derivatization protocol of selected polar metabolites from apple fruit tissue for GC-MS analysis.

    Science.gov (United States)

    Bekele, Elias A; Annaratone, Carlo E P; Hertog, Maarten L A T M; Nicolai, Bart M; Geeraerd, Annemie H

    2014-05-08

    Given the complexity of the plant metabolome exhibiting a wide spectrum of physico-chemical properties, finding the best compromise for GC-MS analysis is a challenging exercise. In this study, the GC-MS protocol for extracting and analyzing polar metabolites from apple tissue is optimized. We found pure methanol extraction to be slightly better as compared to the two phase methanol/chloroform/water extraction in terms of introducing less degradation of the extracted metabolites while being comparable in extraction efficiency and repeatability. The methanol extraction was superior to the single phase methanol/chloroform/water extraction in all performance measures. A multi-response optimization based on a desirability function was applied to optimize the derivatization. This procedure allows searching for optimal parameters while simultaneously considering overall detection enhancement of metabolites from various metabolic classes. A short oximation at a high temperature in combination with a low silylation temperature gave results similar to a longer oximation at low temperature in combination with a high silylation temperature. Increasing silylation time from 0.5 h to 2 h resulted in an improvement of the silylation reaction.

  1. Optimization of saturation-recovery dynamic contrast-enhanced MRI acquisition protocol: monte carlo simulation approach demonstrated with gadolinium MR renography.

    Science.gov (United States)

    Zhang, Jeff L; Conlin, Chris C; Carlston, Kristi; Xie, Luke; Kim, Daniel; Morrell, Glen; Morton, Kathryn; Lee, Vivian S

    2016-07-01

    Dynamic contrast-enhanced (DCE) MRI is widely used for the measurement of tissue perfusion and to assess organ function. MR renography, which is acquired using a DCE sequence, can measure renal perfusion, filtration and concentrating ability. Optimization of the DCE acquisition protocol is important for the minimization of the error propagation from the acquired signals to the estimated parameters, thus improving the precision of the parameters. Critical to the optimization of contrast-enhanced T1 -weighted protocols is the balance of the T1 -shortening effect across the range of gadolinium (Gd) contrast concentration in the tissue of interest. In this study, we demonstrate a Monte Carlo simulation approach for the optimization of DCE MRI, in which a saturation-recovery T1 -weighted gradient echo sequence is simulated and the impact of injected dose (D) and time delay (TD, for saturation recovery) is tested. The results show that high D and/or high TD cause saturation of the peak arterial signals and lead to an overestimation of renal plasma flow (RPF) and glomerular filtration rate (GFR). However, the use of low TD (e.g. 100 ms) and low D leads to similar errors in RPF and GFR, because of the Rician bias in the pre-contrast arterial signals. Our patient study including 22 human subjects compared TD values of 100 and 300 ms after the injection of 4 mL of Gd contrast for MR renography. At TD = 100 ms, we computed an RPF value of 157.2 ± 51.7 mL/min and a GFR of 33.3 ± 11.6 mL/min. These results were all significantly higher than the parameter estimates at TD = 300 ms: RPF = 143.4 ± 48.8 mL/min (p = 0.0006) and GFR = 30.2 ± 11.5 mL/min (p = 0.0015). In conclusion, appropriate optimization of the DCE MRI protocol using simulation can effectively improve the precision and, potentially, the accuracy of the measured parameters. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Laser treatment of port-wine stains

    Directory of Open Access Journals (Sweden)

    Brightman LA

    2015-01-01

    Full Text Available Lori A Brightman,1 Roy G Geronemus,1 Kavitha K Reddy2 1Laser and Skin Surgery Center of New York, New York, NY, USA; 2Department of Dermatology, Boston University School of Medicine, Boston, MA, USA Abstract: Port-wine stains are a type of capillary malformation affecting 0.3% to 0.5% of the population. Port-wine stains present at birth as pink to erythematous patches on the skin and/or mucosa. Without treatment, the patches typically darken with age and may eventually develop nodular thickening or associated pyogenic granuloma. Laser and light treatments provide improvement through selective destruction of vasculature. A variety of vascular-selective lasers may be employed, with the pulsed dye laser being the most common and well studied. Early treatment produces more optimal results. Advances in imaging and laser treatment technologies demonstrate potential to further improve clinical outcomes. Keywords: laser, port-wine stain, capillary vascular malformation, vascular birthmark, selective photothermolysis, photodynamic therapy, intense pulsed light

  3. Development and optimization of a biopreparedness protocol for extracting and detecting avian influenza virus in broiler chicken meat.

    Science.gov (United States)

    Di Pasquale, Simona; Falcone, Emiliana; Knutsson, Rickard; Vaccari, Gabriele; De Medici, Dario; Di Trani, Livia

    2013-09-01

    Detection of avian influenza virus (AIV) in poultry meat is hampered by the lack of an efficient analytical method able to extract and concentrate viral RNA prior to PCR. In this study we developed a method for extracting and detecting AIV from poultry meat by a previously standardized 1-step real-time reverse transcriptase PCR (RRT-PCR) assay. In addition, a new process control, represented by feline calicivirus (FCV), was included in the original protocol, to evaluate all analytical steps from sample preparation to the detection phase. The detection limit was below 1×10(-1) TCID50 of AIV per sample, and the quantification limit corresponded to 1×10(1) TCID50 of AIV per sample. Moreover, the addition of 1×10(2) TCID50/sample of FCV did not affect the quantification and detection limit of the reaction. These results show that the developed assay is suitable for detecting small amounts of AIV in poultry meat. In addition, the developed biopreparedness protocol can be applied to detect AIV in legal or illegal imported broiler chicken meat. The availability of a rapid and sensitive diagnostic method based on molecular identification of AIV in poultry meat provides an important tool in the prevention of AIV circulation.

  4. Cooperative Optimization QoS Cloud Routing Protocol Based on Bacterial Opportunistic Foraging and Chemotaxis Perception for Mobile Internet

    Directory of Open Access Journals (Sweden)

    Shujuan Wang

    2015-01-01

    Full Text Available In order to strengthen the mobile Internet mobility management and cloud platform resources utilization, optimizing the cloud routing efficiency is established, based on opportunistic bacterial foraging bionics, and puts forward a chemotaxis perception of collaborative optimization QoS (Quality of Services cloud routing mechanism. The cloud routing mechanism is based on bacterial opportunity to feed and bacterial motility and to establish the data transmission and forwarding of the bacterial population behavior characteristics. This mechanism is based on the characteristics of drug resistance of bacteria and the structure of the field, and through many iterations of the individual behavior and population behavior the bacteria can be spread to the food gathering area with a certain probability. Finally, QoS cloud routing path would be selected and optimized based on bacterial bionic optimization and hedge mapping relationship between mobile Internet node and bacterial population evolution iterations. Experimental results show that, compared with the standard dynamic routing schemes, the proposed scheme has shorter transmission delay, lower packet error ratio, QoS cloud routing loading, and QoS cloud route request overhead.

  5. Optimization of the Protocol for the Isolation and Refolding of the Extracellular Domain of HER2 Expressed in Escherichia coli.

    Science.gov (United States)

    Dolgikh, V V; Senderskiy, I V; Tetz, G V; Tetz, V V

    2014-04-01

    Receptor 2 of the human epidermal growth factor (HER2/neu, c-erbB2) is a 185 kDa proto-oncogene protein characterized by an overexpression in some oncological diseases, including 30% of mammary glands cancers, as well as tumors in the ovary, stomach and other organs of the human body. Since HER2- tumor status testing is the essential part of a successful cancer treatment, the expression and purification of substantial amounts of the extracellular domain (ECD) of HER2 is an important task. The production of ECD HER2 in Escherichia coli has several advantages over the use of eukaryotic expression systems, but the bulk of the recombinant product in bacteria accumulates as insoluble protein inclusion bodies. In this study, we obtained ECD HER2 in Escherichia coli as insoluble inclusion bodies and elaborated a simple, efficient, and fast protocol for the solubilization, refolding, and isolation of the protein in soluble form.

  6. Optimization of Single- and Dual-Color Immunofluorescence Protocols for Formalin-Fixed, Paraffin-Embedded Archival Tissues.

    Science.gov (United States)

    Kajimura, Junko; Ito, Reiko; Manley, Nancy R; Hale, Laura P

    2016-02-01

    Performance of immunofluorescence staining on archival formalin-fixed paraffin-embedded human tissues is generally not considered to be feasible, primarily due to problems with tissue quality and autofluorescence. We report the development and application of procedures that allowed for the study of a unique archive of thymus tissues derived from autopsies of individuals exposed to atomic bomb radiation in Hiroshima, Japan in 1945. Multiple independent treatments were used to minimize autofluorescence and maximize fluorescent antibody signals. Treatments with NH3/EtOH and Sudan Black B were particularly useful in decreasing autofluorescent moieties present in the tissue. Deconvolution microscopy was used to further enhance the signal-to-noise ratios. Together, these techniques provide high-quality single- and dual-color fluorescent images with low background and high contrast from paraffin blocks of thymus tissue that were prepared up to 60 years ago. The resulting high-quality images allow the application of a variety of image analyses to thymus tissues that previously were not accessible. Whereas the procedures presented remain to be tested for other tissue types and archival conditions, the approach described may facilitate greater utilization of older paraffin block archives for modern immunofluorescence studies.

  7. Optimization of protocols for derivation of mouse embryonic stem cell lines from refractory strains, including the non obese diabetic mouse.

    Science.gov (United States)

    Davies, Timothy J; Fairchild, Paul J

    2012-07-01

    The derivation of pluripotent embryonic stem cells (ESCs) from a variety of genetic backgrounds remains a desirable objective in the generation of mice functionally deficient in genes of interest and the modeling of human disease. Nevertheless, disparity in the ease with which different strains of mice yield ESC lines has long been acknowledged. Indeed, the generation of bona fide ESCs from the non obese diabetic (NOD) mouse, a well-characterized model of human type I diabetes, has historically proved especially difficult to achieve. Here, we report the development of protocols for the derivation of novel ESC lines from C57Bl/6 mice based on the combined use of high concentrations of leukemia inhibitory factor and serum-replacement, which is equally applicable to fresh and cryo-preserved embryos. Further, we demonstrate the success of this approach using Balb/K and CBA/Ca mice, widely considered to be refractory strains. CBA/Ca ESCs contributed to the somatic germ layers of chimeras and displayed a very high competence at germline transmission. Importantly, we were able to use the same protocol for the derivation of ESC lines from nonpermissive NOD mice. These ESCs displayed a normal karyotype that was robustly stable during long-term culture, were capable of forming teratomas in vivo and germline competent chimeras after injection into recipient blastocysts. Further, these novel ESC lines efficiently formed embryoid bodies in vitro and could be directed in their differentiation along the dendritic cell lineage, thus illustrating their potential application to the generation of cell types of relevance to the pathogenesis of type I diabetes.

  8. Optimizing the MRI protocol of the sacroiliac joints in Spondyloarthritis: which para-axial sequence should be used?

    Energy Technology Data Exchange (ETDEWEB)

    Giraudo, Chiara; Weber, Michael; Platzgummer, Hannes; Kainberger, Franz; Schueller-Weidekamm, Claudia [Medical University of Vienna, Vienna General Hospital, Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging und Image-guided Therapy, Vienna (Austria); Magnaldi, Silvia [Fondazione Poliambulanza Istituto Ospedaliero, Dipartimento di Radiologia e Diagnostica per Immagini, Brescia (Italy); Puchner, Antonia [Medical University of Vienna, Vienna General Hospital, Division of Rheumatology, Department of Internal Medicine III, Vienna (Austria)

    2016-01-15

    To assess the diagnostic value of para-axial T2w-TSE (paT2) and fat-suppressed proton density (paPD-FS) MRI sequences for the evaluation of the sacroiliac joint (SIJ) of patients with axial Spondylarthritis (SpA). One hundred and six patients with clinical findings suggestive of SpA underwent an MR protocol of the SIJ with additional paPD-FS (41 patients) and paT2 (105 patients). Acute (bone marrow oedema [BME], enthesitis, capsulitis, synovitis) and chronic findings (erosions, ankylosis) were assessed by paPD-FS and compared with the gold standard post-contrast sequences, whereas chronic features (because of the lack of fat suppression) were evaluated on paT2 and compared with pcT1. paPD-FS demonstrated high sensitivity (98.9 %) and specificity (99.1 %) for BME; sensitivity and specificity for synovitis and enthesitis were 100 %; 85.7 % and 100 %, respectively, for capsulitis. paPD-FS and paT2 showed 100 % sensitivity and specificity for ankylosis; for erosions, paT2 demonstrated 85.3 % sensitivity and 100 % specificity, whereas paPD-FS, respectively, 98 % and 100 %. PaT2 and paPD-FS provided precious information enabling an accurate interpretation of the heterogeneous findings of SpA. paPD-FS showed good results in detecting acute and chronic lesions and its inclusion in a routine MR examination of the SIJ could increase the diagnostic performance of a pre-contrast protocol. (orig.)

  9. Estrogen receptor antibody incubation time and extent of immunoreactivity in invasive carcinoma of the breast: the importance of optimizing antibody avidity.

    Science.gov (United States)

    Goldstein, Neal S; Hunter, Susan; Forbes, Suzy; Odish, Eva; Tehrani, Matab

    2007-06-01

    We noticed that the percentage and intensity of estrogen receptor (ER) antibody (Ab) AB ER 1D5 immunohistochemical (IHC) staining was altered by Ab incubation time and the type of chromogen detection system in invasive breast carcinomas. We studied the impact of these 2 factors on Ab ER 1D5 immunoreactivity. Serial sections from 22 strongly ER-positive invasive breast carcinomas were immunohistochemically stained with Ab clone ER 1D5 using 3 IHC protocols. One IHC protocol used a 12-hour Ab incubation and a supersensitive, labeled streptavidin-biotin chromogen detection system (12 h-Standard), the second IHC protocol used a 2-hour Ab incubation and a supersensitive, labeled streptavidin-biotin chromogen detection system (2 h-SS), and the third protocol used a 2-hour Ab incubation and a polymer-based detection system (2 h-Env). Twenty identical fields on each slide stained with each IHC protocol were evaluated and staining was quantified using image analysis. The mean staining percentages using the 12 h-Standard, 2 h-SS, and 2 h-Env IHC staining protocols were 89%, 72%, and 47%, respectively (P<0.001). Three of the 22 cases (14%) were ER negative (<10% stained area) with the 2 h-Env IHC protocol. Stain intensity was significantly stronger with the 12 h-Standard Ab incubation IHC protocol than either 2-hour Ab incubation protocol (P<0.001). Twelve cases stained with 2-hour Ab incubation IHC protocols had weak visually seen staining: 7 were Allred total score 2 (ER negative) and 5 were Allred total score 3. Ab ER 1D5 avidity is directly related to factors that impact electrostatic forces, one of which is Ab incubation time. Standard automated stainer Ab incubation times of less than 1 hour may be of insufficient duration and result in artificially low levels of ER immunoreactivity. The chromogen detection system in association with the ER 1D5 Ab also alters levels of immunoreactivity. Optimization of IHC staining protocols should include evaluating the Ab incubation

  10. Salt stains from evaporating droplets

    NARCIS (Netherlands)

    Shahidzadeh, N.; Schut, M.F.L.; Desarnaud, J.; Prat, M.; Bonn, D.

    2015-01-01

    The study of the behavior of sessile droplets on solid substrates is not only associated with common everyday phenomena, such as the coffee stain effect, limescale deposits on our bathroom walls, but also very important in many applications such as purification of pharmaceuticals, deicing of

  11. Salt stains from evaporating droplets

    NARCIS (Netherlands)

    Shahidzadeh, N.; Schut, M.F.L.; Desarnaud, J.; Prat, M.; Bonn, D.

    2015-01-01

    The study of the behavior of sessile droplets on solid substrates is not only associated with common everyday phenomena, such as the coffee stain effect, limescale deposits on our bathroom walls, but also very important in many applications such as purification of pharmaceuticals, deicing of airplan

  12. Accelerated staining technique using kitchen microwave oven.

    Science.gov (United States)

    Mukunda, Archana; Narayan, T V; Shreedhar, Balasundhari; Shashidhara, R; Mohanty, Leeky; Shenoy, Sadhana

    2015-01-01

    Histopathological diagnosis of specimens is greatly dependent on good sample preparation and staining. Both of these processes is governed by diffusion of fluids and dyes in and out of the tissue, which is the key to staining. Diffusion of fluids can be accelerated by the application of heat that reduces the time of staining from hours to the minute. We modified an inexpensive model of kitchen microwave oven for staining. This study is an attempt to compare the reliability of this modified technique against the tested technique of routine staining so as to establish the kitchen microwave oven as a valuable diagnostic tool. Sixty different tissue blocks were used to prepare 20 pairs of slides for 4 different stains namely hematoxylin and eosin, Van Gieson's, 0.1% toluidine blue and periodic acid-Schiff. From each tissue block, two bits of tissues were mounted on two different slides. One slide was stained routinely, and the other stained inside a microwave. A pathologist evaluated the stained slides and the results so obtained were analyzed statistically. Microwave staining considerably cut down the staining time from hours to seconds. Microwave staining showed no loss of cellular and nuclear details, uniform-staining characteristics and was of excellent quality. The cellular details, nuclear details and staining characteristics of microwave stained tissues were better than or equal to the routine stained tissue. The overall quality of microwave-stained sections was found to be better than the routine stained tissue in majority of cases.

  13. Resveratrol Ameliorates the Maturation Process of β-Cell-Like Cells Obtained from an Optimized Differentiation Protocol of Human Embryonic Stem Cells

    Science.gov (United States)

    Pezzolla, Daniela; López-Beas, Javier; Lachaud, Christian C.; Domínguez-Rodríguez, Alejandro; Smani, Tarik; Hmadcha, Abdelkrim; Soria, Bernat

    2015-01-01

    Human embryonic stem cells (hESCs) retain the extraordinary capacity to differentiate into different cell types of an adult organism, including pancreatic β-cells. For this particular lineage, although a lot of effort has been made in the last ten years to achieve an efficient and reproducible differentiation protocol, it was not until recently that this aim was roughly accomplished. Besides, several studies evidenced the impact of resveratrol (RSV) on insulin secretion, even though the mechanism by which this polyphenol potentiates glucose-stimulated insulin secretion (GSIS) is still not clear. The aim of this study was to optimize an efficient differentiation protocol that mimics in vivo pancreatic organogenesis and to investigate whether RSV may improve the final maturation step to obtain functional insulin-secreting cells. Our results indicate that treatment of hESCs (HS-181) with activin-A induced definitive endoderm differentiation as detected by the expression of SOX17 and FOXA2. Addition of retinoic acid (RA), Noggin and Cyclopamine promoted pancreatic differentiation as indicated by the expression of the early pancreatic progenitor markers ISL1, NGN3 and PDX1. Moreover, during maturation in suspension culture, differentiating cells assembled in islet-like clusters, which expressed specific endocrine markers such as PDX1, SST, GCG and INS. Similar results were confirmed with the human induced Pluripotent Stem Cell (hiPSC) line MSUH-001. Finally, differentiation protocols incorporating RSV treatment yielded numerous insulin-positive cells, induced significantly higher PDX1 expression and were able to transiently normalize glycaemia when transplanted in streptozotocin (STZ) induced diabetic mice thus promoting its survival. In conclusion, our strategy allows the efficient differentiation of hESCs into pancreatic endoderm capable of generating β-cell-like cells and demonstrates that RSV improves the maturation process. PMID:25774684

  14. Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing.

    Science.gov (United States)

    Sim, James Heng Chiak; Anikst, Victoria; Lohith, Akshar; Pourmand, Nader; Banaei, Niaz

    2015-07-01

    Successful sequencing of the Clostridium difficile genome requires high-quality genomic DNA (gDNA) as the starting material. gDNA extraction using conventional methods is laborious. We describe here an optimized method for the simple extraction of C. difficile gDNA using the QIAamp DNA minikit, which yielded high-quality sequence reads on the Illumina MiSeq platform. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. Synthesis of cis-C-iodo-N-tosyl-aziridines using diiodomethyllithium: reaction optimization, product scope and stability, and a protocol for selection of stationary phase for chromatography.

    Science.gov (United States)

    Boultwood, Tom; Affron, Dominic P; Trowbridge, Aaron D; Bull, James A

    2013-07-05

    The preparation of C-iodo-N-Ts-aziridines with excellent cis-diastereoselectivity has been achieved in high yields by the addition of diiodomethyllithium to N-tosylimines and N-tosylimine-HSO2Tol adducts. This addition-cyclization protocol successfully provided a wide range of cis-iodoaziridines, including the first examples of alkyl-substituted iodoaziridines, with the reaction tolerating both aryl imines and alkyl imines. An ortho-chlorophenyl imine afforded a β-amino gem-diiodide under the optimized reaction conditions due to a postulated coordinated intermediate preventing cyclization. An effective protocol to assess the stability of the sensitive iodoaziridine functional group to chromatography was also developed. As a result of the judicious choice of stationary phase, the iodoaziridines could be purified by column chromatography; the use of deactivated basic alumina (activity IV) afforded high yield and purity. Rearrangements of electron-rich aryl-iodoaziridines have been promoted, selectively affording either novel α-iodo-N-Ts-imines or α-iodo-aldehydes in high yield.

  16. Optimization of diagnostic RT-PCR protocols and sampling procedures for the reliable and cost-effective detection of Cassava brown streak virus.

    Science.gov (United States)

    Abarshi, M M; Mohammed, I U; Wasswa, P; Hillocks, R J; Holt, J; Legg, J P; Seal, S E; Maruthi, M N

    2010-02-01

    Sampling procedures and diagnostic protocols were optimized for accurate diagnosis of Cassava brown streak virus (CBSV) (genus Ipomovirus, family Potyviridae). A cetyl trimethyl ammonium bromide (CTAB) method was optimized for sample preparation from infected cassava plants and compared with the RNeasy plant mini kit (Qiagen) for sensitivity, reproducibility and costs. CBSV was detectable readily in total RNAs extracted using either method. The major difference between the two methods was in the cost of consumables, with the CTAB 10x cheaper (0.53 pounds sterling=US$0.80 per sample) than the RNeasy method (5.91 pounds sterling=US$8.86 per sample). A two-step RT-PCR (1.34 pounds sterling=US$2.01 per sample), although less sensitive, was at least 3-times cheaper than a one-step RT-PCR (4.48 pounds sterling=US$6.72). The two RT-PCR tests revealed consistently the presence of CBSV both in symptomatic and asymptomatic leaves and indicated that asymptomatic leaves can be used reliably for virus diagnosis. Depending on the accuracy required, sampling 100-400 plants per field is an appropriate recommendation for CBSD diagnosis, giving a 99.9% probability of detecting a disease incidence of 6.7-1.7%, respectively. CBSV was detected at 10(-4)-fold dilutions in composite sampling, indicating that the most efficient way to index many samples for CBSV will be to screen pooled samples. The diagnostic protocols described below are reliable and the most cost-effective methods available currently for detecting CBSV.

  17. Etika Berbusana Mahasiswa Stain Samarinda

    Directory of Open Access Journals (Sweden)

    Ida Suryani Wijaya

    2012-06-01

    Full Text Available Ethics is about behavior of human being, such as which one is right or wrong. The ethics is always affecting the human life. The ethics gives people orientation how he/she do manything every time every day. Islamic ethics consists of the way how someone interact each other; how someone should do or not to do, how to sit, how to walk, how to eat or drink, how to sleep, or how to get dressed. Al-Qur’an uses three terms to define about dressing, they are: libas, tsiyah, and sarahi. Dressing has a function as covering the body, as assessoris, as the way to do Islamic taqwa, and as an identiy. Dressing ethics of the female students of STAIN Samarinda has been regulated by the rector regulation No 19 of the year 2002 about relation and dressing ethics for the students of STAIN Samarinda.

  18. [Giemsa stain's 100th year].

    Science.gov (United States)

    Perea-Sasiaín, José

    2003-03-01

    Research work associated with the development of Giemsa stain is revived, with emphasis on the methylene blue polychromes. A short biographical sketch of Dr. Berthold Gustav Carl Giemsa is presented, along with the composition of his original formulation and its mec. HPLC analyses of his azur II indicated the following composition: methylene blue 63.6%, azur B 28.6%, azur A 4.4%, azur C 1.4%, thionin 1.9%. Azur I was not "pure", but rather a mixture of thionin and all of its 3 and 7 N-methylated derivatives. Lillie inferred that it was probably prepared by an acid oxidation process. Applications of Giemsa stain reported in the last 32 years are tabulated.

  19. Hormonal manipulations in the 5-day timed artificial insemination protocol to optimize estrous cycle synchrony and fertility in dairy heifers.

    Science.gov (United States)

    Lima, F S; Ribeiro, E S; Bisinotto, R S; Greco, L F; Martinez, N; Amstalden, M; Thatcher, W W; Santos, J E P

    2013-01-01

    AI was greater for G2P than for control and NG2P on d 32 (control=52.9 vs. NG2P=55.0 vs. G2P=61.7%) and 60 (control=49.0 vs. NG2P=51.6 vs. G2P=59.1%). In study 3, HP attenuated LH release and reduced ovulation (19.0 vs. 48.4%) in response to GnRH compared with LP. Combining GnRH and 2 doses of PGF2α in the 5-d timed AI protocol improved follicle turnover, luteolysis, and P/AI in heifers. Elevated concentrations of progesterone suppressed LH release and are linked with the low ovulatory response to the initial GnRH treatment of the protocol.

  20. Transabdominal Ultrasonography-Defined Optimal and Definitive Bladder-Filling Protocol With Time Trends During Pelvic Radiation for Cervical Cancer.

    Science.gov (United States)

    Umesh, Mahantshetty; Kumar, Deepak P; Chadha, Pranav; Choudary, Rajiv; Kembhavi, Seema; Thakur, Meenakshi; Reena, Engineer; Chopra, Supriya; Shrivastava, Shyamkishore

    2017-01-01

    Advanced radiotherapy techniques have emphasized on the importance of accurate target volume localization and delineation. The aim of this study was to determine time taken to achieve moderate bladder volume under physiological conditions, using transabdominal ultrasound. Patients with cervical cancer undergoing radical radiation with or without concomitant chemotherapy underwent serial ultrasound to estimate bladder filling. With a strict bladder protocol of consuming 1000 mL of water orally over 30 minutes after emptying the bladder, ultrasound was done after 45 minutes from bladder emptying time and repeated at 15-minute interval till 300 (25) mL filling was achieved and repeated every week. Forty-six patients with weekly ultrasound for bladder-filling documentation were evaluated. The mean (standard deviation) bladder volume measured at 45 minutes was 220 (93), 210 (95), 195 (91), 195 (96), and 190 (85) mL (average: 200; median: 195 mL) for the first to fifth week, respectively, and the mean (standard deviation) volume at 75 minutes was 300 (95), 310 (80), 290 (80), 295 (80), and 285 (70) mL (average: 295; median: 300 mL). The mean (standard deviation) time for bladder filling to 300 mL in the first, second, third, fourth, and fifth week was 57 ( 13.5), 67 (16.6), 66 (16.7), 66 (15.5), and 69 (17.1) minutes, respectively. Bladder filling to a definitive moderate volume at a reasonably fixed time period in each week of radiation is well tolerated, feasible, and measurable by weekly transabdominal ultrasound measurements.

  1. An optimized protocol for the generation and functional analysis of human mast cells from CD34(+) enriched cell populations.

    Science.gov (United States)

    Yin, Yuzhi; Bai, Yun; Olivera, Ana; Desai, Avanti; Metcalfe, Dean D

    2017-09-01

    The culture of mast cells from human tissues such a cord blood, peripheral blood or bone marrow aspirates has advanced our understanding of human mast cells (huMC) degranulation, mediator production and response to pharmacologic agents. However, existing methods for huMC culture tend to be laborious and expensive. Combining technical approaches from several of these protocols, we designed a simplified and more cost effective approach to the culture of mast cells from human cell populations including peripheral blood and cryopreserved cells from lymphocytapheresis. On average, we reduced by 30-50 fold the amount of culture media compared to our previously reported method, while the total MC number generated by this method (2.46±0.63×10(6) vs. 2.4±0.28×10(6), respectively, from 1.0×10(8) lymphocytapheresis or peripheral blood mononuclear blood cells [PBMCs]) was similar to our previous method (2.36±0.70×10(6)), resulting in significant budgetary savings. In addition, we compared the yield of huMCs with or without IL-3 added to early cultures in the presence of stem cell factor (SCF) and interlukin-6 (IL-6) and found that the total MC number generated, while higher with IL-3 in the culture, did not reach statistical significance, suggesting that IL-3, often recommended in the culture of huMCs, is not absolutely required. We then performed a functional analysis by flow cytometry using standard methods and which maximized the data we could obtain from cultured cells. We believe these approaches will allow more laboratories to culture and examine huMC behavior going forward. Published by Elsevier B.V.

  2. Development of Sub-optimal Airway Protocols for the International Space Station (ISS) by the Medical Operation Support Team (MOST)

    Science.gov (United States)

    Polk, James D.; Parazynski, Scott; Kelly, Scott; Hurst, Victor, IV; Doerr, Harold K.

    2007-01-01

    Airway management techniques are necessary to establish and maintain a patent airway while treating a patient undergoing respiratory distress. There are situations where such settings are suboptimal, thus causing the caregiver to adapt to these suboptimal conditions. Such occurrences are no exception aboard the International Space Station (ISS). As a result, the NASA flight surgeon (FS) and NASA astronaut cohorts must be ready to adapt their optimal airway management techniques for suboptimal situations. Based on previous work conducted by the Medical Operation Support Team (MOST) and other investigators, the MOST had members of both the FS and astronaut cohorts evaluate two oral airway insertion techniques for the Intubating Laryngeal Mask Airway (ILMA) to determine whether either technique is sufficient to perform in suboptimal conditions within a microgravity environment. Methods All experiments were conducted in a simulated microgravity environment provided by parabolic flight aboard DC-9 aircraft. Each participant acted as a caregiver and was directed to attempt both suboptimal ILMA insertion techniques following a preflight instruction session on the day of the flight and a demonstration of the technique by an anesthesiologist physician in the simulated microgravity environment aboard the aircraft. Results Fourteen participants conducted 46 trials of the suboptimal ILMA insertion techniques. Overall, 43 of 46 trials (94%) conducted were properly performed based on criteria developed by the MOST and other investigators. Discussion The study demonstrated the use of airway management techniques in suboptimal conditions relating to space flight. Use of these techniques will provide a crew with options for using the ILMA to manage airway issues aboard the ISS. Although it is understood that the optimal method for patient care during space flight is to have both patient and caregiver restrained, these techniques provide a needed backup should conditions not present

  3. Optimizing linkage and retention to hypertension care in rural Kenya (LARK hypertension study): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Vedanthan, Rajesh; Kamano, Jemima H; Naanyu, Violet; Delong, Allison K; Were, Martin C; Finkelstein, Eric A; Menya, Diana; Akwanalo, Constantine O; Bloomfield, Gerald S; Binanay, Cynthia A; Velazquez, Eric J; Hogan, Joseph W; Horowitz, Carol R; Inui, Thomas S; Kimaiyo, Sylvester; Fuster, Valentin

    2014-04-27

    Hypertension is the leading global risk factor for mortality. Hypertension treatment and control rates are low worldwide, and delays in seeking care are associated with increased mortality. Thus, a critical component of hypertension management is to optimize linkage and retention to care. This study investigates whether community health workers, equipped with a tailored behavioral communication strategy and smartphone technology, can increase linkage and retention of hypertensive individuals to a hypertension care program and significantly reduce blood pressure among them. The study will be conducted in the Kosirai and Turbo Divisions of western Kenya. An initial phase of qualitative inquiry will assess facilitators and barriers of linkage and retention to care using a modified Health Belief Model as a conceptual framework. Subsequently, we will conduct a cluster randomized controlled trial with three arms: 1) usual care (community health workers with the standard level of hypertension care training); 2) community health workers with an additional tailored behavioral communication strategy; and 3) community health workers with a tailored behavioral communication strategy who are also equipped with smartphone technology. The co-primary outcome measures are: 1) linkage to hypertension care, and 2) one-year change in systolic blood pressure among hypertensive individuals. Cost-effectiveness analysis will be conducted in terms of costs per unit decrease in blood pressure and costs per disability-adjusted life year gained. This study will provide evidence regarding the effectiveness and cost-effectiveness of strategies to optimize linkage and retention to hypertension care that can be applicable to non-communicable disease management in low- and middle-income countries. This trial is registered with (NCT01844596) on 30 April 2013.

  4. Optimization of the derivatization protocol of pentacyclic triterpenes prior to their gas chromatography-mass spectrometry analysis in plant extracts.

    Science.gov (United States)

    Jemmali, Zaineb; Chartier, Agnes; Dufresne, Christelle; Elfakir, Claire

    2016-01-15

    This paper focuses on the application of a two-level full factorial design to optimize the key derivatization step before the GC-FID and GC-MS analysis of pentacyclic triterpenes. The derivatization reaction was screened for influential factors and statistically significant parameters with a p value less than 0.05. A multi-response optimization based on a desirability function was then applied, while simultaneously considering overall detection enhancement of compounds. Results showed that derivatization using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) and trimethylchlorosilane (TMCS) in pyridine (22:13:65v/v/v) for 2h at 30°C was the most efficient method of derivatizing all the hydroxyl and carboxylic acid groups contained in the triterpene structures. The validity of the method was demonstrated using GC-MS analyzes of a mixture containing eleven standards (β-amyrin, α-amyrin, lupeol, erythrodiol, uvaol, betulin, oleanolic acid, betulinic acid, ursolic acid, maslinic acid and corosolic acid). These compounds are representative of different classes of terpene compounds bearing different functional groups such as alcohols, diols, and carboxylic acids. The derivatization procedure was then tested on four plant extracts: apple pomace, salvia sclarea (dried leaves and flowers), sea buckthorn (Hyppophae rhammnoides L.) berries, and B. serrata resin. The identification of triterpenes was based on the comparison of their retention time and mass spectra to those of standards. The presence of compounds already identified in the literature was confirmed and new ones such as maslinic and corosolic acids were identified in apples, sea buckthorn and salvia sclarea. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Optimization of acquisition and contrast injection protocol for C-arm CT imaging in transcatheter aortic valve implantation: initial experience in a swine model.

    Science.gov (United States)

    Numburi, Uma D; Kapadia, Samir R; Schoenhagen, Paul; Tuzcu, E Murat; von Roden, Martin; Halliburton, Sandra S

    2013-02-01

    To determine the optimal C-arm computed tomography (CT) protocol for transcatheter aortic valve implantation (TAVI) in swine. In 6 swine, C-arm CT was performed using 5-s ungated acquisition during sinus rhythm with aortic root (Method 1) or peripheral (Method 2) injection, and during rapid ventricular pacing with root injection (Method 3). Additionally, 24-s ECG-gated acquisitions were performed during sinus rhythm with root (Method 4) or peripheral (Method 5) injection. Aortic root enhancement, presence of artifacts and contrast volumes were compared for all methods. Aortic root measurements were also compared between C-arm CT and multidetector-row computed tomography (MDCT). The best C-arm CT image set was identified and used to predict optimal angiographic projection angles during TAVI; predictions were compared to those from MDCT. Methods 1, 3, 4, and 5 yielded sufficient root enhancement with mild or moderate artifacts and aortic annulus, sinotubular junction, and mid-ascending aorta diameters similar to MDCT. Ungated C-arm CT (Methods 1, 3) required less contrast than ECG-gated C-arm CT (Methods 4, 5). Method 3 was optimal yielding images with high attenuation, few artifacts (2.0), and root measurements similar to MDCT using minimal contrast (36 mL). Predicted angiographic projections from Method 3 were similar to MDCT. Ungated C-arm CT during rapid pacing with aortic root injection required minimal contrast, yielded high attenuation and few artifacts, and aortic root measurements and predicted angiographic planes similar to those from MDCT.

  6. Optimization of synthesis protocols to control the nanostructure and the morphology of metal oxide thin films for memristive applications

    Energy Technology Data Exchange (ETDEWEB)

    Baldi, G., E-mail: giacomo.baldi@cnr.it; Bosi, M.; Attolini, G.; Berzina, T.; Mosca, R.; Ponraj, J. S.; Iannotta, S. [IMEM-CNR Institute, Parco Area delle Scienze 37/A, I-43124 Parma (Italy); Giusti, G.; Nozar, P.; Toccoli, T.; Verucchi, R. [IMEM-CNR Institute, Via alla Cascata 56/C, Povo – I-38123 Trento (Italy); Collini, C.; Lorenzelli, L. [FBK Bruno Kessler Foundation, Via Sommarive 18, I-38123 Trento (Italy)

    2015-03-10

    We propose a multi-technique approach based on in-vacuum synthesis of metal oxides to optimize the memristive properties of devices that use a metal oxide thin film as insulating layer. Pulsed Microplasma Cluster Source (PMCS) is based on supersonic beams seeded by clusters of the metal oxide. Nanocrystalline TiO{sub 2} thin films can be grown at room temperature, controlling the oxide stoichiometry from titanium metal up to a significant oxygen excess. Pulsed Electron beam Deposition (PED) is suitable to grow crystalline thin films on large areas, a step towards producing device arrays with controlled morphology and stoichiometry. Atomic Layer Deposition (ALD) is a powerful technique to grow materials layer-by-layer, finely controlling the chemical and structural properties of the film up to thickness of 50-80 nm. We will present a few examples of metal-insulator-metal structures showing a pinched hysteresis loop in their current-voltage characteristic. The structure, stoichiometry and morphology of the metal oxide layer, either aluminum oxide or titanium dioxide, is investigated by means of scanning electron microscopy (SEM) and by Raman scattering.

  7. Optimized protocol for soluble prokaryotic expression, purification and structural analysis of human placenta specific-1(PLAC1).

    Science.gov (United States)

    Nazari, Mahboobeh; Zarnani, Amir-Hassan; Ghods, Roya; Emamzadeh, Rahman; Najafzadeh, Somayeh; Minai-Tehrani, Arash; Mahmoudian, Jafar; Yousefi, Maryam; Vafaei, Sedigheh; Massahi, Sam; Nejadmoghaddam, Mohammad-Reza

    2017-03-16

    Placenta specific -1 (PLAC1) has been recently introduced as a small membrane-associated protein mainly involved in placental development. Expression of PLAC1 transcript has been documented in almost one hundred cancer cell lines standing for fourteen distinct cancer types. The presence of two disulfide bridges makes difficult to produce functional recombinant PLAC1 in soluble form with high yield. This limitation also complicates the structural studies of PLAC1, which is important for prediction of its physiological roles. To address this issue, we employed an expression matrix consisting of two expression vectors, five different E. coli hosts and five solubilization conditions to optimize production of full and truncated forms of human PLAC1. The recombinant proteins were then characterized using an anti-PLAC1-specific antibody in Western blotting (WB) and enzyme linked immunosorbent assay (ELISA). Structure of full length protein was also investigated using circular dichroism (CD). We demonstrated the combination of Origami™ and pCold expression vector to yield substantial amount of soluble truncated PLAC1 without further need for solubilization step. Full length PLAC1, however, expressed mostly as inclusion bodies with higher yield in Origami™ and Rosetta2. Among solubilization buffers examined, buffer containing Urea 2 M, pH 12 was found to be more effective. Recombinant proteins exhibited excellent reactivity as detected by ELISA and WB. The secondary structure of full length PLAC1 was considered by CD spectroscopy. Taken together, we introduced here a simple, affordable and efficient expression system for soluble PLAC1 production.

  8. Accelerated staining technique using kitchen microwave oven

    Directory of Open Access Journals (Sweden)

    Archana Mukunda

    2015-01-01

    Full Text Available Introduction: Histopathological diagnosis of specimens is greatly dependent on good sample preparation and staining. Both of these processes is governed by diffusion of fluids and dyes in and out of the tissue, which is the key to staining. Diffusion of fluids can be accelerated by the application of heat that reduces the time of staining from hours to the minute. We modified an inexpensive model of kitchen microwave oven for staining. This study is an attempt to compare the reliability of this modified technique against the tested technique of routine staining so as to establish the kitchen microwave oven as a valuable diagnostic tool. Materials and Methods: Sixty different tissue blocks were used to prepare 20 pairs of slides for 4 different stains namely hematoxylin and eosin, Van Gieson′s, 0.1% toluidine blue and periodic acid-Schiff. From each tissue block, two bits of tissues were mounted on two different slides. One slide was stained routinely, and the other stained inside a microwave. A pathologist evaluated the stained slides and the results so obtained were analyzed statistically. Results: Microwave staining considerably cut down the staining time from hours to seconds. Microwave staining showed no loss of cellular and nuclear details, uniform-staining characteristics and was of excellent quality. Interpretation and Conclusion: The cellular details, nuclear details and staining characteristics of microwave stained tissues were better than or equal to the routine stained tissue. The overall quality of microwave-stained sections was found to be better than the routine stained tissue in majority of cases.

  9. The effects of a psychological intervention directed at optimizing immune function: study protocol for a randomized controlled trial.

    Science.gov (United States)

    Schakel, Lemmy; Veldhuijzen, Dieuwke S; van Middendorp, Henriët; Prins, Corine; Joosten, Simone A; Ottenhoff, Tom H M; Visser, Leo G; Evers, Andrea W M

    2017-05-26

    heart rate and skin conductance in response to the psychophysiological tasks after the BCG vaccination. The innovative design features of this study - e.g., combining guided e-health CBT with health-related serious gaming elements and incorporating immunological and psychophysiological challenges - will provide valuable information on the effects of a psychological intervention on both self-reported and physiological health outcomes. This study will offer further insights into the mechanisms underlying the link between psychological factors and health outcomes and is anticipated to contribute to the optimization of health care strategies. Nederlands Trial Register, NTR5610 . Registered on 4 January 2016.

  10. An Improved AODV Routing Protocol Based on Energy Optimization%一种改进的基于能量优化的AODV路由协议

    Institute of Scientific and Technical Information of China (English)

    郭彦芳

    2016-01-01

    Aiming at the problem that node energy is limited fast⁃consuming,and easily leading to network spacing,the paper puts forward an improved AODV routing protocol based on energy optimization (IEO⁃AODV).Based on the AODV routing protocol,and in consideration of the node residual energy and the number of hops to select path,intermediate nodes in the process of routing have a delay relating to their own remaining energy in the forward routing request.The destination node has a delay record,according to the selection of assessment function for optimal routing.Compared with classic AODV,simulation results show that the improved scheme can balance the network energy consumption,and has a larger advantage on packet delivery rate and network prolonged survival time.%针对节点能量有限、消耗过快易导致网络分隔的问题,提出一种改进的基于能量优化的 AODV 路由协议( IEO⁃AODV )。以AODV路由协议为基础,通过综合考虑节点剩余能量和路由跳数进行路径选择,在路由过程中,中间节点在转发路由请求时进行一个与自身剩余能量有关延迟,在目的节点进行一个延迟记录,最后根据评估函数选取最优路由。仿真结果表明,与经典AODV相比,所改进的方案能均衡网络的能量消耗,在分组投递率、延长网络的生存时间等方面有较大的优势。

  11. Optimism

    Science.gov (United States)

    Carver, Charles S.; Scheier, Michael F.; Segerstrom, Suzanne C.

    2010-01-01

    Optimism is an individual difference variable that reflects the extent to which people hold generalized favorable expectancies for their future. Higher levels of optimism have been related prospectively to better subjective well-being in times of adversity or difficulty (i.e., controlling for previous well-being). Consistent with such findings, optimism has been linked to higher levels of engagement coping and lower levels of avoidance, or disengagement, coping. There is evidence that optimism is associated with taking proactive steps to protect one's health, whereas pessimism is associated with health-damaging behaviors. Consistent with such findings, optimism is also related to indicators of better physical health. The energetic, task-focused approach that optimists take to goals also relates to benefits in the socioeconomic world. Some evidence suggests that optimism relates to more persistence in educational efforts and to higher later income. Optimists also appear to fare better than pessimists in relationships. Although there are instances in which optimism fails to convey an advantage, and instances in which it may convey a disadvantage, those instances are relatively rare. In sum, the behavioral patterns of optimists appear to provide models of living for others to learn from. PMID:20170998

  12. Optimization

    CERN Document Server

    Pearce, Charles

    2009-01-01

    Focuses on mathematical structure, and on real-world applications. This book includes developments in several optimization-related topics such as decision theory, linear programming, turnpike theory, duality theory, convex analysis, and queuing theory.

  13. Specimen block counter-staining for localization of GUS expression in transgenic arabidopsis and tobacco

    Science.gov (United States)

    Kim, M. K.; Choi, J-W; Jeon, J-H; Franceschi, V. R.; Davin, L. B.; Lewis, N. G.

    2002-01-01

    A simple counter-staining procedure has been developed for comparative beta-glucuronidase (GUS) expression and anatomical localization in transgenic herbaceous arabidopsis and tobacco. This protocol provides good anatomical visualization for monitoring chimeric gene expression at both the organ and tissue levels. It can be used with different histochemical stains and can be extended to the study of woody species. The specimens are paraffin-embedded, the block is trimmed to reveal internal structure, safranin-O staining solution is briefly applied to the surface of the block, then washed off and, after drying, a drop of immersion oil is placed on the stained surface for subsequent photographic work. This gives tissue counter-staining with good structural preservation without loss of GUS staining product; moreover, sample observation is rapid and efficient compared to existing procedures.

  14. Unsupervised color normalisation for H and E stained histopathology image analysis

    Science.gov (United States)

    Celis, Raúl; Romero, Eduardo

    2015-12-01

    In histology, each dye component attempts to specifically characterise different microscopic structures. In the case of the Hematoxylin-Eosin (H&E) stain, universally used for routine examination, quantitative analysis may often require the inspection of different morphological signatures related mainly to nuclei patterns, but also to stroma distribution. Nevertheless, computer systems for automatic diagnosis are often fraught by color variations ranging from the capturing device to the laboratory specific staining protocol and stains. This paper presents a novel colour normalisation method for H&E stained histopathology images. This method is based upon the opponent process theory and blindly estimates the best color basis for the Hematoxylin and Eosin stains without relying on prior knowledge. Stain Normalisation and Color Separation are transversal to any Framework of Histopathology Image Analysis.

  15. Safranin O staining using a microwave oven.

    Science.gov (United States)

    Kahveci, Z; Minbay, F Z; Cavusoglu, L

    2000-11-01

    We investigated the effects of microwave irradiation on a safranin O staining method for paraffin sections of formalin fixed rabbit larynx. The control sections were stained according to the conventional method, and the experimental sections were stained in microwave oven for 10 sec at 360 W in Weigert's iron hematoxylin, and for 30 sec at 360 W in fast green and 0.1% safranin O staining solutions. Light microscopic examination of the sections revealed that the microwave heating did not adversely affect the staining properties of cartilage tissue compared to the conventional staining method. Small differences such as darker staining of the matrix and shrinkage of the cytoplasm was observed in some microwave treated sections. The present study revealed that microwave application can be used safely for the safranin O method with the advantage of reduced staining time.

  16. Analysis and Optimization of Lightweight TCP/IP Protocol Stack Mechanism%轻量级TCP/IP协议栈机制分析与优化

    Institute of Scientific and Technical Information of China (English)

    袁中书; 陆阳

    2015-01-01

    Lightweight TCP/IP protocol stack ( LwIP ) is mainly used in resource-constrained embedded devices. In order to meet the real-time requirement of the embedded device, this paper analyzes the internal mechanism of LwIP, conducts a performance bottleneck analysis by experimental measurements, and designs the optimization program of LwIP. The main performance bottlenecks of LwIP are memory copy and verification process. Accordingly,the optimized algorithms of memory copy and checksum are presented. Additionally,in order to meet the higher priority requirement of the urgent data,this paper presents the management mechanism of the priority,and ensures that the emergency packets take precedence over ordinary data packets. Experimental tests are presented to prove that these optimization methods improve the real-time performance of LwIP.%轻量级TCP/IP协议栈( LwIP)主要应用于资源受限的嵌入式设备。为满足嵌入式设备对实时性的要求,分析LwIP的内部机制,对其进行性能瓶颈分析,并根据分析结果设计、实施LwIP的实时性和优先级管理优化方案。 LwIP的主要性能瓶颈是内存拷贝和校验过程,据此给出优化后的内存拷贝算法和校验算法。为满足紧急数据对更高优先级的要求,给出LwIP协议栈优先级管理机制,能够确保高优先级标记的紧急数据包优先传输于普通数据包。实验结果表明,该优化方法可以显著提高LwIP的实时性能。

  17. Platinum blue staining of cells grown in electrospun scaffolds.

    Science.gov (United States)

    Yusuf, Mohammed; Millas, Ana Luiza G; Estandarte, Ana Katrina C; Bhella, Gurdeep K; McKean, Robert; Bittencourt, Edison; Robinson, Ian K

    2014-01-01

    Fibroblast cells grown in electrospun polymer scaffolds were stained with platinum blue, a heavy metal stain, and imaged using scanning electron microscopy. Good contrast on the cells was achieved compared with samples that were gold sputter coated. The cell morphology could be clearly observed, and the cells could be distinguished from the scaffold fibers. Here we optimized the required concentration of platinum blue for imaging cells grown in scaffolds and show that a higher concentration causes platinum aggregation. Overall, platinum blue is a useful stain for imaging cells because of its enhanced contrast using scanning electron microscopy (SEM). In the future it would be useful to investigate cell growth and morphology using three-dimensional imaging methods.

  18. Staining tomato fruit cuticle and exocarp tissues.

    Science.gov (United States)

    Graham, E T

    1997-05-01

    Immature fruit of tomato, Lycopersicon esculentum (Celebrity), was examined to observe the cuticle, its interface with the epidermis, and the general histology of the outer exocarp. Paraffin sections were stained first with Bismarck brown Y. Structures already stained in various hues of brown were stained again with either azure B, aluminum hematoxylin and alcian blue SGX, or the periodic acid-Schiff (PAS) reaction. Bismarck brown-azure B displayed the cuticle in strong contrast with subjacent tissue; however, nuclei were not easily identified at low magnification. Bismarck brown-hematoxylin-alcian blue produced a sharply contrasted combination of yellow cuticle, bright blue cell walls and purple nuclei. Nuclei stained purple with hematoxylin were easily identified at x100. Bismarck brown-PAS stained the cuticle golden brown and subjacent tissues mageta red. Surprisingly, epidermal cells stained specifically and intensely with PAS while pretreatment with an aldehyde blockade and omission of periodic acid prevented staining of all other tissues.

  19. Embedding, serial sectioning and staining of zebrafish embryos using JB-4 resin.

    Science.gov (United States)

    Sullivan-Brown, Jessica; Bisher, Margaret E; Burdine, Rebecca D

    2011-01-01

    Histological techniques are critical for observing tissue and cellular morphology. In this paper, we outline our protocol for embedding, serial sectioning, staining and visualizing zebrafish embryos embedded in JB-4 plastic resin-a glycol methacrylate-based medium that results in excellent preservation of tissue morphology. In addition, we describe our procedures for staining plastic sections with toluidine blue or hematoxylin and eosin, and show how to couple these stains with whole-mount RNA in situ hybridization. We also describe how to maintain and visualize immunofluorescence and EGFP signals in JB-4 resin. The protocol we outline-from embryo preparation, embedding, sectioning and staining to visualization-can be accomplished in 3 d. Overall, we reinforce that plastic embedding can provide higher resolution of cellular details and is a valuable tool for cellular and morphological studies in zebrafish.

  20. Optimization on BitTorrent Protocol for Video Application%面向视频应用的BitTorrent协议优化

    Institute of Scientific and Technical Information of China (English)

    李敏宁; 鱼滨; 杨力

    2015-01-01

    BitTorrent protocol is a file sharing protocol based on P2P (Peer to Peer),with"the more users the download faster" feature. It reflects the superiority of the system especially for large files. In recent years,video media streams are a class file that the most amounts of Internet users occupied. With the further increase of consumer bandwidth,more and more people want to get the multimedia applica-tions such as video on demand. The traditional C/S architecture,when a sharp increase is conducted in the number of users,prone to over-load the server,using the server cluster or distributed system to cause the cost increases. BitTorrent can better reduce server load and im-prove the scalability and robustness of the system. But BitTorrent is designed for ordinary share large files,selecting the file fragments are disorder conduction,and cannot effectively support on-demand and live video for large files. In this paper,for video-on-demand needs of large files,fragment selection algorithm is optimized of BitTorrent protocol,realizing on-demand and live of video files.%BitTorrent协议是一种基于P2P(Peer to Peer)的文件共享协议,具有"用户越多,下载速度越快"的特点,尤其是针对大文件的下载,更能体现出系统的优越性.视频媒体流是近年来网络用户占有量最多的一类文件,随着消费者带宽的进一步增加,越来越多的人希望得到像视频点播这样的多媒体应用.传统的C/S架构在当用户数目急剧增加时,容易产生服务器过载现象,使用服务器集群或分布式系统成本增大.BitTorrent能够较好地降低服务器负担,提高系统的扩展性和健壮性.但是BitTorrent针对普通大文件的共享设计,对文件的片段选择是无序进行的,不能有效地支持视频大文件的点播和直播.文中针对视频大文件的点播需求,对BitTorrent协议的片段选择算法进行优化,实现了视频文件的点播和直播.

  1. Flat mount preparation for observation and analysis of zebrafish embryo specimens stained by whole mount in situ hybridization.

    Science.gov (United States)

    Cheng, Christina N; Li, Yue; Marra, Amanda N; Verdun, Valerie; Wingert, Rebecca A

    2014-07-17

    The zebrafish embryo is now commonly used for basic and biomedical research to investigate the genetic control of developmental processes and to model congenital abnormalities. During the first day of life, the zebrafish embryo progresses through many developmental stages including fertilization, cleavage, gastrulation, segmentation, and the organogenesis of structures such as the kidney, heart, and central nervous system. The anatomy of a young zebrafish embryo presents several challenges for the visualization and analysis of the tissues involved in many of these events because the embryo develops in association with a round yolk mass. Thus, for accurate analysis and imaging of experimental phenotypes in fixed embryonic specimens between the tailbud and 20 somite stage (10 and 19 hours post fertilization (hpf), respectively), such as those stained using whole mount in situ hybridization (WISH), it is often desirable to remove the embryo from the yolk ball and to position it flat on a glass slide. However, performing a flat mount procedure can be tedious. Therefore, successful and efficient flat mount preparation is greatly facilitated through the visual demonstration of the dissection technique, and also helped by using reagents that assist in optimal tissue handling. Here, we provide our WISH protocol for one or two-color detection of gene expression in the zebrafish embryo, and demonstrate how the flat mounting procedure can be performed on this example of a stained fixed specimen. This flat mounting protocol is broadly applicable to the study of many embryonic structures that emerge during early zebrafish development, and can be implemented in conjunction with other staining methods performed on fixed embryo samples.

  2. Adenosine-stress dynamic myocardial perfusion imaging using 128-slice dual-source CT: optimization of the CT protocol to reduce the radiation dose.

    Science.gov (United States)

    Kim, Sung Mok; Kim, Yoo Na; Choe, Yeon Hyeon

    2013-04-01

    The aim of this study was to compare the radiation dose and image quality of different adenosine-stress dynamic myocardial perfusion CT protocols using a 128-slice dual-source computed tomography (DSCT) scanner. We included 330 consecutive patients with suspected coronary artery disease. Protocols employed the following dynamic scan parameters: protocol I, a 30-s scan with a fixed tube current (FTC, n = 172); protocol II, a 30-s scan using an automatic tube current modulation (ATCM) technique (n = 108); protocol III, a 14-s scan using an ATCM (n = 50). To determine the scan interval for protocol III, we analyzed time-attenuation curves of 26 patients with myocardial perfusion who had been scanned using protocol I or II. The maximum attenuation difference between normal and abnormal myocardium occurred at 18.0 s to 30.3 s after initiation of contrast injection. Myocardial perfusion images of FTC and ATCM were of diagnostic image quality based on visual analysis. The mean radiation dose associated with protocols I, II, and III was 12.1 ± 1.6 mSv, 7.7 ± 2.5 mSv, and 3.8 ± 1.3 mSv, respectively (p < 0.01). Use of a dose-modulation technique and a 14-s scan duration for adenosine-stress CT enables significant dose reduction while maintaining diagnostic image quality.

  3. Unconditionally Secure Protocols

    DEFF Research Database (Denmark)

    Meldgaard, Sigurd Torkel

    the secure computation. Especially we look at the communication complexity of protocols in this model, and perfectly secure protocols. We show general protocols for any finite functionality with statistical security and optimal communication complexity (but exponential amount of preprocessing). And for two......This thesis contains research on the theory of secure multi-party computation (MPC). Especially information theoretically (as opposed to computationally) secure protocols. It contains results from two main lines of work. One line on Information Theoretically Secure Oblivious RAMS, and how...... they are used to speed up secure computation. An Oblivious RAM is a construction for a client with a small $O(1)$ internal memory to store $N$ pieces of data on a server while revealing nothing more than the size of the memory $N$, and the number of accesses. This specifically includes hiding the access pattern...

  4. Damage to microvessels during pused laser treatment of port-wine stains

    Science.gov (United States)

    Svaasand, Lars O.; Fiskerstrand, Elisanne J.; Norvang Nilsen, Lill T.; Stopps, E. K. S.; Nelson, J. Stuart; Berns, Michael W.

    1996-01-01

    Selective photothermolysis with pulsed lasers is presumably the most successful therapy for port wine stain birthmarks (flammeus nevi). Selectivity is obtained by using an optical wavelength corresponding to high absorption in blood together with small absorption in tissue. Further on, the pulse length is selected to be long enough to allow heat to diffuse into the vessel wall, but simultaneously short enough to prevent thermal damage to perivascular tissues. The optimal wavelength and pulse length are therefore dependent on vessel diameter, vessel wall thickness and depth in dermis. The present work, that is based on analytical mathematical modeling, demonstrates that in the case of a 0.45 ms long pulse at 585 nm wavelength vessels of diameter in the range of 40 - 60 micrometers require minimum optical fluence. Smaller vessels require higher fluence because the amount of heat needed to heat the wall then becomes a substantial fraction of the absorbed optical energy, and larger vessels require higher dose because the attenuation of light is blood prevents the blood in central part of the lumen to participate in the heating process. Further on, it is shown that the commonly used dose in the range of 6 - 7 J/cm2 is expected to inflict vessel rupture rather than thermolysis is superficially located vessels. The present analysis might serve to draw guide lines for a protocol where the optical energy, wavelength and pulse length are optimized with respect to vessel diameter and depth.

  5. Acetic orcein staining of prefixed tissue sections.

    Science.gov (United States)

    Reynolds, C; Lillie, R D

    1978-05-01

    Acetic orcein stains formol- and Carnoy-fixed tissues, coloring mast cells, nuclei, basophilic cytoplasm, cerebral corpora amylacea, and cartilage strongly; keratin and erythrocytes moderately; muscle and collagen weakly. Guinea pig Brunner gland and rat colonic goblet cell mucins did not stain. The red nuclear stain contrasts well with the Prussian blue reaction of hemosiderin and the ferric ferricyanide (Turnbull's blue) reaction of enterochromaffin. A weak (0.01%) fast-green FCF stain changes collagen and sometimes smooth muscle to green, without impairing nucleic acid or mast cell staining. Picroindigocarmine gives blue collagen, yellow muscle, and red elastin, nucleic acids and mast cells. Picro-methyl blue tends to override the red nuclear stain. Carnoy fixation is somewhat better for nuclei, formol for basophil cytoplasms.

  6. Tissue Staining (Chromoscopy of the Gastrointestinal Tract

    Directory of Open Access Journals (Sweden)

    M Brian Fennerty

    1999-01-01

    Full Text Available Tissue staining, or chomoscopy, is used as an adjunctive technique during gastrointestinal endoscopy. Chemical agents are applied to the gastrointestinal mucosal surface to identify specific epithelia or to enhance the mucosal surface characteristics of the gastrointestinal epithelium. This aids in the recognition of subtle lesions (ie, polyps or allows directed targeting of biopsies (ie, sprue or Barrett’s esophagus to increase the yield of endoscopic diagnostic accuracy. The four endoscopic tissue-staining techniques in use are vital staining, contrast staining (chromoscopy, reactive staining and tattooing. Some of the agents used for endoscopic tissue staining and the uses of chromoscopy in identifying pathology of the esophagus, stomach, small bowel and colon during endoscopy are discussed.

  7. Erbium doped stain etched porous silicon

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez-Diaz, B. [Departamento de Fisica Basica, Universidad de La Laguna, Avda. Astrofisico Francisco Sanchez, 38204 La Laguna, S/C de Tenerife (Spain); Diaz-Herrera, B. [Departamento de Energia Fotovoltaica, Instituto Tecnologico de Energias Renovables (ITER), Poligono Industrial de Granadilla, 38611 S/C Tenerife (Spain); Guerrero-Lemus, R. [Departamento de Fisica Basica, Universidad de La Laguna, Avda. Astrofisico Francisco Sanchez, 38204 La Laguna, S/C de Tenerife (Spain)], E-mail: rglemus@ull.es; Mendez-Ramos, J.; Rodriguez, V.D. [Departamento de Fisica Fundamental, Experimental Electronica y Sistemas, Universidad de La Laguna, Avda. Astrofisico Francisco Sanchez, 38204 La Laguna, S/C de Tenerife (Spain); Hernandez-Rodriguez, C. [Departamento de Fisica Basica, Universidad de La Laguna, Avda. Astrofisico Francisco Sanchez, 38204 La Laguna, S/C de Tenerife (Spain); Martinez-Duart, J.M. [Departamento de Fisica Aplicada, C-XII, Universidad Autonoma de Madrid, 28049 Cantoblanco, Madrid (Spain)

    2008-01-15

    In this work a simple erbium doping process applied to stain etched porous silicon layers (PSLs) is proposed. This doping process has been developed for application in porous silicon solar cells, where conventional erbium doping processes are not affordable because of the high processing cost and technical difficulties. The PSLs were formed by immersion in a HF/HNO{sub 3} solution to properly adjust the porosity and pore thickness to an optimal doping of the porous structure. After the formation of the porous structure, the PSLs were analyzed by means of nitrogen BET (Brunauer, Emmett and Teller) area measurements and scanning electron microscopy. Subsequently, the PSLs were immersed in a saturated erbium nitrate solution in order to cover the porous surface. Then, the samples were subjected to a thermal process to activate the Er{sup 3+} ions. Different temperatures and annealing times were used in this process. The photoluminescence of the PSLs was evaluated before and after the doping processes and the composition was analyzed by Fourier transform IR spectroscopy.

  8. The Simplest Protocol for Oblivious Transfer

    DEFF Research Database (Denmark)

    Chou, Tung; Orlandi, Claudio

    2015-01-01

    Oblivious Transfer (OT) is the fundamental building block of cryptographic protocols. In this paper we describe the simplest and most efficient protocol for 1-out-of-n OT to date, which is obtained by tweaking the Diffie-Hellman key-exchange protocol. The protocol achieves UC-security against...... optimizations) is at least one order of magnitude faster than previous work. Category / Keywords: cryptographic protocols / Oblivious Transfer, UC Security, Elliptic Curves, Efficient Implementation...

  9. Simple and cost effective apparatus for silver staining of polyacrylamide gels with sequential reagents addition and real time monitoring.

    Science.gov (United States)

    Maurye, Praveen; Basu, Arpita; Gupta, Angshuman

    2014-06-01

    Highly reproducible results in molecular biology depend a lot on effective staining and destaining methods. Silver staining of polyacrylamide DNA and protein gel has been adopted widely in the molecular biology laboratories for detecting a very low nanogram range of sample. An efficient staining of a polyacrylamide gel requires a number of well controlled and highly sensitive steps that often becomes tiresome when done manually or when there are a number of gels to be stained simultaneously. Since, silver staining is a multistep procedure that requires proper fixation and exchange of substance, a reliable protocol is necessary and a simple apparatus may be an added advantage to carry out the steps with ease and safety. Here, we describe a simple and cost effective device made from off-the-shelf components for some established silver staining protocols. Staining is done on a tray while six graduated bottles with a liquid delivery stopcock each, is connected to the tray through silicon tubing. The used up solution is drained off completely from the staining tray through a liquid outlet stopcock using vacuum pressure. The system is fixed with a camera connected to a computer for effective control of the staining process in each step. The apparatus provides the researchers with efficient staining and real time monitoring of gels without the need for handling toxic chemicals.

  10. A PET/MRI study towards finding the optimal [{sup 18}F]Fluciclovine PET protocol for detection and characterisation of primary prostate cancer

    Energy Technology Data Exchange (ETDEWEB)

    Elschot, Mattijs; Sandsmark, Elise; Tessem, May-Britt [NTNU, Norwegian University of Science and Technology, Deparment of Circulation and Medical Imaging, Faculty of Medicine, Trondheim (Norway); Selnaes, Kirsten M.; Bathen, Tone F. [NTNU, Norwegian University of Science and Technology, Deparment of Circulation and Medical Imaging, Faculty of Medicine, Trondheim (Norway); Trondheim University Hospital, St. Olavs Hospital, Trondheim (Norway); Krueger-Stokke, Brage [NTNU, Norwegian University of Science and Technology, Deparment of Circulation and Medical Imaging, Faculty of Medicine, Trondheim (Norway); Trondheim University Hospital, Department of Radiology, St. Olavs Hospital, Trondheim (Norway); Stoerkersen, Oeystein [Trondheim University Hospital, Department of Pathology, St. Olavs Hospital, Trondheim (Norway); Moestue, Siver A. [NTNU, Norwegian University of Science and Technology, Deparment of Circulation and Medical Imaging, Faculty of Medicine, Trondheim (Norway); NTNU, Norwegian University of Science and Technology, Department of Laboratory Medicine, Children' s and Women' s Health, Faculty of Medicine, Trondheim (Norway); Bertilsson, Helena [Trondheim University Hospital, Department of Urology, St. Olavs Hospital, Trondheim (Norway); NTNU, Norwegian University of Science and Technology, Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Trondheim (Norway)

    2017-04-15

    [{sup 18}F]Fluciclovine PET imaging shows promise for the assessment of prostate cancer. The purpose of this PET/MRI study is to optimise the PET imaging protocol for detection and characterisation of primary prostate cancer, by quantitative evaluation of the dynamic uptake of [{sup 18}F]Fluciclovine in cancerous and benign tissue. Patients diagnosed with high-risk primary prostate cancer underwent an integrated [{sup 18}F]Fluciclovine PET/MRI exam before robot-assisted radical prostatectomy with extended pelvic lymph node dissection. Volumes-of-interest (VOIs) of selected organs (prostate, bladder, blood pool) and sub-glandular prostate structures (tumour, benign prostatic hyperplasia (BPH), inflammation, healthy tissue) were delineated on T2-weighted MR images, using whole-mount histology samples as a reference. Three candidate windows for optimal PET imaging were identified based on the dynamic curves of the mean and maximum standardised uptake value (SUV{sub mean} and SUV{sub max}, respectively). The statistical significance of differences in SUV between VOIs were analysed using Wilcoxon rank sum tests (p<0.05, adjusted for multiple testing). Twenty-eight (28) patients [median (range) age: 66 (55-72) years] were included. An early (W1: 5-10 minutes post-injection) and two late candidate windows (W2: 18-23; W3: 33-38 minutes post-injection) were selected. Late compared with early imaging was better able to distinguish between malignant and benign tissue [W3, SUV{sub mean}: tumour vs. BPH 2.5 vs. 2.0 (p<0.001), tumour vs. inflammation 2.5 vs. 1.7 (p<0.001), tumour vs. healthy tissue 2.5 vs. 2.0 (p<0.001); W1, SUV{sub mean}: tumour vs. BPH 3.1 vs. 3.1 (p=0.771), tumour vs inflammation 3.1 vs. 2.2 (p=0.021), tumour vs. healthy tissue 3.1 vs. 2.5 (p<0.001)] as well as between high-grade and low/intermediate-grade tumours (W3, SUV{sub mean}: 2.6 vs. 2.1 (p=0.040); W1, SUV{sub mean}: 3.1 vs. 2.8 (p=0.173)). These differences were relevant to the peripheral zone, but

  11. Properties of blue-stained wood

    Directory of Open Access Journals (Sweden)

    Miha Humar

    2008-07-01

    Full Text Available Discoloration of wood is frequently caused by blue-stain fungi. Among them Aureobasidium pullulans and Sclerophoma pithyophila are reported as the most important staining organism. In previous researches, it was generally considered that blue-stain fungi do not influence mechanical properties. However, there were some opposite results published as well. In order to elucidate this issue, specimens made of Scots pine (Pinus sylvestris sapwood were exposed to two blue stain fungi A. pullulans and S. pithyophila for periods between two and eight weeks. FTIR, weight, colour and non-destructive modulus of elasticity measurements were performed before and after exposure. The results showed that blue stain fungi, besides considerable discoloration, do not cause any significant damage to wood. Surprisingly the non-destructive MoE analysis showed that modulus of elasticity even slightly increase after fungal exposure.

  12. Methods of staining and visualization of sphingolipid enriched and non-enriched plasma membrane regions of Arabidopsis thaliana with fluorescent dyes and lipid analogues

    Directory of Open Access Journals (Sweden)

    Blachutzik Jörg O

    2012-08-01

    Full Text Available Abstract Background Sterols and Sphingolipids form lipid clusters in the plasma membranes of cell types throughout the animal and plant kingdoms. These lipid domains provide a medium for protein signaling complexes at the plasma membrane and are also observed to be principal regions of membrane contact at the inception of infection. We visualized different specific fluorescent lipophilic stains of the both sphingolipid enriched and non-sphingolipid enriched regions in the plasma membranes of live protoplasts of Arabidopsis thaliana. Results Lipid staining protocols for several fluorescent lipid analogues in plants are presented. The most emphasis was placed on successful protocols for the single and dual staining of sphingolipid enriched regions and exclusion of sphingolipid enriched regions on the plasma membrane of Arabidopsis thaliana protoplasts. A secondary focus was placed to ensure that these staining protocols presented still maintain cell viability. Furthermore, the protocols were successfully tested with the spectrally sensitive dye Laurdan. Conclusion Almost all existing staining procedures of the plasma membrane with fluorescent lipid analogues are specified for animal cells and tissues. In order to develop lipid staining protocols for plants, procedures were established with critical steps for the plasma membrane staining of Arabidopsis leaf tissue and protoplasts. The success of the plasma membrane staining protocols was additionally verified by measurements of lipid dynamics by the fluorescence recovery after photobleaching technique and by the observation of new phenomena such as time dependent lipid polarization events in living protoplasts, for which a putative physiological relevance is suggested.

  13. A simple and rapid fluorescence in situ hybridization microwave protocol for reliable dicentric chromosome analysis.

    Science.gov (United States)

    Cartwright, Ian M; Genet, Matthew D; Kato, Takamitsu A

    2013-03-01

    Fluorescence in situhybridization (FISH) is an extremely effective and sensitive approach to analyzing chromosome aberrations. Until recently, this procedure has taken multiple days to complete. The introduction of telomeric and centromeric peptide nucleic acid (PNA) probes has reduced the procedure's duration to several hours, but the protocols still call for a high temperature (80-90°C) step followed by 1-3 h of hybridization. The newest method to speed up the FISH protocol is the use of a microwave to shorten the heating element to less than a minute; however this protocol still calls for a 1-h hybridization period. We have utilized PNA centromere/telomere probes in conjunction with a microwave oven to show telomere and centromere staining in as little as 30 s. We have optimized the hybridization conditions to increase the sensitivity and effectiveness of the new protocol and can effectively stain chromosomes in 2 min and 30 s of incubation. We have found that our new approach to FISH produces extremely clear and distinct signals. Radiation-induced dicentric formation in mouse and human fibroblast cells was analyzed by two individual scorers and the observed dicentrics matched very well.

  14. Optimization of the protocols for in vitro culture and induction of hepatic differentiation of rat mesenchymal stem cells%骨髓间充质干细胞体外培养及肝向分化方案的优化

    Institute of Scientific and Technical Information of China (English)

    向俊西; 郑幸龙; 祝旭龙; 杨丽斐; 高睿; 李建辉; 刘学民; 吕毅

    2015-01-01

    目的 优化一套简便、可靠、稳定的大鼠骨髓间充质干细胞分离、培养、鉴定及肝向分化的方案.方法 采用全骨髓差速贴壁法分离提取大鼠骨髓间充质干细胞,通过优化的1.5 h差速贴壁结合12 h首次全量换液方法,及体外改良培养方案实现细胞高效纯化扩增.流式细胞术表面标志物检测结合成脂、成骨、成软骨诱导分化鉴定细胞群.采用添加bFGF、HGF、EGF等多种生长因子的三步诱导法促使骨髓间充质干细胞向肝系分化,并进行形态学、免疫学、基因水平评估.结果 分离纯化的细胞群阳性表达CD29、CD44、CD90,阴性表达CD34、CD45,经成脂、成骨、成软骨诱导液作用后,油红O、茜素红、甲苯胺蓝染色均呈阳性.经三步法肝向诱导处理后,细胞群呈肝样细胞形态改变,表达肝脏特异性标志物ALB、AFP,肝系相关基因表达水平呈时间依赖性逐渐上升.结论 优化后的方案能够简便、可靠、稳定地获得高纯度的大鼠骨髓间充质干细胞,并能在特定微环境作用下实现肝向分化.%Objective To optimize the protocols for isolation, in vitro culture, identification and induction of hepatic differentiation of rat bone marrow mesenchymal stem cells (BMSCs). Methods Rat BMSCs were separated and purified by differential adherent culture for 1.5 h with the first medium change at 12 h. The surface markers of BMSCs were detected by flow cytometry. The cells were induced to differentiate into adipogenic, osteogenic, and chondrogenesis lineages. A 3-step protocol including sequential addition of growth factors, cytokines and hormones was used to induce the BMSCs to differentiate into hepatocyte-like cells. Results The cells isolated using this protocol were positive for CD29, CD44, and CD90 and negative for CD29 and CD45. The adipogenic, osteogenic, and chondrogenic differentiation of the BMSCs were verified by Oil red, Alizarin red, and toluidine blue staining

  15. (dtltt) protocol

    African Journals Online (AJOL)

    2013-03-01

    Mar 1, 2013 ... Keywords: multi-access, multiservice, network, synchronous, asynchronous, traffic, timed-token. 1. ... 12, 13 ] SAFENET [14], Manufacturing Automation. Protocol (MAP) ...... ken circulation on mobile Ad Hoc Networks. 21th In-.

  16. Microwave oven-based technique for immunofluorescent staining of paraffin-embedded tissues.

    Science.gov (United States)

    Long, Delwin J; Buggs, Colleen

    2008-02-01

    Immunohistochemical analysis of formalin-fixed paraffin-embedded tissues can be challenging due to potential modifications of protein structure by exposure to formalin. Heat-induced antigen retrieval techniques can reverse reactions between formalin and proteins that block antibody recognition. Interactions between antibodies and antigens are further enhanced by microwave irradiation, which has simplified immunohistochemical staining protocols. In this report, we modify a technique for antigen retrieval and immunofluorescent staining of formalin-fixed paraffin-embedded tissues by showing that it works well with several antibodies and buffers. This microwave-assisted method for antigen retrieval and immunofluorescent staining eliminates the need for blocking reagents and extended washes, which greatly simplifies the protocol allowing one to complete the analysis in less than 3 h.

  17. DNA DIFFERENTIAL STAINING AND ITS CLINICAL APPLICATION

    Institute of Scientific and Technical Information of China (English)

    庄维城; 潘瑞彭; 欧阳仁荣; 杜心垿; 蒋莉芳; 陈小龙; 宣政华; 奚志红

    1992-01-01

    DNA differential stain is a simple method distinguishing cells of proliferative from quiescent stage. Double stranded DNA in quiescent cells is easily denatured by weak acid into single strand. As double stranded nucleic acid combined with methyl green and single stranded nucleic acid with pyronin, we make use of methyl green pyronin staining method to the cells treated with weak acid to distinguish proliferating from quiescent cells. This paper reports the observation of leukemia cells in the bone marrow smears of 100 cases of untreated acute leukemia by DNA differential staining method. The percentage of Go cells was lowest in ALL and highest in APL.

  18. Surface staining of small intestinal biopsies

    DEFF Research Database (Denmark)

    Poulsen, Steen Seier

    1977-01-01

    Small intestinal biopsies are most often by routine examined under a stereo-microscope, prior to embedding for histological examination. This is done in order to get a view of the appearance of the mucosal pattern, especially villus configuration. The distinctness of the surface pattern however......, is improved considerably if the biopsies are stained with Alcian Green and/or PAS before they are examined. In the present paper a detailed description is given of staining of small intestinal biopsies as whole mounts. The difference between the unstained and the stained biopsies is illustrated by a few...

  19. Optimizing Rehabilitation for Phantom Limb Pain Using Mirror Therapy and Transcranial Direct Current Stimulation: A Randomized, Double-Blind Clinical Trial Study Protocol.

    Science.gov (United States)

    Pinto, Camila Bonin; Saleh Velez, Faddi Ghassan; Bolognini, Nadia; Crandell, David; Merabet, Lotfi B; Fregni, Felipe

    2016-07-06

    Despite the multiple available pharmacological and behavioral therapies for the management of chronic phantom limb pain (PLP) in lower limb amputees, treatment for this condition is still a major challenge and the results are mixed. Given that PLP is associated with maladaptive brain plasticity, interventions that promote cortical reorganization such as non-invasive brain stimulation and behavioral methods including transcranial direct current stimulation (tDCS) and mirror therapy (MT), respectively, may prove to be beneficial to control pain in PLP. Due to its complementary effects, a combination of tDCS and MT may result in synergistic effects in PLP. The objective of this study is to evaluate the efficacy of tDCS and MT as a rehabilitative tool for the management of PLP in unilateral lower limb amputees. A prospective, randomized, placebo-controlled, double-blind, factorial, superiority clinical trial will be carried out. Participants will be eligible if they meet the following inclusion criteria: lower limb unilateral traumatic amputees that present PLP for at least 3 months after the amputated limb has completely healed. Participants (N=132) will be randomly allocated to the following groups: (1) active tDCS and active MT, (2) sham tDCS and active MT, (3) active tDCS and sham MT, and (4) sham tDCS and sham MT. tDCS will be applied with the anodal electrode placed over the primary motor cortex (M1) contralateral to the amputation side and the cathode over the contralateral supraorbital area. Stimulation will be applied at the same time of the MT protocol with the parameters 2 mA for 20 minutes. Pain outcome assessments will be performed at baseline, before and after each intervention session, at the end of MT, and in 2 follow-up visits. In order to assess cortical reorganization and correlate with clinical outcomes, participants will undergo functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) before and after the

  20. Optimization of killer assays for yeast selection protocols Optimización de la actividad killer para protocolos de selección de levaduras

    Directory of Open Access Journals (Sweden)

    C. A. Lopes

    2010-12-01

    Full Text Available A new optimized semiquantitative yeast killer assay is reported for the first time. The killer activity of 36 yeast isolates belonging to three species, namely, Metschnikowia pulcherrima, Wickerhamomyces anomala and Torulaspora delbrueckii, was tested with a view to potentially using these yeasts as biocontrol agents against the wine spoilage species Pichia guilliermondii and Pichia membranifaciens. The effectiveness of the classical streak-based (qualitative method and the new semiquantitative techniques was compared. The percentage of yeasts showing killer activity was found to be higher by the semiquantitative technique (60% than by the qualitative method (45%. In all cases, the addition of 1% NaCl into the medium allowed a better observation of the killer phenomenon. Important differences were observed in the killer capacity of different isolates belonging to a same killer species. The broadest spectrum of action was detected in isolates of W. anomala NPCC 1023 and 1025, and M. pulcherrima NPCC 1009 and 1013. We also brought experimental evidence supporting the importance of the adequate selection of the sensitive isolate to be used in killer evaluation. The new semiquantitative method proposed in this work enables to visualize the relationship between the number of yeasts tested and the growth of the inhibition halo (specific productivity. Hence, this experimental approach could become an interesting tool to be taken into account for killer yeast selection protocols.En este trabajo se presenta un nuevo ensayo semicuantitativo que optimiza la detección de actividad killer en levaduras. Se evaluó la actividad killer de 36 cepas pertenecientes a las especies Metschnikowia pulcherrima, Wickerhamomyces anomala y Torulaspora delbrueckii, en vista del potencial uso de estas levaduras como agentes de biocontrol frente a las especies contaminantes de vinos Pichia guilliermondii y Pichia membranifaciens. Se comparó la efectividad de la técnica cl

  1. Quantitative and qualitative comparison of MR imaging of the temporomandibular joint at 1.5 and 3.0 T using an optimized high-resolution protocol.

    Science.gov (United States)

    Manoliu, Andrei; Spinner, Georg; Wyss, Michael; Erni, Stefan; Ettlin, Dominik A; Nanz, Daniel; Ulbrich, Erika J; Gallo, Luigi M; Andreisek, Gustav

    2016-01-01

    To quantitatively and qualitatively compare MRI of the temporomandibular joint (TMJ) using an optimized high-resolution protocol at 3.0 T and a clinical standard protocol at 1.5 T. A phantom and 12 asymptomatic volunteers were MR imaged using a 2-channel surface coil (standard TMJ coil) at 1.5 and 3.0 T (Philips Achieva and Philips Ingenia, respectively; Philips Healthcare, Best, Netherlands). Imaging protocol consisted of coronal and oblique sagittal proton density-weighted turbo spin echo sequences. For quantitative evaluation, a spherical phantom was imaged. Signal-to-noise ratio (SNR) maps were calculated on a voxelwise basis. For qualitative evaluation, all volunteers underwent MRI of the TMJ with the jaw in closed position. Two readers independently assessed visibility and delineation of anatomical structures of the TMJ and overall image quality on a 5-point Likert scale. Quantitative and qualitative measurements were compared between field strengths. The quantitative analysis showed similar SNR for the high-resolution protocol at 3.0 T compared with the clinical protocol at 1.5 T. The qualitative analysis showed significantly better visibility and delineation of clinically relevant anatomical structures of the TMJ, including the TMJ disc and pterygoid muscle as well as better overall image quality at 3.0 T than at 1.5 T. The presented results indicate that expected gains in SNR at 3.0 T can be used to increase the spatial resolution when imaging the TMJ, which translates into increased visibility and delineation of anatomical structures of the TMJ. Therefore, imaging at 3.0 T should be preferred over 1.5 T for imaging the TMJ.

  2. A supravital cytodiagnostic stain for urinary sediments.

    Science.gov (United States)

    Sternheimer, R

    1975-02-24

    A mixture of aqueous solutions of National fast blue, a copper-phthalocyanine dye, and pyronin B, a red xanthene dye, when added to fresh urinary sediment, supravitally stains benign or malignant cells and the various types of casts and their inclusions. The stain facilitates identification of the formed elements and particularly aids in the differentiation of polymorphonuclear leukocytes from lymphocytes, histiocytes, plasma cells, and renal tubular cells. A variable staining of casts and their inclusions has been observed. Tumor cells may be recognized by nuclear abnormalities or, in case of hyperchromatic tendency, by a very rapid and early uptake of dye preceding that of the surrounding cells. The staining method is rapid and simple enough for routine urinalysis and screening procedures.

  3. Accounting for patient size in the optimization of dose and image quality of pelvis cone beam CT protocols on the Varian OBI system.

    Science.gov (United States)

    Wood, Tim J; Moore, Craig S; Horsfield, Carl J; Saunderson, John R; Beavis, Andrew W

    2015-01-01

    The purpose of this study was to develop size-based radiotherapy kilovoltage cone beam CT (CBCT) protocols for the pelvis. Image noise was measured in an elliptical phantom of varying size for a range of exposure factors. Based on a previously defined "small pelvis" reference patient and CBCT protocol, appropriate exposure factors for small, medium, large and extra-large patients were derived which approximate the image noise behaviour observed on a Philips CT scanner (Philips Medical Systems, Best, Netherlands) with automatic exposure control (AEC). Selection criteria, based on maximum tube current-time product per rotation selected during the radiotherapy treatment planning scan, were derived based on an audit of patient size. It has been demonstrated that 110 kVp yields acceptable image noise for reduced patient dose in pelvic CBCT scans of small, medium and large patients, when compared with manufacturer's default settings (125 kVp). Conversely, extra-large patients require increased exposure factors to give acceptable images. 57% of patients in the local population now receive much lower radiation doses, whereas 13% require higher doses (but now yield acceptable images). The implementation of size-based exposure protocols has significantly reduced radiation dose to the majority of patients with no negative impact on image quality. Increased doses are required on the largest patients to give adequate image quality. The development of size-based CBCT protocols that use the planning CT scan (with AEC) to determine which protocol is appropriate ensures adequate image quality whilst minimizing patient radiation dose.

  4. High contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy

    Science.gov (United States)

    Tapia, Juan C.; Kasthuri, Narayanan; Hayworth, Kenneth; Schalek, Richard; Lichtman, Jeff W.; Smith, Stephen J; Buchanan, JoAnn

    2013-01-01

    Conventional heavy metal post staining methods on thin sections lend contrast but often cause contamination. To avoid this problem, we tested several en bloc staining techniques to contrast tissue in serial sections mounted on solid substrates for examination by Field Emission Scanning Electron Microscope (FESEM). Because FESEM section imaging requires that specimens have higher contrast and greater electrical conductivity than transmission electron microscope (TEM) samples, our technique utilizes osmium impregnation (OTO) to make the samples conductive while heavily staining membranes for segmentation studies. Combining this step with other classic heavy metal en bloc stains including uranyl acetate, lead aspartate, copper sulfate and lead citrate produced clean, highly contrasted TEM and SEM samples of insect, fish, and mammalian nervous system. This protocol takes 7–15 days to prepare resin embedded tissue, cut sections and produce serial section images. PMID:22240582

  5. New Grocott Stain without Using Chromic Acid.

    Science.gov (United States)

    Shiogama, Kazuya; Kitazawa, Kayo; Mizutani, Yasuyoshi; Onouchi, Takanori; Inada, Ken-Ichi; Tsutsumi, Yutaka

    2015-01-01

    We established a new "ecological" Grocott stain for demonstrating fungi, based upon a 4R principle of refusal, reduction, reuse, and recycle of waste management. Conventional Grocott stain employs environmentally harsh 5% chromic acid for oxidization. Initially, we succeeded in reducing the concentration of chromic acid from 5% to 1% by incubating the solution at 60°C and using five-fold diluted chromic acid solution at which point it was reusable. Eventually, we reached the refusal level where 1% periodic acid oxidization was efficient enough, when combined with preheating of sections in the electric jar, microwave oven, or pressure pan. For convenience sake, we recommend pressure pan heating in tap water for 10 min. Stainability of fungi in candidiasis and aspergillosis was comparable with conventional Grocott stain, while Mucor hyphae showed enhanced staining. The modified sequence was further applicable to detecting a variety of mycotic pathogens in paraffin sections. Our environmentally-friendly Grocott stain also has the advantage of avoiding risk of human exposure to hexavalent chromium solution in the histopathology laboratory. The simple stain sequence is can be easily applied worldwide.

  6. The evaluation and planning of light dose in photodynamic therapy for port wine stains

    Science.gov (United States)

    Zhang, Feng-juan; Hu, Xiaoming; Zhang, Qi-shen

    2014-11-01

    Photodynamic therapy (PDT) is one of the best available treatment for dermatology, especially for port wine stains (PWS), in which the efficacy is associated with the light dose, the photosensitizer concentration, the oxygen concentration and so on. Accurate control of the light dose will help doctors develop more effective treatment protocols, and reduce the treatment cost. Considering the characters of PWS, a binocular vision system composed of a camera, a digital projector and a computing unit is designed. An accurate 3D modeling of patients was achieved using a gray coding structured light, and then the lesions were segmented based on HSV space. Subsequently, each 3D point is fit on the surface by a nearest neighbor algorithm and the surface normal can be obtained. Three dimensional localization of lesion provide digital objective basis for automatic control of light device. The irradiance on the surface at a given angle can be assessed, and the optimum angle for the treatment can be solved and optimized by the doctor to improve irradiation areas.

  7. A father protocol for quantum broadcast channels

    CERN Document Server

    Dupuis, F; Dupuis, Fr\\'ed\\'eric; Hayden, Patrick

    2006-01-01

    We present a new protocol for quantum broadcast channels based on the fully quantum Slepian-Wolf protocol. The protocol yields an achievable rate region for entanglement-assisted transmission of quantum information through a quantum broadcast channel that can be considered the quantum analogue of Marton's region for classical broadcast channels. The protocol can be adapted to yield achievable rate regions for unassisted quantum communication and for entanglement-assisted classical communication. Regularized versions of all three rate regions are provably optimal.

  8. Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging.

    Science.gov (United States)

    Bauman, Tyler M; Ricke, Emily A; Drew, Sally A; Huang, Wei; Ricke, William A

    2016-04-08

    Immunohistochemistry is a commonly used clinical and research lab detection technique for investigating protein expression and localization within tissues. Many semi-quantitative systems have been developed for scoring expression using immunohistochemistry, but inherent subjectivity limits reproducibility and accuracy of results. Furthermore, the investigation of spatially overlapping biomarkers such as nuclear transcription factors is difficult with current immunohistochemistry techniques. We have developed and optimized a system for simultaneous investigation of multiple proteins using high throughput methods of multiplexed immunohistochemistry and multispectral imaging. Multiplexed immunohistochemistry is performed by sequential application of primary antibodies with secondary antibodies conjugated to horseradish peroxidase or alkaline phosphatase. Different chromogens are used to detect each protein of interest. Stained slides are loaded into an automated slide scanner and a protocol is created for automated image acquisition. A spectral library is created by staining a set of slides with a single chromogen on each. A subset of representative stained images are imported into multispectral imaging software and an algorithm for distinguishing tissue type is created by defining tissue compartments on images. Subcellular compartments are segmented by using hematoxylin counterstain and adjusting the intrinsic algorithm. Thresholding is applied to determine positivity and protein co-localization. The final algorithm is then applied to the entire set of tissues. Resulting data allows the user to evaluate protein expression based on tissue type (ex. epithelia vs. stroma) and subcellular compartment (nucleus vs. cytoplasm vs. plasma membrane). Co-localization analysis allows for investigation of double-positive, double-negative, and single-positive cell types. Combining multispectral imaging with multiplexed immunohistochemistry and automated image acquisition is an

  9. Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures.

    Science.gov (United States)

    Minas, Konstantinos; McEwan, Neil R; Newbold, Charles Jamie; Scott, Karen P

    2011-12-01

    The quality and yield of extracted DNA are critical for the majority of downstream applications in molecular biology. Moreover, molecular techniques such as quantitative real-time PCR (qPCR) are becoming increasingly widespread; thus, validation and cross-laboratory comparison of data require standardization of upstream experimental procedures. DNA extraction methods depend on the type and size of starting material(s) used. As such, the extraction of template DNA is arguably the most significant variable when cross-comparing data from different laboratories. Here, we describe a reliable, inexpensive and rapid method of DNA purification that is equally applicable to small or large scale or high-throughput purification of DNA. The protocol relies on a CTAB-based buffer for cell lysis and further purification of DNA with phenol : chloroform : isoamyl alcohol. The protocol has been used successfully for DNA purification from rumen fluid and plant cells. Moreover, after slight alterations, the same protocol was used for large-scale extraction of DNA from pure cultures of Gram-positive and Gram-negative bacteria. The yield of the DNA obtained with this method exceeded that from the same samples using commercial kits, and the quality was confirmed by successful qPCR applications.

  10. A simple cost-effective modification improves the quality of immunocytochemical staining in cervical scrape samples characterized by presence of excess mucus

    Science.gov (United States)

    Pawar, Sagar; Mahantshetty, Umesh; Deodhar, Kedar; Teni, Tanuja

    2014-01-01

    Immunocytochemistry (ICC) is a very important tool in a diverse range of biomedical research as well as in diagnostic cytopathology. Smears prepared from cervical scrapes contain a large amount of overlying mucus that interferes with the standard immunocytochemical staining protocol. A modified ICC protocol is described, which involves pretreatment of these smears with 1 mg/ml solution of Ambroxol hydrochloride in methanol for 1 hour. Source of Ambroxol hydrochloride was a 30 mg Mucolite™ tablet, at a cost of 1.70 rupees (∼3·5 US cents) per tablet. This mucolytic solution effectively clears the mucus, facilitating the accessibility of the antibody to the antigenic determinants. This pretreatment resulted in the increased percentage of positively stained cells as well as staining intensity, leading to improved overall ICC staining and score. This is a novel modification that can be cost-effectively applied in ICC staining protocols for cytology samples characterized by the presence of excess mucus. PMID:25620823

  11. Immunoperoxidase staining of cervicovaginal smears after radiotherapy.

    Science.gov (United States)

    Wachtel, M S; Thaler, H T; Gangi, M D; Hajdu, S I

    1992-01-01

    Cervicovaginal smears from 2 women with postirradiation dysplasia, 4 women with postirradiation squamous cell carcinoma of the cervix, 30 women with irradiation atypia and 5 healthy, nonirradiated women were stained immunohistochemically with six keratin antibodies. For four of the antibodies--CK19 (BA17), EMA, PKK-1 and CAM 5.2--squamous cells showing irradiation atypia, postirradiation dysplasia or postirradiation squamous cell carcinoma were more likely to stain positively than were nonirradiated squamous cells. For three of the antibodies in which multiple squamous cells stained positively, the proportion of squamous cells showing postirradiation dysplasia or postirradiation squamous cell carcinoma staining strongly was equal to or greater than the corresponding overall proportion for squamous cells showing irradiation atypia. This was statistically significant with only one antibody, PKK-1. No statistically significant differences were seen in staining of irradiated and nonirradiated squamous cells by MAK-6 and AE1:AE3. The data show that some keratin antigens are more often expressed in the irradiated groups and that there may be differences in the degree of antigen expression between squamous cells showing postirradiation dysplasia or postirradiation squamous cell carcinoma and squamous cells showing irradiation atypia.

  12. Intravital staining with methylene blue in tympanoplasty.

    Science.gov (United States)

    Vaiman, Michael; Sarfaty, Shlomo; Gavriel, Haim; Kraus, Moshe; Kaplan, Daniel; Puterman, Max

    2010-09-01

    Objective of the study is to investigate usefulness of the methylene blue staining for the operation of tympanoplasty in surgical training process with randomized, controlled trial. Two hospitals were involved: Department of Otolaryngology, Assaf Harofeh Medical Center, and Department of Otolaryngology Head and Neck Surgery, Soroka University Medical Center. Tympanoplasty with graft placement was performed by young surgeons on 30 patients (30 ears) with anterior perforations using intraoperative staining of tympanoplasty grafts with methylene blue (Group 1). The same number of patients/ears was operated by the young surgeons without intraoperative staining (Group 2). 76 patients operated without staining by experienced surgeons served as a control group. Results showed tympanic membrane healing (graft take) in 30 (100%) cases in Group 1 and in 26 (86.66%) cases in Group 2. The pure-tone audiogram testing revealed significant improvement of hearing in all successful cases (p < 0.05). No side immediate or postponed effects were detected. We conclude that intravital staining with methylene blue in tympanoplasty simplifies the operation and could assist in better visualization and proper placement of the graft. This technique could be most useful in a training process for resident surgeons.

  13. Optimizing the scan protocol in whole-brain perfusion imaging with 320-MDCT%320排容积CT全脑灌注成像扫描协议优化研究

    Institute of Scientific and Technical Information of China (English)

    曹国全; 许化致; 潘克华; 陈伟建; 郭翔

    2014-01-01

    目的 探讨320排容积CT全脑灌注成像扫描协议优化的可行性.方法 20名健康志愿者按随机数字表法分为对照组和试验组,对照组7例,选择标准灌注扫描协议(19圈容积采集);试验组13例,通过合理改变采集间隔,减少扫描期相,采用一组新的灌注扫描协议(11圈容积采集).图像分析感兴趣区(ROI)设为两侧额叶白质、顶叶白质、半卵圆区、基底节区、枕叶、小脑,大小约(20±2)mm2.计算得到各感兴趣区的灌注参数值,包括脑血容量(rCBV)、达峰时间(TTP)、脑血流量(rCBF)、平均通过时间(MTT)及延迟时间(DT).结果 试验组剂量长度乘积(DLP)和有效剂量(E)较对照组降低了42.02%.两组不同层面左右两侧ROI区的各灌注参数的差异无统计学意义.两组组间上述各个对应部位的ROI区各灌注参数无明显差别.结论 优化后的扫描协议得到了与厂家推荐的标准协议无差异的全脑灌注参数值且降低了辐射剂量,推荐常规使用.%Objective To evaluate the feasibility of optimized scan protocol in whole-brain perfusion imaging with 320-MDCT scanner.Methods Twenty healthy volunteers were randomly divided into control group (13 patients) and test group (7 patients).The standard perfusion scan protocol (collecting 19 volumes)was applied in control group.The optimized perfusion CT scan protocol(collecting ll volumes)formulated by reducing scanning phases reasonably and changing the collection intervals was applied in test group.The regions of interest(ROI) with area of(20 ± 2)mm2 were located in the bilateral frontal white matter,parietal white matter,centrum semiovate,basal ganglia,occipital lobe and cerebellum.Bilateral perfusion values from ROI were measured,including cerebral blood volume(CBV),mean transit time (TTP),cerebral blood flow (CBF),mean transit time (MTT) and delay time (DT).Results Dose length product (DLP)and effective dose (ED)in optimized protocol were decreased 42.02

  14. Hybrid protocol of remote implementations of quantum operations

    Science.gov (United States)

    Zhao, Ning Bo; Wang, An Min

    2007-12-01

    We propose a protocol of remote implementations of quantum operations by hybridizing bidirectional quantum-state teleportation (BQST) [Huelga , Phys. Rev. A 63, 042303 (2001)] and the Wang protocol [Wang, Phys. Rev. A 74, 032317 (2006)]. The protocol is available for remote implementations of quantum operations in the restricted sets specified in the paper. We also give a proof of the protocol and point out its optimization. As an extension, this hybrid protocol can be reduced to the BQST and Wang protocols.

  15. Improved conventional and microwave-assisted silylation protocols for simultaneous gas chromatographic determination of tocopherols and sterols: Method development and multi-response optimization.

    Science.gov (United States)

    Poojary, Mahesha M; Passamonti, Paolo

    2016-12-09

    This paper reports on improved conventional thermal silylation (CTS) and microwave-assisted silylation (MAS) methods for simultaneous determination of tocopherols and sterols by gas chromatography. Reaction parameters in each of the methods developed were systematically optimized using a full factorial design followed by a central composite design. Initially, experimental conditions for CTS were optimized using a block heater. Further, a rapid MAS was developed and optimized. To understand microwave heating mechanisms, MAS was optimized by two distinct modes of microwave heating: temperature-controlled MAS and power-controlled MAS, using dedicated instruments where reaction temperature and microwave power level were controlled and monitored online. Developed methods: were compared with routine overnight derivatization. On a comprehensive level, while both CTS and MAS were found to be efficient derivatization techniques, MAS significantly reduced the reaction time. The optimal derivatization temperature and time for CTS found to be 55°C and 54min, while it was 87°C and 1.2min for temperature-controlled MAS. Further, a microwave power of 300W and a derivatization time 0.5min found to be optimal for power-controlled MAS. The use of an appropriate derivatization solvent, such as pyridine, was found to be critical for the successful determination. Catalysts, like potassium acetate and 4-dimethylaminopyridine, enhanced the efficiency slightly. The developed methods showed excellent analytical performance in terms of linearity, accuracy and precision. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Visualizing peripheral nerve regeneration by whole mount staining.

    Directory of Open Access Journals (Sweden)

    Xin-peng Dun

    Full Text Available Peripheral nerve trauma triggers a well characterised sequence of events both proximal and distal to the site of injury. Axons distal to the injury degenerate, Schwann cells convert to a repair supportive phenotype and macrophages enter the nerve to clear myelin and axonal debris. Following these events, axons must regrow through the distal part of the nerve, re-innervate and finally are re-myelinated by Schwann cells. For nerve crush injuries (axonotmesis, in which the integrity of the nerve is maintained, repair may be relatively effective whereas for nerve transection (neurotmesis repair will likely be very poor as few axons may be able to cross between the two parts of the severed nerve, across the newly generated nerve bridge, to enter the distal stump and regenerate. Analysing axon growth and the cell-cell interactions that occur following both nerve crush and cut injuries has largely been carried out by staining sections of nerve tissue, but this has the obvious disadvantage that it is not possible to follow the paths of regenerating axons in three dimensions within the nerve trunk or nerve bridge. To try and solve this problem, we describe the development and use of a novel whole mount staining protocol that allows the analysis of axonal regeneration, Schwann cell-axon interaction and re-vascularisation of the repairing nerve following nerve cut and crush injuries.

  17. Visualizing Peripheral Nerve Regeneration by Whole Mount Staining

    Science.gov (United States)

    Dun, Xin-peng; Parkinson, David B.

    2015-01-01

    Peripheral nerve trauma triggers a well characterised sequence of events both proximal and distal to the site of injury. Axons distal to the injury degenerate, Schwann cells convert to a repair supportive phenotype and macrophages enter the nerve to clear myelin and axonal debris. Following these events, axons must regrow through the distal part of the nerve, re-innervate and finally are re-myelinated by Schwann cells. For nerve crush injuries (axonotmesis), in which the integrity of the nerve is maintained, repair may be relatively effective whereas for nerve transection (neurotmesis) repair will likely be very poor as few axons may be able to cross between the two parts of the severed nerve, across the newly generated nerve bridge, to enter the distal stump and regenerate. Analysing axon growth and the cell-cell interactions that occur following both nerve crush and cut injuries has largely been carried out by staining sections of nerve tissue, but this has the obvious disadvantage that it is not possible to follow the paths of regenerating axons in three dimensions within the nerve trunk or nerve bridge. To try and solve this problem, we describe the development and use of a novel whole mount staining protocol that allows the analysis of axonal regeneration, Schwann cell-axon interaction and re-vascularisation of the repairing nerve following nerve cut and crush injuries. PMID:25738874

  18. Blood culture gram stain, acridine orange stain and direct sensitivity-based antimicrobial therapy of bloodstream infection in patients with trauma

    Directory of Open Access Journals (Sweden)

    Behera B

    2010-01-01

    Full Text Available Purpose: The purpose of this study was to ascertain if the simple practice of Gram stain, acridine orange stain and direct sensitivity determination of positive blood culture bottles could be used to guide early and appropriate treatment in trauma patients with clinical suspicion of sepsis. The study also aimed to evaluate the error in interpreting antimicrobial sensitivity by direct method when compared to standard method and find out if specific antibiotic-organism combination had more discrepancies. Findings from consecutive episodes of blood stream infection at an Apex Trauma centre over a 12-month period are summarized. Materials and Methods: A total of 509 consecutive positive blood cultures were subjected to Gram staining. AO staining was done in BacT/ALERT-positive Gram-stain negative blood cultures. Direct sensitivity was performed from 369 blood culture broths, showing single type of growth in Gram and acridine orange staining. Results of direct sensitivity were compared to conventional sensitivity for errors. Results: No ′very major′ discrepancy was found in this study. About 5.2 and 1.8% minor error rates were noted in gram-positive and gram-negative bacteria, respectively, while comparing the two methods. Most of the discrepancies in gram-negative bacteria were noted in β lactam - β lactamase inhibitor combinations. Direct sensitivity testing was not reliable for reporting of methicillin and vancomycin resistance in Staphylococci. Conclusions: Gram stain result together with direct sensitivity testing is required for optimizing initial antimicrobial therapy in trauma patients with clinical suspicion of sepsis. Gram staining and AO staining proved particularly helpful in the early detection of candidaemia.

  19. 2D Projection Analysis of GPCR Complexes by Negative Stain Electron Microscopy.

    Science.gov (United States)

    Peisley, Alys; Skiniotis, Georgios

    2015-01-01

    While electron cryo-microscopy (cryo-EM) of biological specimens is the preferred single particle EM method for structure determination, its application is very challenging for the typically small (offer a simple and powerful tool for the rapid evaluation of sample characteristics, such as homogeneity or oligomeric state. When coupled to single particle classification and averaging, negative stain EM can provide valuable information on the overall architecture and dynamics of protein complexes. Here we provide a concise protocol for negative stain imaging and two-dimensional (2D) projection analysis of GPCR complexes, including notes for the intricacies of the application in these biological systems.

  20. Potential of 80-kV high-resolution cone-beam CT imaging combined with an optimized protocol for neurological surgery

    Energy Technology Data Exchange (ETDEWEB)

    Kanayama, Seisaku; Hara, Takayuki [Toranomon Hospital, Department of Neurosurgery, Tokyo (Japan); Hamada, Yusuke [Toranomon Hospital, Department of Radiology, Tokyo (Japan); Matsumaru, Yuji [Toranomon Hospital, Department of Neuro-Endovascular Therapy, Tokyo (Japan)

    2014-11-05

    With the development of computed tomography (CT) and magnetic resonance imaging (MRI), the use of conventional X-ray angiography including digital subtraction angiography (DSA) for diagnosis has decreased, as it is an invasive technique with a risk of neurological complications. However, X-ray angiography imaging technologies have progressed markedly, along with the development of endovascular treatments. A newly developed angiography technique using cone-beam CT (CBCT) technology provides higher spatial resolution than conventional CT. Herein, we describe the potential of this technology for neurosurgical operations with reference to clinical cases. Two hundred twenty-five patients who received 80-kV high-resolution CBCT from July 2011 to June 2014 for preoperative examinations were included in this study. For pathognomonical cases, images were taken with suitable reconstruction modes and contrast protocols. Cases were compared with intraoperative findings or images from other modalities. We observed the following pathognomonical types: (1) imaging of the distal dural ring (DDR) and the surrounding structure for paraclinoid aneurysms, (2) imaging of thin blood vessels, and (3) imaging of both brain tumors and their surrounding anatomy. Our devised 80-kV high-resolution CBCT imaging system provided clear visualization of detailed anatomy when compared with other modalities in almost all cases. Only two cases provided poor visualization due to movement artifact. Eighty-kilovolt high-resolution CBCT has the potential to provide detailed anatomy for neurosurgical operations when utilizing suitable modes and contrast protocols. (orig.)

  1. The Language of Stained-Glass Windows

    Science.gov (United States)

    Brew, Charl Anne

    2010-01-01

    The splendor and beauty of stained glass punctuates any room. In this article, the author describes a cross-curriculum project which incorporated the French classes' research and written study of France in the Middle Ages. For the project the author suggested Sainte-Chapelle which is considered a reliquary and was built by Louis IX to house the…

  2. Corneal staining after treatment with topical tetracycline

    NARCIS (Netherlands)

    R. Lapid-Gortzak; C.P. Nieuwendaal; A.R. Slomovic; L. Spanjaard

    2006-01-01

    Purpose: The purpose of this paper is to report a case of corneal staining after treatment with topical tetracycline. Methods: A patient with crystalline keratopathy caused by Streptococcus viridans after corneal transplantation was treated topically with tetracycline eye drops, based on results of

  3. Autofluorescence of routinely hematoxylin and eosin- stained ...

    African Journals Online (AJOL)

    SERVER

    2008-03-04

    Mar 4, 2008 ... histological method, and staining by this dying method is dependant partly upon ... procedure that is specific for it, or for the chemical group to which it belongs ... Hematoxylin was found to have no effect on the inten- ... Hair pulp. -. - Inner root ... Autofluorescence of interstitial tissue makes structures such as ...

  4. STAINING OF VACCINIA ANTIGEN BY IMMUNOURANIUM TECHNIQUE,

    Science.gov (United States)

    An attempt to follow morphologically the development of vaccinia antigen in helium-lanthanum ( HeLa ) cells is reported. The conversion of rabbit...antisera to vaccinia virus and the preparation of vaccinia-infected HeLa cells for electron microscopy are described. With specific staining, viral

  5. The Language of Stained-Glass Windows

    Science.gov (United States)

    Brew, Charl Anne

    2010-01-01

    The splendor and beauty of stained glass punctuates any room. In this article, the author describes a cross-curriculum project which incorporated the French classes' research and written study of France in the Middle Ages. For the project the author suggested Sainte-Chapelle which is considered a reliquary and was built by Louis IX to house the…

  6. Can magnetic resonance imaging be an alternative to computed tomography in immunocompromised patients with suspected fungal infections? Feasibility of a speed optimized examination protocol at 3 Tesla.

    Science.gov (United States)

    Nagel, Sebastian Niko; Wyschkon, Sebastian; Schwartz, Stefan; Hamm, Bernd; Elgeti, Thomas

    2016-04-01

    To prospectively evaluate a short MRI examination protocol for the detection of nodular pulmonary infiltrates in immunocompromised patients with hematologic diseases and suspected invasive fungal infections. Patients with nodular infiltrates on CT scans were examined on a 3T MRI scanner. The standardized protocol included axial T2-weighted fast spin echo (FSE) sequences +/- fat saturation (FS), and axial T1-weighted gradient echo (GRE) sequences. Long and short axis diameters of nodular infiltrates and visibility were assessed on MR images at least six months after the CT scan, blinded to patient and examination data. Inter- and intra-reader reliability was assessed in two patients. Statistical testing included Wilcoxon-test, Cohen's kappa, and intra-class correlation coefficients. Bland-Altman plots were created to visualize differences in the measurements. In all 13 patients MRI examinations were completed successfully (average examination time 12 min and maximum breath-hold time of 8s). CT detected 409 nodules. Sensitivity of MRI was 93.2% when using all sequences in combination; considering nodules >5mm, sensitivity increased to 97.9%. Reliability analysis showed excellent correlations with an intra-class correlation coefficient of at least 0.89 for T2 FSE (95% CI 0.79-0.93, p<0.01) images for the intra-, and the lowest of 0.77 for T2 FSE (95% CI 0.55-0.89, p<0.01) images for the inter-reader comparison. Agreement on nodule visibility was at least kappa=0.95 (p<0.01) for the intra- and 0.72 (p<0.01) for the inter-reader analysis. With an average examination time of 12 min, pulmonary MRI at 3T is feasible in immunocompromised patients with hematologic diseases and suspected invasive fungal infections. MRI might serve as an alternative diagnostic tool during follow-up examinations. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Improved Whole-Blood-Staining Device

    Science.gov (United States)

    Sams, Clarence F.; Crucian, Brian; Paul, Bonnie; Melton, Shannon; Guess, Terry

    2012-01-01

    Dramatic improvements have been made in NASA s Whole Blood Staining Device (WBSD) since it was last described in "Whole-Blood-Staining Device," NASA Tech Briefs, Vol. 23, No. 10 (October 1999), page 64. The new system has a longer shelf life, a simpler and more effective operational procedure, improved interface with instrumentation, and shorter processing time. More specifically, the improvements have targeted bag and locking clip materials, sampling ports, and air pocket prevention. The WBSD stains whole blood collected during spaceflight for subsequent flow cytometric analysis. In short, the main device stains white blood cells by use of monoclonal antibodies conjugated to various fluorochromes, followed by lysing and fixing of the cells by use of a commercial reagent that has been diluted according to NASA safety standards. This system is compact, robust, and does not require electric power, precise mixing, or precise incubation times. Figure 1 depicts the present improved version for staining applications, which is a poly(tetrafluoroethylene) bag with a Luer-lock port and plastic locking clips. An InterLink (or equivalent) intravenous- injection port screws into the Luer-lock port. The inflatable/collapsible nature of the bag facilitates loading and helps to minimize the amount of air trapped in the fully loaded bag. Some additional uses have been identified for the device beyond whole blood staining. The WBSD has been configured for functional assays that require culture of live cells by housing sterile culture media, mitogens, and fixatives prior to use [Figure 2(a)]. Simple injection of whole blood allows cell-stimulation culture to be performed in reduced gravity conditions, and product stabilization prior to storage, while protecting astronauts from liquid biohazardous materials. Also, the improved WBSD has reconstituted powdered injectable antibiotics by mixing them with diluent liquids [Figure 2(b)]. Although such mixing can readily be performed on

  8. Histology protocols

    Directory of Open Access Journals (Sweden)

    CarloAlberto Redi

    2010-06-01

    Full Text Available Tim D. Hewitson & Ian A. Darby (Eds Humana press, Totowa, New Jersey (USA Series: Springer Protocols Methods in Molecular Biology, Volume 611, 2010 Pages: 230; € 83.15 ISBN: 978-1-60327-344-2 Impressive as it can sounds in the era that Biology see a clear dominance of reductionism with the idea that complexity can be disentagled more and more thanks to the use of molecular tools, the reader will remain fascinated by this slim and agile volume devoted to bring together what apparently are two separeted words: molecular biology and histology. Simply remembering to the youngest scientists.....

  9. Rapid and simultaneous detection of Mycobacterium tuberculosis complex and Beijing/W genotype in sputum by an optimized DNA extraction protocol and a novel multiplex real-time PCR.

    Science.gov (United States)

    Leung, Eric T Y; Zheng, L; Wong, Rity Y K; Chan, Edward W C; Au, T K; Chan, Raphael C Y; Lui, Grace; Lee, Nelson; Ip, Margaret

    2011-07-01

    Rapid diagnosis and genotyping of Mycobacterium tuberculosis by molecular methods are often limited by the amount and purity of DNA extracted from body fluids. In this study, we evaluated 12 DNA extraction methods and developed a highly sensitive protocol for mycobacterial DNA extraction directly from sputa using surface-coated magnetic particles. We have also developed a novel multiplex real-time PCR for simultaneous identification of M. tuberculosis complex and the Beijing/W genotype (a hypervirulent sublineage of M. tuberculosis) by using multiple fluorogenic probes targeting both the M. tuberculosis IS6110 and the Rv0927c-pstS3 intergenic region. With reference strains and clinical isolates, our real-time PCR accurately identified 20 non-Beijing/W and 20 Beijing/W M. tuberculosis strains from 17 different species of nontuberculosis Mycobacterium (NTM). Further assessment of our DNA extraction protocol and real-time PCR with 335 nonduplicate sputum specimens correctly identified all 74 M. tuberculosis culture-positive specimens. In addition, 15 culture-negative specimens from patients with confirmed tuberculosis were also identified. No cross-reactivity was detected with NTM specimens (n = 31). The detection limit of the assay is 10 M. tuberculosis bacilli, as determined by endpoint dilution analysis. In conclusion, an optimized DNA extraction protocol coupled with a novel multiprobe multiplex real-time PCR for the direct detection of M. tuberculosis, including Beijing/W M. tuberculosis, was found to confer high sensitivity and specificity. The combined procedure has the potential to compensate for the drawbacks of conventional mycobacterial culture in routine clinical laboratory setting, such as the lengthy incubation period and the limitation to viable organisms.

  10. Optimization of a sperm-oviduct binding assay mimicking in vivo conditions. Adoption of sperm separation methods and protocols for analysing sperm motility and intracellular Ca2+ level

    OpenAIRE

    Narud, Birgitte

    2014-01-01

    English: An in vitro model that mimics the interactions between spermatozoa and oviductal epithelial cells can be used to increase the knowledge about the function of the oviduct and the formation of a sperm reservoir in vivo. The aim of the present study was to optimize methods for culturing bovine epithelial cells (BOECs) bi-dimensionally on plastic and three-dimensionally on polyester membrane. These cells were used in a sperm binding assay for evaluation of sperm-BOEC binding and relea...

  11. Photodynamic therapy for port wine stains

    Science.gov (United States)

    Li, Junheng

    1998-11-01

    Previous therapies for port wine stains usually cause unacceptable scarring or obtain poor effect. Because port wine is a congenital vasculopathy consisting of an abnormal network of capillaries in the upper dermis with an overlying normal epidermis and the researchers found the tumor blood vessels were occluded accompanying the necrosis of the tumor after PDT. The author and his colleagues started a series of animal and clinical studies since 1991 about photodynamic therapy for port wine stain an they established the method of PDT for PWS. The clinical studies of over 1500 cases proved that PWS can be cured by PDT without scar formation because there is no thermal effect involved. No relapse was found within a maximum follow-up of six years.

  12. Whole-Mount DAPI Staining and Measurement of DNA Content in Plant Cells.

    Science.gov (United States)

    Schnittger, Arp; Hülskamp, Martin

    2007-01-01

    INTRODUCTIONDuring development, many plant cells undergo endoreduplication, whereby ploidy increases to a multiple of the normal 2C content. For example, trichome development is accompanied by an increase in ploidy to 32C, indicating that trichome cells undergo four rounds of endoreduplication. In the protocol described here, DNA levels, and hence developmental progress in the corresponding cells, are measured by staining the DNA with a fluorescent marker and then quantifying the fluorescence of individual nuclei.

  13. Standardized Relative Quantification of Immunofluorescence Tissue Staining

    OpenAIRE

    sprotocols

    2015-01-01

    Authors: Oriol Arqués, Irene Chicote, Stephan Tenbaum, Isabel Puig & Héctor G. Palmer ### Abstract The detection of correlations between the expression levels or sub-cellular localization of different proteins with specific characteristics of human tumors, such as e.g. grade of malignancy, may give important hints of functional associations. Here we describe the method we use for relative quantification of immunofluorescence staining of tumor tissue sections, which allows us to co...

  14. A staining method for assessing the viability of Esteya vermicola conidia.

    Science.gov (United States)

    Wang, Yunbo; Thang, NguyenTrong; Li, Zheng; Zhang, Yongan; Li, Jingjie; Xue, Jianjie; Gu, Lijuan; Hong, VuThuy; Mira, Lee; Sung, Changkeun

    2014-07-01

    The viability of conidia of Esteya vermicola, a potentially important biocontrol agent against the pinewood nematode Bursaphelenchus xylophilus, is usually determined by cultivation for 18-48 h in culture medium. As an alternative to this labor-intensive method, we have developed a rapid, simple, and low-cost staining method for assessing E vermicola conidia survival rates. A mixture of neutral red and methylene blue was found to be the most optimal among several stains that also included safranin O and Janus green B. This mixture stained nonviable conidia blue, in contrast to viable conidia, which were stained red in the cytoplasm and blue in the cell wall. This method may be particularly useful for traditional research laboratories, as it provides rapid results using common, relatively inexpensive laboratory equipment.

  15. A Survey of Pediatric CT Protocols and Radiation Doses in South Korean Hospitals to Optimize the Radiation Dose for Pediatric CT Scanning.

    Science.gov (United States)

    Hwang, Jae-Yeon; Do, Kyung-Hyun; Yang, Dong Hyun; Cho, Young Ah; Yoon, Hye-Kyung; Lee, Jin Seong; Koo, Hyun Jung

    2015-12-01

    Children are at greater risk of radiation exposure than adults because the rapidly dividing cells of children tend to be more radiosensitive and they have a longer expected life time in which to develop potential radiation injury. Some studies have surveyed computed tomography (CT) radiation doses and several studies have established diagnostic reference levels according to patient age or body size; however, no survey of CT radiation doses with a large number of patients has yet been carried out in South Korea. The aim of the present study was to investigate the radiation dose in pediatric CT examinations performed throughout South Korea. From 512 CT (222 brain CT, 105 chest CT, and 185 abdominopelvic CT) scans that were referred to our tertiary hospital, a dose report sheet was available for retrospective analysis of CT scan protocols and dose, including the volumetric CT dose index (CTDIvol), dose-length product (DLP), effective dose, and size-specific dose estimates (SSDE). At 55.2%, multiphase CT was the most frequently performed protocol for abdominopelvic CT. Tube current modulation was applied most often in abdominopelvic CT and chest CT, accounting for 70.1% and 62.7%, respectively. Regarding the CT dose, the interquartile ranges of the CTDIvol were 11.1 to 22.5 (newborns), 16.6 to 39.1 (≤1 year), 14.6 to 41.7 (2-5 years), 23.5 to 44.1 (6-10 years), and 31.4 to 55.3 (≤15 years) for brain CT; 1.3 to 5.7 (≤1 year), 3.9 to 6.8 (2-5 years), 3.9 to 9.3 (6-10 years), and 7.7 to 13.8 (≤15 years) for chest CT; and 4.0 to 7.5 (≤1 year), 4.2 to 8.9 (2-5 years), 5.7 to 12.4 (6-10 years), and 7.6 to 16.6 (≤15 years) for abdominopelvic CT. The SSDE and CTDIvol were well correlated for patients CT in South Korea. The CTDIvol, DLP, and effective dose were generally lower than in German and UK surveys, except in certain age groups.

  16. Aptamer Stainings for Super-resolution Microscopy.

    Science.gov (United States)

    de Castro, Maria Angela Gomes; Rammner, Burkhard; Opazo, Felipe

    2016-01-01

    Fluorescence microscopy is an invaluable tool to visualize molecules in their biological context with ease and flexibility. However, studies using conventional light microscopy have been limited to the resolution that light diffraction allows (i.e., ~200 nm). This limitation has been recently circumvented by several types of advanced fluorescence microscopy techniques, which have achieved resolutions of up to ~10 nm. The resulting enhanced imaging precision has helped to find important cellular details that were not visible using diffraction-limited instruments. However, it has also revealed that conventional stainings using large affinity tags, such as antibodies, are not accurate enough for these imaging techniques. Since aptamers are substantially smaller than antibodies, they could provide a real advantage in super-resolution imaging. Here we compare the live staining of transferrin receptors (TfnR) obtained with different fluorescently labeled affinity probes: aptamers, specific monoclonal antibodies, or the natural receptor ligand transferrin. We observed negligible differences between these staining strategies when imaging is performed with conventional light microscopy (i.e., laser scanning confocal microscopy). However, a clear superiority of the aptamer tag over antibodies became apparent in super-resolved images obtained with stimulated emission depletion (STED) microscopy.

  17. A simple metal staining procedure for identification and visualization of single cells by LA-ICP-MS.

    Science.gov (United States)

    Herrmann, A J; Techritz, S; Jakubowski, N; Haase, A; Luch, A; Panne, U; Mueller, L

    2017-05-21

    High lateral resolution of metal detection in single cells by use of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) demands powerful staining methods. In this work different staining procedures for the single cell analysis with LA-ICP-MS were optimized. An iridium intercalator was utilized to stain the cell nuclei whereas the whole cell was stained by the use of maleimido-mono-amide-DOTA (mDOTA) complexing lanthanide(iii) ions. The content of the artificially introduced metals per cell was quantified using a matrix matched calibration approach based on cellulose membranes onto which standards were spotted by a microarray spotter. Absolute metal stain amounts in the range of 2.34 to 9.81 femtomole per cell were determined. The metal staining procedures allow direct identification and visualization of single cells and their cell compartments by element microscopy without the use of bright field images of the sample.

  18. A simple technique for staining of platyhelminths with the lactophnol cotton blue stain.

    Science.gov (United States)

    Henedi, Adawia A M; El-Azazy, Osama M E

    2013-08-01

    This paper describes a simple technique for staining of flatworms using lactophenol cotton blue (LPCB). The staining was tested on 2 trematode species: Heterophyes heterophyes and Mesostephanus appendiculatus, and one cestode: Diplopylidium acanthotetra, which were collected from the intestine of stray cats in Kuwait. The specimens were mounted in a small amount of the LPCB stain on a clean slide for 2-3 minutes before covering with a cover slip. The technique rapidly and clearly differentiated the internal structures of the helminthes. Its speed and simplicity are advantages over other staining methods. It is easily used in wide-scale surveys where a large number of platyhelminths have to be identified and it is suitable for field studies.

  19. Optimization of Electronic Commerce Authentication Protocol Based on QoS Quantitative Assessment%基于QoS量化评估的电子商务认证协议优化

    Institute of Scientific and Technical Information of China (English)

    刘彩霞

    2016-01-01

    通过对电子商务的认证协议进行优化设计,可以提高电子商务商家的服务质量( QoS)。当前方法多采用多地址差错控制协议对电子商务进行认证,随着服务对象数量的增加和数据链路规模的扩大,准确度会大幅下降。提出基于最小竞争窗口树形层状拓扑的电子商务认证协议,实现对商家的QoS量化评估。构建电子商务认证协议的网络结构模型和数据传输模型,对商家的服务质量QoS信息进行信息模型构建和预测算法描述,引入最小竞争窗口树形层状拓扑改进对电子商务认证协议进行优化。实验结果表明,采用该方法进行商家的QoS量化评估,具有较好的服务质量预测能力,可以准确指导商家改善服务质量,提高线上交易的安全性和可靠性,展示了较好的应用价值。%Through the study of the optimization design of the authentication protocol of electronic commerce, can improve the quality of service ( QoS) of e-commerce businesses. Current method with multiple address error control protocol for electronic commerce certification, with the increase of number of the service object and the ex-pansion of data link, its accuracy will have fallen sharply. Based on minimum contention window of tree layer topol-ogy electronic commerce authentication protocol was proposed, to realize QoS quantitative evaluation to the busi-nessman. Construction of electronic commerce network structure model of authentication protocol and the data trans-mission model, quality of service QoS information of business information model building and forecasting algorithm is described, the introduction of minimum contention window tree layer topology improved authentication protocol is optimized to the electronic commerce. The experimental results show that the QoS of quantitative evaluation using this method to the businessman, has good prediction ability, service quality can accurately guide the

  20. [Multicenter trial for optimization of bolus tracking settings and contrast material injection protocol in arterial dominant phase of dynamic computed tomography for diagnosis of hepatocellular carcinoma].

    Science.gov (United States)

    Yoshikawa, Shushi; Okada, Masahiro; Kondo, Hiroshi; Sou, Hironobu; Murakami, Takamichi; Kanematsu, Masayuki; Ichikawa, Tomoaki; Hayakawa, Akiko; Shiosakai, Kazuhito; Awai, Kazuo; Yoshimitsu, Kengo; Yamashita, Yasuyuki

    2014-08-01

    Alongside current improvements in the performance of computer tomography (CT) systems, there has been an increase in the use of bolus tracking (BT) to acquire arterial dominant phase images for dynamic CT at optimal timing for characterization of liver focal lesions. However, optimal BT settings have not been established. In the present study, methods of contrast enhancement and BT setting values were evaluated using a multicenter post-marketing surveillance study on contrast media used in patients with chronic hepatitis and/or cirrhosis who had undergone liver dynamic CT for diagnosis of hepatocellular carcinoma, conducted by Daiichi Sankyo Co., Ltd. The results suggested the contrast injection method to be clinically useful if the amount of iodine per kilogram of body weight is set at 600 mg/kg and the injection duration at 30 s. To achieve a good arterial dominant scan under conditions where the injection duration is fixed at 30 s or the average injection duration is 34 s using the fixed injection rate method, the scan delay time should ideally to be set to longer than 13 s. If using the BT method, we recommend that the BT settings should be revalidated in reference to our results.

  1. 基于多路由协议的株间锄草机器人结构和控制优化设计%Control Optimization Design and Structure of Plant Weeding Robot Based on Muti-routing Protocols

    Institute of Scientific and Technical Information of China (English)

    李伟; 江民夏; 汪小志; 余良俊

    2016-01-01

    In order to obtain the ideal effect of mechanical weeding between seedlings,it presents a new structural optimi-zation method of weeding robot.It adopts the multi-objective optimization model to design the terminal structure of wee-ding, the cooperative control of multiple weeding robot with multiple routing protocols,greatly improving the work efficien-cy of field weeding robot.Based on the established mechanical weeding tooth trajectory mathematical model, it was com-bined with the requirements of modern agriculture to the limit and mechanical weeding parameters.The multi-objective optimization model is established,and the optimization toolbox of Matlab to obtain the optimal solution and its application in multi robot routing protocol system control framework.In order to verify the validity of the optimization method,experi-ments are carried out in collaboration of multi field weeding robot, it found through experiments, the multi routing wee-ding robot after optimization,not only greatly improves the operation speed and the weeding efficiency,but also reduce the crop loss rate, which provides a theoretical basis for the design of rotary tillage weeding machine in large scale.%为获得理想的苗间机械锄草效果,提出了一种新的锄草机器人结构优化方法.该方法主要采用多目标优化模型对锄草末端结构进行设计,采用多路由协议对多锄草机器人进行协同控制,大大提高了田间锄草机器人的工作效率.在建立了机械锄草齿运动轨迹数学模型的基础上,结合现代农艺对机械锄草参数的限定及要求,建立了多目标优化模型,并利用MatLab优化工具箱得到最优解,将其应用在多机器人系统控制的多路由协议框架中.为了验证优化方法的有效性,在田间对多锄草机器人协同作业进行了试验,结果表明:优化后的多路由锄草机器人不仅大大提高了作业速度和锄草效率,而且降低了作物苗损失率,为大型中耕除

  2. Optimization of retroviral-mediated gene transfer to human NOD/SCID mouse repopulating cord blood cells through a systematic analysis of protocol variables.

    Science.gov (United States)

    Hennemann, B; Conneally, E; Pawliuk, R; Leboulch, P; Rose-John, S; Reid, D; Chuo, J Y; Humphries, R K; Eaves, C J

    1999-05-01

    Retroviral transduction of human hematopoietic stem cells is still limited by lack of information about conditions that will maximize stem cell self-renewal divisions in vitro. To address this, we first compared the kinetics of entry into division of single human CD34+CD38- cord blood (CB) cells exposed in vitro to three different flt3-ligand (FL)-containing cytokine combinations. Of the three combinations tested, FL + hyperinterleukin 6 (HIL-6) yielded the least clones and these developed at a slow rate. With either FL + Steel factor (SF) + HIL-6 + thrombopoietin (TPO) or FL + SF + interleukin 3 (IL-3) + IL-6 + granulocyte-colony-stimulating factor (G-CSF), >90% of the cells that formed clones within 6 days undertook their first division within 4 days, although not until after 24 hours. These latter two, more stimulatory, cytokine combinations then were used to assess the effect of duration of cytokine exposure on the efficiency of transducing primitive CB cells with a gibbon ape leukemia virus-pseudotyped murine retroviral vector containing the enhanced green fluorescent protein (GFP) cDNA and the neomycin resistance gene. Fresh lin- CB cells exposed once to medium containing this virus plus cytokines on fibronectin-coated dishes yielded 23% GFP+ CD34+ cells and 52-57% G418-resistant CFC when assessed after 2 days. Prestimulation of the target cells (before exposing them to virus) with either the four or five cytokine combination increased their susceptibility. In both cases, the effect of prestimulation assessed using the same infection protocol was maximal with 2 days of prestimulation and resulted in 47-54% GFP+ CD34+ cells and 67-69% G418-resistant CFC. Repeated daily addition of new virus (up to three times), with assessment of the cells 2 days after the last addition of fresh virus, gave only a marginal improvement in the proportion of transduced CD34+ cells and CFC, but greatly increased the proportion of transduced LTC-IC (from 40% to >99

  3. Partners for the optimal organisation of the healthcare continuum for high users of health and social services: protocol of a developmental evaluation case study design.

    Science.gov (United States)

    Hudon, Catherine; Chouinard, Maud-Christine; Couture, Martine; Brousselle, Astrid; Couture, Eva Marjorie; Dubois, Marie-France; Fortin, Martin; Freund, Tobias; Loignon, Christine; Mireault, Jean; Pluye, Pierre; Roberge, Pasquale; Rodriguez, Charo

    2014-12-02

    Case management allows us to respond to the complex needs of a vulnerable clientele through a structured approach that promotes enhanced interaction between partners. Syntheses on the subject converge towards a need for a better description of the relationships between programmes and their local context, as well as the characteristics of the clienteles and programmes that contribute to positive impacts. The purpose of this project is thus to describe and evaluate the case management programmes of four health and social services centres in the Saguenay-Lac- Saint-Jean region of Québec, Canada, in order to inform their improvement while creating knowledge on case management that can be useful in other contexts. This research relies on a multiple embedded case study design based on a developmental evaluation approach. We will work with the case management programme for high users of hospital services of each centre. Three different units of analysis will be interwoven to obtain an in-depth understanding of each case, that is: (1) health and social services centre and local services network, (2) case management programme and (3) patients who are high users of services. Two strategies for programme evaluation (logic models and implementation analysis) will guide the mixed data collection based on qualitative and quantitative methods. This data collection will rely on: (1) individual interviews and focus groups; (2) participant observation; (3) document analysis; (4) clinical and administrative data and (5) questionnaires. Description and comparison of cases, and integration of qualitative and quantitative data will be used to guide the data analysis. The study protocol was approved by the Ethics Research Boards of the four health and social services centres (HSSCs) involved. Findings will be disseminated by publications in peer-reviewed journals, conferences, and policy and practice partners in local and national government. Published by the BMJ Publishing Group

  4. Partners for the optimal organisation of the healthcare continuum for high users of health and social services: protocol of a developmental evaluation case study design

    Science.gov (United States)

    Hudon, Catherine; Chouinard, Maud-Christine; Couture, Martine; Brousselle, Astrid; Couture, Eva Marjorie; Dubois, Marie-France; Fortin, Martin; Freund, Tobias; Loignon, Christine; Mireault, Jean; Pluye, Pierre; Roberge, Pasquale; Rodriguez, Charo

    2014-01-01

    Introduction Case management allows us to respond to the complex needs of a vulnerable clientele through a structured approach that promotes enhanced interaction between partners. Syntheses on the subject converge towards a need for a better description of the relationships between programmes and their local context, as well as the characteristics of the clienteles and programmes that contribute to positive impacts. The purpose of this project is thus to describe and evaluate the case management programmes of four health and social services centres in the Saguenay-Lac- Saint-Jean region of Québec, Canada, in order to inform their improvement while creating knowledge on case management that can be useful in other contexts. Methods and analysis This research relies on a multiple embedded case study design based on a developmental evaluation approach. We will work with the case management programme for high users of hospital services of each centre. Three different units of analysis will be interwoven to obtain an in-depth understanding of each case, that is: (1) health and social services centre and local services network, (2) case management programme and (3) patients who are high users of services. Two strategies for programme evaluation (logic models and implementation analysis) will guide the mixed data collection based on qualitative and quantitative methods. This data collection will rely on: (1) individual interviews and focus groups; (2) participant observation; (3) document analysis; (4) clinical and administrative data and (5) questionnaires. Description and comparison of cases, and integration of qualitative and quantitative data will be used to guide the data analysis. Ethics and dissemination The study protocol was approved by the Ethics Research Boards of the four health and social services centres (HSSCs) involved. Findings will be disseminated by publications in peer-reviewed journals, conferences, and policy and practice partners in local and

  5. Generalized routing protocols for multihop relay networks

    KAUST Repository

    Khan, Fahd Ahmed

    2011-07-01

    Performance of multihop cooperative networks depends on the routing protocols employed. In this paper we propose the last-n-hop selection protocol, the dual path protocol, the forward-backward last-n-hop selection protocol and the forward-backward dual path protocol for the routing of data through multihop relay networks. The average symbol error probability performance of the schemes is analysed by simulations. It is shown that close to optimal performance can be achieved by using the last-n-hop selection protocol and its forward-backward variant. Furthermore we also compute the complexity of the protocols in terms of number of channel state information required and the number of comparisons required for routing the signal through the network. © 2011 IEEE.

  6. An in vitro analysis model for investigating the staining effect of various chlorhexidine-based mouthwashes

    Science.gov (United States)

    Kouadio, Alain-Ayepa; Struillou, Xavier; Bories, Céline; Bouler, Jean-Michel; Badran, Zahi

    2017-01-01

    Background There are different mouthwashes containing chlorhexidine in different concentrations, as well as various excipients. Chlorhexidine induce stains or discoloration in teeth and mucous membranes. The aim of this work was to design a model to reproduce in vitro staining associated with the use of different mouthwashes containing chlorhexidine. Material and Methods We used as substrates of natural teeth and elephant ivory slices. Different incubation baths were conducted over 21 days in culture dishes at 37°C. At the beginning of experiment before incubation (D0) and after 21 days (D21) of incubation with different mouthwashes, pictures of substrates were taken in a standardized manner and an image analysis software was used to analyse and quantify the staining under the various conditions by using the 3 main colours (Red, Green, Blue, RGB). Results The results of this work demonstrate a very good reproducibility of the protocol, and secondly, a different expression statistically significant of the primary blue colour. We suggest that for a given concentration of chlorhexidine, the staining effects may vary depending on the excipients used. Conclusions This replicable model, easy to implement over a relatively short duration, can be used for evaluation of existing mouthwashes, and to test the excipients anti discoloration proposed by manufacturers. Key words:In vitro, chlorhexidine, mouthwashes, dental stain, tooth discoloration.

  7. Improved dose calculation accuracy for low energy brachytherapy by optimizing dual energy CT imaging protocols for noise reduction using sinogram affirmed iterative reconstruction.

    Science.gov (United States)

    Landry, Guillaume; Gaudreault, Mathieu; van Elmpt, Wouter; Wildberger, Joachim E; Verhaegen, Frank

    2016-03-01

    The goal of this study was to evaluate the noise reduction achievable from dual energy computed tomography (CT) imaging (DECT) using filtered backprojection (FBP) and iterative image reconstruction algorithms combined with increased imaging exposure. We evaluated the data in the context of imaging for brachytherapy dose calculation, where accurate quantification of electron density ρe and effective atomic number Zeff is beneficial. A dual source CT scanner was used to scan a phantom containing tissue mimicking inserts. DECT scans were acquired at 80 kVp/140Sn kVp (where Sn stands for tin filtration) and 100 kVp/140Sn kVp, using the same values of the CT dose index CTDIvol for both settings as a measure for the radiation imaging exposure. Four CTDIvol levels were investigated. Images were reconstructed using FBP and sinogram affirmed iterative reconstruction (SAFIRE) with strength 1,3 and 5. From DECT scans two material quantities were derived, Zeff and ρe. DECT images were used to assign material types and the amount of improperly assigned voxels was quantified for each protocol. The dosimetric impact of improperly assigned voxels was evaluated with Geant4 Monte Carlo (MC) dose calculations for an (125)I source in numerical phantoms. Standard deviations for Zeff and ρe were reduced up to a factor ∼2 when using SAFIRE with strength 5 compared to FBP. Standard deviations on Zeff and ρe as low as 0.15 and 0.006 were achieved for the muscle insert representing typical soft tissue using a CTDIvol of 40 mGy and 3mm slice thickness. Dose calculation accuracy was generally improved when using SAFIRE. Mean (maximum absolute) dose errors of up to 1.3% (21%) with FBP were reduced to less than 1% (6%) with SAFIRE at a CTDIvol of 10 mGy. Using a CTDIvol of 40mGy and SAFIRE yielded mean dose calculation errors of the order of 0.6% which was the MC dose calculation precision in this study and no error was larger than ±2.5% as opposed to errors of up to -4% with FPB. This

  8. Optimal cut-off criteria for duplex ultrasound for the diagnosis of restenosis in stented carotid arteries: Review and protocol for a diagnostic study

    Directory of Open Access Journals (Sweden)

    Brown Martin M

    2009-07-01

    cohort we will enrol a minimum of 300 patients treated with a stent. All patients undergo regular DUS examination at the yearly follow-up visit according to the ICSS protocol. To avoid verification bias, an additional computed tomography angiography (CTA will be performed as a reference test in all consecutive patients, regardless of the degree of stenosis on the initial DUS test.

  9. Detecting the apoptosis of dopamine neurons with immunohistochemical staining and double-staining technique

    Institute of Scientific and Technical Information of China (English)

    Jiguo Zhang; Jing Zhang; Feng Zhang; Yunsheng Gao

    2006-01-01

    BACKGROUND: It is proved that the onset of Parkinson disease companies with neuronal apoptosis of dopamine in substantia nigra of midbrain. Previous researches on neuronal apoptosis of dopamine were analyzed on their consecutive tissue sections with immunohistochemical single-labeling method, immunofluorescence and electron microscope, and there are significant differences.OBJECTIVE: To observe the feasibility of neuronal apoptosis of dopamine with in situ end labeling and tyrosine-hydroxylase antibody immunohistochemical double-labeling staining technique.DESIGN: Controlled study.SETTING: College of Pharmacology of Taishan Medical College; College of Management of Taishan Medical College.MATERIALS: Wistar rats with 2 weeks old and of clean grade were provided by the Animal Center of Taishan Medical College. In situ end labeling kit (terminal deoxynucleotidyl transferase, mixed reactive solution of nucleotide, transfusion-POD), monoclonal antibody of rat antibody against tyrosine hydroxylase (Boehriuser).METHODS: The experiment was completed at the Pharmacological Laboratory of Taishan Medical College from February to December 2005. Tissue from midbrain of rats was taken out to make paraffin sections to observe the neuronal apoptosis of dopamine under microscope with in situ end labeling and tyrosine-hydroxylase antibody immunohistochemical double-labeling staining technique.MAIN OUTCOME MEASURES: Neuronal apoptosis of dopamine with in situ end labeling and tyrosine-hydroxylase antibody immunohistochemical double-labeling staining technique.RESULTS:① After double-labeling staining,two kinks of positive products were observed in neurons of dopamine which were suffered from apoptosis. One stained with tyrosine hydroxylase was hyacinthine, and the other stained with in situ end labeling was buffy. Cells of positive products stained with in situ end labeling shaped as strap and bend and was distributed in clustering.Cytoplasm was hyacinthine, staining was symmetrical

  10. The Optimal Protocol of Extraction and Purification of Large Fragment DNA%大片段DNA提取和纯化的优化方案

    Institute of Scientific and Technical Information of China (English)

    陈琰; 艾云灿

    2011-01-01

    [ Objective ] The aim was to study the optimum proposal of big segment DNA extraction and purification. [ Method] Based on traditional SDS extraction, the extraction and purification process of big segment DNA were improved. [ Result] A optimized scheme of DNA extraetion and purification was established, based on this scheme, DNA with big segment and high purity were obtained. [ Conclusion] All those provided references for big segment DNA extraction and purification in the future.%[目的]研究大片段DNA提取和纯化的优化方案研究.[方法]在传统SDS提取法的基础上,对大片段DNA的提取和纯化过程进行了改进.[结果]建立了一种优化的DNA提取和纯化的方案,通过该方案能够得到片段大、纯度高的DNA.[结论]为今后大片段DNA的提取和纯化提供了参考.

  11. Improved dose calculation accuracy for low energy brachytherapy by optimizing dual energy CT imaging protocols for noise reduction using sinogram affirmed iterative reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Landry, Guillaume [Maastricht University Medical Center (Netherlands). Dept. of Radiation Oncology (MAASTRO); Munich Univ. (Germany). Dept. of Medical Physics; Gaudreault, Mathieu [Maastricht University Medical Center (Netherlands). Dept. of Radiation Oncology (MAASTRO); Laval Univ., QC (Canada). Dept. de Radio-Oncologie et Centre de Recherche en Cancerologie; Laval Univ., QC (Canada). Dept. de Physique, de Genie Physique et d' Optique; Elmpt, Wouter van [Maastricht University Medical Center (Netherlands). Dept. of Radiation Oncology (MAASTRO); Wildberger, Joachim E. [Maastricht University Medical Center (Netherlands). Dept. of Radiology; Verhaegen, Frank [Maastricht University Medical Center (Netherlands). Dept. of Radiation Oncology (MAASTRO); McGill Univ. Montreal, QC (Canada). Dept. of Oncology

    2016-05-01

    The goal of this study was to evaluate the noise reduction achievable from dual energy computed tomography (CT) imaging (DECT) using filtered backprojection (FBP) and iterative image reconstruction algorithms combined with increased imaging exposure. We evaluated the data in the context of imaging for brachytherapy dose calculation, where accurate quantification of electron density ρ{sub e} and effective atomic number Z{sub eff} is beneficial. A dual source CT scanner was used to scan a phantom containing tissue mimicking inserts. DECT scans were acquired at 80 kVp/140Sn kVp (where Sn stands for tin filtration) and 100 kVp/140Sn kVp, using the same values of the CT dose index CTDI{sub vol} for both settings as a measure for the radiation imaging exposure. Four CTDI{sub vol} levels were investigated. Images were reconstructed using FBP and sinogram affirmed iterative reconstruction (SAFIRE) with strength 1,3 and 5. From DECT scans two material quantities were derived, Z{sub eff} and ρ{sub e}. DECT images were used to assign material types and the amount of improperly assigned voxels was quantified for each protocol. The dosimetric impact of improperly assigned voxels was evaluated with Geant4 Monte Carlo (MC) dose calculations for an {sup 125}I source in numerical phantoms. Standard deviations for Z{sub eff} and ρ{sub e} were reduced up to a factor ∝2 when using SAFIRE with strength 5 compared to FBP. Standard deviations on Z{sub eff} and ρ{sub e} as low as 0.15 and 0.006 were achieved for the muscle insert representing typical soft tissue using a CTDI{sub vol} of 40 mGy and 3 mm slice thickness. Dose calculation accuracy was generally improved when using SAFIRE. Mean (maximum absolute) dose errors of up to 1.3% (21%) with FBP were reduced to less than 1% (6%) with SAFIRE at a CTDI{sub vol} of 10 mGy. Using a CTDI{sub vol} of 40mGy and SAFIRE yielded mean dose calculation errors of the order of 0.6% which was the MC dose calculation precision in this study and

  12. Rimmed vacuoles and the added value of SMI-31 staining in diagnosing sporadic inclusion body myositis.

    Science.gov (United States)

    van der Meulen, M F; Hoogendijk, J E; Moons, K G; Veldman, H; Badrising, U A; Wokke, J H

    2001-07-01

    Problems in diagnosing sporadic inclusion body myositis may arise if all clinical features fit a diagnosis of polymyositis, but the muscle biopsy shows some rimmed vacuoles. Recently, immunohistochemistry with an antibody directed against phosphorylated neurofilament (SMI-31) has been advocated as a diagnostic test for sporadic inclusion body myositis. The aims of the present study were to define a quantitative criterion to differentiate sporadic inclusion body myositis from polymyositis based on the detection of rimmed vacuoles in the haematoxylin-eosin staining and to evaluate the additional diagnostic value of the SMI-31 staining. Based on clinical criteria and creatine kinase levels in patients with endomysial infiltrates, 18 patients complied with the diagnosis of sporadic inclusion body myositis, and 17 with the diagnosis of polymyositis. A blinded observer counted the abnormal fibres in haematoxylin-eosin-stained sections and in SMI-31-stained sections. The optimal cut-off in the haematoxylin-eosin test was 0.3% vacuolated fibres. Adding the SMI-31 staining significantly increased the positive predictive value from 87 to 100%, but increased the negative predictive value only to small extent. We conclude that (1) patients with clinical and laboratory features of polymyositis, including response to treatment, may show rimmed vacuoles in their muscle biopsy and that (2) adding the SMI-31 stain can be helpful in differentiating patients who respond to treatment from patients who do not.

  13. Establishment and Optimization of Protocol for Genomic DNA Extraction from Seeds of Jatropha curcas%麻疯树(Jatropha curcas L.)种子总DNA提取方法的建立和优化

    Institute of Scientific and Technical Information of China (English)

    李静; 曾德贤; 吴子欢; 范林元; 刘飞虎

    2011-01-01

    A protocol to extract genomic DNA from seeds of Jatropha curcas was established and optimized in order to overleap seedling cultnre and decrease the experimental time. Considering the high contents of proteins. polyphenols and polysaccharides in the seeds, this protocol applied efficient procedures based on CTAB method to remove the secondary metabolites and impuriy. Antioxidant PVP was used to remove polyphenols when sample was homogenized , whereas the cell nuchlear separation buffer was used to remove polysacchandes, and then phenol - chloroform - isoamyl alcohol ( volume proportion = 25 ∶ 24∶ 1 ) extraction to get rid of proteins. The obtained genomic DNA with satisfied concentration and quality couH be used in the test of electrophoresis and ISSR-PCR amplification.%用种子提取DNA可省却培育幼苗过程而加快实验进度,为此建立了麻疯树(Jatropha curcas L.)种子DNA提取方法.针对麻疯树种子富含蛋白质、多酚及多糖等次生物质的特点,基于CTAB法进行优化,在研磨种子时加入抗氧化剂PVP去除多酚,接着用核分离缓冲液去除多糖,再通过酚-氯仿-异戊醇(体积比=25:24:1)抽提去除蛋白质.所提取的麻疯树种子总DNA浓度和质量均较高,经琼脂糖凝胶电泳和ISSR-PCR扩增得到了非常清晰的DNA条带.

  14. Preparation of Cytokine-activated NK Cells for Use in Adoptive Cell Therapy in Cancer Patients: Protocol Optimization and Therapeutic Potential.

    Science.gov (United States)

    van Ostaijen-ten Dam, Monique M; Prins, Henk-Jan; Boerman, Gerharda H; Vervat, Carly; Pende, Daniela; Putter, Hein; Lankester, Arjan; van Tol, Maarten J D; Zwaginga, Jaap J; Schilham, Marco W

    2016-01-01

    Cell-based immunotherapy using donor-derived natural killer (NK) cells after allogeneic hematopoietic stem cell transplantation may be an attractive treatment of residual leukemia. This study aimed to optimize clinical grade production of a cytokine-activated NK-cell product. NK cells were isolated either by double depletion (CD3(-), CD19(-)) or by sequential depletion and enrichment (CD3(-,) CD56(+)) via CliniMACS from leukapheresis material and cultured in vitro with interleukin (IL)-2 or IL-15. Both NK cell isolation procedures yielded comparable recovery of NK cells and levels of T-cell contamination. After culture with cytokines, the CD3(-)CD56(+) procedure resulted in NK cells of higher purity, that is, less T cells and monocytes, higher viability, and a slightly higher yield than the CD3(-)CD19- procedure. CD69, NKp44, and NKG2A expression were higher on CD3(-)CD56(+) products, whereas lysis of Daudi cells was comparable. Five days of culture led to higher expression of CD69, NKp44, and NKp30 and lysis of K562 and Daudi cell lines. Although CD69 expression and lysis of Daudi cells were slightly higher in cultures with IL-2, T-cell contamination was lower with IL-15. Therefore, further experiments were performed with CD3(-)CD56(+) products cultured with IL-15. Cryopreservation of IL-15-activated NK cells resulted in a loss of cytotoxicity (>92%), whereas thawing of isolated, uncultured NK cells followed by culture with IL-15 yielded cells with about 43% of the original lytic activity. Five-day IL-15-activated NK cells lysed tumor target cell lines and primary leukemic blasts, providing the basis for NK cell–based immunotherapeutic strategies in a clinical setting.

  15. Oil Red O and Hematoxylin and Eosin Staining for Quantification of Atherosclerosis Burden in Mouse Aorta and Aortic Root.

    Science.gov (United States)

    Andrés-Manzano, M Jesús; Andrés, Vicente; Dorado, Beatriz

    2015-01-01

    Methods for staining tissues with Oil Red O and hematoxylin-eosin are classical histological techniques that are widely used to quantify atherosclerotic burden in mouse tissues because of their ease of use, reliability, and the large amount of information they provide. These stains can provide quantitative data about the impact of a genetic or environmental factor on atherosclerotic burden and on the initiation, progression, or regression of the disease, and can also be used to evaluate the efficacy of drugs designed to prevent or treat atherosclerosis. This chapter provides protocols for quantifying atherosclerotic burden in mouse aorta and aortic root, including methods for dissection, Oil Red O staining, hematoxylin-eosin staining, and image analysis.

  16. Mac protocols for cyber-physical systems

    CERN Document Server

    Xia, Feng

    2015-01-01

    This book provides a literature review of various wireless MAC protocols and techniques for achieving real-time and reliable communications in the context of cyber-physical systems (CPS). The evaluation analysis of IEEE 802.15.4 for CPS therein will give insights into configuration and optimization of critical design parameters of MAC protocols. In addition, this book also presents the design and evaluation of an adaptive MAC protocol for medical CPS, which exemplifies how to facilitate real-time and reliable communications in CPS by exploiting IEEE 802.15.4 based MAC protocols. This book wil

  17. Barriers and facilitators to the dissemination of DECISION+, a continuing medical education program for optimizing decisions about antibiotics for acute respiratory infections in primary care: A study protocol

    Directory of Open Access Journals (Sweden)

    Gagnon Marie-Pierre

    2011-01-01

    decision making regarding the use of antibiotics in acute respiratory infections, to facilitate its dissemination in primary care on a large scale. Our results should help continuing medical educators develop a continuing medical education program in shared decision making for other clinically relevant topics. This will help optimize clinical decisions in primary care.

  18. Port wine stain on a child's face (image)

    Science.gov (United States)

    Port wine stains are always present at birth. In an infant, they are flat, pink, vascular lesions. Common locations ... may be present anywhere on the body. Port wine stains may appear in association with other syndromes.

  19. Comparison between Giemsa and Van Geison stains in ...

    African Journals Online (AJOL)

    Rukevwe S. Abraka

    2016-09-14

    Sep 14, 2016 ... identification of collagen fibers of great importance. Stains such as Van ... Both cation and anion contain ... already large molecules, solutions of neutral stains are ... Differentiate in 2% aqueous ferric chloride until elastic tissue.

  20. Laser therapy in plastic surgery: decolorization in port wine stains

    Science.gov (United States)

    Peszynski-Drews, Cezary; Wolf, Leszek

    1996-03-01

    For the first time laserotherapy is described as a method of port wine stain decolorization in plastic surgery. The authors present their 20-year experience in the treatment of port wine stains with the argon laser and dye laser.

  1. Scrub typhus hepatitis confirmed by immunohistochemical staining

    Institute of Scientific and Technical Information of China (English)

    Jong-Hoon Chung; Sung-Chul Lim; Na-Ra Yun; Sung-Heui Shin; Choon-Mee Kim; Dong-Min Kim

    2012-01-01

    Scrub typhus is an acute febrile disease caused by Orientia tsutsugamushi (O.tsutsugamushi).We report herein the case of a woman who presented with fever and elevated serum levels of liver enzymes and who was definitively diagnosed with scrub typhus by histopathological examination of liver biopsy specimens,serological tests and nested polymerase chain reaction.Immunohistochemical staining using a monoclonal anti-O.tsutsugamushi antibody showed focally scattered positive immunoreactions in the cytoplasm of some hepatocytes.This case suggests that scrub typhus hepatitis causes mild focal inflammation due to direct liver damage without causing piecemeal necrosis or interface hepatitis.Thus,scrub typhus hepatitis differs from acute viral hepatitis secondary to liver damage due to host immune responses,which causes severe Iobular disarray with diffuse hepatocytic degeneration,necrosis and apoptosis as well as findings indicative of hepatic cholestasis,such as hepatic bile plugs or brown pigmentation of hepatocytes.

  2. Several staining techniques to enhance the visibility of Acanthamoeba cysts.

    Science.gov (United States)

    El-Sayed, Nagwa Mostafa; Hikal, Wafaa Mohamed

    2015-03-01

    Acanthamoeba is one of the most common free-living amoebae. It is widespread in the environment and can infect humans causing keratitis. Delayed diagnosis or misdiagnosis leads to extensive corneal inflammation and profound visual loss. Therefore, accurate and rapid diagnosis of Acanthamoeba keratitis is essential for successful treatment and good prognosis. This study was designed to use different staining techniques to facilitate the identification of Acanthamoeba cysts. Acanthamoeba cysts were isolated by cultivation of either corneal scraping specimens or tap water samples onto non-nutrient agar plates seeded with Escherichia coli. Subcultures were done from positive cultures until unique cysts were isolated. Acanthamoeba cysts were stained temporarily using iodine, eosin, methylene blue, and calcofluor white (CFW) stains and as permanent slides after processing for mounting using modified trichrome, Gimenez and Giemsa staining. These stains were compared on the basis of staining quality including clarity of morphological details, differentiation between cytoplasm and nuclei, color and contrast, and also other characteristics of the staining techniques, including ease of handling, time taken for the procedure, and cost effectiveness. The cysts of Acanthamoeba were recognized in the form of double-walled cysts: the outer wall (ectocyst) that was being differentiated from the variably stained surrounding background and the inner wall (endocyst) that was sometimes stellated, polygonal, round, or oval and visualized as separate from the spherical, sometimes irregular, outline of the ectocyst. Regarding the temporary stains, it was found that they were efficient for visualizing the morphological details of Acanthamoeba cysts. In CFW staining, Acanthamoeba cysts appeared as bluish-white or turquoise oval halos although the internal detail was not evident. On the other hand, the results of permanent-stained slides showed the most consistent stain for identification of

  3. Immunocytochemical and Immunohistochemical Staining with Peptide Antibodies.

    Science.gov (United States)

    Friis, Tina; Pedersen, Klaus Boberg; Hougaard, David; Houen, Gunnar

    2015-01-01

    Peptide antibodies are particularly useful for immunocytochemistry (ICC) and immunohistochemistry (IHC), where antigens may denature due to fixation of tissues and cells. Peptide antibodies can be made to any defined sequence, including unknown putative proteins and posttranslationally modified sequences. Moreover, the availability of large amounts of the antigen (peptide) allows inhibition/adsorption controls, which are important in ICC/IHC, due to the many possibilities for false-positive reactions caused by immunoglobulin Fc receptors, nonspecific reactions, and cross-reactivity of primary and secondary antibodies with other antigens and endogenous immunoglobulins, respectively. Here, simple protocols for ICC and IHC are described together with recommendations for appropriate controls.

  4. Guided protein extraction from formalin-fixed tissues for quantitative multiplex analysis avoids detrimental effects of histological stains.

    Science.gov (United States)

    Becker, Karl-Friedrich; Schott, Christina; Becker, Ingrid; Höfler, Heinz

    2008-05-01

    Formalin fixed and paraffin embedded (FFPE) tissues are the basis for histopathological diagnosis of many diseases around the world. For translational research and routine diagnostics, protein analysis from FFPE tissues is very important. We evaluated the potential influence of six histological stains, including hematoxylin (Mayer and Gill), fast red, light green, methyl blue and toluidine blue, for yield, electrophoretic mobility in 1-D gels, and immunoreactivity of proteins isolated from formalin-fixed breast cancer tissues. Proteins extracted from stained FFPE tissues using a recently established technique were compared with proteins obtained from the same tissues but without prior histological staining. Western blot and quantitative protein lysate microarray analysis demonstrated that histological staining can result in decreased protein yield but may not have much influence on immunoreactivity and electrophoretic mobility. Interestingly, not all staining protocols tested are compatible with subsequent protein analysis. The commonly used hematoxylin staining was found to be suitable for multiplexed quantitative protein measurement technologies although protein extraction was less efficient. For best results we suggest a guided protein extraction method, in which an adjacent hematoxylin/eosin-stained tissue section is used to control dissection of an unstained specimen for subsequent protein extraction and quantification for research and diagnosis.

  5. In situ microliter-droplet anodic stripping voltammetry of copper stained on the gold label after galvanic replacement reaction enlargement for ultrasensitive immunoassay of proteins.

    Science.gov (United States)

    Qin, Xiaoli; Xu, Aigui; Wang, Linchun; Liu, Ling; Chao, Long; He, Fang; Tan, Yueming; Chen, Chao; Xie, Qingji

    2016-05-15

    We report a new protocol for ultrasensitive electrochemical sandwich-type immunosensing, on the basis of signal amplification by gold-label/copper-staining, galvanic replacement reactions (GRRs), and in situ microliter-droplet anodic stripping voltammetry (ASV) after an enhanced cathodic preconcentration of copper. First, a sandwich-type immuno-structure is appropriately assembled at a glassy carbon electrode. Second, copper is selectively stained on the catalytic surfaces of second antibody-conjugated Au nanoparticles through CuSO4-ascorbic acid redox reaction, and the GRRs between HAuCl4 and the stained copper are used to amplify the quantity of copper. Finally, the corresponding antigen is determined based on simultaneous chemical-dissolution/cathodic-preconcentration of copper for in-situ ASV analysis directly at the immunoelectrode. Cyclic voltammetry, electrochemical impedance spectroscopy, quartz crystal microbalance and scanning electron microscopy are used for film characterization and/or process monitoring. Under optimized conditions, ultrasensitive analyses of human immunoglobulin G (IgG) and human carbohydrate antigen 125 (CA125) are achieved. The limits of detection are 0.3 fg mL(-1) (equivalent to 7 IgG molecules in the 6 μL sample employed) for IgG (S/N=3) and 1.3 nU mL(-1) for CA125 (S/N=3), respectively, which are amongst the best reported to date for the two proteins. The theoretical feasibility of such a single-molecule-level amperometric immunoassay is also discussed based on the immunological reaction thermodynamics. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. 21 CFR 864.1850 - Dye and chemical solution stains.

    Science.gov (United States)

    2010-04-01

    ... synthetic or natural dyes or nondye chemicals in solutions used in staining cells and tissues for diagnostic... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Dye and chemical solution stains. 864.1850 Section... (CONTINUED) MEDICAL DEVICES HEMATOLOGY AND PATHOLOGY DEVICES Biological Stains § 864.1850 Dye and...

  7. 7 CFR 28.442 - Middling Yellow Stained Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Middling Yellow Stained Color. 28.442 Section 28.442... Stained Color. Middling Yellow Stained Color is American Upland cotton which in color is deeper than Middling Tinged Color. below color grade cotton...

  8. 7 CFR 28.441 - Strict Middling Yellow Stained Color.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Strict Middling Yellow Stained Color. 28.441 Section... Strict Middling Yellow Stained Color. Strict Middling Yellow Stained Color is color which is deeper than that of Strict Middling Tinged Color....

  9. Spiral CT and optimization of the modalities of the iodinated intravenous contrast material: Experimental studies in human pathology; Tomodensitometrie spiralee et optimisation des protocoles d'injection du contraste iode intra-veineux: etudes experimentales en pathologie humaine

    Energy Technology Data Exchange (ETDEWEB)

    Bonaldi, V

    1998-06-19

    Spiral (or helical) CT represents the most recent improvement in the field of computed assisted tomography (CAT scan). The capabilities of this new imaging modality are much superior to these of conventional CT scanning; then result from the rapid acquisition and from the volumetric nature of the derived data set. The short time of data acquisition had made mandatory the revision of protocols for intravenous administration of iodinated contrast material. By the means of several studies, carried out on pathologic and healthy patients, we have attempted to improve knowledge in factors influencing CT attenuation values after injection of contrast material, in the aim of improving contrast administration performed during spiral CT scanning. Anatomical landmarks that we have studied till now have been liver, the pancreas, the kidney and the cervical spine. In addition, a paired based methodology has been used. The volumetric set of data derived from spiral CT scanning leads to optimal post-processing tasks, the most interesting being related to cine-display and multiplanar reformatting; both modalities have been evaluated, about the pancreas and the musculo-skeletal system respectively. Conversely, this new modality, as for other imaging modalities, is responsible for additional costs derived from restless increase in the number of images to be dealt with and from the occurrence of new tasks (in post-processing particularly). The place of spiral CT in diagnostic strategies among other modern imaging modalities should be assessed, especially with respect to Magnetic Resonance Imaging (MRI). (author)

  10. Microfluidic Cell Cycle Analysis of Spread Cells by DAPI Staining

    Directory of Open Access Journals (Sweden)

    Jing Sun

    2017-01-01

    Full Text Available Single-cell cell cycle analysis is an emerging technique that requires detailed exploration of the image analysis process. In this study, we established a microfluidic single-cell cell cycle analysis method that can analyze cells in small numbers and in situ on a microfluidic chip. In addition, factors that influenced the analysis were carefully investigated. U87 or HeLa cells were seeded and attached to microfluidic channels before measurement. Cell nucleic DNA was imaged by 4′-6-diamidino-2-phenylindole (DAPI staining under a fluorescent microscope and subsequently fluorescent intensities of the cell nuclei DNA were converted to depict histograms for cell cycle phases. DAPI concentration, microscopic magnification, exposure time and cell number were examined for optimal cell cycle analysis conditions. The results showed that as few as a few hundred cells could be measured by DAPI staining in the range of 0.4–0.6 μg/mL to depict histograms with typical cell cycle phase distribution. Microscopic magnification during image acquisition, however, could distort the phase distribution. Exposure time did not significantly affect the cell cycle analysis. Furthermore, cell cycle inhibitor rapamycin treatment changed the cell cycle phase distribution as expected. In conclusion, a method for microfluidic single-cell cell cycle analysis of spread cells in situ was developed. Factors such as dye concentration and microscopic magnification had more influence on cell cycle phase distribution. Further studies will focus on detail differentiation of cell cycle phases and the application of such a method for biological meanings.

  11. Multi-stained whole slide image alignment in digital pathology

    Science.gov (United States)

    Déniz, Oscar; Toomey, David; Conway, Catherine; Bueno, Gloria

    2015-03-01

    In Digital Pathology, one of the most simple and yet most useful feature is the ability to view serial sections of tissue simultaneously on a computer monitor. This enables the pathologist to evaluate the histology and expression of multiple markers for a patient in a single review. However, the rate limiting step in this process is the time taken for the pathologist to open each individual image, align the sections within the viewer, with a maximum of four slides at a time, and then manually move around the section. In addition, due to tissue processing and pre-analytical steps, sections with different stains have non-linear variations between the two acquisitions, that is, they will stretch and change shape from section to section. To date, no solution has come close to a workable solution to automatically align the serial sections into one composite image. This research work address this problem to obtain an automated serial section alignment tool enabling the pathologists to simply scroll through the various sections in a single viewer. To this aim a multi-resolution intensity-based registration method using mutual information as a similarity metric, an optimizer based on an evolutionary process and a bilinear transformation has been used. To characterize the performance of the algorithm 40 cases x 5 different serial sections stained with hematoxiline-eosine (HE), estrogen receptor (ER), progesterone receptor (PR), Ki67 and human epidermal growth factor receptor 2 (Her2), have been considered. The qualitative results obtained are promising, with average computation time of 26.4s for up to 14660x5799 images running interpreted code.

  12. Optimizing synchrotron microCT for high-throughput phenotyping of zebrafish

    Science.gov (United States)

    La Rivière, Patrick J.; Clark, Darin; Rojek, Alexandra; Vargas, Phillip; Xiao, Xianghui; DeCarlo, Francesco; Kindlmann, Gordon; Cheng, Keith

    2010-09-01

    We are creating a state-of-the-art 2D and 3D imaging atlas of zebrafish development. The atlas employs both 2D histology slides and 3D benchtop and synchrotron micro CT results. Through this atlas, we expect to document normal and abnormal organogenesis, to reveal new levels of structural detail, and to advance image informatics as a form of systems biology. The zebrafish has become a widely used model organism in biological and biomedical research for studies of vertebrate development and gene function. In this work, we will report on efforts to optimize synchrotron microCT imaging parameters for zebrafish at crucial developmental stages. The aim of these studies is to establish protocols for high-throughput phenotyping of normal, mutant and diseased zebrafish. We have developed staining and embedding protocols using different heavy metal stains (osmium tetroxide and uranyl acetate) and different embedding media (Embed 812 and glycol methacrylate). We have explored the use of edge subtraction and multi-energy techniques for contrast enhancement and we have examined the use of different sample-detector distances with unstained samples to explore and optimize phase-contrast enhancement effects. We will report principally on our efforts to optimize energy choice for single- and multi-energy studies as well as our efforts to optimize the degree of phase contrast enhancement.

  13. Automated single-slide staining device. [in clinical bacteriology

    Science.gov (United States)

    Wilkins, J. R.; Mills, S. M.

    1975-01-01

    An automatic single-slide Gram staining device is described. A timer-actuated solenoid controls the dispensing of gentian violet, Gram iodine solution, decolorizer, and 1% aqueous safranin in proper sequence and for the time required for optimum staining. The amount of stain or reagent delivered is controlled by means of stopcocks below each solenoid. Used stains and reagents can be flushed automatically or manually. Smears Gram stained automatically are equal in quality to those prepared manually. The time to complete one Gram cycle is 4.80 min.

  14. A PROGRAMMED LABOUR - PROTOCOL

    Directory of Open Access Journals (Sweden)

    Savita

    2014-12-01

    Full Text Available A Prospective randomized Clinical study of outcome of labour following. “A Programmed labour. Protocol” was done at Department of OBG, MRMC Gulbarga. The Protocol was aimed with dual. Objective of Providing Pain relief during labour and teaching the goal of safe motherhood by optimizing objective outcome. AIMS AND OBJECTIVES: Shortening of duration of labour. Effect of labour analgesia. Monitoring of the events during labour. Lowering the incidence of operative deliveries. METHODS: 100 cases primi pregnant women admitted in labour room are randomly selected. It is designed to apply to low risk primi parous, singleton cephalic presentation without evidence of CPD and spontaneous onset of labour. RESULTS: Shortened duration of all the stages of Labour, especially significant reduction in duration of active phase of labour. CONCLUSION: The programmed labour is simple easy and effective method for painless and safe delivery.

  15. Evaluation of Decalcification Techniques for Rat Femurs Using HE and Immunohistochemical Staining

    Directory of Open Access Journals (Sweden)

    Haixia Liu

    2017-01-01

    Full Text Available Aim. In routine histopathology, decalcification is an essential step for mineralized tissues. The purpose of this study is to evaluate the effects of different decalcification solutions on the morphological and antigenicity preservation in Sprague Dawley (SD rat femurs. Materials and Methods. Four different decalcification solutions were employed to remove the mineral substances from rat femurs, including 10% neutral buffered EDTA, 3% nitric acid, 5% nitric acid, and 8% hydrochloric acid/formic acid. Shaking and low temperature were used to process the samples. The stainings of hematoxylin-eosin (HE and immunohistochemical (IHC were employed to evaluate the bone morphology and antigenicity. Key Findings. Different decalcification solutions may affect the quality of morphology and the staining of paraffin-embedded sections in pathological examinations. Among four decalcifying solutions, 3% nitric acid is the best decalcifying agent for HE staining. 10% neutral buffered EDTA and 5% nitric acid are the preferred decalcifying agents for IHC staining. Significance. The current study investigated the effects of different decalcifying agents on the preservation of the bone structure and antigenicity, which will help to develop suitable protocols for the analyses of the bony tissue.

  16. Enabling Multiphoton and Second Harmonic Generation Imaging in Paraffin-Embedded and Histologically Stained Sections.

    Science.gov (United States)

    Monaghan, Michael G; Kroll, Sebastian; Brucker, Sara Y; Schenke-Layland, Katja

    2016-06-01

    Nonlinear microscopy, namely multiphoton imaging and second harmonic generation (SHG), is an established noninvasive technique useful for the imaging of extracellular matrix (ECM). Typically, measurements are performed in vivo on freshly excised tissues or biopsies. In this article, we describe the effect of rehydrating paraffin-embedded sections on multiphoton and SHG emission signals and the acquisition of nonlinear images from hematoxylin and eosin (H&E)-stained sections before and after a destaining protocol. Our results reveal that bringing tissue sections to a physiological state yields a significant improvement in nonlinear signals, particularly in SHG. Additionally, the destaining of sections previously processed with H&E staining significantly improves their SHG emission signals during imaging, thereby allowing sufficient analysis of collagen in these sections. These results are important for researchers and pathologists to obtain additional information from paraffin-embedded tissues and archived samples to perform retrospective analysis of the ECM or gain additional information from rare samples.

  17. Protocol Implementation Generator

    DEFF Research Database (Denmark)

    Carvalho Quaresma, Jose Nuno; Probst, Christian W.

    2010-01-01

    necessary tools. In this paper, we present the Protocol Implementation Generator (PiG), a framework that can be used to add protocol generation to protocol negotiation, or to easily share and implement new protocols throughout a network. PiG enables the sharing, verification, and translation...... of communication protocols. With it, partners can suggest a new protocol by sending its specification. After formally verifying the specification, each partner generates an implementation, which can then be used for establishing communication. We also present a practical realisation of the Protocol Implementation...... Generator framework based on the LySatool and a translator from the LySa language into C or Java....

  18. The PULSAR primary care protocol: a stepped-wedge cluster randomized controlled trial to test a training intervention for general practitioners in recovery-oriented practice to optimize personal recovery in adult patients.

    Science.gov (United States)

    Enticott, Joanne C; Shawyer, Frances; Brophy, Lisa; Russell, Grant; Fossey, Ellie; Inder, Brett; Mazza, Danielle; Vasi, Shiva; Weller, Penelope June; Wilson-Evered, Elisabeth; Edan, Vrinda; Meadows, Graham

    2016-12-20

    General practitioners (GPs) in Australia play a central role in the delivery of mental health care. This article describes the PULSAR (Principles Unite Local Services Assisting Recovery) Primary Care protocol, a novel mixed methods evaluation of a training intervention for GPs in recovery-oriented practice. The aim of the intervention is to optimize personal recovery in patients consulting study GPs for mental health issues. The intervention mixed methods design involves a stepped-wedge cluster randomized controlled trial testing the outcomes of training in recovery-oriented practice, together with an embedded qualitative study to identify the contextual enablers and challenges to implementing recovery-oriented practice. The project is conducted in Victoria, Australia between 2013 and 2017. Eighteen general practices and community health centers are randomly allocated to one of two steps (nine months apart) to start an intervention comprising GP training in the delivery of recovery-oriented practice. Data collection consists of cross-sectional surveys collected from patients of participating GPs at baseline, and again at the end of Steps 1 and 2. The primary outcome is improvement in personal recovery using responses to the Questionnaire about the Process of Recovery. Secondary outcomes are improvements in patient-rated measures of personal recovery and wellbeing, and of the recovery-oriented practice they have received, using the INSPIRE questionnaire, the Warwick-Edinburgh Mental Well-being Scale, and the Kessler Psychological Distress Scale. Participant data will be analyzed in the group that the cluster was assigned to at each study time point. Another per-protocol dataset will contain all data time-stamped according to the date of intervention received at each cluster site. Qualitative interviews with GPs and patients at three and nine months post-training will investigate experiences and challenges related to implementing recovery-oriented practice in primary

  19. Quantification of intracellular polyhydroxyalkanoates by virtue of personalized flow cytometry protocol.

    Science.gov (United States)

    Saranya, V; Poornimakkani; Krishnakumari, M S; Suguna, P; Binuramesh, C; Abirami, P; Rajeswari, V; Ramachandran, K B; Shenbagarathai, R

    2012-11-01

    Polyhydroxyalkanoates (PHAs) are natural polyesters produced by microbes, a potential alternative to synthetic plastics. Various methods ranging from gravimetry to spectrophotometry are routinely used for qualitative analysis of extracted PHA. There is a great need for accurate quantification of intracellular PHA during bioprocess. Hence, the present study aims to improvise the existing Nile red-based flow cytometry protocol. It was achieved using respective cells in a non-PHA accumulating state as gating control to minimize non-specific staining. The optimal Nile red concentration required for PHA staining is 5 × 10(3) pg mL(-1), which is ~10(3)-fold less than that of earlier reports. Further, it was inferred that flow-based quantification was more accurate than the gravimetric method. The intracellular PHA content was highest in Pseudomonas sp. MNNG-S (52.06 %) among the Pseudomonas strains tested by the flow-based method. Both gravimetric and flow-based cell cycle analyses revealed that DNA synthesis (S phase) and PHA production (log phase) are synchronous at 24-48 h of culture. This study supports flow-based PHA quantification for real time online measurement of intracellular PHA for bioreactor monitoring, control and optimization enduing industrial applications.

  20. SELECT OF OPTIMAL SLEEP STATE IN ADAPTIVE SMAC USING DPM

    National Research Council Canada - National Science Library

    Elham Hajian; Kamal Jamshidi; Ali Bohlooli

    2010-01-01

    .... Therefore, optimal energy consumption for wsn protocols is a necessity. In a number of proposed protocols periodic sleep and wake is used for energy use reduction but these protocols result in increased end to end delay...

  1. IgG Subclass Staining in Routine Renal Biopsy Material.

    Science.gov (United States)

    Hemminger, Jessica; Nadasdy, Gyongyi; Satoskar, Anjali; Brodsky, Sergey V; Nadasdy, Tibor

    2016-05-01

    Immunofluorescence staining plays a vital role in nephropathology, but the panel of antibodies used has not changed for decades. Further classification of immunoglobulin (Ig)G-containing immune-type deposits with IgG subclass staining (IgG1, IgG2, IgG3, and IgG4) has been shown to be of diagnostic utility in glomerular diseases, but their value in the evaluation of renal biopsies has not been addressed systematically in large renal biopsy material. Between January 2007 and June 2014, using direct immunofluorescence, we stained every renal biopsy for the IgG subclasses if there was moderate to prominent glomerular IgG staining and/or IgG-predominant or IgG-codominant glomerular staining. The total number of biopsies stained was 1084, which included 367 cases of membranous glomerulonephritis, 307 cases of lupus nephritis, 74 cases of fibrillary glomerulonephritis, 53 cases of proliferative glomerulonephritis with monoclonal IgG deposits, and 25 cases of antiglomerular basement membrane disease, among others. We found that monoclonality of IgG deposits cannot always be reliably determined on the basis of kappa and lambda light chain staining alone, particularly if concomitant (frequently nonspecific) IgM staining is present. In IgG heavy and heavy and light chain deposition disease (3 cases), subclass staining is very helpful, and in proliferative glomerulonephritis with monoclonal IgG deposits subclass staining is necessary. IgG subclass staining is useful in differentiating primary from secondary membranous glomerulonephritis. In proliferative glomerulonephritis with polyclonal IgG deposition, IgG1 dominance/codominance with concomitant IgG3 and IgG2 but weak or absent IgG4 staining favors an underlying autoimmune disease. IgG subclass staining is a very useful diagnostic method in a selected cohort of renal biopsies, particularly in biopsies with glomerulonephritis with monoclonal IgG deposits.

  2. Optimized MOL-PCR for Characterization of Microbial Pathogens.

    Science.gov (United States)

    Wuyts, Véronique; Roosens, Nancy H C; Bertrand, Sophie; Marchal, Kathleen; De Keersmaecker, Sigrid C J

    2016-01-06

    Characterization of microbial pathogens is necessary for surveillance, outbreak detection, and tracing of outbreak sources. This unit describes a multiplex oligonucleotide ligation-PCR (MOL-PCR) optimized for characterization of microbial pathogens. With MOL-PCR, different types of markers, like unique sequences, single-nucleotide polymorphisms (SNPs) and indels, can be simultaneously analyzed in one assay. This assay consists of a multiplex ligation for detection of the markers, a singleplex PCR for signal amplification, and hybridization to MagPlex-TAG beads for readout on a Luminex platform after fluorescent staining. The current protocol describes the MOL-PCR, as well as methods for DNA isolation, probe design, and data interpretation and it is based on an optimized MOL-PCR assay for subtyping of Salmonella Typhimurium.

  3. Efficacy test of a toothpaste in reducing extrinsic dental stain

    Science.gov (United States)

    Agustanti, A.; Ramadhani, S. A.; Adiatman, M.; Rahardjo, A.; Callea, M.; Yavuz, I.; Maharani, D. A.

    2017-08-01

    This clinical trial compared the external dental stain reduction achieved by tested toothpaste versus placebo in adult patients. In this double-blind, parallel, randomised clinical trial, 45 female volunteers with a mean age of 20 years old were included. All study subjects front teeth were topically applicated with Silver Diamine Fluoride (SDF) to create external dental stains. Subjects were randomized into test (n=22) and control (n=23) groups. Toothpastes were used for two days to analyse the effects of removing external stains on the labial surfaces of all anterior teeth. VITA Easyshade Advance 4.0 was used to measure dental extrinsic stains changes. The analysis showed statistically significant efficacy of the tested toothpaste in reducing external dental stain caused by SDF, comparing to the placebo toothpaste, after one and two days of usage. The tested toothpaste was effective in reducing dental stain.

  4. Post-staining electroblotting for efficient and reliable peptide blotting.

    Science.gov (United States)

    Lee, Der-Yen; Chang, Geen-Dong

    2015-01-01

    Post-staining electroblotting has been previously described to transfer Coomassie blue-stained proteins from polyacrylamide gel onto polyvinylidene difluoride (PVDF) membranes. Actually, stained peptides can also be efficiently and reliably transferred. Because of selective staining procedures for peptides and increased retention of stained peptides on the membrane, even peptides with molecular masses less than 2 kDa such as bacitracin and granuliberin R are transferred with satisfactory results. For comparison, post-staining electroblotting is about 16-fold more sensitive than the conventional electroblotting for visualization of insulin on the membrane. Therefore, the peptide blots become practicable and more accessible to further applications, e.g., blot overlay detection or immunoblotting analysis. In addition, the efficiency of peptide transfer is favorable for N-terminal sequence analysis. With this method, peptide blotting can be normalized for further analysis such as blot overlay assay, immunoblotting, and N-terminal sequencing for identification of peptide in crude or partially purified samples.

  5. Optimization, validation, and application of a real-time PCR protocol for quantification of viable bacterial cells in municipal sewage sludge and biosolids using reporter genes and Escherichia coli.

    Science.gov (United States)

    van Frankenhuyzen, Jessica K; Trevors, Jack T; Flemming, Cecily A; Lee, Hung; Habash, Marc B

    2013-11-01

    Biosolids result from treatment of sewage sludge to meet jurisdictional standards, including pathogen reduction. Once government regulations are met, materials can be applied to agricultural lands. Culture-based methods are used to enumerate pathogen indicator microorganisms but may underestimate cell densities, which is partly due to bacteria existing in a viable but non-culturable physiological state. Viable indicators can also be quantified by realtime polymerase chain reaction (qPCR) used with propidium monoazide (PMA), a dye that inhibits amplification of DNA found extracellularly or in dead cells. The objectives of this study were to test an optimized PMA-qPCR method for viable pathogen detection in wastewater solids and to validate it by comparing results to data obtained by conventional plating. Reporter genes from genetically marked Pseudomonas sp. UG14Lr and Agrobacterium tumefaciens 542 cells were spiked into samples of primary sludge, and anaerobically digested and Lystek-treated biosolids as cell-free DNA, dead cells, viable cells, and mixtures of live and dead cells, followed by DNA extraction with and without PMA, and qPCR. The protocol was then used for Escherichia coli quantification in the three matrices, and results compared to plate counts. PMA-qPCR selectively detected viable cells, while inhibiting signals from cell-free DNA and DNA found in membrane-compromised cells. PMA-qPCR detected 0.5-1 log unit more viable E. coli cells in both primary solids and dewatered biosolids than plate counts. No viable E. coli was found in Lystek-treated biosolids. These data suggest PMA-qPCR may more accurately estimate pathogen cell numbers than traditional culture methods.

  6. Optimized AODV routing protocol based on reverse route search in leisure time and route learning%基于闲时逆寻和路由学习机制的优化AODV路由协议

    Institute of Scientific and Technical Information of China (English)

    杜青松; 朱江; 张尔扬

    2011-01-01

    对AODV协议在不同MANET网络环境中的性能缺陷进行了研究,提出了节点闲时反向路由搜索机制和邻居节点路由监听学习机制,并进一步提出了优化的AODV路由协议O-AODV.利用O-AODV协议在MANET网络中产生多个局部路由,从而增加网络中的路由冗余度,提高路由发现的效率,加快故障路由的本地修复.仿真实验结果表明,O-AODV协议提高了分组投递率,降低了端到端延时,有效地减少了网络中的重路由开销,在大规模和拓扑变化快的网络环境中优于AODV协议.%An optimized AODV routing protocol (0-AODV) which integrated RRSL mechanism (reverse route search in leisure time) and route learning mechanism was proposed. According to O-AODV, many local routes were produced in MANET and route redundancy was increased, therefore improved the efficiency of routing discovery, speeded up the local repair procedure of break routes, and decreased the overhead of route rediscovery. Simulation results indicate that O-AODV can improve packet delivery ratio and decrease the end-to-end packet delay, its performance is superior to AODV in large scale and fast changing MANET.

  7. WSN中具有引导距离和位置意识的GEAR路由优化协议%GEAR Routing Optimization Protocol Based on Guiding Distance and Location Aware in Wireless Sensor Network

    Institute of Scientific and Technical Information of China (English)

    任秀丽; 谭振江

    2015-01-01

    Focus on the problems of big energy consumption and short survival time of the network,GEAR routing optimization protocol( GLGEAR)was proposed based on Guiding Distance and Location Aware in wireless sensor network. When GLGEAR select the next sensor node,the concept of guiding distance was introduced to modify the formula of estimated cost for routing more optimized,so that it could reduce the energy consumption during data transmission. For finding the suitable sensor node which was closer to the target area,GLGEAR designed a new node selection method. The method could reduce the computational complexity and shorten the path setup time. At the same time GLGEAR also designed strategies to solve the problems of routing holes and the failure of data transmission. Simulation results indicated that GLGEAR is more effective and available than TO-GEAR in network lifetime,energy consumption of path setup,and success rate of data transmission.%针对无线传感器网络能量消耗大和网络生存时间短的问题,提出了一种具有引导距离和位置意识的GEAR路由优化协议( GLGEAR)。该协议在选择下一跳节点时,引入了引导距离这个概念,改进了估计代价计算公式,使选路更加优化,从而减少数据传输时的能量消耗;为了找到离目标区域更近的邻居节点,设计了新的节点选择方法,降低了计算的复杂性,缩短了路径的建立时间。同时,该协议给出了路由空洞和数据传输失败时的解决策略,使GLGEAR协议具有更好的可靠性。仿真结果表明,该协议在网络生存时间,路径生成能量消耗,数据传输成功率等方面的性能表现优于TO-GEAR等协议。

  8. AUTOFLUORESCENCE IN PAP STAIN IN THE SPUTUM OF SUSPECTED PULMONARY TUBERCULOSIS AND COMPARE WITH OTHER AFB STAINS

    Directory of Open Access Journals (Sweden)

    Mani

    2016-02-01

    Full Text Available BACKGROUND Tuberculosis is an infectious disease caused by mycobacterium tuberculosis. It primarily affect lungs and can also affect intestine, meninges, bones and Joints, lymph node, skin and other tissues of the body. There are various methods for the diagnosis of tuberculosis, such as sputum examination of tubercular bacilli by Ziehl-Neelsen staining, demonstration of tubercular bacilli by Auramine–Rhodamine staining and culture in LJ medium. Papanicolaou stain is widely used in routine cytological evaluation of samples derived from the respiratory tract and eosin to be responsible for the autofluorescence. MATERIAL AND METHOD Present study was done clinically suspected tubercular patients from January to July 2015. On all received samples ZN stain, fluorescent stain and PAP stain was applied. RESULT Among the clinically suspected patients 650 (35.35% was diagnosed with tuberculosis. Male-to-female ratio was 2.76:1, Tuberculosis was diagnosed in 315 (16.75% cases with Ziehl-Neelsen staining with fluorescent staining in 611 (32.79% cases and Autofluorescence in 650 (35.35% cases. CONCLUSION In present study, fever was chief clinical complaint. Males are more diagnosed with tuberculosis than females. Autofluorescent staining is slightly more sensitive than the Auramine–Rhodamine and more ZN staining in demonstration of AFB in the samples.

  9. [Imaging port wine stain by optical coherence tomography].

    Science.gov (United States)

    Zhao, Shi-Yong; Yu, Xin; Qiu, Hai-Xia; Huang, Nai-Yan; Wang, Tian-Shi; Xue, Ping; Gu, Ying

    2010-12-01

    Optical coherence tomography is an appropriate imaging method for biomedical science, due to its advantages of noninvasive nature, high resolution and fast imaging speed. Because most biological tissues have the characteristic of high scattering coefficient, OCT system can just obtain the structural images several millimeters below the surface of the tissues. The superficial depth of OCT's penetration limits application in dermatology field. As a common disease, the port wine stain (PWS) is a indication of OCT, because of its superficial lesion and significant expansion of blood vessels. To get deeper penetration in the skin, the authors employed 1 310 nm superluminescent diode as light source, optimized the light intensity ratio of reference delay arm and sample arm and control polarization, and the research of PWS imaging in vivo was accomplished. Besides, OCT is able to gather clear image and key characteristic parameters, such as the depth of epidermis layer, the diameter of blood vessel, etc. OCT will play an important role in the diagnosis and therapy of PWS.

  10. Lasers or light sources for treating port-wine stains

    DEFF Research Database (Denmark)

    Faurschou, Annesofie; Olesen, Anne Braae; Leonardi-Bee, Jo;

    2011-01-01

    Port-wine stains are birthmarks caused by malformations of blood vessels in the skin. Port-wine stains manifest themselves in infancy as a flat, red mark and do not regress spontaneously but may, if untreated, become darker and thicker in adult life. The profusion of various lasers and light...... sources makes it difficult to decide which equipment is the best for treating port-wine stains....

  11. Efficient staining of actinomycetoma and eumycetoma grains using henna extract.

    Science.gov (United States)

    Zakout, Y M; Batran, S E

    2015-01-01

    The use of natural, nontoxic, convenient and eco-friendly dyes for histopathological diagnosis avoids some of the synthetic dyes' hazards. I used an aqueous extract of henna at a concentration of 20 g/ml and acidified with acetic acid to stain mycetoma grains. Henna stained mycetoma grains orange-red to brown. The engulfed mycetoma grains within inflammatory cells stained well with henna extract compared to hematoxylin and eosin (H & E) and hexamine silver.

  12. TREATMENTS TO MINIMIZE EXTRACTIVES STAIN IN WESTERN RED CEDAR

    Directory of Open Access Journals (Sweden)

    Rod Stirling,

    2012-04-01

    Full Text Available Under certain conditions involving uneven exposure to weather, stains related to the extractives can reduce the aesthetic appeal of western red cedar in exterior applications such as fence boards, siding, and sidewall shingles. Selected chemical treatments were evaluated for their ability to inhibit the formation of extractives stain. DDACarbonate, alkyl amine oxide, and combinations thereof delayed extractives stain formation in an accelerated field test, with higher loadings having greater effect.

  13. Comparing mRNA levels using in situ hybridization of a target gene and co-stain

    OpenAIRE

    Wunderlich, Zeba; Bragdon, Meghan D.; Angela H. DePace

    2014-01-01

    In situ hybridization is an important technique for measuring the spatial expression patterns of mRNA in cells, tissues, and whole animals. However, mRNA levels cannot be compared across experiments using typical protocols. Here we present a semi-quantitative method to compare mRNA levels of a gene across multiple samples. This method yields an estimate of the error in the measurement to allow statistical comparison. Our method uses a typical in situ hybridization protocol to stain for a targ...

  14. 3D reconstruction of multiple stained histology images

    Directory of Open Access Journals (Sweden)

    Yi Song

    2013-01-01

    Full Text Available Context: Three dimensional (3D tissue reconstructions from the histology images with different stains allows the spatial alignment of structural and functional elements highlighted by different stains for quantitative study of many physiological and pathological phenomena. This has significant potential to improve the understanding of the growth patterns and the spatial arrangement of diseased cells, and enhance the study of biomechanical behavior of the tissue structures towards better treatments (e.g. tissue-engineering applications. Methods: This paper evaluates three strategies for 3D reconstruction from sets of two dimensional (2D histological sections with different stains, by combining methods of 2D multi-stain registration and 3D volumetric reconstruction from same stain sections. Setting and Design: The different strategies have been evaluated on two liver specimens (80 sections in total stained with Hematoxylin and Eosin (H and E, Sirius Red, and Cytokeratin (CK 7. Results and Conclusion: A strategy of using multi-stain registration to align images of a second stain to a volume reconstructed by same-stain registration results in the lowest overall error, although an interlaced image registration approach may be more robust to poor section quality.

  15. Histopathological evaluation of ocular microsporidiosis by different stains

    Directory of Open Access Journals (Sweden)

    Sharma Savitri

    2006-06-01

    Full Text Available Abstract Background There is limited data on comparing stains in the detection of microsporidia in corneal biopsies. Hence we wanted to evaluate various stains for their ability to detect microsporidia in corneal tissue sections. Methods Four cases diagnosed with microsporidiosis on Hematoxylin and Eosin and Periodic Acid Schiff's stained sections of the corneal button between January 2002 and December 2004, were included. Further sections were prospectively stained with calcofluor white, Gram, Giemsa, Masson's trichrome, acridine orange, Gomori's methenamine silver, Gram's chromotrope and modified acid fast stain. The stained sections were analyzed for the spore characteristics in terms of size, shape, color contrast, cell wall morphology, waist band in cytoplasm and ease of detection. Results All sections showed microsporidial spores as 3 – 5 μm, oval bodies. 1% acid fast, Gram's chromotrope and GMS stains provided a reliable diagnosis of microsporidia as diagnostic waist band could be identified and good contrast helped distinguish the spores from inflammatory debris. Conclusion Considering the ease of performance, cost effectiveness and rapidity of the technique, 1% acid fast stain and Gram's chromotrope stain are ideal for the detection of microsporidia.

  16. Effects of Hoechst33342 staining on the viability and flow cytometric sex-sorting of frozen-thawed ram sperm.

    Science.gov (United States)

    Quan, Guo Bo; Ma, Yuan; Li, Jian; Wu, Guo Quan; Li, Dong Jiang; Ni, Yi Na; Lv, Chun Rong; Zhu, Lan; Hong, Qiong Hua

    2015-02-01

    Cytometric sorting of frozen-thawed sperm can overcome difficulties caused by the unavailability of sorting facilities on farms where semen is collected from male livestock. In order to optimize the cytometric sex-sorting procedure, effects of Hoechst33342 staining on the viability and cytometric sorting efficiency of frozen-thawed ram sperm were evaluated. The frozen-thawed sperm were stained with Hoechst33342 at various dye concentrations (80 μM, 120 μM, 160 μM, 200 μM, 240 μM, or 320 μM) for 45 min to evaluate effects of dye dose. The frozen-thawed sperm were stained with 160 μM Hoechst33342 for various durations (0 min, 15 min, 30 min, 45 min, 60 min, 75 min, or 90 min) to evaluate effects of staining duration. Sperm motility and moving velocity were analyzed using a computer-assisted sperm analysis system (CASAS). Acrosome status, membrane integrity, and distribution of phosphatidylserine (PS) in Hoechst33342-stained sperm were analyzed using flow cytometry after staining with fluorescein isothiocyanate-labeled lectin from pisum sativum (FITC-PSA), Annexin V, or propidium iodide (PI). The fertility of Hoechst33342-stained sperm was analyzed by in vitro fertilization (IVF). A high-speed cell sorter was used to evaluate effects of Hoechst33342 staining on cytometric sex-sorting of frozen-thawed sperm. The motility, moving velocity, membrane integrity, and PS distribution of Hoechst33342-stained sperm were significantly different from that of immediately thawed sperm (Pram sperm. Results of cytometric sorting indicated that frozen-thawed sperm can be efficiently sorted into two sperm populations with X and Y chromosome when the Hoechst33342 concentration was 160 μM. Moreover, when the staining duration was equal to or longer than 45 min, the frozen-thawed sperm can be successfully sorted in the presence of 160μM Hoechst33342. In conclusion, Hoechst33342 staining can detrimentally influence viability of frozen-thawed ram sperm except acrosome and in vitro

  17. A simple cost-effective modification improves the quality of immunocytochemical staining in cervical scrape samples characterized by presence of excess mucus

    OpenAIRE

    Pawar, Sagar; Mahantshetty, Umesh; Deodhar, Kedar; Teni, Tanuja

    2014-01-01

    Immunocytochemistry (ICC) is a very important tool in a diverse range of biomedical research as well as in diagnostic cytopathology. Smears prepared from cervical scrapes contain a large amount of overlying mucus that interferes with the standard immunocytochemical staining protocol. A modified ICC protocol is described, which involves pretreatment of these smears with 1 mg/ml solution of Ambroxol hydrochloride in methanol for 1 hour. Source of Ambroxol hydrochloride was a 30 mg Mucolite™ tab...

  18. A simple cost-effective modification improves the quality of immunocytochemical staining in cervical scrape samples characterized by presence of excess mucus

    OpenAIRE

    Pawar, Sagar; Mahantshetty, Umesh; Deodhar, Kedar; Teni, Tanuja

    2014-01-01

    Immunocytochemistry (ICC) is a very important tool in a diverse range of biomedical research as well as in diagnostic cytopathology. Smears prepared from cervical scrapes contain a large amount of overlying mucus that interferes with the standard immunocytochemical staining protocol. A modified ICC protocol is described, which involves pretreatment of these smears with 1 mg/ml solution of Ambroxol hydrochloride in methanol for 1 hour. Source of Ambroxol hydrochloride was a 30 mg Mucolite™ tab...

  19. Embryonic and induced pluripotent stem cell staining and sorting with the live-cell fluorescence imaging probe CDy1.

    Science.gov (United States)

    Kang, Nam-Young; Yun, Seong-Wook; Ha, Hyung-Ho; Park, Sung-Jin; Chang, Young-Tae

    2011-06-30

    Detecting and isolating specific types of cells is crucial to understanding a variety of biological processes, including development, aging, regeneration and pathogenesis; this understanding, in turn, allows the use of cells for therapeutic purposes, for which stem cells have emerged recently as invaluable materials. The current methods of isolation and characterization of stem cells depend on cell morphology in culture or on immunostaining of specific markers. These methods are, however, time consuming and involve the use of antibodies that may often make the cells unsuitable for further study. We recently developed a fluorescent small molecule named CDy1 (compound of designation yellow 1) that selectively stains live embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). This protocol describes detailed procedures for staining ESC and iPSC in live conditions and for fluorescence-activated cell sorting (FACS) of ESC using CDy1. Cell staining, image acquisition and FACS can be done within 6 h.

  20. Performance Analysis of AODV-UI Routing Protocol With Energy Consumption Improvement Under Mobility Models in Hybrid Ad hoc Network

    OpenAIRE

    Abdusy Syarif; Riri Fitri Sari

    2011-01-01

    In mobile ad hoc networks (MANETs), routing protocol plays the most important role. In the last decade, Ad hoc On-demand Distance Vector (AODV) routing protocol becomes the attention of focussed research on MANETs world wide. A lot of protocols had been proposed to improve and optimize AODV routing protocol to achieve the best in quest of reliable protocol. In this paper, we present some improvement suggestion to AODV routing protocol. Our proposed protocol, called AODV-UI, improved AODV in g...

  1. Research on Protocol Migration

    Institute of Scientific and Technical Information of China (English)

    汪芸; 顾冠群; 等

    1996-01-01

    This paper elaborates the concept and model of protocol migration in network interconnection.Migration strategies and principles are discussed and several cases are studied in detail which show the basic procedure and techniques used in protocol migration.

  2. Selection of optimal ovary stimulation protocol for patients with unexplained infertility%原因不明性不孕患者促排卵治疗方案的优选

    Institute of Scientific and Technical Information of China (English)

    黄仲英; 李尚为; 马黔红

    2011-01-01

    目的 研究三种促排卵方案对原因不明性不孕患者的治疗效果,为优化选择促排卵治疗方案提供依据.方法 将73例诊断为原因不明性不孕患者共101周期纳入研究分为三组,分别予克罗米酚(CC组)、克罗米酚加人绝经期促性腺激素(HMG)(CC+HMG组),以及人绝经期促性腺激素(HMG组)三种方案促排卵.采用阴道超声监测卵泡发育,并联合尿促黄体生成素(LH)和Insler宫颈黏液评分以确定HCG注射时间,肌注HCG后30~40 h指导同房,在确定排卵后3 d开始肌注黄体酮支持.结果 三组在年龄、不孕年限、窦卵泡数及基础内分泌方面无统计学差异.CC组的卵泡期[(16.32±1.73)d]显著长于CC+HMG组[(15.3±1.49)d]和HMG组[(13.85±1.19)d](P<0.05);注射HCG日子宫内膜厚度为(7.44±0.96)nml,少于CC+HMG组[(9.15±0.85)mill]和HMG组[(9.52±1.36)mm];排卵个数为(1.84±0.86)个,少于CC+HMG组[(2.06 ±0.75)个]和HMG组[(2.48±0.68)个].三组妊娠率分别为12.9%、24.24%和26.92%,CC+HMG组和HMG组妊娠率显著高于CC组,但两组间无统计学差异(P<0.05).HMG组周期取消率最高,达18.75%.CC组1例、CC+HMG组1例、HMG组2例发生中度卵巢过度刺激综合征(OHSS).双胎2例,均发生于HMG组.结论 对原因不明性不孕患者进行促排卵治疗,采用CC+HMG方案促排卵治疗效果优于CC方案、与HMG方案无统计学差异,但周期取消率、OHSS及多胎发生风险低于HMG方案,推荐采用.%Objective To select optimal ovary stimulation protocol for patients with unexplained infertility( UI). Methods Seventy three patients (101 cycles) with UI were subjected to three ovary stimulation protocols: clomiphene citrate ( CC ) , CC + human menopausal gonadotropin ( HMG) , or HMG. Trans-vaginal B-ultrasonic scanning combined with urine LH detection and cervical mucus evaluation by Insler scoring system were used to determine appropriate time of HCG injection . Timed intercourse was recommended 30-40 h after

  3. Comparing mRNA levels using in situ hybridization of a target gene and co-stain.

    Science.gov (United States)

    Wunderlich, Zeba; Bragdon, Meghan D; DePace, Angela H

    2014-06-15

    In situ hybridization is an important technique for measuring the spatial expression patterns of mRNA in cells, tissues, and whole animals. However, mRNA levels cannot be compared across experiments using typical protocols. Here we present a semi-quantitative method to compare mRNA levels of a gene across multiple samples. This method yields an estimate of the error in the measurement to allow statistical comparison. Our method uses a typical in situ hybridization protocol to stain for a target gene and an internal standard, which we refer to as a co-stain. As a proof of concept, we apply this method to multiple lines of transgenic Drosophila embryos, harboring constructs that express reporter genes to different levels. We generated this test set by mutating enhancer sequences to contain different numbers of binding sites for Zelda, a transcriptional activator. We demonstrate that using a co-stain with in situ hybridization is an effective method to compare mRNA levels across samples. This method requires only minor modifications to existing in situ hybridization protocols and uses straightforward analysis techniques. This strategy can be broadly applied to detect quantitative, spatially resolved changes in mRNA levels.

  4. Lasers or light sources for treating port-wine stains

    DEFF Research Database (Denmark)

    Faurschou, Annesofie; Olesen, Anne Braae; Leonardi-Bee, Jo;

    2011-01-01

    Port-wine stains are birthmarks caused by malformations of blood vessels in the skin. Port-wine stains manifest themselves in infancy as a flat, red mark and do not regress spontaneously but may, if untreated, become darker and thicker in adult life. The profusion of various lasers and light...

  5. THIONIN STAINING OF PARAFFIN AND PLASTIC EMBEDDED SECTIONS OF CARTILAGE

    NARCIS (Netherlands)

    BULSTRA, SK; DRUKKER, J; KUIJER, R; BUURMAN, WA; VANDERLINDEN, AJ

    1993-01-01

    The usefulness of thionin for staining cartilage sections embedded in glycol methacrylate (GMA) and the effect of decalcification on cartilage sections embedded in paraffin and GMA were assessed. Short decalcification periods using 5% formic acid or 10% EDTA did not influence the staining properties

  6. Hematoxylin and safranin O staining of frozen sections.

    Science.gov (United States)

    Tran, D; Golick, M; Rabinovitz, H; Rivlin, D; Elgart, G; Nordlow, B

    2000-03-01

    Currently the hematoxylin and eosin staining procedure is the most popular among Mohs surgeons for histology. However, safranin O, a cheaper and relatively safer stain which is predominantly used for plant histology, should be considered as it offers similar or improved accuracy in the diagnosis of frozen sections of basal and squamous cell carcinomas.

  7. News from the Biological Stain Commission No. 10

    DEFF Research Database (Denmark)

    Lyon, H O

    2011-01-01

    In the 10th issue of News from the Biological Stain Commission (BSC), under the heading of Regulatory affairs, the Biological Stain Commission's International Affairs Committee presents information from the meeting of ISO/TC 212/WG 1 held in London, UK, on 16-17 November 2009. Furthermore, the it...

  8. THIONIN STAINING OF PARAFFIN AND PLASTIC EMBEDDED SECTIONS OF CARTILAGE

    NARCIS (Netherlands)

    BULSTRA, SK; DRUKKER, J; KUIJER, R; BUURMAN, WA; VANDERLINDEN, AJ

    The usefulness of thionin for staining cartilage sections embedded in glycol methacrylate (GMA) and the effect of decalcification on cartilage sections embedded in paraffin and GMA were assessed. Short decalcification periods using 5% formic acid or 10% EDTA did not influence the staining properties

  9. Alcian blue-stained particles in a eutrophic lake

    DEFF Research Database (Denmark)

    Worm, J.; Søndergaard, Morten

    1998-01-01

    We used a neutral solution of Alcian Blue to stain transparent particles in eutrophic Lake Frederiksborg Slotss0, Denmark. Alcian Blue-stained particles (ABSP) appeared to be similar to the so-called transparent exopolymer particles (TEP) identified with an acidic solution of Alcian Blue. Our...

  10. The effect of selected staining techniques on bull sperm morphometry.

    Science.gov (United States)

    Banaszewska, Dorota; Andraszek, Katarzyna; Czubaszek, Magdalena; Biesiada-Drzazga, Barbara

    2015-08-01

    Sperm morphometry has some value as an indicator of reproductive capacity in males. In laboratory practice a variety of slide-staining methods are used during morphological evaluation of semen to predict male fertility. The aim of this study was to determine the effect of staining of semen using four different techniques on the morphometry of the bull sperm cell. The material for the study consisted of semen collected from test bulls of the Black-and-White variety of Holstein-Friesians. The results obtained in the study indicate differences in the dimensions of bull sperm heads when different slide staining techniques were used. The most similar results for sperm head dimensions were obtained in the case of SpermBlue(®) and eosin+gentian violet complex, although statistically significant differences were found between all the staining techniques. Extreme values were noted for the other staining techniques - lowest for the Papanicolaou and highest for silver nitrate, which may indicate more interference in the cell by the reagents used in the staining process. However, silver nitrate staining was best at identifying the structures of the sperm cell. Hence it is difficult to determine which of the staining methods most faithfully reveals the dimensions and shape of the bull sperm.

  11. Pyogenic granuloma, port-wine stain and pregnancy.

    Science.gov (United States)

    Rodins, Karl; Gramp, Dallas; James, Daniel; Kumar, Sandeep

    2011-11-01

    We present a novel case of pyogenic granuloma occurring within a port-wine stain in two sequential pregnancies at different sites. There was no history of precipitating events such as trauma. We discuss why a pyogenic granuloma may occur within a port-wine stain and how pregnancy may increase the likelihood of this occurring.

  12. Topological Design of Protocols

    CERN Document Server

    Jaffe, Arthur; Wozniakowski, Alex

    2016-01-01

    We give a topological simulation for tensor networks that we call the two-string model. In this approach we give a new way to design protocols, and we discover a new multipartite quantum communication protocol. We introduce the notion of topologically compressed transformations. Our new protocol can implement multiple, non-local compressed transformations among multi-parties using one multipartite resource state.

  13. Vertical Protocol Composition

    DEFF Research Database (Denmark)

    Groß, Thomas; Mödersheim, Sebastian Alexander

    2011-01-01

    The security of key exchange and secure channel protocols, such as TLS, has been studied intensively. However, only few works have considered what happens when the established keys are actually used—to run some protocol securely over the established “channel”. We call this a vertical protocol com...

  14. Multistep level sections to detect occult fallopian tube carcinoma in risk-reducing salpingo-oophorectomies from women with BRCA mutations: implications for defining an optimal specimen dissection protocol.

    Science.gov (United States)

    Rabban, Joseph T; Krasik, Ellen; Chen, Lee-May; Powell, Catherine B; Crawford, Beth; Zaloudek, Charles J

    2009-12-01

    exhaustive multistep level sectioning of all remaining tubal and ovarian blocks from both these women confirmed the original benign diagnosis in 1 woman but in the other woman, the deepest levels of 1 ovarian block revealed a single 1-mm nodule of cancer at the base of an ovarian surface epithelial invagination. This specimen was one of the first RRSO cases in our experience and on review of the original report, this ovary was not dissected into multiple slices along its short axis but was only bivalved along its long axis. We propose that there does not seem to be any diagnostic value in automatically performing multistep deeper level sections of RRSO specimens if the tissue is sectioned appropriately and if the specimen is sliced at intervals that are no more than 3 mm thick. Guidelines for evaluation of RRSO specimens should emphasize the use of an optimal dissection protocol and the importance of thin tissue slice intervals.

  15. Staining in firearm barrels after experimental contact shots.

    Science.gov (United States)

    Schyma, C; Bauer, K; Brünig, J; Courts, C; Madea, B

    2017-02-10

    After contact shots to the head biological traces inside firearm barrels can be found. This study was conducted to simulate and to evaluate such staining. Five current handguns of four inch barrel length in the calibre .22 long rifle, 7.65mm Browning, 9mm Luger and .38 special were used to perform 24 contact shots on silicone coated, gelatine filled box models using the triple contrast method. The staining was documented by endoscopy and swabs gathered from both ends of the barrel were analysed by quantitative PCR. With the exception of the .22 revolver, all firearms showed distinct staining which decreased from the muzzle to the rear end of the barrel. The pattern was varied, showing droplets, elongated forms or stripes. In 14 of 24 shots, staining reached the chamber. The staining results were comparable to real suicide cases.

  16. Mapping stain distribution in pathology slides using whole slide imaging

    Directory of Open Access Journals (Sweden)

    Fang-Cheng Yeh

    2014-01-01

    Full Text Available Background: Whole slide imaging (WSI offers a novel approach to digitize and review pathology slides, but the voluminous data generated by this technology demand new computational methods for image analysis. Materials and Methods: In this study, we report a method that recognizes stains in WSI data and uses kernel density estimator to calculate the stain density across the digitized pathology slides. The validation study was conducted using a rat model of acute cardiac allograft rejection and another rat model of heart ischemia/reperfusion injury. Immunohistochemistry (IHC was conducted to label ED1 + macrophages in the tissue sections and the stained slides were digitized by a whole slide scanner. The whole slide images were tessellated to enable parallel processing. Pixel-wise stain classification was conducted to classify the IHC stains from those of the background and the density distribution of the identified IHC stains was then calculated by the kernel density estimator. Results: The regression analysis showed a correlation coefficient of 0.8961 between the number of IHC stains counted by our stain recognition algorithm and that by the manual counting, suggesting that our stain recognition algorithm was in good agreement with the manual counting. The density distribution of the IHC stains showed a consistent pattern with those of the cellular magnetic resonance (MR images that detected macrophages labeled by ultrasmall superparamagnetic iron-oxide or micron-sized iron-oxide particles. Conclusions: Our method provides a new imaging modality to facilitate clinical diagnosis. It also provides a way to validate/correlate cellular MRI data used for tracking immune-cell infiltration in cardiac transplant rejection and cardiac ischemic injury.

  17. Offset-sparsity decomposition for automated enhancement of color microscopic image of stained specimen in histopathology

    Science.gov (United States)

    Kopriva, Ivica; Hadžija, Marijana Popović; Hadžija, Mirko; Aralica, Gorana

    2015-07-01

    We propose an offset-sparsity decomposition method for the enhancement of a color microscopic image of a stained specimen. The method decomposes vectorized spectral images into offset terms and sparse terms. A sparse term represents an enhanced image, and an offset term represents a "shadow." The related optimization problem is solved by computational improvement of the accelerated proximal gradient method used initially to solve the related rank-sparsity decomposition problem. Removal of an image-adapted color offset yields an enhanced image with improved colorimetric differences among the histological structures. This is verified by a no-reference colorfulness measure estimated from 35 specimens of the human liver, 1 specimen of the mouse liver stained with hematoxylin and eosin, 6 specimens of the mouse liver stained with Sudan III, and 3 specimens of the human liver stained with the anti-CD34 monoclonal antibody. The colorimetric difference improves on average by 43.86% with a 99% confidence interval (CI) of [35.35%, 51.62%]. Furthermore, according to the mean opinion score, estimated on the basis of the evaluations of five pathologists, images enhanced by the proposed method exhibit an average quality improvement of 16.60% with a 99% CI of [10.46%, 22.73%].

  18. On using Mobile IP Protocols

    Directory of Open Access Journals (Sweden)

    Fayza A. Nada

    2006-01-01

    Full Text Available The recent advances in wireless communication technology and the unprecedented growth of the Internet have paved the way for wireless networking and IP mobility. Mobile Internet protocol has been designed within the IETF to support the mobility of users who wish to connect to the Internet and maintain communications as they move from place to place. This study describes and summarizes the current Internet draft for mobile IP (MIPv4 with its major components: agent discovery, registration and tunneling. In addition, we outline the available encapsulation techniques and route optimization procedure. In the end, we describe the design of the new protocol for transparent routing of IPv6 packets to mobile IPv6 nodes operating in the Internet.

  19. Blind Collective Signature Protocol

    Directory of Open Access Journals (Sweden)

    Nikolay A. Moldovyan

    2011-06-01

    Full Text Available Using the digital signature (DS scheme specified by Belarusian DS standard there are designed the collective and blind collective DS protocols. Signature formation is performed simultaneously by all of the assigned signers, therefore the proposed protocols can be used also as protocols for simultaneous signing a contract. The proposed blind collective DS protocol represents a particular implementation of the blind multisignature schemes that is a novel type of the signature schemes. The proposed protocols are the first implementations of the multisignature schemes based on Belarusian signature standard.

  20. Homogeneous luminescent stain etched porous silicon elaborated by a new multi-step stain etching method

    Energy Technology Data Exchange (ETDEWEB)

    Hajji, M., E-mail: mhajji2001@yahoo.fr [Laboratoire de Photovoltaïque, Centre de Recherche et des Technologies de l’Energie, Technopôle de Borj-Cédria BP 95, Hammam-Lif 2050 (Tunisia); Institut Supérieur d’Electronique et de Communication de Sfax, route Menzel Chaker Km 0.5, BP 868, Sfax 3018 (Tunisia); Khalifa, M.; Slama, S. Ben; Ezzaouia, H. [Laboratoire de Photovoltaïque, Centre de Recherche et des Technologies de l’Energie, Technopôle de Borj-Cédria BP 95, Hammam-Lif 2050 (Tunisia)

    2013-11-01

    This paper presents a new method to produce porous silicon which derived from the conventional stain etching (SE) method. But instead of one etching step that leads to formation of porous layer, the substrate is subjected to an initial etching step with a duration Δt{sub 0} followed by a number of supplementary short steps that differs from a layer to another. The duration of the initial step is just the necessary time to have a homogenous porous layer on the whole surface of the substrate. It was found that this duration is largely dependent of the doping type and level of the silicon substrate. The duration of supplementary steps was kept as short as possible to prevent the formation of bubbles on the silicon surface during silicon dissolution which leads generally to inhomogeneous porous layers. It is found from surface investigation by atomic force microscopy (AFM) that multistep stain etching (MS-SE) method allows to produce homogeneous porous silicon nanostructures compared to the conventional SE method. The chemical composition of the obtained porous layers has been evaluated using Fourier transform infrared spectroscopy (FTIR). Photoluminescence (PL) measurement shows that porous layers produced by SE and MS-SE methods have comparable spectra indicating that those layers are composed of nanocrystallites with comparable sizes. But the intensity of photoluminescence of layer elaborated by MS-SE method is higher than that elaborated by the SE method. Total reflectance characteristics show that the presented method allows the production of porous silicon layers with controllable thicknesses and optical properties. Results for porous silicon layers elaborated on heavily doped n-type silicon show that the reflectance can be reduced to values less than 3% in the major part of the spectrum.

  1. 如何优化胚胎冻存方案改善患者妊娠结局%How to improve the pregnancy outcome by optimizing embryo cryopreservation protocol

    Institute of Scientific and Technical Information of China (English)

    张玥; 张云山; 薛凤霞

    2015-01-01

    Objective To investigate how to optimize the protocol of embryo cryopreservation to improve the success of frozen-thawed embryo transfer (FET), reduce multiple pregnancy rate and increase the cumulative pregnancy rate from one oocyte retrieval process. Methods The clinical data of 1 166 FET cycles were retrospectively analyzed and separated into different groups:445 for vitrification and 721 for slow-freezing. The vitrification group was divided into single embryo (28 cy⁃cles), double embryos (71 cycles) and triple embryos (346 cycles). 0-1 optimal embryo was called O0-1 group (235 cycles), 2 optimal embryos were called O2 group (80 cycles), 3 optimal embryos were called O3 group (130 cycles). The difference preg⁃nancy outcomes (implantation rate, clinical pregnancy, abortion rate and live-birth rate) were compared between groups. Results (1) There were significantly higher embryo survival rate(98.3%vs 73.1%), embryo recovery rate without damaging (83.3%vs 62.1%), implantation rate(36.8%vs 29.9%), clinical pregnancy(57.1%vs 44.0%) and live-birth rate(47.9%vs 34.5%) in vitrification group than those of slow freezing group(P0.05). Conclusion Vitrification technology can improve the clinical pregnancy and live-birth rate, and decrease multiple preg⁃nancy rate. Two optimal embryos in one tube are supposed to be the preferred method for embryo cryopreservation.%目的:探讨如何优化胚胎冻存的方案以提高胚胎解冻移植的成功率,降低多胎率,增加一次取卵的累积妊娠率。方法回顾性分析1166个冻融胚胎移植(FET)周期的临床资料,分为玻璃化冷冻组(445)和慢速程序冷冻组(721);445个玻璃化冷冻FET周期分为单胚组(28个周期)、双胚组(71个周期)、三胚组(346个周期)。0~1个优胚为O0~1组(235个周期)、2个优胚为O2组(80个周期),3个优胚为O3组(130个周期)。比较各组之间的妊娠结局(着床率、临床妊娠率、流

  2. Fetal cell detection in maternal blood : A study in 236 samples using erythroblast morphology, DAB and HbF staining, and FISH analysis

    NARCIS (Netherlands)

    Oosterwijk, JC; Mesker, WE; Ouwerkerk-van Velzen, MCM; Knepfle, CFHM; Wiesmeijer, KC; Beverstock, GC; van Ommen, GJB; Kanhai, HHH; Tanke, HJ

    1998-01-01

    A protocol to detect fetal nucleated red blood cells (NRBCs) was tested in 217 pregnant women and in 19 nonpregnant controls. All the pregnant women were sampled after chorionic villus sampling (CVS); 20 were also sampled pre-CVS. NRBC recognition was based upon morphology by using staining of hemog

  3. Microscopic analysis of MTT stained boar sperm cells

    Directory of Open Access Journals (Sweden)

    B.M. van den Berg

    2015-06-01

    Full Text Available The ability of sperm cells to develop colored formazan by reduction of MTT was used earlier to develop a spectrophotometric assay to determine the viability of sperm cells for several mammalian species. It was the objective of the present study to visualize microscopically the location of the formazan in boar sperm cells. The MTT staining process of boar sperm cells can be divided into a series of morphological events. Incubation of the sperm cells in the presence of MTT resulted after a few min in a diffuse staining of the midpiece of the sperm cells. Upon further incubation the staining of the midpiece became more intense, and gradually the formation of packed formazan granules became more visible. At the same time, a small formazan stained granule appeared medially on the sperm head, which increased in size during further incubation. After incubation for about 1 h the midpiece granules were intensely stained and more clearly distinct as granules, while aggregation of sperm cells occurred. Around 90% of the sperm cells showed these staining events. At the end of the staining the formazan granules have disappeared from both the sperm cells and medium, whereas formazan crystals appeared as thin crystal threads, that became heavily aggregated in the incubation medium. It was concluded that formazan is taken up by lipid droplets in the cytoplasm. Further, the use of the MTT assay to test for sperm viability should be regarded as a qualitative assay, whereas its practical use at artificial insemination (AI Stations is limited.

  4. Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel.

    Directory of Open Access Journals (Sweden)

    Weizhong Tang

    Full Text Available To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA, (dC, (dG and (dT to silver staining could be ranged as (dA > (dG > (dC > (dT from high to low. It was unexpected that oligo (dT was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt. The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.

  5. Microscopic analysis of MTT stained boar sperm cells.

    Science.gov (United States)

    van den Berg, B M

    2015-01-01

    The ability of sperm cells to develop colored formazan by reduction of MTT was used earlier to develop a spectrophotometric assay to determine the viability of sperm cells for several mammalian species. It was the objective of the present study to visualize microscopically the location of the formazan in boar sperm cells. The MTT staining process of boar sperm cells can be divided into a series of morphological events. Incubation of the sperm cells in the presence of MTT resulted after a few min in a diffuse staining of the midpiece of the sperm cells. Upon further incubation the staining of the midpiece became more intense, and gradually the formation of packed formazan granules became more visible. At the same time, a small formazan stained granule appeared medially on the sperm head, which increased in size during further incubation. After incubation for about 1 h the midpiece granules were intensely stained and more clearly distinct as granules, while aggregation of sperm cells occurred. Around 90% of the sperm cells showed these staining events. At the end of the staining the formazan granules have disappeared from both the sperm cells and medium, whereas formazan crystals appeared as thin crystal threads, that became heavily aggregated in the incubation medium. It was concluded that formazan is taken up by lipid droplets in the cytoplasm. Further, the use of the MTT assay to test for sperm viability should be regarded as a qualitative assay, whereas its practical use at artificial insemination (AI) Stations is limited.

  6. C4d staining as immunohistochemical marker in inflammatory myopathies.

    Science.gov (United States)

    Pytel, Peter

    2014-10-01

    The diagnosis of an inflammatory myopathy is often established based on basic histologic studies. Additional immunohistochemical studies are sometimes required to support the diagnosis and the classification of inflammatory myopathies. Staining for major histocompatibility complex 1 (MHC1) often shows increased sarcolemmal labeling in inflammatory myopathies. Endomysial capillary staining C5b-9 (membrane attack complex) is a feature that is reported as frequently associated with dermatomyositis. Immunohistochemical staining for C4d is widely used for various applications including the assessment of antibody-mediated rejection after solid organ transplantation. In the context of dermatomyositis, C4d staining has been described in skin biopsies but not in muscle biopsies. A total of 32 muscle biopsy specimens were examined. The hematoxylin and eosin-stained slides were reviewed, and immunohistochemical studies for MHC1, C5b-9, and C4d were conducted. The staining observed for C5b-9 and C4d was compared. Overall, the staining pattern for C4d mirrored the one observed for C5b-9 in the examined muscle biopsy specimens. There was high and statistically significant (P<0.0001) correlation between the staining seen with these 2 antibodies. Both antibodies labeled the cytoplasm of degenerating necrotic myofibers. In addition, both antibodies showed distinct endomysial capillary labeling in a subset of dermatomyositis. Areas with perifascicular atrophy often exhibited the most prominent vascular labeling for C4d and C5b-9. In conclusion, C4d and C5b-9 show similar expression patterns in muscle biopsies of patients with inflammatory myopathies and both highlight the presence of vascular labeling associated with dermatomyositis. C4d antibodies are widely used and may offer an alternative for C5b-9 staining.

  7. Differential fluorescent staining of Listeria monocytogenes and a whey food soil for quantitative analysis of surface hygiene.

    Science.gov (United States)

    Whitehead, Kathryn A; Benson, Paul; Verran, Joanna

    2009-09-30

    The accurate monitoring of surface cleanliness in terms of bacterial contamination is usually carried out using methods such as plate counts or replica plating. However these methods take at least eighteen hours to obtain results and do not determine the presence or amount of residual organic material on a surface, which may interfere with cleaning and disinfection. This work describes the application of fluorescent stains to cells (Listeria monocytogenes) and food soil (solubilized whey) to optimize a dual staining method that can be used in the quantitative analysis of surface cleanability. Seven different stains were tested at a range of concentrations (0.3%-0.001 mg/ml) and application methods. The best stain combination for differential staining of L. monocytogenes and whey food soil was 0.1 mg/ml rhodamine B with 0.1 g/ml DAPI. Differential staining of the cells and soil occurred regardless of the application method. This method has been successfully used to demonstrate the hygienic status of surfaces in an industrial situation. This novel work enables quantitative assessment of soils and cells on surfaces.

  8. anolyte as an alternative bleach for stained cotton fabrics

    African Journals Online (AJOL)

    user

    anolyte, colour change, sodium hypochlorite, bleach, stain ... Cotton is a natural fibre that is high in demand worldwide. ... various dyes are commonly used in the processing and .... prepared an hour before any test was carried out whereby ...

  9. The electrical conduction variation in stained carbon nanotubes

    Science.gov (United States)

    Sun, Shih-Jye; Wei Fan, Jun; Lin, Chung-Yi

    2012-01-01

    Carbon nanotubes become stained from coupling with foreign molecules, especially from adsorbing gas molecules. The charge exchange, which is due to the orbital hybridization, occurred in the stained carbon nanotube induces electrical dipoles that consequently vary the electrical conduction of the nanotube. We propose a microscopic model to evaluate the electrical current variation produced by the induced electrical dipoles in a stained zigzag carbon nanotube. It is found that stronger orbital hybridization strengths and larger orbital energy differences between the carbon nanotube and the gas molecules help increasing the induced electrical dipole moment. Compared with the stain-free carbon nanotube, the induced electrical dipoles suppress the current in the nanotube. In the carbon nanotubes with induced dipoles the current increases as a result of increasing orbital energy dispersion via stronger hybridization couplings. In particular, at a fixed hybridization coupling, the current increases with the bond length for the donor-carbon nanotube but reversely for the acceptor-carbon nanotube.

  10. Snakebite management in Iran: Devising a protocol

    Directory of Open Access Journals (Sweden)

    Seyed Mostafa Monzavi

    2014-01-01

    Full Text Available Background: Snakebite in Iran has been a health concern. However, management of snakebite is not standardized and varies from center to center. This study is aimed at devising an evidence-based comprehensive protocol for snakebite management in Iran, to reduce unnecessary variations in practice. Materials and Methods: A narrative search in electronic databases was performed. Fifty peer-reviewed articles, guidelines, and textbooks were reviewed and practical details were extracted. Our currently used protocol in the Mashhad Toxicology Center was supplemented with this information. Consequently an improved wide-range protocol was developed. The protocol was then discussed and amended within a focus group comprised of medical toxicologists and internal medicine specialists. The amended version was finally discussed with expert physicians specialized in different areas of medicine, to be optimized by supplementing other specific considerations. Results: During a one-year process, the protocol was finalized. The final version of the protocol, which was designed in six steps, comprised of three components: A schematic algorithm, a severity grading scale, and instructions for supportive and adjunctive treatments. The algorithm pertains to both Viperidae and Elapidae snakebite envenomations and consists of a planned course of action and dosing of antivenom, based on the severity of the envenomation. Conclusion: Snakebite envenomation is a clinical toxicologic emergency, which needs to be treated in a timely and organized manner. Hence, a multi-aspect protocol was designed to improve the clinical outcomes, reduce unnecessary administration of antivenom, and help physicians make more proper clinical judgments.

  11. Encryption Switching Protocols

    OpenAIRE

    Couteau, Geoffroy; Peters, Thomas; Pointcheval, David

    2016-01-01

    International audience; We formally define the primitive of encryption switching protocol (ESP), allowing to switch between two encryption schemes. Intuitively, this two-party protocol converts given ciphertexts from one scheme into ciphertexts of the same messages under the other scheme, for any polynomial number of switches, in any direction. Although ESP is a special kind of two-party computation protocol, it turns out that ESP implies general two-party computation (2-PC) under natural con...

  12. Solute concentration-dependent contact angle hysteresis and evaporation stains.

    Science.gov (United States)

    Li, Yueh-Feng; Sheng, Yu-Jane; Tsao, Heng-Kwong

    2014-07-08

    The presence of nonvolatile solutes in a liquid drop on a solid surface can affect the wetting properties. Depending on the surface-activity of the solutes, the extent of contact angle hysteresis (CAH) can vary with their concentration and the pattern of the evaporation stain is altered accordingly. In this work, four types of concentration-dependent CAH and evaporation stains are identified for a water drop containing polymeric additives on polycarbonate. For polymers without surface-activity such as dextran, advancing and receding contact angles (θa and θr) are independent of solute concentrations, and a concentrated stain is observed in the vicinity of the drop center after complete evaporation. For polymers with weak surface-activity such as poly(ethylene glycol) (PEG), both θa and θr are decreased by solute addition, and the stain pattern varies with increasing PEG concentration, including a concentrated stain and a mountain-like island. For polymers with intermediate surface-activity such as sodium polystyrenesulfonate (NaPSS), θa descends slightly, but θr decreases significantly after the addition of a substantial amount of NaPSS, and a ring-like stain pattern is observed. Moreover, the size of the ring stain can be controlled by NaPSS concentration. For polymers with strong surface-activity such as poly(vinylpyrrolidone) (PVP), θa remains essentially a constant, but θr is significantly lowered after the addition of a small amount of PVP, and the typical ring-like stain is seen.

  13. News from the Biological Stain Commission, No. 17

    DEFF Research Database (Denmark)

    Lyon, H O

    2016-01-01

    In the 17(th) issue of News from the Biological Stain Commission (BSC) under the heading of Regulatory affairs, the Biological Stain Commission's International Affairs Committee presents information from the 20(th) meeting of ISO/TC 212 Clinical laboratory testing and in vitro diagnostic test sys...... systems held on October 15 - 17, 2014 in Toronto, Canada, and from the 29(th) meeting of CEN/TC 140 In vitro diagnostic medical devices held on February 3, 2015 in Berlin, Germany....

  14. Multiparty Quantum Cryptographic Protocol

    Institute of Scientific and Technical Information of China (English)

    M. Ramzan; M. K. Khan

    2008-01-01

    We propose a multiparty quantum cryptographic protocol. Unitary operators applied by Bob and Charlie, on their respective qubits of a tripartite entangled state encoding a classical symbol that can be decoded at Alice's end with the help of a decoding matrix. Eve's presence can be detected by the disturbance of the decoding matrix. Our protocol is secure against intercept-resend attacks. Furthermore, it is efficient and deterministic in the sense that two classical bits can be transferred per entangled pair of qubits. It is worth mentioning that in this protocol, the same symbol can be used for key distribution and Eve's detection that enhances the effciency of the protocol.

  15. Black Stain and Dental Caries: A Review of the Literature

    Directory of Open Access Journals (Sweden)

    Tomasz Żyła

    2015-01-01

    Full Text Available Black stain is characterized as a dark line or an incomplete coalescence of dark dots localized on the cervical third of the tooth. Over the last century, the etiology of black stain has been the subject of much debate. Most of the studies concerning this issue were conducted in pediatric population. According to the reviewed articles published between 2001 and 2014, the prevalence of black stain varies from 2.4% to 18% with equal sex distribution. The majority of the authors confirm the correlation between the presence of black stain and lower caries experience. The microflora of this deposit is dominated by Actinomyces spp. and has lower cariogenic potential than nondiscolored dental plaque. Iron/copper and sulfur complexes are thought to be responsible for the dark color. In patients with black stain saliva has higher calcium concentrations and higher buffering capacity. Factors such as dietary habits, socioeconomic status, and iron supplementation may be contributing to the formation of black stain.

  16. [Morphology and diagnosis of the oral protozoans Trichomonas tenax and Entamoeba gingivalis using the Giemsa-Romanovsky stain].

    Science.gov (United States)

    Vráblic, J; Vodrázka, J; Tomová, S; Staník, R; Catár, G

    1998-11-01

    In the microscopic diagnosis of Trichomonas tenax and Entamoeba gingivalis is the technically and time not demanding native preparation of a culture, in which both protozoans can be detected according to their typical motility, determining. In the permanent preparation of the culture stained according to Giemsa-Romanovsky, which has also documentary character, are all of the characteristic cell organelles stainable, enabling so their detection without their typical motility. Staining according to Giemsa-Romanovsky is technically simple and not time consuming, not very laborious, low cost and the coloration is permanent, that means optimal for the diagnostic of oral protozoans in permanent preparations. (Fig. 5, Ref. 4.)

  17. 基于SMAC的无线传感器网络MAC协议的分析与优化%Analysis and Optimization of MAC Protocol of SMAC-based Wireless Sensor Network

    Institute of Scientific and Technical Information of China (English)

    赵雪莹

    2011-01-01

    首先对MAC协议进行了相关介绍.然后重点介绍了一种基于竞争的无线传感器网络MAC层协议S-MAC协议.其核心是提出了一种新的无线传感器网络的MAC协议设计方案.基于动态调整占空比的思想,提出了ATC-SMAC协议.该协议在S-MAC协议的基础上改进了固定占空比的劣势,根据每个节点上的数据包的平均延迟调整占空比.通过动态地调整每个节点的占空比,使不同流量的节点拥有不同的工作时间,协议根据不同节点的流量情况自适应地对其占空比进行调整.经过仿真试验,得到ATC-MAC在网络端对端延迟、能量消耗以及吞吐量方面较S-MAC协议都有比较明显的提高.%The MAC protocol is introduced. A wireless sensor network MAC layer protocol based on competition named S-MAC protocol is analyzed. The core of this paper is the design scheme of MAC protocol of a new wireless sensor network, and the ATC-SMAC protocol based on the dynamic adjustment of duty cycle is proposed. This protocol improved the disadvantages of fixed duty cycle of S-MAC, and used the strategy of adjusting the duty cycle according to average packet delay on one node. Nodes with different traffic owned different work time according the duty cycle dynamic adjustment of each node. The protocol dynamically adjusted the duty cycle according to the traffic of each node. According to the simulation, the ATC-MAC is better than S-MAC in end to end delay, energy consumption and throughput.

  18. Composing Interfering Abstract Protocols

    Science.gov (United States)

    2016-04-01

    Fähndrich and K. R. M. Leino. Heap monotonic typestate. In IWACO 2003. [11] X. Feng. Local rely-guarantee reasoning . In POPL ’09. [12] T. Freeman...While protocol-based techniques to reason about interference abound, they do not address two practical concerns: the decidability of protocol...46 C Examples using Informal Extensions 48 C.1 Monotonic Counter

  19. Optimization of Solid-state Fermentation for Two Streptomyces Stains Against Banana Fusarium Wilt and Selection of Its Additive%2株抗香蕉枯萎病菌链霉菌固态发酵工艺的优化及混合菌载体的选择

    Institute of Scientific and Technical Information of China (English)

    莫坤联; 曾涛; 陈汉清; 郭刚; 曾会才

    2013-01-01

      将具有抗香蕉枯萎病菌活性链霉菌通过固体发酵的优化,提高其菌丝生长以及孢子产量,并选择合适的吸附载体,为后期的香蕉枯萎病大田生物防治研究提供技术基础。采用单因子和4因子3水平正交试验法优化白刺链霉菌BWL15-4菌株及不吸水链霉菌BWL58菌株的固态法发酵培养基配方,通过单因子试验探讨了初始pH、接种量以及培养温度对2株菌生长情况的影响,并以孢子存活量多少确定了混合菌株的最适载体。BWL58优化后的固态发酵条件为:pH 7.0左右,接种量2%,发酵温度28℃。培养基配方为:无机盐水占大米重量的150%,黄豆粉占大米重量的5%,麸皮占大米重量的20%,沙土占大米重量的30%。BWL15-4优化后的固体发酵条件为:初始pH 6.3左右,接种量3%,发酵温度29.5℃。培养基配方为无机盐水占大米重量的130%,黄豆粉占大米重量的10%,麸皮占大米重量的20%,沙土占大米重量的20%。按照此优化条件进行固态发酵,白刺链霉菌BWL58菌株及不吸水链霉菌BWL15-4菌株孢子含量可分别达到1013 cfu/g和1012 cfu/g数量级以上。从面粉、高岭土、非耕作层土中通过筛选得到了混合菌的最佳填料为非耕作层。当非耕作层土与混合菌以2:1的比例混合时,在常温下保存3个月后,孢子数只降低一个数量级。%In this study, the solid-state fermentation conditions of two isolates that against Fusarium oxysporum f. sp. Cubense causing banana panama wilt were optimized. The purpose of this project was to increase the yield of mycelium and spores; the additive was optimized as well, for the biological control of banana panama wilt. The optimization of media for the isolates was by the 4 factors 3 levels orthogonal experiments, and their solid-state fermentation conditions was performed by determining the effects of pH, amount of inoculums, and temperature designed by

  20. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...... as possible. Evaluations show that the proposed protocol provides considerable gains over the standard tree splitting protocol applying SIC. The improvement comes at the expense of an increased feedback and receiver complexity....

  1. AUTOMATED ASSESSMENT OF EPIDERMAL THICKNESS AND VASCULAR DENSITY OF PORT WINE STAINS OCT IMAGE

    Directory of Open Access Journals (Sweden)

    CHENGMING WANG

    2014-01-01

    Full Text Available Optical coherence tomography (OCT enables in vivo imaging of port wine stains (PWS lesions. The knowledge of vascular structure and epidermal thickness (ET of PWS may aid the objective diagnosis and optimal treatment. To obtain the structural parameters more rapidly and avoid user intervention, an automated algorithm of energy map is introduced based on intensity and edge information to extract the skin surface using dynamic programming method. Subsequently, an averaged A-scan analysis is performed to obtain the mean ET and the relative intensity of dermis indicating the corresponding vascular density. This approach is currently successfully applied in clinical diagnosis and shows promising guidance and assessment of PDT treatment.

  2. VITRAIL: Acquisition, Modeling, and Rendering of Stained Glass.

    Science.gov (United States)

    Thanikachalam, Niranjan; Baboulaz, Loic; Prandoni, Paolo; Trumpler, Stefan; Wolf, Sophie; Vetterli, Martin

    2016-10-01

    Stained glass windows are designed to reveal their powerful artistry under diverse and time-varying lighting conditions; virtual relighting of stained glass, therefore, represents an exceptional tool for the appreciation of this age old art form. However, as opposed to most other artifacts, stained glass windows are extremely difficult if not impossible to analyze using controlled illumination because of their size and position. In this paper, we present novel methods built upon image based priors to perform virtual relighting of stained glass artwork by acquiring the actual light transport properties of a given artifact. In a preprocessing step, we build a material-dependent dictionary for light transport by studying the scattering properties of glass samples in a laboratory setup. We can now use the dictionary to recover a light transport matrix in two ways: under controlled illuminations the dictionary constitutes a sparsifying basis for a compressive sensing acquisition, while in the case of uncontrolled illuminations the dictionary is used to perform sparse regularization. The proposed basis preserves volume impurities and we show that the retrieved light transport matrix is heterogeneous, as in the case of real world objects. We present the rendering results of several stained glass artifacts, including the Rose Window of the Cathedral of Lausanne, digitized using the presented methods.

  3. Catalytic activity in individual cracking catalyst particles imaged throughout different life stages by selective staining

    Science.gov (United States)

    Buurmans, Inge L. C.; Ruiz-Martínez, Javier; Knowles, William V.; van der Beek, David; Bergwerff, Jaap A.; Vogt, Eelco T. C.; Weckhuysen, Bert M.

    2011-11-01

    Fluid catalytic cracking (FCC) is the major conversion process used in oil refineries to produce valuable hydrocarbons from crude oil fractions. Because the demand for oil-based products is ever increasing, research has been ongoing to improve the performance of FCC catalyst particles, which are complex mixtures of zeolite and binder materials. Unfortunately, there is limited insight into the distribution and activity of individual zeolitic domains at different life stages. Here we introduce a staining method to visualize the structure of zeolite particulates and other FCC components. Brønsted acidity maps have been constructed at the single particle level from fluorescence microscopy images. By applying a statistical methodology to a series of catalysts deactivated via industrial protocols, a correlation is established between Brønsted acidity and cracking activity. The generally applicable method has clear potential for catalyst diagnostics, as it determines intra- and interparticle Brønsted acidity distributions for industrial FCC materials.

  4. Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

    Science.gov (United States)

    Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

    2013-01-01

    Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

  5. A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis

    Science.gov (United States)

    Gering, E.; Atkinson, C.T.

    2004-01-01

    Measures of parasitemia by intraerythrocytic hematozoan parasites are normally expressed as the number of infected erythrocytes per n erythrocytes and are notoriously tedious and time consuming to measure. We describe a protocol for generating rapid counts of nucleated erythrocytes from digital micrographs of thin blood smears that can be used to estimate intensity of hematozoan infections in nonmammalian vertebrate hosts. This method takes advantage of the bold contrast and relatively uniform size and morphology of erythrocyte nuclei on Giemsa-stained blood smears and uses ImageJ, a java-based image analysis program developed at the U.S. National Institutes of Health and available on the internet, to recognize and count these nuclei. This technique makes feasible rapid and accurate counts of total erythrocytes in large numbers of microscope fields, which can be used in the calculation of peripheral parasitemias in low-intensity infections.

  6. Computer-aided diagnosis system for classifying benign and malignant thyroid nodules in multi-stained FNAB cytological images.

    Science.gov (United States)

    Gopinath, Balasubramanian; Shanthi, Natesan

    2013-06-01

    An automated computer-aided diagnosis system is developed to classify benign and malignant thyroid nodules using multi-stained fine needle aspiration biopsy (FNAB) cytological images. In the first phase, the image segmentation is performed to remove the background staining information and retain the appropriate foreground cell objects in cytological images using mathematical morphology and watershed transform segmentation methods. Subsequently, statistical features are extracted using two-level discrete wavelet transform (DWT) decomposition, gray level co-occurrence matrix (GLCM) and Gabor filter based methods. The classifiers k-nearest neighbor (k-NN), Elman neural network (ENN) and support vector machine (SVM) are tested for classifying benign and malignant thyroid nodules. The combination of watershed segmentation, GLCM features and k-NN classifier results a lowest diagnostic accuracy of 60 %. The highest diagnostic accuracy of 93.33 % is achieved by ENN classifier trained with the statistical features extracted by Gabor filter bank from the images segmented by morphology and watershed transform segmentation methods. It is also observed that SVM classifier results its highest diagnostic accuracy of 90 % for DWT and Gabor filter based features along with morphology and watershed transform segmentation methods. The experimental results suggest that the developed system with multi-stained thyroid FNAB images would be useful for identifying thyroid cancer irrespective of staining protocol used.

  7. IPv6 Protocol Analyzer

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    With the emerging of next generation Intemet protocol (IPv6), it is expected to replace the current version of Internet protocol (IPv4) that will be exhausted in the near future. Besides providing adequate address space, some other new features are included into the new 128 bits of IP such as IP auto configuration, quality of service, simple routing capability, security, mobility and multicasting. The current protocol analyzer will not be able to handle IPv6 packets. This paper will focus on developing protocol analyzer that decodes IPv6 packet. IPv6 protocol analyzer is an application module,which is able to decode the IPv6 packet and provide detail breakdown of the construction of the packet. It has to understand the detail construction of the IPv6, and provide a high level abstraction of bits and bytes of the IPv6 packet.Thus it increases network administrators' understanding of a network protocol,helps he/she in solving protocol related problem in a IPv6 network environment.

  8. Sperm viability staining in ecology and evolution: potential pitfalls

    DEFF Research Database (Denmark)

    Holman, Luke

    2009-01-01

    The causes and consequences of variation in sperm quality, survival and ageing are active areas of research in ecology and evolution. In order to address these topics, many recent studies have measured sperm viability using fluorescent staining. Although sperm viability staining has produced...... a number of interesting results, it has some potential pitfalls that have rarely been discussed. In the present paper, I review the major findings of ecology and evolution studies employing sperm viability staining and outline the method's principle limitations. The key problem is that the viability assay...... may itself kill sperm, which is likely to confound many common experimental designs in addition to producing artificially low estimates of sperm viability. I further suggest that sperm number should be routinely measured in sperm viability studies, as it may be an important but overlooked source...

  9. A cytokeratin- and calretinin-negative staining sarcomatoid malignant mesothelioma.

    Science.gov (United States)

    Hurtuk, Michael G; Carbone, Michele

    2004-01-01

    Malignant Mesothelioma, or mesothelioma, is a mesothelial-based malignancy that may occur in the pleura, pericardium and peritoneum. Mesothelioma is a very aggressive cancer with limited treatment, and a median survival of about 1 year. At times, the diagnosis of mesothelioma may be problematic. The final diagnosis of mesothelioma relies on histology and often is dependent upon immunohistochemistry. It is generally assumed that mesotheliomas must stain positive for cytokeratin and calretinin and negative staining for these markers would rule out the diagnosis. We encountered a patient with a pleural-based, cytokeratin- and calretinin-negative sarcomatoid malignancy. These negative stainings would rule out the diagnosis of mesothelioma but, after careful consideration of the patient's clinical records, and additional histological and immunohistochemical studies, we conclude that this patient suffered from mesothelioma of the sarcomatoid type.

  10. MEGARA Optics: stain removal in PBM2Y prisms

    Science.gov (United States)

    Aguirre-Aguirre, D.; Izazaga-Pérez, R.; Villalobos-Mendoza, B.; Carrasco, E.; Gil de Paz, A.; Gallego, J.; Iglesias, J.

    2017-01-01

    MEGARA is the new integral-field and multi-object optical spectrograph for the GTC. For medium and high resolution, the dispersive elements are volume phase holographic gratings, sandwiched between two flat windows and two prisms of high optical precision. The prisms are made of Ohara PBM2Y optical glass. After the prisms polishing process, some stains appeared on the surfaces. For this, in this work is shown the comparative study of five different products (muriatic acid, paint remover, sodium hydroxide, aqua regia and rare earth liquid polish) used for trying to eliminate the stains of the HR MEGARA prisms. It was found that by polishing with the hands the affected area, and using a towel like a kind of pad, and polish during five minutes using rare earth, the stains disappear completely affecting only a 5% the rms of the surface quality. Not so the use of the other products that did not show any apparent result.

  11. Chromosome-specific staining to detect genetic rearrangements

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

    2013-04-09

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  12. Chromosome-specific staining to detect genetic rearrangements

    Science.gov (United States)

    Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

    2013-04-09

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  13. Stain-free histopathology by programmable supercontinuum pulses

    Science.gov (United States)

    Tu, Haohua; Liu, Yuan; Turchinovich, Dmitry; Marjanovic, Marina; Lyngsø, Jens K.; Lægsgaard, Jesper; Chaney, Eric J.; Zhao, Youbo; You, Sixian; Wilson, William L.; Xu, Bingwei; Dantus, Marcos; Boppart, Stephen A.

    2016-08-01

    The preparation, staining, visualization and interpretation of histological images of tissue is well accepted as the gold standard process for the diagnosis of disease. These methods have a long history of development, and are used ubiquitously in pathology, despite being highly time- and labour-intensive. Here, we introduce a unique optical imaging platform and methodology for label-free multimodal multiphoton microscopy that uses a novel photonic-crystal fibre source to generate tailored chemical contrast based on programmable supercontinuum pulses. We demonstrate the collection of optical signatures of the tumour microenvironment, including evidence of mesoscopic biological organization, tumour cell migration and (lymph-) angiogenesis collected directly from fresh ex vivo mammary tissue. Acquisition of these optical signatures and other cellular or extracellular features, which are largely absent from histologically processed and stained tissue, combined with an adaptable platform for optical alignment-free programmable-contrast imaging, offers the potential to translate stain-free molecular histopathology into routine clinical use.

  14. Effectiveness and mode of action of whitening dentifrices on enamel extrinsic stains.

    Science.gov (United States)

    Alshara, Salem; Lippert, Frank; Eckert, George J; Hara, Anderson T

    2014-01-01

    This study was conducted in order to investigate the mode of action and the whitening effect of whitening dentifrices. Two hundred fifty-six bovine enamel specimens (10 × 10 mm(2)) were prepared, partially stained, and assigned into eight groups (n = 32): six whitening dentifrices, one nonwhitening and deionized water (negative control), and further divided in two subgroups (n = 16), according to the test model: chemical (dentifrice slurry treatment only) or chemo-mechanical (slurry + toothbrushing). Specimens were treated w