Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities

DEFF Research Database (Denmark)

Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.

2017-01-01

Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...

Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells

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Isabel Correa

2018-03-01

Full Text Available Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1 specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.

Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells.

Science.gov (United States)

Correa, Isabel; Ilieva, Kristina M; Crescioli, Silvia; Lombardi, Sara; Figini, Mariangela; Cheung, Anthony; Spicer, James F; Tutt, Andrew N J; Nestle, Frank O; Karagiannis, Panagiotis; Lacy, Katie E; Karagiannis, Sophia N

2018-01-01

Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires.

Evaluation of Antigen-Conjugated Fluorescent Beads to Identify Antigen-Specific B Cells

Science.gov (United States)

Correa, Isabel; Ilieva, Kristina M.; Crescioli, Silvia; Lombardi, Sara; Figini, Mariangela; Cheung, Anthony; Spicer, James F.; Tutt, Andrew N. J.; Nestle, Frank O.; Karagiannis, Panagiotis; Lacy, Katie E.; Karagiannis, Sophia N.

2018-01-01

Selection of single antigen-specific B cells to identify their expressed antibodies is of considerable interest for evaluating human immune responses. Here, we present a method to identify single antibody-expressing cells using antigen-conjugated fluorescent beads. To establish this, we selected Folate Receptor alpha (FRα) as a model antigen and a mouse B cell line, expressing both the soluble and the membrane-bound forms of a human/mouse chimeric antibody (MOv18 IgG1) specific for FRα, as test antibody-expressing cells. Beads were conjugated to FRα using streptavidin/avidin-biotin bridges and used to select single cells expressing the membrane-bound form of anti-FRα. Bead-bound cells were single cell-sorted and processed for single cell RNA retrotranscription and PCR to isolate antibody heavy and light chain variable regions. Variable regions were then cloned and expressed as human IgG1/k antibodies. Like the original clone, engineered antibodies from single cells recognized native FRα. To evaluate whether antigen-coated beads could identify specific antibody-expressing cells in mixed immune cell populations, human peripheral blood mononuclear cells (PBMCs) were spiked with test antibody-expressing cells. Antigen-specific cells could comprise up to 75% of cells selected with antigen-conjugated beads when the frequency of the antigen-positive cells was 1:100 or higher. In PBMC pools, beads conjugated to recombinant antigens FRα and HER2 bound antigen-specific anti-FRα MOv18 and anti-HER2 Trastuzumab antibody-expressing cells, respectively. From melanoma patient-derived B cells selected with melanoma cell line-derived protein-coated fluorescent beads, we generated a monoclonal antibody that recognized melanoma antigen-coated beads. This approach may be further developed to facilitate analysis of B cells and their antibody profiles at the single cell level and to help unravel humoral immune repertoires. PMID:29628923

Identifying Emerging Trends of Financial Business Method Patents

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Won Sang Lee

2017-09-01

Full Text Available Financial technology has become an important part of the banking industry in recent times. This study attempts to propose a framework to identify emerging areas and trends using financial business method patents. Based on the abstracts of financial business method patents registered at the United States Patent and Trademark Office, this study first applies latent Dirichlet allocation to identify emerging topics. The probability of the annual occurrence of each topic is adjusted through the exponentially weighted moving average to reflect the importance of the recent probability of topics. Each topic is classified as “hot” or “cold” depending on whether the exponentially weighted moving average of the probabilities exceeds the threshold. We applied survival analysis to the time gap of recurrently becoming hot from a cold status with the associated factor of financial business method patents. The findings suggest that the topic with the short granted period and high forward citation is likely to become hot. In addition, the topic that is aged and specific in narrow areas is likely to continuously change into the hot or cold status. The approach proposed in this study contributes toward understanding topic emergence in the financial area and pursuing sustainable development.

Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.

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Sedaghat, Nafiseh; Fathy, Mahmood; Modarressi, Mohammad Hossein; Shojaie, Ali

2016-09-07

Testicular cancer is the most common cancer in men aged between 15 and 35 and more than 90% of testicular neoplasms are originated at germ cells. Recent research has shown the impact of microRNAs (miRNAs) in different types of cancer, including testicular germ cell tumor (TGCT). MicroRNAs are small non-coding RNAs which affect the development and progression of cancer cells by binding to mRNAs and regulating their expressions. The identification of functional miRNA-mRNA interactions in cancers, i.e. those that alter the expression of genes in cancer cells, can help delineate post-regulatory mechanisms and may lead to new treatments to control the progression of cancer. A number of sequence-based methods have been developed to predict miRNA-mRNA interactions based on the complementarity of sequences. While necessary, sequence complementarity is, however, not sufficient for presence of functional interactions. Alternative methods have thus been developed to refine the sequence-based interactions using concurrent expression profiles of miRNAs and mRNAs. This study aims to find functional cancer-specific miRNA-mRNA interactions in TGCT. To this end, the sequence-based predicted interactions are first refined using an ensemble learning method, based on two well-known methods of learning miRNA-mRNA interactions, namely, TaLasso and GenMiR++. Additional functional analyses were then used to identify a subset of interactions to be most likely functional and specific to TGCT. The final list of 13 miRNA-mRNA interactions can be potential targets for identifying TGCT-specific interactions and future laboratory experiments to develop new therapies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Using network screening methods to determine locations with specific safety issues: A design consistency case study.

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Butsick, Andrew J; Wood, Jonathan S; Jovanis, Paul P

2017-09-01

The Highway Safety Manual provides multiple methods that can be used to identify sites with promise (SWiPs) for safety improvement. However, most of these methods cannot be used to identify sites with specific problems. Furthermore, given that infrastructure funding is often specified for use related to specific problems/programs, a method for identifying SWiPs related to those programs would be very useful. This research establishes a method for Identifying SWiPs with specific issues. This is accomplished using two safety performance functions (SPFs). This method is applied to identifying SWiPs with geometric design consistency issues. Mixed effects negative binomial regression was used to develop two SPFs using 5 years of crash data and over 8754km of two-lane rural roadway. The first SPF contained typical roadway elements while the second contained additional geometric design consistency parameters. After empirical Bayes adjustments, sites with promise (SWiPs) were identified. The disparity between SWiPs identified by the two SPFs was evident; 40 unique sites were identified by each model out of the top 220 segments. By comparing sites across the two models, candidate road segments can be identified where a lack design consistency may be contributing to an increase in expected crashes. Practitioners can use this method to more effectively identify roadway segments suffering from reduced safety performance due to geometric design inconsistency, with detailed engineering studies of identified sites required to confirm the initial assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

High-Throughput Screening to Identify Regulators of Meiosis-Specific Gene Expression in Saccharomyces cerevisiae.

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Kassir, Yona

2017-01-01

Meiosis and gamete formation are processes that are essential for sexual reproduction in all eukaryotic organisms. Multiple intracellular and extracellular signals feed into pathways that converge on transcription factors that induce the expression of meiosis-specific genes. Once triggered the meiosis-specific gene expression program proceeds in a cascade that drives progress through the events of meiosis and gamete formation. Meiosis-specific gene expression is tightly controlled by a balance of positive and negative regulatory factors that respond to a plethora of signaling pathways. The budding yeast Saccharomyces cerevisiae has proven to be an outstanding model for the dissection of gametogenesis owing to the sophisticated genetic manipulations that can be performed with the cells. It is possible to use a variety selection and screening methods to identify genes and their functions. High-throughput screening technology has been developed to allow an array of all viable yeast gene deletion mutants to be screened for phenotypes and for regulators of gene expression. This chapter describes a protocol that has been used to screen a library of homozygous diploid yeast deletion strains to identify regulators of the meiosis-specific IME1 gene.

Identifying States along the Hematopoietic Stem Cell Differentiation Hierarchy with Single Cell Specificity via Raman Spectroscopy.

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Ilin, Yelena; Choi, Ji Sun; Harley, Brendan A C; Kraft, Mary L

2015-11-17

A major challenge for expanding specific types of hematopoietic cells ex vivo for the treatment of blood cell pathologies is identifying the combinations of cellular and matrix cues that direct hematopoietic stem cells (HSC) to self-renew or differentiate into cell populations ex vivo. Microscale screening platforms enable minimizing the number of rare HSCs required to screen the effects of numerous cues on HSC fate decisions. These platforms create a strong demand for label-free methods that accurately identify the fate decisions of individual hematopoietic cells at specific locations on the platform. We demonstrate the capacity to identify discrete cells along the HSC differentiation hierarchy via multivariate analysis of Raman spectra. Notably, cell state identification is accurate for individual cells and independent of the biophysical properties of the functionalized polyacrylamide gels upon which these cells are cultured. We report partial least-squares discriminant analysis (PLS-DA) models of single cell Raman spectra enable identifying four dissimilar hematopoietic cell populations across the HSC lineage specification. Successful discrimination was obtained for a population enriched for long-term repopulating HSCs (LT-HSCs) versus their more differentiated progeny, including closely related short-term repopulating HSCs (ST-HSCs) and fully differentiated lymphoid (B cells) and myeloid (granulocytes) cells. The lineage-specific differentiation states of cells from these four subpopulations were accurately identified independent of the stiffness of the underlying biomaterial substrate, indicating subtle spectral variations that discriminated these populations were not masked by features from the culture substrate. This approach enables identifying the lineage-specific differentiation stages of hematopoietic cells on biomaterial substrates of differing composition and may facilitate correlating hematopoietic cell fate decisions with the extrinsic cues that

Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities.

Science.gov (United States)

Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B; Papamarkou, Theodore; Huber, Kilian V M; Mutz, Cornelia; Toretsky, Jeffrey A; Bennett, Keiryn L; Olsen, Jesper V; Brunak, Søren; Kovar, Heinrich; Superti-Furga, Giulio

2017-01-01

Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes. Using a multilevel experimental approach including quantitative phosphoproteomics, we analyzed the molecular rationale behind the disease-specific synergistic effect of simultaneous application of PKC412 and IGF1R inhibitors. The mechanism of the drug synergy between these inhibitors is different from the sum of the mechanisms of the single agents. The combination effectively inhibited pathway crosstalk and averted feedback loop repression, in EWS-FLI1-dependent manner. Mol Cancer Ther; 16(1); 88-101. ©2016 AACR. ©2016 American Association for Cancer Research.

Tissue-type-specific transcriptome analysis identifies developing xylem-specific promoters in poplar.

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Ko, Jae-Heung; Kim, Hyun-Tae; Hwang, Ildoo; Han, Kyung-Hwan

2012-06-01

Plant biotechnology offers a means to create novel phenotypes. However, commercial application of biotechnology in crop improvement programmes is severely hindered by the lack of utility promoters (or freedom to operate the existing ones) that can drive gene expression in a tissue-specific or temporally controlled manner. Woody biomass is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, developing xylem (DX)-specific modification of the feedstock is highly desirable. To develop utility promoters that can drive transgene expression in a DX-specific manner, we used the Affymetrix Poplar Genome Arrays to obtain tissue-type-specific transcriptomes from poplar stems. Subsequent bioinformatics analysis identified 37 transcripts that are specifically or strongly expressed in DX cells of poplar. After further confirmation of their DX-specific expression using semi-quantitative PCR, we selected four genes (DX5, DX8, DX11 and DX15) for in vivo confirmation of their tissue-specific expression in transgenic poplars. The promoter regions of the selected DX genes were isolated and fused to a β-glucuronidase (GUS)-reported gene in a binary vector. This construct was used to produce transgenic poplars via Agrobacterium-mediated transformation. The GUS expression patterns of the resulting transgenic plants showed that these promoters were active in the xylem cells at early seedling growth and had strongest expression in the developing xylem cells at later growth stages of poplar. We conclude that these DX promoters can be used as a utility promoter for DX-specific biomass engineering. © 2012 The Authors. Plant Biotechnology Journal © 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

Methods To Identify Aptamers against Cell Surface Biomarkers

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Frédéric Ducongé

2011-09-01

Full Text Available Aptamers are nucleic acid-based ligands identified through a process of molecular evolution named SELEX (Systematic Evolution of Ligands by Exponential enrichment. During the last 10-15 years, numerous aptamers have been developed specifically against targets present on or associated with the surface of human cells or infectious pathogens such as viruses, bacteria, fungi or parasites. Several of the aptamers have been described as potent probes, rivalling antibodies, for use in flow cytometry or microscopy. Some have also been used as drugs by inhibiting or activating functions of their targets in a manner similar to neutralizing or agonistic antibodies. Additionally, it is straightforward to conjugate aptamers to other agents without losing their affinity and they have successfully been used in vitro and in vivo to deliver drugs, siRNA, nanoparticles or contrast agents to target cells. Hence, aptamers identified against cell surface biomarkers represent a promising class of ligands. This review presents the different strategies of SELEX that have been developed to identify aptamers for cell surface-associated proteins as well as some of the methods that are used to study their binding on living cells.

A comparison study of size-specific dose estimate calculation methods

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Parikh, Roshni A. [Rainbow Babies and Children' s Hospital, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Department of Radiology, Cleveland, OH (United States); University of Michigan Health System, Department of Radiology, Ann Arbor, MI (United States); Wien, Michael A.; Jordan, David W.; Ciancibello, Leslie; Berlin, Sheila C. [Rainbow Babies and Children' s Hospital, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Department of Radiology, Cleveland, OH (United States); Novak, Ronald D. [Rainbow Babies and Children' s Hospital, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Department of Radiology, Cleveland, OH (United States); Rebecca D. Considine Research Institute, Children' s Hospital Medical Center of Akron, Center for Mitochondrial Medicine Research, Akron, OH (United States); Klahr, Paul [CT Clinical Science, Philips Healthcare, Highland Heights, OH (United States); Soriano, Stephanie [Rainbow Babies and Children' s Hospital, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Department of Radiology, Cleveland, OH (United States); University of Washington, Department of Radiology, Seattle, WA (United States)

2018-01-15

The size-specific dose estimate (SSDE) has emerged as an improved metric for use by medical physicists and radiologists for estimating individual patient dose. Several methods of calculating SSDE have been described, ranging from patient thickness or attenuation-based (automated and manual) measurements to weight-based techniques. To compare the accuracy of thickness vs. weight measurement of body size to allow for the calculation of the size-specific dose estimate (SSDE) in pediatric body CT. We retrospectively identified 109 pediatric body CT examinations for SSDE calculation. We examined two automated methods measuring a series of level-specific diameters of the patient's body: method A used the effective diameter and method B used the water-equivalent diameter. Two manual methods measured patient diameter at two predetermined levels: the superior endplate of L2, where body width is typically most thin, and the superior femoral head or iliac crest (for scans that did not include the pelvis), where body width is typically most thick; method C averaged lateral measurements at these two levels from the CT projection scan, and method D averaged lateral and anteroposterior measurements at the same two levels from the axial CT images. Finally, we used body weight to characterize patient size, method E, and compared this with the various other measurement methods. Methods were compared across the entire population as well as by subgroup based on body width. Concordance correlation (ρ{sub c}) between each of the SSDE calculation methods (methods A-E) was greater than 0.92 across the entire population, although the range was wider when analyzed by subgroup (0.42-0.99). When we compared each SSDE measurement method with CTDI{sub vol,} there was poor correlation, ρ{sub c}<0.77, with percentage differences between 20.8% and 51.0%. Automated computer algorithms are accurate and efficient in the calculation of SSDE. Manual methods based on patient thickness provide

Recent advances in cross-cultural measurement in psychiatric epidemiology: utilizing 'what matters most' to identify culture-specific aspects of stigma.

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Yang, Lawrence Hsin; Thornicroft, Graham; Alvarado, Ruben; Vega, Eduardo; Link, Bruce George

2014-04-01

While stigma measurement across cultures has assumed growing importance in psychiatric epidemiology, it is unknown to what extent concepts arising from culture have been incorporated. We utilize a formulation of culture-as the everyday interactions that 'matter most' to individuals within a cultural group-to identify culturally-specific stigma dynamics relevant to measurement. A systematic literature review from January 1990 to September 2012 was conducted using PsycINFO, Medline and Google Scholar to identify articles studying: (i) mental health stigma-related concepts; (ii) ≥ 1 non-Western European cultural group. From 5292 abstracts, 196 empirical articles were located. The vast majority of studies (77%) utilized adaptations of existing Western-developed stigma measures to new cultural groups. Extremely few studies (2.0%) featured quantitative stigma measures derived within a non-Western European cultural group. A sizeable amount (16.8%) of studies employed qualitative methods to identify culture-specific stigma processes. The 'what matters most' perspective identified cultural ideals of the everyday activities that comprise 'personhood' of 'preserving lineage' among specific Asian groups, 'fighting hard to overcome problems and taking advantage of immigration opportunities' among specific Latino-American groups, and 'establishing trust among religious institutions due to institutional discrimination' among African-American groups. These essential cultural interactions shaped culture-specific stigma manifestations. Mixed method studies (3.6%) corroborated these qualitative results. Quantitatively-derived, culturally-specific stigma measures were lacking. Further, the vast majority of qualitative studies on stigma were conducted without using stigma-specific frameworks. We propose the 'what matters most' approach to address this key issue in future research.

Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA

Science.gov (United States)

Periasamy, Vengadesh; Rizan, Nastaran; Al-Ta’ii, Hassan Maktuff Jaber; Tan, Yee Shin; Tajuddin, Hairul Annuar; Iwamoto, Mitsumasa

2016-01-01

The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology. PMID:27435636

Building America Guidance for Identifying and Overcoming Code, Standard, and Rating Method Barriers

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Cole, P. C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Halverson, M. A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2013-09-01

This guidance document was prepared using the input from the meeting summarized in the draft CSI Roadmap to provide Building America research teams and partners with specific information and approaches to identifying and overcoming potential barriers to Building America innovations arising in and/or stemming from codes, standards, and rating methods.

Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome.

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Matthew R Mason

Full Text Available Oral infections have a strong ethnic predilection; suggesting that ethnicity is a critical determinant of oral microbial colonization. Dental plaque and saliva samples from 192 subjects belonging to four major ethnicities in the United States were analyzed using terminal restriction fragment length polymorphism (t-RFLP and 16S pyrosequencing. Ethnicity-specific clustering of microbial communities was apparent in saliva and subgingival biofilms, and a machine-learning classifier was capable of identifying an individual's ethnicity from subgingival microbial signatures. The classifier identified African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity. The data demonstrates a significant association between ethnic affiliation and the composition of the oral microbiome; to the extent that these microbial signatures appear to be capable of discriminating between ethnicities.

PCR-RFLP Method to Identify Salmonid Species of Economic Importance

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Andreea Dudu

2011-05-01

Full Text Available The identification of different fish species by molecular methods has become necessary to avoid both the incorrect labelling of individuals involved in repopulation programmes and the commercial frauds on the fish market. Different fish species of great economical importance, like the salmonids, which are very much requested for their meat, can be identified using molecular techniques such as PCR-RFLP. The method is based on the amplification of a target region from the genome by PCR reaction followed by endonucleases digestion to detect the polymorphism of restriction fragments. In our study we analysed the following salmonid species from Romania: Salmo trutta fario, Salmo labrax, Salvelinus fontinalis, Onchorhynchus mykiss, Thymallus thymallus and Hucho hucho. In order to discriminate between the analysed species we amplified a fragment of mitochondrial genome comprising tRNAGlu/ cytochrome b/ tRNAThr/ tRNAPro/ D-loop/ tRNAPhe, followed by digestion with a specific restriction enzyme. The direct digestion of unpurified PCR products generated species-specific restriction patterns and proved to be a simple, reliable, inexpensive and fast method. Thus, it may be successfully utilized in specialized laboratories for the correct identification of the fish species for multiple purposes, including the traceability of fish food products.

PCR-RFLP diagnostic method for identifying Globodera species in Slovenia

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Sasa ŠIRCA

2011-01-01

Full Text Available Species identification within the genus Globodera is based on the morphological and morphometrical characters of the cysts and second stage juveniles, and these are included in the majority of identification keys. Morphometrical methods are fast and can be applied to most of samples but they demand a trained and experienced specialist. Furthermore, some morphometrical characters may overlap between populations and beetwen species, leading to inaccurate identification. To confirm and complement the morphometrical identification of Globodera species molecular methods have been developed. Sequences of the internal transcribed spacer regions ITS1 and ITS2 of the rDNA gene cluster proved to be useful for identifying nematode species identification. A PCR-RFLP molecular method was used to identify Globodera rostochiensis, G. pallida, G. tabacum and G. achilleae. Globodera rostochiensis, G. pallida, G. tabacum and G. achilleae can be distinguished with PCR-RFLP analysis of the rDNA ITS fragment using five restriction enzymes. The RFLP patterns of G. rostochiensis, G. tabacum and G. achilleae were species-specific, while those of G. pallida varied. South American populations of G. pallida differed from other populations as their RFLP patterns were demonstrated to be distinct by in silico restriction of the ITS sequences deposited at NCBI.

Methods to identify the unexplored diversity of microbial exopolysaccharides.

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Rühmann, Broder; Schmid, Jochen; Sieber, Volker

2015-01-01

Microbial exopolysaccharides (EPS) are a structurally very diverse class of molecules. A number of them have found their application in rather diverging fields that extend from medicine, food, and cosmetics on the one side to construction, drilling, and chemical industry on the other side. The analysis of microbial strains for their competence in polysaccharide production has therefore been a major issue in the past, especially in the search for new polysaccharide variants among natural strain isolates. Concerning the fact that nearly all microbes carry the genetic equipment for the production of polysaccharides under specific conditions, the naturally provided EPS portfolio seems to be still massively underexplored. Therefore, there is a need for high throughput screening techniques capable of identifying novel variants of bacterial EPS with properties superior to the already described ones, or even totally new ones. A great variety of different techniques has been used in screening approaches for identifying microorganisms that are producing EPS in substantial amounts. Mucoid growth is often the method of choice for visual identification of EPS producing strains. Depending on the thickening characteristics of the polysaccharide, observation of viscosity in culture broth can also be an option to evaluate EPS production. Precipitation with different alcohols represents a common detection, isolation, and purification method for many EPS. A more quantitative approach is found in the total carbohydrate content analysis, normally determined, e.g., by phenol-sulfuric-acid-method. In addition, recently a new and reliable method for the detailed analysis of the monomeric composition and the presence of rare sugars and sugar substitutions has become available, which could give a first hint of the polymer structure of unknown EPS. This minireview will compare available methods and novel techniques and discuss their benefits and disadvantages.

Methods to identify the unexplored diversity of microbial exopolysaccharides

Directory of Open Access Journals (Sweden)

Broder eRühmann

2015-06-01

Full Text Available Microbial exopolysaccharides (EPS are a structurally very diverse class of molecules. A number of them have found their application in rather diverging fields that extend from medicine, food and cosmetics on the one side to construction, drilling and chemical industry on the other side. The analysis of microbial strains for their competence in polysaccharide production has therefore been a major issue in the past, especially in the search for new polysaccharide variants among natural strain isolates. Concerning the fact that nearly all microbes carry the genetic equipment for the production of polysaccharides under specific conditions, the naturally provided EPS portfolio seems to be still massively underexplored. Therefore, there is a need for high throughput screening techniques capable of identifying novel variants of bacterial exopolysaccharides with properties superior to the already described ones, or even totally new ones. A great variety of different techniques has been used in screening approaches for identifying microorganisms that are producing EPS in substantial amounts. Mucoid growth is often the method of choice for visual identification of EPS producing strains. Depending on the thickening characteristics of the polysaccharide, observation of viscosity in culture broth can also be an option to evaluate EPS production. Precipitation with different alcohols represents a common detection, isolation and purification method for many EPS. A more quantitative approach is found in the total carbohydrate content analysis, normally determined e.g. by phenol-sulfuric-acid-method. In addition, recently a new and reliable method for the detailed analysis of the monomeric composition and the presence of rare sugars and sugar substitutions has become available, which could give a first hint of the polymer structure of unknown EPS. This minireview will compare available methods and novel techniques and discuss their benefits and disadvantages.

Betweenness-Based Method to Identify Critical Transmission Sectors for Supply Chain Environmental Pressure Mitigation.

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Liang, Sai; Qu, Shen; Xu, Ming

2016-02-02

To develop industry-specific policies for mitigating environmental pressures, previous studies primarily focus on identifying sectors that directly generate large amounts of environmental pressures (a.k.a. production-based method) or indirectly drive large amounts of environmental pressures through supply chains (e.g., consumption-based method). In addition to those sectors as important environmental pressure producers or drivers, there exist sectors that are also important to environmental pressure mitigation as transmission centers. Economy-wide environmental pressure mitigation might be achieved by improving production efficiency of these key transmission sectors, that is, using less upstream inputs to produce unitary output. We develop a betweenness-based method to measure the importance of transmission sectors, borrowing the betweenness concept from network analysis. We quantify the betweenness of sectors by examining supply chain paths extracted from structural path analysis that pass through a particular sector. We take China as an example and find that those critical transmission sectors identified by betweenness-based method are not always identifiable by existing methods. This indicates that betweenness-based method can provide additional insights that cannot be obtained with existing methods on the roles individual sectors play in generating economy-wide environmental pressures. Betweenness-based method proposed here can therefore complement existing methods for guiding sector-level environmental pressure mitigation strategies.

Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

Science.gov (United States)

Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

2017-09-05

In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

From viral genome to specific peptide epitopes: methods for identifying porcine T cell epitopes based on in silico predictions, in vitro identification and ex vivo verification

DEFF Research Database (Denmark)

Pedersen, Lasse Eggers; Rasmussen, Michael; Harndah, Mikkel

2013-01-01

to predict likely candidates for peptide-SLA binding. These results were combined with binding predictions generated by the algorithm, NetMHCpan (http://www.cbs.dtu.dk/services/NetMHCpan/) in order to select peptide candidates for in vitro analysis. The correlation between high affinity and high stability.......000 peptides. T cell epitopes were identified using peptide-SLA complexes assembled into fluorescent tetramers to stain swine influenza specific CTLs derived from immunized animals and MHC-defined pigs vaccinated against foot-and-mouth disease virus. These results demonstrate the broad applicability of methods...... originally developed for analysis of human leukocyte antigen (HLA) presentation of peptides. The methods presented provide a timely and cost-effective approach to CTL epitope discovery that can be applied to diseases of swine and of other mammalian species of interest....

Transcriptome Analysis of Mycobacteria-Specific CD4+ T Cells Identified by Activation-Induced Expression of CD154.

Science.gov (United States)

Kunnath-Velayudhan, Shajo; Goldberg, Michael F; Saini, Neeraj K; Johndrow, Christopher T; Ng, Tony W; Johnson, Alison J; Xu, Jiayong; Chan, John; Jacobs, William R; Porcelli, Steven A

2017-10-01

Analysis of Ag-specific CD4 + T cells in mycobacterial infections at the transcriptome level is informative but technically challenging. Although several methods exist for identifying Ag-specific T cells, including intracellular cytokine staining, cell surface cytokine-capture assays, and staining with peptide:MHC class II multimers, all of these have significant technical constraints that limit their usefulness. Measurement of activation-induced expression of CD154 has been reported to detect live Ag-specific CD4 + T cells, but this approach remains underexplored and, to our knowledge, has not previously been applied in mycobacteria-infected animals. In this article, we show that CD154 expression identifies adoptively transferred or endogenous Ag-specific CD4 + T cells induced by Mycobacterium bovis bacillus Calmette-Guérin vaccination. We confirmed that Ag-specific cytokine production was positively correlated with CD154 expression by CD4 + T cells from bacillus Calmette-Guérin-vaccinated mice and show that high-quality microarrays can be performed from RNA isolated from CD154 + cells purified by cell sorting. Analysis of microarray data demonstrated that the transcriptome of CD4 + CD154 + cells was distinct from that of CD154 - cells and showed major enrichment of transcripts encoding multiple cytokines and pathways of cellular activation. One notable finding was the identification of a previously unrecognized subset of mycobacteria-specific CD4 + T cells that is characterized by the production of IL-3. Our results support the use of CD154 expression as a practical and reliable method to isolate live Ag-specific CD4 + T cells for transcriptomic analysis and potentially for a range of other studies in infected or previously immunized hosts. Copyright © 2017 by The American Association of Immunologists, Inc.

Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities

DEFF Research Database (Denmark)

Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B.

2017-01-01

Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any...... including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong...

An HTS-compatible 3D colony formation assay to identify tumor-specific chemotherapeutics.

Science.gov (United States)

Horman, Shane R; To, Jeremy; Orth, Anthony P

2013-12-01

There has been increasing interest in the development of cellular behavior models that take advantage of three-dimensional (3D) cell culture. To enable assessment of differential perturbagen impacts on cell growth in 2D and 3D, we have miniaturized and adapted for high-throughput screening (HTS) the soft agar colony formation assay, employing a laser-scanning cytometer to image and quantify multiple cell types simultaneously. The assay is HTS compatible, providing high-quality, image-based, replicable data for multiple, co-cultured cell types. As proof of concept, we subjected colorectal carcinoma colonies in 3D soft agar to a mini screen of 1528 natural product compounds. Hit compounds from the primary screen were rescreened in an HTS 3D co-culture matrix containing colon stromal cells and cancer cells. By combining tumor cells and normal, nontransformed colon epithelial cells in one primary screening assay, we were able to obtain differential IC50 data, thereby distinguishing tumor-specific compounds from general cytotoxic compounds. Moreover, we were able to identify compounds that antagonized tumor colony formation in 3D only, highlighting the importance of this assay in identifying agents that interfere with 3D tumor structural growth. This screening platform provides a fast, simple, and robust method for identification of tumor-specific agents in a biologically relevant microenvironment.

Hypocretin neuron-specific transcriptome profiling identifies the sleep modulator Kcnh4a.

Science.gov (United States)

Yelin-Bekerman, Laura; Elbaz, Idan; Diber, Alex; Dahary, Dvir; Gibbs-Bar, Liron; Alon, Shahar; Lerer-Goldshtein, Tali; Appelbaum, Lior

2015-10-01

Sleep has been conserved throughout evolution; however, the molecular and neuronal mechanisms of sleep are largely unknown. The hypothalamic hypocretin/orexin (Hcrt) neurons regulate sleep\\wake states, feeding, stress, and reward. To elucidate the mechanism that enables these various functions and to identify sleep regulators, we combined fluorescence cell sorting and RNA-seq in hcrt:EGFP zebrafish. Dozens of Hcrt-neuron-specific transcripts were identified and comprehensive high-resolution imaging revealed gene-specific localization in all or subsets of Hcrt neurons. Clusters of Hcrt-neuron-specific genes are predicted to be regulated by shared transcription factors. These findings show that Hcrt neurons are heterogeneous and that integrative molecular mechanisms orchestrate their diverse functions. The voltage-gated potassium channel Kcnh4a, which is expressed in all Hcrt neurons, was silenced by the CRISPR-mediated gene inactivation system. The mutant kcnh4a (kcnh4a(-/-)) larvae showed reduced sleep time and consolidation, specifically during the night, suggesting that Kcnh4a regulates sleep.

Investigations regarding the lowering of specific intellectual property risks identified in the production process

Directory of Open Access Journals (Sweden)

Pakocs Ramona

2017-01-01

Full Text Available The main purpose of this research is to decrease the emergence of specific intellectual property risks within the production process as well as increasing risk management performance of IP by preventing them. In order to achieve this, previous studies regarding the main specific intellectual property risks from industrial companies were analyzed together with their managerial methods as well as the possibility of reducing their emergence. As a result of the research conducted were identified five types of intellectual property risks that have a high potential of emergence in the production process, namely: the risk of production of goods in violation of IP rights; the know-how, production knowledge and trade secret disclosure risk; the technological risk of unprotected utility models; the technological risk of unprotected integrated circuits topographies and finally the risk of product counterfeit. In order to achieve the main purpose of our investigation, we have proposed new formulas for estimating the specific intellectual property risks identified in the production process. Their purpose was to minimalize the risk’s negative effects on industrial companies and to increase the managerial performance from the intellectual property domain through a new type of management appropriately named: intellectual property management. The research is finalized with a case study regarding the lapse of rights of a patented invention. Based on a case analysis, it was proved that the exploitation of an invention without a contract represents a counterfeit.

SMM-system: A mining tool to identify specific markers in Salmonella enterica.

Science.gov (United States)

Yu, Shuijing; Liu, Weibing; Shi, Chunlei; Wang, Dapeng; Dan, Xianlong; Li, Xiao; Shi, Xianming

2011-03-01

This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html. Copyright © 2011 Elsevier B.V. All rights reserved.

An Efficient Stepwise Statistical Test to Identify Multiple Linked Human Genetic Variants Associated with Specific Phenotypic Traits.

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Iksoo Huh

Full Text Available Recent advances in genotyping methodologies have allowed genome-wide association studies (GWAS to accurately identify genetic variants that associate with common or pathological complex traits. Although most GWAS have focused on associations with single genetic variants, joint identification of multiple genetic variants, and how they interact, is essential for understanding the genetic architecture of complex phenotypic traits. Here, we propose an efficient stepwise method based on the Cochran-Mantel-Haenszel test (for stratified categorical data to identify causal joint multiple genetic variants in GWAS. This method combines the CMH statistic with a stepwise procedure to detect multiple genetic variants associated with specific categorical traits, using a series of associated I × J contingency tables and a null hypothesis of no phenotype association. Through a new stratification scheme based on the sum of minor allele count criteria, we make the method more feasible for GWAS data having sample sizes of several thousands. We also examine the properties of the proposed stepwise method via simulation studies, and show that the stepwise CMH test performs better than other existing methods (e.g., logistic regression and detection of associations by Markov blanket for identifying multiple genetic variants. Finally, we apply the proposed approach to two genomic sequencing datasets to detect linked genetic variants associated with bipolar disorder and obesity, respectively.

Use of stream water pH and specific conductance measurements to identify ground water discharges of fly ash leachate

International Nuclear Information System (INIS)

Price, R.M.

1992-01-01

Low pH and high specific conductance are typical chemical characteristics of coal fly ash leachate. Measurements of these parameters in streams adjacent to a fly ash facility were used to identify areas of ground water discharge into the streams. In-situ specific conductance and pH were determined at approximately 50 surface water stations from on-site and off-site streams. The results of the in-situ determinations were used to select twelve surface water stations for more detailed chemical analyses. The chemical character of the stream water affected by ground water discharges was similar to the water quality of sedimentation ponds which received drainage from the fly ash embankment. The results indicated that in-situ measurements of indicator parameters such as pH and specific conductance can be used as a screening method for identifying surface water quality impacts at fly ash facilities

Comparison of Whole-Cell SELEX Methods for the Identification of Staphylococcus Aureus-Specific DNA Aptamers

OpenAIRE

Moon, Jihea; Kim, Giyoung; Park, Saet Byeol; Lim, Jongguk; Mo, Changyeun

2015-01-01

Whole-cell Systemic Evolution of Ligands by Exponential enrichment (SELEX) is the process by which aptamers specific to target cells are developed. Aptamers selected by whole-cell SELEX have high affinity and specificity for bacterial surface molecules and live bacterial targets. To identify DNA aptamers specific to Staphylococcus aureus, we applied our rapid whole-cell SELEX method to a single-stranded ssDNA library. To improve the specificity and selectivity of the aptamers, we designed, s...

Quality control methods in accelerometer data processing: identifying extreme counts.

Directory of Open Access Journals (Sweden)

Carly Rich

Full Text Available Accelerometers are designed to measure plausible human activity, however extremely high count values (EHCV have been recorded in large-scale studies. Using population data, we develop methodological principles for establishing an EHCV threshold, propose a threshold to define EHCV in the ActiGraph GT1M, determine occurrences of EHCV in a large-scale study, identify device-specific error values, and investigate the influence of varying EHCV thresholds on daily vigorous PA (VPA.We estimated quantiles to analyse the distribution of all accelerometer positive count values obtained from 9005 seven-year old children participating in the UK Millennium Cohort Study. A threshold to identify EHCV was derived by differentiating the quantile function. Data were screened for device-specific error count values and EHCV, and a sensitivity analysis conducted to compare daily VPA estimates using three approaches to accounting for EHCV.Using our proposed threshold of ≥ 11,715 counts/minute to identify EHCV, we found that only 0.7% of all non-zero counts measured in MCS children were EHCV; in 99.7% of these children, EHCV comprised < 1% of total non-zero counts. Only 11 MCS children (0.12% of sample returned accelerometers that contained negative counts; out of 237 such values, 211 counts were equal to -32,768 in one child. The medians of daily minutes spent in VPA obtained without excluding EHCV, and when using a higher threshold (≥19,442 counts/minute were, respectively, 6.2% and 4.6% higher than when using our threshold (6.5 minutes; p<0.0001.Quality control processes should be undertaken during accelerometer fieldwork and prior to analysing data to identify monitors recording error values and EHCV. The proposed threshold will improve the validity of VPA estimates in children's studies using the ActiGraph GT1M by ensuring only plausible data are analysed. These methods can be applied to define appropriate EHCV thresholds for different accelerometer models.

LC-QTOF-MS identification of porcine-specific peptide in heat treated pork identifies candidate markers for meat species determination.

Science.gov (United States)

Sarah, S A; Faradalila, W N; Salwani, M S; Amin, I; Karsani, S A; Sazili, A Q

2016-05-15

The purpose of this study was to identify porcine-specific peptide markers from thermally processed meat that could differentiate pork from beef, chevon and chicken meat. In the initial stage, markers from tryptic digested protein of chilled, boiled and autoclaved pork were identified using LC-QTOF-MS. An MRM method was then established for verification. A thorough investigation of LC-QTOF-MS data showed that only seven porcine-specific peptides were consistently detected. Among these peptides, two were derived from lactate dehydrogenase, one from creatine kinase, and four from serum albumin protein. However, MRM could only detect four peptides (EVTEFAK, LVVITAGAR, FVIER and TVLGNFAAFVQK) that were consistently present in pork samples. In conclusion, meat species determination through a tandem mass spectrometry platform shows high potential in providing scientifically valid and reliable results even at peptide level. Besides, the specificity and selectivity offered by the proteomics approach also provide a robust platform for Halal authentication. Copyright © 2015 Elsevier Ltd. All rights reserved.

Scientometric methods for identifying emerging technologies

Science.gov (United States)

Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

2015-11-03

Provided is a method of generating a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain.

Method for identifying particulate fluoride compounds

Energy Technology Data Exchange (ETDEWEB)

Tufts, B J

1960-01-01

A method is described for identifying particulates containing fluorides and other complex fluorine compounds such as fluorosilicate in samples collected on membrane filters. The filter is treated with lead chloride to precipitate lead chlorofluoride at each fluoride-containing spot. This microspot is identified by examination in a light microscope. Sulfate and phosphate, which also precipitate if present, can be distinguished and do not interfere. Calibrations are given for the fluorides and the more insoluble salts, relating the original particle size to the reaction site size. Thus, the mass of the particles can be calculated. Results of some field tests in an area of fluoride pollution are given, and compared with standard testing procedures.

Building America Guidance for Identifying and Overcoming Code, Standard, and Rating Method Barriers

Energy Technology Data Exchange (ETDEWEB)

Cole, Pamala C.; Halverson, Mark A.

2013-09-01

The U.S. Department of Energy’s (DOE) Building America program implemented a new Codes and Standards Innovation (CSI) Team in 2013. The Team’s mission is to assist Building America (BA) research teams and partners in identifying and resolving conflicts between Building America innovations and the various codes and standards that govern the construction of residences. A CSI Roadmap was completed in September, 2013. This guidance document was prepared using the information in the CSI Roadmap to provide BA research teams and partners with specific information and approaches to identifying and overcoming potential barriers to Building America (BA) innovations arising in and/or stemming from codes, standards, and rating methods. For more information on the BA CSI team, please email: CSITeam@pnnl.gov

Sparse feature selection identifies H2A.Z as a novel, pattern-specific biomarker for asymmetrically self-renewing distributed stem cells

Directory of Open Access Journals (Sweden)

Yang Hoon Huh

2015-03-01

Full Text Available There is a long-standing unmet clinical need for biomarkers with high specificity for distributed stem cells (DSCs in tissues, or for use in diagnostic and therapeutic cell preparations (e.g., bone marrow. Although DSCs are essential for tissue maintenance and repair, accurate determination of their numbers for medical applications has been problematic. Previous searches for biomarkers expressed specifically in DSCs were hampered by difficulty obtaining pure DSCs and by the challenges in mining complex molecular expression data. To identify such useful and specific DSC biomarkers, we combined a novel sparse feature selection method with combinatorial molecular expression data focused on asymmetric self-renewal, a conspicuous property of DSCs. The analysis identified reduced expression of the histone H2A variant H2A.Z as a superior molecular discriminator for DSC asymmetric self-renewal. Subsequent molecular expression studies showed H2A.Z to be a novel “pattern-specific biomarker” for asymmetrically self-renewing cells, with sufficient specificity to count asymmetrically self-renewing DSCs in vitro and potentially in situ.

Comparative Evaluations of Four Specification Methods for Real-Time Systems

Science.gov (United States)

1989-12-01

December 1989 Comparative Evaluations of Four Specification Methods for Real - Time Systems David P. Wood William G. Wood Specification and Design Methods...Methods for Real - Time Systems Abstract: A number of methods have been proposed in the last decade for the specification of system and software requirements...and software specification for real - time systems . Our process for the identification of methods that meet the above criteria is described in greater

A Novel Method to Identify Differential Pathways in Hippocampus Alzheimer's Disease.

Science.gov (United States)

Liu, Chun-Han; Liu, Lian

2017-05-08

BACKGROUND Alzheimer's disease (AD) is the most common type of dementia. The objective of this paper is to propose a novel method to identify differential pathways in hippocampus AD. MATERIAL AND METHODS We proposed a combined method by merging existed methods. Firstly, pathways were identified by four known methods (DAVID, the neaGUI package, the pathway-based co-expressed method, and the pathway network approach), and differential pathways were evaluated through setting weight thresholds. Subsequently, we combined all pathways by a rank-based algorithm and called the method the combined method. Finally, common differential pathways across two or more of five methods were selected. RESULTS Pathways obtained from different methods were also different. The combined method obtained 1639 pathways and 596 differential pathways, which included all pathways gained from the four existing methods; hence, the novel method solved the problem of inconsistent results. Besides, a total of 13 common pathways were identified, such as metabolism, immune system, and cell cycle. CONCLUSIONS We have proposed a novel method by combining four existing methods based on a rank product algorithm, and identified 13 significant differential pathways based on it. These differential pathways might provide insight into treatment and diagnosis of hippocampus AD.

Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos.

Directory of Open Access Journals (Sweden)

Rong-Ping Zhang

Full Text Available Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM and the pectoral muscle (PM of two genetically different duck breeds, Heiwu duck (H and Peking duck (P, at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P at the same developmental stage (embryonic 15 days. Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG were used to functionally annotate DEGs (differentially expression genes. The DEGs identified in Experiment 1 were mainly involved in focal adhesion, the PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05. In Experiment 2, the DEGs were associated with only the ribosome signaling pathway (corrected P-value<0.05. In addition, quantitative real-time PCR was used to confirm 15 of the differentially expressed genes originally detected by RNA-Seq. A comparative transcript analysis of the leg and pectoral muscles of two duck breeds not only

Identifying Teaching Methods that Engage Entrepreneurship Students

Science.gov (United States)

Balan, Peter; Metcalfe, Mike

2012-01-01

Purpose: Entrepreneurship education particularly requires student engagement because of the complexity of the entrepreneurship process. The purpose of this paper is to describe how an established measure of engagement can be used to identify relevant teaching methods that could be used to engage any group of entrepreneurship students.…

Identifying Method of Drunk Driving Based on Driving Behavior

Directory of Open Access Journals (Sweden)

Xiaohua Zhao

2011-05-01

Full Text Available Drunk driving is one of the leading causes contributing to traffic crashes. There are numerous issues that need to be resolved with the current method of identifying drunk driving. Driving behavior, with the characteristic of real-time, was extensively researched to identify impaired driving behaviors. In this paper, the drives with BACs above 0.05% were defined as drunk driving state. A detailed comparison was made between normal driving and drunk driving. The experiment in driving simulator was designed to collect the driving performance data of the groups. According to the characteristics analysis for the effect of alcohol on driving performance, seven significant indicators were extracted and the drunk driving was identified by the Fisher Discriminant Method. The discriminant function demonstrated a high accuracy of classification. The optimal critical score to differentiate normal from drinking state was found to be 0. The evaluation result verifies the accuracy of classification method.

The development of a patient-specific method for physiotherapy goal setting: a user-centered design.

Science.gov (United States)

Stevens, Anita; Köke, Albère; van der Weijden, Trudy; Beurskens, Anna

2018-08-01

To deliver client-centered care, physiotherapists need to identify the patients' individual treatment goals. However, practical tools for involving patients in goal setting are lacking. The purpose of this study was to improve the frequently used Patient-Specific Complaints instrument in Dutch physiotherapy, and to develop it into a feasible method to improve physiotherapy goal setting. An iterative user-centered design was conducted in co-creation with the physiotherapists and patients, in three phases. Their needs and preferences were identified by means of group meetings and questionnaires. The new method was tested in several field tests in physiotherapy practices. Four main objectives for improvement were formulated: clear instructions for the administration procedure, targeted use across the physiotherapy process, client-activating communication skills, and a client-centered attitude of the physiotherapist. A theoretical goal-setting framework and elements of shared decision making were integrated into the new-called, Patient-Specific Goal-setting method, together with a practical training course. The user-centered approach resulted in a goal-setting method that is fully integrated in the physiotherapy process. The new goal-setting method contributes to a more structured approach to goal setting and enables patient participation and goal-oriented physiotherapy. Before large-scale implementation, its feasibility in physiotherapy practice needs to be investigated. Implications for rehabilitation Involving patients and physiotherapists in the development and testing of a goal-setting method, increases the likelihood of its feasibility in practice. The integration of a goal-setting method into the physiotherapy process offers the opportunity to focus more fully on the patient's goals. Patients should be informed about the aim of every step of the goal-setting process in order to increase their awareness and involvement. Training physiotherapists to use a patient-specific

Method of detecting genetic deletions identified with chromosomal abnormalities

Energy Technology Data Exchange (ETDEWEB)

Gray, Joe W; Pinkel, Daniel; Tkachuk, Douglas

2013-11-26

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 acids probes are typically of a complexity greater tha 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, particlularly 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 ut genetically different diseases, and for many prognostic and diagnostic applications.

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

Directory of Open Access Journals (Sweden)

Karp Peter D

2004-06-01

Full Text Available Abstract Background The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to assign function to 40–60% of sequences. In addition, large numbers of sequences may have non-specific annotations (e.g., thiolase family protein. Pathway holes occur when a genome appears to lack the enzymes needed to catalyze reactions in a pathway. If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database. Results We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases. Our program not only identifies potential candidate sequences for pathway holes, but combines data from multiple, heterogeneous sources to assess the likelihood that a candidate has the required function. Our algorithm emulates the manual sequence annotation process, considering not only evidence from homology searches, but also considering evidence from genomic context (i.e., is the gene part of an operon? and functional context (e.g., are there functionally-related genes nearby in the genome? to determine the posterior belief that a candidate has the required function. The method can be applied across an entire metabolic pathway network and is generally applicable to any pathway database. The program uses a set of sequences encoding the required activity in other genomes to identify candidate proteins in the genome of interest, and then evaluates each candidate by using a simple Bayes classifier to determine the probability that the candidate has the desired function. We achieved 71% precision at a

Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program.

Directory of Open Access Journals (Sweden)

Dunja Knapp

Full Text Available Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.

19 CFR 134.43 - Methods of marking specific articles.

Science.gov (United States)

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Methods of marking specific articles. 134.43...; DEPARTMENT OF THE TREASURY COUNTRY OF ORIGIN MARKING Method and Location of Marking Imported Articles § 134.43 Methods of marking specific articles. (a) Marking previously required by certain provisions of the...

Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study

DEFF Research Database (Denmark)

Druley, Todd E; Wang, Lihua; Lin, Shiow J

2016-01-01

from six pedigrees. OBFC1 (chromosome 10) is involved in telomere maintenance, and falls within a linkage peak recently reported from an analysis of telomere length in LLFS families. Two different algorithms for single gene associations identified three genes with an enrichment of variation......BACKGROUND: The Long Life Family Study (LLFS) is an international study to identify the genetic components of various healthy aging phenotypes. We hypothesized that pedigree-specific rare variants at longevity-associated genes could have a similar functional impact on healthy phenotypes. METHODS......: We performed custom hybridization capture sequencing to identify the functional variants in 464 candidate genes for longevity or the major diseases of aging in 615 pedigrees (4,953 individuals) from the LLFS, using a multiplexed, custom hybridization capture. Variants were analyzed individually...

Carbapenem inactivation: a very affordable and highly specific method for phenotypic detection of carbapenemase-producing Pseudomonas aeruginosa isolates compared with other methods.

Science.gov (United States)

Akhi, Mohammad Taghi; Khalili, Younes; Ghotaslou, Reza; Kafil, Hossein Samadi; Yousefi, Saber; Nagili, Behroz; Goli, Hamid Reza

2017-06-01

This investigation was undertaken to compare phenotypic and molecular methods for detection of carbapenemase-producing Pseudomonas aeruginosa. A total of 245 non-duplicated isolates of P. aeruginosa were collected from hospitalized patients. Disc diffusion method was used to identify carbapenem-resistant bacteria. Three phenotypic methods, including Modified Hodge Test (MHT), Modified Carba NP (MCNP) test and Carbapenem Inactivation Method (CIM) were used for investigation of carbapenemase production. In addition, polymerase chain reaction (PCR) was used to detect carbapenemase encoding genes. Of 245 P. aeruginosa isolates investigated, 121 isolates were carbapenem-resistant. Among carbapenem-resistant isolates, 40, 39 and 35 isolates exhibited positive results using MHT, MCNP test and CIM, respectively. PCR indicated the presence of carbapenemase genes in 35 of carbapenem-resistant isolates. MHT showed low sensitivity and specificity for carbapenemase detection among P. aeruginosa isolates in comparison to PCR. CIM was most affordable and highly specific than MCNP test compared with the molecular method.

Identifying essential genes in bacterial metabolic networks with machine learning methods

Science.gov (United States)

2010-01-01

Background Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell. However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective. Results We developed a machine learning technique to identify essential genes using the experimental data of genome-wide knock-out screens from one bacterial organism to infer essential genes of another related bacterial organism. We used a broad variety of topological features, sequence characteristics and co-expression properties potentially associated with essentiality, such as flux deviations, centrality, codon frequencies of the sequences, co-regulation and phyletic retention. An organism-wise cross-validation on bacterial species yielded reliable results with good accuracies (area under the receiver-operator-curve of 75% - 81%). Finally, it was applied to drug target predictions for Salmonella typhimurium. We compared our predictions to the viability of experimental knock-outs of S. typhimurium and identified 35 enzymes, which are highly relevant to be considered as potential drug targets. Specifically, we detected promising drug targets in the non-mevalonate pathway. Conclusions Using elaborated features characterizing network topology, sequence information and microarray data enables to predict essential genes from a bacterial reference organism to a related query organism without any knowledge about the essentiality of genes of the query organism. In general, such a method is beneficial for inferring drug targets when experimental data about genome-wide knockout screens is not available for the investigated organism. PMID:20438628

An Investigation to Validate the Grammar and Phonology Screening (GAPS) Test to Identify Children with Specific Language Impairment

Science.gov (United States)

van der Lely, Heather K. J.; Payne, Elisabeth; McClelland, Alastair

2011-01-01

Background The extraordinarily high incidence of grammatical language impairments in developmental disorders suggests that this uniquely human cognitive function is “fragile”. Yet our understanding of the neurobiology of grammatical impairments is limited. Furthermore, there is no “gold-standard” to identify grammatical impairments and routine screening is not undertaken. An accurate screening test to identify grammatical abilities would serve the research, health and education communities, further our understanding of developmental disorders, and identify children who need remediation, many of whom are currently un-diagnosed. A potential realistic screening tool that could be widely administered is the Grammar and Phonology Screening (GAPS) test – a 10 minute test that can be administered by professionals and non-professionals alike. Here we provide a further step in evaluating the validity and accuracy (sensitivity and specificity) of the GAPS test in identifying children who have Specific Language Impairment (SLI). Methods and Findings We tested three groups of children; two groups aged 3;6–6:6, a typically developing (n = 30) group, and a group diagnosed with SLI: (n = 11) (Young (Y)-SLI), and a further group aged 6;9–8;11 with SLI (Older (O)-SLI) (n = 10) who were above the test age norms. We employed a battery of language assessments including the GAPS test to assess the children's language abilities. For Y-SLI children, analyses revealed a sensitivity and specificity at the 5th and 10th percentile of 1.00 and 0.98, respectively, and for O-SLI children at the 10th and 15th percentile .83 and .90, respectively. Conclusions The findings reveal that the GAPS is highly accurate in identifying impaired vs. non-impaired children up to 6;8 years, and has moderate-to-high accuracy up to 9 years. The results indicate that GAPS is a realistic tool for the early identification of grammatical abilities and impairment in young children. A larger

Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

NARCIS (Netherlands)

van Leeuwen, E.M.; Karssen, L.C.; Deelen, J.; Isaacs, A.; Medina-Gomez, C.; Mbarek, H.; Kanterakis, A.; Trompet, S.; Postmus, I.; Verweij, N.; van Enckevort, D.; Huffman, J.E.; White, C.C.; Feitosa, M.F.; Bartz, T.M.; Manichaikul, A.; Joshi, P.K.; Peloso, G.M.; Deelen, P.; Dijk, F.; Willemsen, G.; de Geus, E.J.C.; Milaneschi, Y.; Penninx, B.W.J.H.; Francioli, L.C.; Menelaou, A.; Pulit, S.L.; Rivadeneira, F.; Hofman, A.; Oostra, B.A.; Franco, O.H.; Mateo Leach, I.; Beekman, M.; de Craen, A.J.; Uh, H.W.; Trochet, H.; Hocking, L.J.; Porteous, D.J.; Sattar, N.; Packard, C.J.; Buckley, B.M.; Brody, J.A.; Bis, J.C.; Rotter, J.I.; Mychaleckyj, J.C.; Campbell, H.; Duan, Q.; Lange, L.A.; Wilson, J.F.; Hayward, C.; Polasek, O.; Vitart, V.; Rudan, I.; Wright, A.F.; Rich, S.S.; Psaty, B.M.; Borecki, I.B.; Kearney, P.M.; Stott, D.J.; Cupples, L.A.; Jukema, J.W.; van der Harst, P.; Sijbrands, E.J.; Hottenga, J.J.; Uitterlinden, A.G.; Swertz, M.A.; van Ommen, G.J.B; Bakker, P.I.W.; Slagboom, P.E.; Boomsma, D.I.; Wijmenga, C.; van Duijn, C.M.

2015-01-01

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (∼35,000 samples) with the population-specific reference panel created

Validation of a Consensus Method for Identifying Delirium from Hospital Records

Science.gov (United States)

Kuhn, Elvira; Du, Xinyi; McGrath, Keith; Coveney, Sarah; O'Regan, Niamh; Richardson, Sarah; Teodorczuk, Andrew; Allan, Louise; Wilson, Dan; Inouye, Sharon K.; MacLullich, Alasdair M. J.; Meagher, David; Brayne, Carol; Timmons, Suzanne; Davis, Daniel

2014-01-01

Background Delirium is increasingly considered to be an important determinant of trajectories of cognitive decline. Therefore, analyses of existing cohort studies measuring cognitive outcomes could benefit from methods to ascertain a retrospective delirium diagnosis. This study aimed to develop and validate such a method for delirium detection using routine medical records in UK and Ireland. Methods A point prevalence study of delirium provided the reference-standard ratings for delirium diagnosis. Blinded to study results, clinical vignettes were compiled from participants' medical records in a standardised manner, describing any relevant delirium symptoms recorded in the whole case record for the period leading up to case-ascertainment. An expert panel rated each vignette as unlikely, possible, or probable delirium and disagreements were resolved by consensus. Results From 95 case records, 424 vignettes were abstracted by 5 trained clinicians. There were 29 delirium cases according to the reference standard. Median age of subjects was 76.6 years (interquartile range 54.6 to 82.5). Against the original study DSM-IV diagnosis, the chart abstraction method gave a positive likelihood ratio (LR) of 7.8 (95% CI 5.7–12.0) and the negative LR of 0.45 (95% CI 0.40–0.47) for probable delirium (sensitivity 0.58 (95% CI 0.53–0.62); specificity 0.93 (95% CI 0.90–0.95); AUC 0.86 (95% CI 0.82–0.89)). The method diagnosed possible delirium with positive LR 3.5 (95% CI 2.9–4.3) and negative LR 0.15 (95% CI 0.11–0.21) (sensitivity 0.89 (95% CI 0.85–0.91); specificity 0.75 (95% CI 0.71–0.79); AUC 0.86 (95% CI 0.80–0.89)). Conclusions This chart abstraction method can retrospectively diagnose delirium in hospitalised patients with good accuracy. This has potential for retrospectively identifying delirium in cohort studies where routine medical records are available. This example of record linkage between hospitalisations and epidemiological data may lead to

Fluorescently labeled dengue viruses as probes to identify antigen-specific memory B cells by multiparametric flow cytometry.

Science.gov (United States)

Woda, Marcia; Mathew, Anuja

2015-01-01

Low frequencies of memory B cells in the peripheral blood make it challenging to measure the functional and phenotypic characteristics of this antigen experienced subset of B cells without in vitro culture. To date, reagents are lacking to measure ex vivo frequencies of dengue virus (DENV)-specific memory B cells. We wanted to explore the possibility of using fluorescently labeled DENV as probes to detect antigen-specific memory B cells in the peripheral blood of DENV immune individuals. Alexa Fluor dye-labeled DENV yielded viable virus that could be stored at -80°C for long periods of time. Using a careful gating strategy and methods to decrease non-specific binding, we were able to identify a small frequency of B cells from dengue immune individuals that bound labeled DENV. Sorted DENV(+) B cells from immune, but not naïve donors secreted antibodies that bound DENV after in vitro stimulation. Overall, Alexa Fluor dye-labeled DENVs are useful reagents to enable the detection and characterization of memory B cells in DENV immune individuals. Copyright © 2014 Elsevier B.V. All rights reserved.

Allele-specific deletions in mouse tumors identify Fbxw7 as germline modifier of tumor susceptibility.

Directory of Open Access Journals (Sweden)

Jesus Perez-Losada

Full Text Available Genome-wide association studies (GWAS have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5-10%. There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p = 0.001, but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility.

Phospho-specific flow cytometry identifies aberrant signaling in indolent B-cell lymphoma

Directory of Open Access Journals (Sweden)

Blix Egil S

2012-10-01

Full Text Available Abstract Background Knowledge about signaling pathways in malignant cells may provide prognostic and diagnostic information in addition to identify potential molecular targets for therapy. B-cell receptor (BCR and co-receptor CD40 signaling is essential for normal B cells, and there is increasing evidence that signaling via BCR and CD40 plays an important role in the pathogenesis of B-cell lymphoma. The aim of this study was to investigate basal and induced signaling in lymphoma B cells and infiltrating T cells in single-cell suspensions of biopsies from small cell lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL and marginal zone lymphoma (MZL patients. Methods Samples from untreated SLL/CLL and MZL patients were examined for basal and activation induced signaling by phospho-specific flow cytometry. A panel of 9 stimulation conditions targeting B and T cells, including crosslinking of the B cell receptor (BCR, CD40 ligand and interleukins in combination with 12 matching phospho-protein readouts was used to study signaling. Results Malignant B cells from SLL/CLL patients had higher basal levels of phosphorylated (p-SFKs, p-PLCγ, p-ERK, p-p38, p-p65 (NF-κB, p-STAT5 and p-STAT6, compared to healthy donor B cells. In contrast, anti-BCR induced signaling was highly impaired in SLL/CLL and MZL B cells as determined by low p-SFK, p-SYK and p-PLCγ levels. Impaired anti-BCR-induced p-PLCγ was associated with reduced surface expression of IgM and CD79b. Similarly, CD40L-induced p-ERK and p-p38 were also significantly reduced in lymphoma B cells, whereas p-p65 (NF-κB was equal to that of normal B cells. In contrast, IL-2, IL-7 and IL-15 induced p-STAT5 in tumor-infiltrating T cells were not different from normal T cells. Conclusions BCR signaling and CD40L-induced p-p38 was suppressed in malignant B cells from SLL/CLL and MZL patients. Single-cell phospho-specific flow cytometry for detection of basal as well as activation

An Efficient Approach for Identifying Stable Lobes with Discretization Method

Directory of Open Access Journals (Sweden)

Baohai Wu

2013-01-01

Full Text Available This paper presents a new approach for quick identification of chatter stability lobes with discretization method. Firstly, three different kinds of stability regions are defined: absolute stable region, valid region, and invalid region. Secondly, while identifying the chatter stability lobes, three different regions within the chatter stability lobes are identified with relatively large time intervals. Thirdly, stability boundary within the valid regions is finely calculated to get exact chatter stability lobes. The proposed method only needs to test a small portion of spindle speed and cutting depth set; about 89% computation time is savedcompared with full discretization method. It spends only about10 minutes to get exact chatter stability lobes. Since, based on discretization method, the proposed method can be used for different immersion cutting including low immersion cutting process, the proposed method can be directly implemented in the workshop to promote machining parameters selection efficiency.

Extending existing structural identifiability analysis methods to mixed-effects models.

Science.gov (United States)

Janzén, David L I; Jirstrand, Mats; Chappell, Michael J; Evans, Neil D

2018-01-01

The concept of structural identifiability for state-space models is expanded to cover mixed-effects state-space models. Two methods applicable for the analytical study of the structural identifiability of mixed-effects models are presented. The two methods are based on previously established techniques for non-mixed-effects models; namely the Taylor series expansion and the input-output form approach. By generating an exhaustive summary, and by assuming an infinite number of subjects, functions of random variables can be derived which in turn determine the distribution of the system's observation function(s). By considering the uniqueness of the analytical statistical moments of the derived functions of the random variables, the structural identifiability of the corresponding mixed-effects model can be determined. The two methods are applied to a set of examples of mixed-effects models to illustrate how they work in practice. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparison of whole-cell SELEX methods for the identification of Staphylococcus aureus-specific DNA aptamers.

Science.gov (United States)

Moon, Jihea; Kim, Giyoung; Park, Saet Byeol; Lim, Jongguk; Mo, Changyeun

2015-04-15

Whole-cell Systemic Evolution of Ligands by Exponential enrichment (SELEX) is the process by which aptamers specific to target cells are developed. Aptamers selected by whole-cell SELEX have high affinity and specificity for bacterial surface molecules and live bacterial targets. To identify DNA aptamers specific to Staphylococcus aureus, we applied our rapid whole-cell SELEX method to a single-stranded ssDNA library. To improve the specificity and selectivity of the aptamers, we designed, selected, and developed two categories of aptamers that were selected by two kinds of whole-cell SELEX, by mixing and combining FACS analysis and a counter-SELEX process. Using this approach, we have developed a biosensor system that employs a high affinity aptamer for detection of target bacteria. FAM-labeled aptamer sequences with high binding to S. aureus, as determined by fluorescence spectroscopic analysis, were identified, and aptamer A14, selected by the basic whole-cell SELEX using a once-off FACS analysis, and which had a high binding affinity and specificity, was chosen. The binding assay was evaluated using FACS analysis. Our study demonstrated the development of a set of whole-cell SELEX derived aptamers specific to S. aureus; this approach can be used in the identification of other bacteria.

Comparison of Whole-Cell SELEX Methods for the Identification of Staphylococcus Aureus-Specific DNA Aptamers

Directory of Open Access Journals (Sweden)

Jihea Moon

2015-04-01

Full Text Available Whole-cell Systemic Evolution of Ligands by Exponential enrichment (SELEX is the process by which aptamers specific to target cells are developed. Aptamers selected by whole-cell SELEX have high affinity and specificity for bacterial surface molecules and live bacterial targets. To identify DNA aptamers specific to Staphylococcus aureus, we applied our rapid whole-cell SELEX method to a single-stranded ssDNA library. To improve the specificity and selectivity of the aptamers, we designed, selected, and developed two categories of aptamers that were selected by two kinds of whole-cell SELEX, by mixing and combining FACS analysis and a counter-SELEX process. Using this approach, we have developed a biosensor system that employs a high affinity aptamer for detection of target bacteria. FAM-labeled aptamer sequences with high binding to S. aureus, as determined by fluorescence spectroscopic analysis, were identified, and aptamer A14, selected by the basic whole-cell SELEX using a once-off FACS analysis, and which had a high binding affinity and specificity, was chosen. The binding assay was evaluated using FACS analysis. Our study demonstrated the development of a set of whole-cell SELEX derived aptamers specific to S. aureus; this approach can be used in the identification of other bacteria.

Testing of toxicity based methods to develop site specific clean up objectives - phase 1: Toxicity protocol screening and applicability

International Nuclear Information System (INIS)

Hamilton, H.; Kerr, D.; Thorne, W.; Taylor, B.; Zadnik, M.; Goudey, S.; Birkholz, D.

1994-03-01

A study was conducted to develop a cost-effective and practical protocol for using bio-assay based toxicity assessment methods for remediation of decommissioned oil and gas production, and processing facilities. The objective was to generate site-specific remediation criteria for contaminated sites. Most companies have used the chemical-specific approach which, however, did not meet the ultimate land use goal of agricultural production. The toxicity assessment method described in this study dealt with potential impairment to agricultural crop production and natural ecosystems. Human health concerns were not specifically addressed. It was suggested that chemical-specific methods should be used when human health concerns exist. . Results showed that toxicity tests will more directly identify ecological stress caused by site contamination than chemical-specific remediation criteria, which can be unnecessarily protective. 11 refs., 7 tabs., 6 figs

Validation of a consensus method for identifying delirium from hospital records.

Directory of Open Access Journals (Sweden)

Elvira Kuhn

Full Text Available Delirium is increasingly considered to be an important determinant of trajectories of cognitive decline. Therefore, analyses of existing cohort studies measuring cognitive outcomes could benefit from methods to ascertain a retrospective delirium diagnosis. This study aimed to develop and validate such a method for delirium detection using routine medical records in UK and Ireland.A point prevalence study of delirium provided the reference-standard ratings for delirium diagnosis. Blinded to study results, clinical vignettes were compiled from participants' medical records in a standardised manner, describing any relevant delirium symptoms recorded in the whole case record for the period leading up to case-ascertainment. An expert panel rated each vignette as unlikely, possible, or probable delirium and disagreements were resolved by consensus.From 95 case records, 424 vignettes were abstracted by 5 trained clinicians. There were 29 delirium cases according to the reference standard. Median age of subjects was 76.6 years (interquartile range 54.6 to 82.5. Against the original study DSM-IV diagnosis, the chart abstraction method gave a positive likelihood ratio (LR of 7.8 (95% CI 5.7-12.0 and the negative LR of 0.45 (95% CI 0.40-0.47 for probable delirium (sensitivity 0.58 (95% CI 0.53-0.62; specificity 0.93 (95% CI 0.90-0.95; AUC 0.86 (95% CI 0.82-0.89. The method diagnosed possible delirium with positive LR 3.5 (95% CI 2.9-4.3 and negative LR 0.15 (95% CI 0.11-0.21 (sensitivity 0.89 (95% CI 0.85-0.91; specificity 0.75 (95% CI 0.71-0.79; AUC 0.86 (95% CI 0.80-0.89.This chart abstraction method can retrospectively diagnose delirium in hospitalised patients with good accuracy. This has potential for retrospectively identifying delirium in cohort studies where routine medical records are available. This example of record linkage between hospitalisations and epidemiological data may lead to further insights into the inter-relationship between acute

Issues in identifying germ tube positive yeasts by conventional methods.

Science.gov (United States)

Yazdanpanah, Atta; Khaithir, Tzar Mohd Nizam

2014-01-01

Candida speciation is vital for epidemiology and management of candidiasis. Nonmolecular conventional methods often fail to identify closely related germ tube positive yeasts from clinical specimens. The present study was conducted to identify these yeasts and to highlight issues in conventional versus molecular methods of identification. A total of 98 germ tube positive yeasts from high vaginal swabs were studied over a 12-month period. Isolates were examined with various methods including growth at 42 °C and 45 °C on Sabouraud dextrose agar (SDA), color development on CHROMagar Candida medium, chlamydospore production on corn meal agar at 25 °C, carbohydrate assimilation using ID 32C system, and polymerase chain reaction using a single pair of primers targeting the hyphal wall protein 1 (Hwp1) gene. Of all the isolates studied, 97 were molecularly confirmed as C. albicans and one isolate was identified as C. dubliniensis. No C. africana was detected in this study. The molecular method used in our study was an accurate and useful tool for discriminating C. albicans, C. dubliniensis, and C. africana. The conventional methods, however, were less accurate and riddled with many issues that will be discussed in further details. © 2013 Wiley Periodicals, Inc.

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome.

Science.gov (United States)

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O'Connor, Timothy D; Abecasis, Gonçalo R; Wojcik, Genevieve L; Gignoux, Christopher R; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E; Bustamante, Carlos; Beaty, Terri H; Mathias, Rasika A; Barnes, Kathleen C; Qin, Zhaohui S

2017-04-21

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.

Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes

Science.gov (United States)

Trinkle-Mulcahy, Laura; Boulon, Séverine; Lam, Yun Wah; Urcia, Roby; Boisvert, François-Michel; Vandermoere, Franck; Morrice, Nick A.; Swift, Sam; Rothbauer, Ulrich; Leonhardt, Heinrich; Lamond, Angus

2008-01-01

The identification of interaction partners in protein complexes is a major goal in cell biology. Here we present a reliable affinity purification strategy to identify specific interactors that combines quantitative SILAC-based mass spectrometry with characterization of common contaminants binding to affinity matrices (bead proteomes). This strategy can be applied to affinity purification of either tagged fusion protein complexes or endogenous protein complexes, illustrated here using the well-characterized SMN complex as a model. GFP is used as the tag of choice because it shows minimal nonspecific binding to mammalian cell proteins, can be quantitatively depleted from cell extracts, and allows the integration of biochemical protein interaction data with in vivo measurements using fluorescence microscopy. Proteins binding nonspecifically to the most commonly used affinity matrices were determined using quantitative mass spectrometry, revealing important differences that affect experimental design. These data provide a specificity filter to distinguish specific protein binding partners in both quantitative and nonquantitative pull-down and immunoprecipitation experiments. PMID:18936248

An assessment of two methods for identifying undocumented levees using remotely sensed data

Science.gov (United States)

Czuba, Christiana R.; Williams, Byron K.; Westman, Jack; LeClaire, Keith

2015-01-01

Many undocumented and commonly unmaintained levees exist in the landscape complicating flood forecasting, risk management, and emergency response. This report describes a pilot study completed by the U.S. Geological Survey in cooperation with the U.S. Army Corps of Engineers to assess two methods to identify undocumented levees by using remotely sensed, high-resolution topographic data. For the first method, the U.S. Army Corps of Engineers examined hillshades computed from a digital elevation model that was derived from light detection and ranging (lidar) to visually identify potential levees and then used detailed site visits to assess the validity of the identifications. For the second method, the U.S. Geological Survey applied a wavelet transform to a lidar-derived digital elevation model to identify potential levees. The hillshade method was applied to Delano, Minnesota, and the wavelet-transform method was applied to Delano and Springfield, Minnesota. Both methods were successful in identifying levees but also identified other features that required interpretation to differentiate from levees such as constructed barriers, high banks, and bluffs. Both methods are complementary to each other, and a potential conjunctive method for testing in the future includes (1) use of the wavelet-transform method to rapidly identify slope-break features in high-resolution topographic data, (2) further examination of topographic data using hillshades and aerial photographs to classify features and map potential levees, and (3) a verification check of each identified potential levee with local officials and field visits.

Method of identifying features in indexed data

Science.gov (United States)

Jarman, Kristin H [Richland, WA; Daly, Don Simone [Richland, WA; Anderson, Kevin K [Richland, WA; Wahl, Karen L [Richland, WA

2001-06-26

The present invention is a method of identifying features in indexed data, especially useful for distinguishing signal from noise in data provided as a plurality of ordered pairs. Each of the plurality of ordered pairs has an index and a response. The method has the steps of: (a) providing an index window having a first window end located on a first index and extending across a plurality of indices to a second window end; (b) selecting responses corresponding to the plurality of indices within the index window and computing a measure of dispersion of the responses; and (c) comparing the measure of dispersion to a dispersion critical value. Advantages of the present invention include minimizing signal to noise ratio, signal drift, varying baseline signal and combinations thereof.

Identifying Creatively Gifted Students: Necessity of a Multi-Method Approach

Science.gov (United States)

Ambrose, Laura; Machek, Greg R.

2015-01-01

The process of identifying students as creatively gifted provides numerous challenges for educators. Although many schools assess for creativity in identifying students for gifted and talented services, the relationship between creativity and giftedness is often not fully understood. This article reviews commonly used methods of creativity…

A method to identify aperiodic disturbances in the ionosphere

Science.gov (United States)

Wang, J.-S.; Chen, Z.; Huang, C.-M.

2014-05-01

In this paper, variations in the ionospheric F2 layer's critical frequency are decomposed into their periodic and aperiodic components. The latter include disturbances caused both by geophysical impacts on the ionosphere and random noise. The spectral whitening method (SWM), a signal-processing technique used in statistical estimation and/or detection, was used to identify aperiodic components in the ionosphere. The whitening algorithm adopted herein is used to divide the Fourier transform of the observed data series by a real envelope function. As a result, periodic components are suppressed and aperiodic components emerge as the dominant contributors. Application to a synthetic data set based on significant simulated periodic features of ionospheric observations containing artificial (and, hence, controllable) disturbances was used to validate the SWM for identification of aperiodic components. Although the random noise was somewhat enhanced by post-processing, the artificial disturbances could still be clearly identified. The SWM was then applied to real ionospheric observations. It was found to be more sensitive than the often-used monthly median method to identify geomagnetic effects. In addition, disturbances detected by the SWM were characterized by a Gaussian-type probability density function over all timescales, which further simplifies statistical analysis and suggests that the disturbances thus identified can be compared regardless of timescale.

Identifying Heterogeneities in Subsurface Environment using the Level Set Method

Energy Technology Data Exchange (ETDEWEB)

Lei, Hongzhuan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lu, Zhiming [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Vesselinov, Velimir Valentinov [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2016-08-25

These are slides from a presentation on identifying heterogeneities in subsurface environment using the level set method. The slides start with the motivation, then explain Level Set Method (LSM), the algorithms, some examples are given, and finally future work is explained.

[Study on commercial specification of atractylodes based on Delphi method].

Science.gov (United States)

Wang, Hao; Chen, Li-Xiao; Huang, Lu-Qi; Zhang, Tian-Tian; Li, Ying; Zheng, Yu-Guang

2016-03-01

This research adopts "Delphi method" to evaluate atractylodes traditional traits and rank correlation. By using methods of mathematical statistics the relationship of the traditional identification indicators and atractylodes goods rank correlation was analyzed, It is found that the main characteristics affectingatractylodes commodity specifications and grades of main characters wereoil points of transaction,color of transaction,color of surface,grain of transaction,texture of transaction andspoilage. The study points out that the original "seventy-six kinds of medicinal materials commodity specification standards of atractylodes differentiate commodity specification" is not in conformity with the actual market situation, we need to formulate corresponding atractylodes medicinal products specifications and grades.This study combined with experimental results "Delphi method" and the market actual situation, proposed the new draft atractylodes commodity specifications and grades, as the new atractylodes commodity specifications and grades standards. It provides a reference and theoretical basis. Copyright© by the Chinese Pharmaceutical Association.

A multiplex PCR-based method to identify strongylid parasite larvae recovered from ovine faecal cultures and/or pasture samples.

Science.gov (United States)

Bisset, S A; Knight, J S; Bouchet, C L G

2014-02-24

A multiplex PCR-based method was developed to overcome the limitations of microscopic examination as a means of identifying individual infective larvae from the wide range of strongylid parasite species commonly encountered in sheep in mixed sheep-cattle grazing situations in New Zealand. The strategy employed targets unique species-specific sequence markers in the second internal transcribed spacer (ITS-2) region of ribosomal DNA of the nematodes and utilises individual larval lysates as reaction templates. The basic assay involves two sets of reactions designed to target the ten strongylid species most often encountered in ovine faecal cultures under New Zealand conditions (viz. Haemonchus contortus, Teladorsagia circumcincta, Trichostrongylus axei, Trichostrongylus colubriformis, Trichostrongylus vitrinus, Cooperia curticei, Cooperia oncophora, Nematodirus spathiger, Chabertia ovina, and Oesophagostomum venulosum). Five species-specific primers, together with a pair of "generic" (conserved) primers, are used in each of the reactions. Two products are generally amplified, one by the generic primer pair regardless of species (providing a positive PCR control) and the other (whose size is indicative of the species present) by the appropriate species-specific primer in combination with one or other of the generic primers. If necessary, any larvae not identified by these reactions can subsequently be tested using primers designed specifically to detect those species less frequently encountered in ovine faecal cultures (viz. Ostertagia ostertagi, Ostertagia leptospicularis, Cooperia punctata, Nematodirus filicollis, and Bunostomum trigonocephalum). Results of assays undertaken on >5500 nematode larvae cultured from lambs on 16 different farms distributed throughout New Zealand indicated that positive identifications were initially obtained for 92.8% of them, while a further 4.4% of reactions gave a generic but no visible specific product and 2.8% gave no discernible

The validity of the family history method for identifying Alzheimer disease.

Science.gov (United States)

Li, G; Aryan, M; Silverman, J M; Haroutunian, V; Perl, D P; Birstein, S; Lantz, M; Marin, D B; Mohs, R C; Davis, K L

1997-05-01

To examine the validity of the family history method for identifying Alzheimer disease (AD) by comparing family history and neuropathological diagnoses. Seventy-seven former residents of the Jewish Home and Hospital for the Aged, New York, NY, with neuropathological evaluations on record were blindly assessed for the presence of dementia and, if present, the type of dementia through family informants by telephone interviews. The Alzheimer's Disease Risk Questionnaire was used to collect demographic information and screen for possible dementia. If dementia was suspected, the Dementia Questionnaire was administered to assess the course and type of dementia, i.e., primary progressive dementia (PPD, likely AD), multiple infarct dementia, mixed dementia (i.e., PPD and multiple infarct dementia), and other dementias based on the modified Diagnostic and Statistical Manual of Mental Disorders, Third Edition, criteria. Sixty (77.9%) of 77 elderly subjects were classified as having dementia and 17 (22.1%) were without dementia by family history evaluation. Of the 60 elderly subjects with dementia, 57 (95%) were found at autopsy to have had neuropathological changes related to dementia. The sensitivity of the family history diagnosis for dementia with related neuropathological change was 0.84 (57 of 68) and the specificity was 0.67 (6 of 9). Using family history information to differentiate the type of dementia, the sensitivity for definite or probable AD (with or without another condition) was 0.69 (36 of 51) and the specificity was 0.73 (19 of 26). The majority (9 of 15) of patients testing false negative for PPD had a history of stroke associated with onset of memory changes, excluding a diagnosis of PPD. Identifying dementia, in general, and AD, in particular, has an acceptable sensitivity and specificity. As is true for direct clinical diagnosis, the major issue associated with misclassifying AD in a family history assessment is the masking effects of a coexisting non

Methods of checking general safety criteria in UML statechart specifications

International Nuclear Information System (INIS)

Pap, Zsigmond; Majzik, Istvan; Pataricza, Andras; Szegi, Andras

2005-01-01

This paper describes methods and tools for safety analysis of UML statechart specifications. A comprehensive set of general safety criteria including completeness and consistency is applied in automated analysis. Analysis techniques are based on OCL expressions, graph transformations and reachability analysis. Two canonical intermediate representations of the statechart specification are introduced. They are suitable for straightforward implementation of checker methods and for the support of the proof of the correctness and soundness of the applied analysis. One of them also serves as a basis of the metamodel of a variant of UML statecharts proposed for the specification of safety-critical control systems. The analysis is extended to object-oriented specifications. Examples illustrate the application of the checker methods implemented by an automated tool-set

Measuring Health Information Dissemination and Identifying Target Interest Communities on Twitter: Methods Development and Case Study of the @SafetyMD Network.

Science.gov (United States)

Kandadai, Venk; Yang, Haodong; Jiang, Ling; Yang, Christopher C; Fleisher, Linda; Winston, Flaura Koplin

2016-05-05

Little is known about the ability of individual stakeholder groups to achieve health information dissemination goals through Twitter. This study aimed to develop and apply methods for the systematic evaluation and optimization of health information dissemination by stakeholders through Twitter. Tweet content from 1790 followers of @SafetyMD (July-November 2012) was examined. User emphasis, a new indicator of Twitter information dissemination, was defined and applied to retweets across two levels of retweeters originating from @SafetyMD. User interest clusters were identified based on principal component analysis (PCA) and hierarchical cluster analysis (HCA) of a random sample of 170 followers. User emphasis of keywords remained across levels but decreased by 9.5 percentage points. PCA and HCA identified 12 statistically unique clusters of followers within the @SafetyMD Twitter network. This study is one of the first to develop methods for use by stakeholders to evaluate and optimize their use of Twitter to disseminate health information. Our new methods provide preliminary evidence that individual stakeholders can evaluate the effectiveness of health information dissemination and create content-specific clusters for more specific targeted messaging.

A simple method to identify areas of environmental risk due to manure application.

Science.gov (United States)

Flores, Héctor; Arumí, José Luis; Rivera, Diego; Lagos, L Octavio

2012-06-01

The management of swine manure is becoming an important environmental issue in Chile. One option for the final disposal of manure is to use it as a biofertilizer, but this practice could impact the surrounding environment. To assess the potential environmental impacts of the use of swine manure as a biofertilizer, we propose a method to identify zones of environmental risk through indices. The method considers two processes: nutrient runoff and solute leaching, and uses available information about soils, crops and management practices (irrigation, fertilization, and rotation). We applied the method to qualitatively assess the environmental risk associated with the use of swine manure as a biofertilizer in an 8,000-pig farm located in Central Chile. Results showed that the farm has a moderate environmental risk, but some specific locations have high environmental risks, especially those associated with impacts on areas surrounding water resources. This information could assist the definition of better farm-level management practices, as well as the preservation of riparian vegetation acting as buffer strips. The main advantage of our approach is that it combines qualitative and quantitative information, including particular situations or field features based on expert knowledge. The method is flexible, simple, and can be easily extended or adapted to other processes.

A Statistical Method of Identifying Interactions in Neuron–Glia Systems Based on Functional Multicell Ca2+ Imaging

Science.gov (United States)

Nakae, Ken; Ikegaya, Yuji; Ishikawa, Tomoe; Oba, Shigeyuki; Urakubo, Hidetoshi; Koyama, Masanori; Ishii, Shin

2014-01-01

Crosstalk between neurons and glia may constitute a significant part of information processing in the brain. We present a novel method of statistically identifying interactions in a neuron–glia network. We attempted to identify neuron–glia interactions from neuronal and glial activities via maximum-a-posteriori (MAP)-based parameter estimation by developing a generalized linear model (GLM) of a neuron–glia network. The interactions in our interest included functional connectivity and response functions. We evaluated the cross-validated likelihood of GLMs that resulted from the addition or removal of connections to confirm the existence of specific neuron-to-glia or glia-to-neuron connections. We only accepted addition or removal when the modification improved the cross-validated likelihood. We applied the method to a high-throughput, multicellular in vitro Ca2+ imaging dataset obtained from the CA3 region of a rat hippocampus, and then evaluated the reliability of connectivity estimates using a statistical test based on a surrogate method. Our findings based on the estimated connectivity were in good agreement with currently available physiological knowledge, suggesting our method can elucidate undiscovered functions of neuron–glia systems. PMID:25393874

A simple method for identifying parameter correlations in partially observed linear dynamic models.

Science.gov (United States)

Li, Pu; Vu, Quoc Dong

2015-12-14

Parameter estimation represents one of the most significant challenges in systems biology. This is because biological models commonly contain a large number of parameters among which there may be functional interrelationships, thus leading to the problem of non-identifiability. Although identifiability analysis has been extensively studied by analytical as well as numerical approaches, systematic methods for remedying practically non-identifiable models have rarely been investigated. We propose a simple method for identifying pairwise correlations and higher order interrelationships of parameters in partially observed linear dynamic models. This is made by derivation of the output sensitivity matrix and analysis of the linear dependencies of its columns. Consequently, analytical relations between the identifiability of the model parameters and the initial conditions as well as the input functions can be achieved. In the case of structural non-identifiability, identifiable combinations can be obtained by solving the resulting homogenous linear equations. In the case of practical non-identifiability, experiment conditions (i.e. initial condition and constant control signals) can be provided which are necessary for remedying the non-identifiability and unique parameter estimation. It is noted that the approach does not consider noisy data. In this way, the practical non-identifiability issue, which is popular for linear biological models, can be remedied. Several linear compartment models including an insulin receptor dynamics model are taken to illustrate the application of the proposed approach. Both structural and practical identifiability of partially observed linear dynamic models can be clarified by the proposed method. The result of this method provides important information for experimental design to remedy the practical non-identifiability if applicable. The derivation of the method is straightforward and thus the algorithm can be easily implemented into a

Method for investigating management impact to causes and consequences of specific hazards MIMIX

Energy Technology Data Exchange (ETDEWEB)

Heikkilae, J; Rouhiainen, V; Suokas, J [VTT Manufacturing Technology, Tampere (Finland). Safety Engineering; Rasmussen, B [Risoe National Lab., Roskilde (Denmark)

1996-12-31

Method for Investigating Management Impact to Causes and Consequences of Specific Hazards (MIMIX) is a new method for the identification of deficiencies in managerial means and practices used for maintaining and improving safety in a plant. MIMIX is a part of TOMHID methodology which is aimed for overall identification of hazards in a chemical plant. However, MIMIX can be used independently. This report includes guidelines for carrying out a MIMIX analysis. Some experiences from TOMHID analysis case studies, forms and other supporting material (appendix A) and an example of the preparation of incident scenarios (appendix B) are also included in the report. MIMIX consists of three main stages: preparation of incident scenarios, worker interviews and management interviews. A couple of incident scenarios are prepared to support the worker interviews. In each worker interview, such undesired conditions in the plant which promote errors and violations affecting the incident described in a scenario are identified. Deficiencies in managerial means and practices used for correcting the identified undesired conditions are investigated with management interviews. (author)

Method for investigating management impact to causes and consequences of specific hazards MIMIX

Energy Technology Data Exchange (ETDEWEB)

Heikkilae, J.; Rouhiainen, V.; Suokas, J. [VTT Manufacturing Technology, Tampere (Finland). Safety Engineering; Rasmussen, B. [Risoe National Lab., Roskilde (Denmark)

1995-12-31

Method for Investigating Management Impact to Causes and Consequences of Specific Hazards (MIMIX) is a new method for the identification of deficiencies in managerial means and practices used for maintaining and improving safety in a plant. MIMIX is a part of TOMHID methodology which is aimed for overall identification of hazards in a chemical plant. However, MIMIX can be used independently. This report includes guidelines for carrying out a MIMIX analysis. Some experiences from TOMHID analysis case studies, forms and other supporting material (appendix A) and an example of the preparation of incident scenarios (appendix B) are also included in the report. MIMIX consists of three main stages: preparation of incident scenarios, worker interviews and management interviews. A couple of incident scenarios are prepared to support the worker interviews. In each worker interview, such undesired conditions in the plant which promote errors and violations affecting the incident described in a scenario are identified. Deficiencies in managerial means and practices used for correcting the identified undesired conditions are investigated with management interviews. (author)

On-line method to identify control rod drops in Pressurized Water Reactors

International Nuclear Information System (INIS)

Souza, T.J.; Martinez, A.S.; Medeiros, J.A.C.C.; Palma, D.A.P.; Gonçalves, A.C.

2014-01-01

Highlights: • On-line method to identify control rod drops in PWR reactors. • Identification method based on the readings of the ex-core detector. • Recognition of the patterns in the ex-core detector responses. - Abstract: A control rod drop event in PWR reactors leads to an unsafe operating condition. It is important to quickly identify the rod to minimise undesirable effects in such a scenario. The goal of this work is to develop an online method to identify control rod drops in PWR reactors. The method entails the construction of a tool based on ex-core detector responses. It proposes to recognize patterns in the neutron ex-core detectors responses and thus to make an online identification of a control rod drop in the core during the reactor operation. The results of the study, as well as the behaviour of the detector responses demonstrated the feasibility of this method

A Systematic Review of Validated Methods for Identifying Cerebrovascular Accident or Transient Ischemic Attack Using Administrative Data

Science.gov (United States)

Andrade, Susan E.; Harrold, Leslie R.; Tjia, Jennifer; Cutrona, Sarah L.; Saczynski, Jane S.; Dodd, Katherine S.; Goldberg, Robert J.; Gurwitz, Jerry H.

2012-01-01

Purpose To perform a systematic review of the validity of algorithms for identifying cerebrovascular accidents (CVAs) or transient ischemic attacks (TIAs) using administrative and claims data. Methods PubMed and Iowa Drug Information Service (IDIS) searches of the English language literature were performed to identify studies published between 1990 and 2010 that evaluated the validity of algorithms for identifying CVAs (ischemic and hemorrhagic strokes, intracranial hemorrhage and subarachnoid hemorrhage) and/or TIAs in administrative data. Two study investigators independently reviewed the abstracts and articles to determine relevant studies according to pre-specified criteria. Results A total of 35 articles met the criteria for evaluation. Of these, 26 articles provided data to evaluate the validity of stroke, 7 reported the validity of TIA, 5 reported the validity of intracranial bleeds (intracerebral hemorrhage and subarachnoid hemorrhage), and 10 studies reported the validity of algorithms to identify the composite endpoints of stroke/TIA or cerebrovascular disease. Positive predictive values (PPVs) varied depending on the specific outcomes and algorithms evaluated. Specific algorithms to evaluate the presence of stroke and intracranial bleeds were found to have high PPVs (80% or greater). Algorithms to evaluate TIAs in adult populations were generally found to have PPVs of 70% or greater. Conclusions The algorithms and definitions to identify CVAs and TIAs using administrative and claims data differ greatly in the published literature. The choice of the algorithm employed should be determined by the stroke subtype of interest. PMID:22262598

CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens.

Science.gov (United States)

Bais, Preeti; Namburi, Sandeep; Gatti, Daniel M; Zhang, Xinyu; Chuang, Jeffrey H

2017-10-01

We present CloudNeo, a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data. Tumor-specific mutant peptides can be detected by the immune system through their interactions with the human leukocyte antigen complex, and neoantigen presence has recently been shown to correlate with anti T-cell immunity and efficacy of checkpoint inhibitor therapy. However computing capabilities to identify neoantigens from genomic sequencing data are a limiting factor for understanding their role. This challenge has grown as cancer datasets become increasingly abundant, making them cumbersome to store and analyze on local servers. Our cloud-based pipeline provides scalable computation capabilities for neoantigen identification while eliminating the need to invest in local infrastructure for data transfer, storage or compute. The pipeline is a Common Workflow Language (CWL) implementation of human leukocyte antigen (HLA) typing using Polysolver or HLAminer combined with custom scripts for mutant peptide identification and NetMHCpan for neoantigen prediction. We have demonstrated the efficacy of these pipelines on Amazon cloud instances through the Seven Bridges Genomics implementation of the NCI Cancer Genomics Cloud, which provides graphical interfaces for running and editing, infrastructure for workflow sharing and version tracking, and access to TCGA data. The CWL implementation is at: https://github.com/TheJacksonLaboratory/CloudNeo. For users who have obtained licenses for all internal software, integrated versions in CWL and on the Seven Bridges Cancer Genomics Cloud platform (https://cgc.sbgenomics.com/, recommended version) can be obtained by contacting the authors. jeff.chuang@jax.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Specific surface area evaluation method by using scanning electron microscopy

International Nuclear Information System (INIS)

Petrescu, Camelia; Petrescu, Cristian; Axinte, Adrian

2000-01-01

Ceramics are among the most interesting materials for a large category of applications, including both industry and health. Among the characteristic of the ceramic materials, the specific surface area is often difficult to evaluate.The paper presents a method of evaluation for the specific surface area of two ceramic powders by means of scanning electron microscopy measurements and an original method of computing the specific surface area.Cumulative curves are used to calculate the specific surface area under assumption that the values of particles diameters follow a normal logarithmic distribution. For two powder types, X7R and NPO the results are the following: - for the density ρ (g/cm 2 ), 5.5 and 6.0, respectively; - for the average diameter D bar (μm), 0.51 and 0.53, respectively; - for σ, 1.465 and 1.385, respectively; - for specific surface area (m 2 /g), 1.248 and 1.330, respectively. The obtained results are in good agreement with the values measured by conventional methods. (authors)

Identifying influential spreaders in complex networks based on kshell hybrid method

Science.gov (United States)

Namtirtha, Amrita; Dutta, Animesh; Dutta, Biswanath

2018-06-01

Influential spreaders are the key players in maximizing or controlling the spreading in a complex network. Identifying the influential spreaders using kshell decomposition method has become very popular in the recent time. In the literature, the core nodes i.e. with the largest kshell index of a network are considered as the most influential spreaders. We have studied the kshell method and spreading dynamics of nodes using Susceptible-Infected-Recovered (SIR) epidemic model to understand the behavior of influential spreaders in terms of its topological location in the network. From the study, we have found that every node in the core area is not the most influential spreader. Even a strategically placed lower shell node can also be a most influential spreader. Moreover, the core area can also be situated at the periphery of the network. The existing indexing methods are only designed to identify the most influential spreaders from core nodes and not from lower shells. In this work, we propose a kshell hybrid method to identify highly influential spreaders not only from the core but also from lower shells. The proposed method comprises the parameters such as kshell power, node's degree, contact distance, and many levels of neighbors' influence potential. The proposed method is evaluated using nine real world network datasets. In terms of the spreading dynamics, the experimental results show the superiority of the proposed method over the other existing indexing methods such as the kshell method, the neighborhood coreness centrality, the mixed degree decomposition, etc. Furthermore, the proposed method can also be applied to large-scale networks by considering the three levels of neighbors' influence potential.

Serum Metabolomics to Identify the Liver Disease-Specific Biomarkers for the Progression of Hepatitis to Hepatocellular Carcinoma

Science.gov (United States)

Gao, Rong; Cheng, Jianhua; Fan, Chunlei; Shi, Xiaofeng; Cao, Yuan; Sun, Bo; Ding, Huiguo; Hu, Chengjin; Dong, Fangting; Yan, Xianzhong

2015-12-01

Hepatocellular carcinoma (HCC) is a common malignancy that has region specific etiologies. Unfortunately, 85% of cases of HCC are diagnosed at an advanced stage. Reliable biomarkers for the early diagnosis of HCC are urgently required to reduced mortality and therapeutic expenditure. We established a non-targeted gas chromatography-time of flight-mass spectrometry (GC-TOFMS) metabolomics method in conjunction with Random Forests (RF) analysis based on 201 serum samples from healthy controls (NC), hepatitis B virus (HBV), liver cirrhosis (LC) and HCC patients to explore the metabolic characteristics in the progression of hepatocellular carcinogenesis. Ultimately, 15 metabolites were identified intimately associated with the process. Phenylalanine, malic acid and 5-methoxytryptamine for HBV vs. NC, palmitic acid for LC vs. HBV, and asparagine and β-glutamate for HCC vs. LC were screened as the liver disease-specific potential biomarkers with an excellent discriminant performance. All the metabolic perturbations in these liver diseases are associated with pathways for energy metabolism, macromolecular synthesis, and maintaining the redox balance to protect tumor cells from oxidative stress.

Systematic screening of isogenic cancer cells identifies DUSP6 as context-specific synthetic lethal target in melanoma

DEFF Research Database (Denmark)

Wittig-Blaich, Stephanie; Wittig, Rainer; Schmidt, Steffen

2017-01-01

Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few technolo......Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few...... technologies are available for the systematic downstream evaluation of these results to identify novel starting points of future cancer therapies. We improved and extended a site-specific recombination-based system for systematic analysis of the individual functions of a large number of candidate genes......, a library of 108 isogenic melanoma cell lines was constructed and 8 genes were identified that significantly reduced viability in a discovery screen and in an independent validation screen. Here, we demonstrate the broad applicability of this recombination-based method and we proved its potential...

Chapter 9: Metering Cross-Cutting Protocol. The Uniform Methods Project: Methods for Determining Energy-Efficiency Savings for Specific Measures

Energy Technology Data Exchange (ETDEWEB)

Mort, Dan [ADM Associates, Inc. Sacramento, CA (United States)

2017-09-01

Estimated energy savings are calculated as the difference between the energy use during the baseline period and the energy use during the post installation period of the EEM. This chapter describes the physical properties measured in the process of evaluating EEMs and the specific metering methods for several types of measurements. Skill-level requirements and other operating considerations are discussed, including where, when, and how often measurements should be made. The subsequent section identifies metering equipment types and their respective measurement accuracies. This is followed by sections containing suggestions regarding proper data handling procedures and the categorization and definition of several load types.

Novel HTS strategy identifies TRAIL-sensitizing compounds acting specifically through the caspase-8 apoptotic axis.

Directory of Open Access Journals (Sweden)

Darren Finlay

Full Text Available Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand (TRAIL is potentially a very important therapeutic as it shows selectivity for inducing apoptosis in cancer cells whilst normal cells are refractory. TRAIL binding to its cognate receptors, Death Receptors-4 and -5, leads to recruitment of caspase-8 and classical activation of downstream effector caspases, leading to apoptosis. As with many drugs however, TRAIL's usefulness is limited by resistance, either innate or acquired. We describe here the development of a novel 384-well high-throughput screening (HTS strategy for identifying potential TRAIL-sensitizing agents that act solely in a caspase-8 dependent manner. By utilizing a TRAIL resistant cell line lacking caspase-8 (NB7 compared to the same cells reconstituted with the wild-type protein, or with a catalytically inactive point mutant of caspase-8, we are able to identify compounds that act specifically through the caspase-8 axis, rather than through general toxicity. In addition, false positive hits can easily be "weeded out" in this assay due to their activity in cells lacking caspase-8-inducible activity. Screening of the library of pharmacologically active compounds (LOPAC was performed as both proof-of-concept and to discover potential unknown TRAIL sensitizers whose mechanism is caspase-8 mediated. We identified known TRAIL sensitizers from the library and identified new compounds that appear to sensitize specifically through caspase-8. In sum, we demonstrate proof-of-concept and discovery of novel compounds with a screening strategy optimized for the detection of caspase-8 pathway-specific TRAIL sensitizers. This screen was performed in the 384-well format, but could easily be further miniaturized, allows easy identification of artifactual false positives, and is highly scalable to accommodate diverse libraries.

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

KAUST Repository

Olimpieri, Pier Paolo

2013-06-26

MOTIVATION: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. RESULTS: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. AVAILABILITY: http://www.biocomputing.it/proABC. CONTACT: anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Science.gov (United States)

Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

2016-01-19

Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

Science.gov (United States)

Tycko, Josh; Myer, Vic E.; Hsu, Patrick D.

2016-01-01

Summary Advances in the development of delivery, repair, and specificity strategies for the CRISPR-Cas9 genome engineering toolbox are helping researchers understand gene function with unprecedented precision and sensitivity. CRISPR-Cas9 also holds enormous therapeutic potential for the treatment of genetic disorders by directly correcting disease-causing mutations. Although the Cas9 protein has been shown to bind and cleave DNA at off-target sites, the field of Cas9 specificity is rapidly progressing with marked improvements in guide RNA selection, protein and guide engineering, novel enzymes, and off-target detection methods. We review important challenges and breakthroughs in the field as a comprehensive practical guide to interested users of genome editing technologies, highlighting key tools and strategies for optimizing specificity. The genome editing community should now strive to standardize such methods for measuring and reporting off-target activity, while keeping in mind that the goal for specificity should be continued improvement and vigilance. PMID:27494557

System and method for deriving a process-based specification

Science.gov (United States)

Hinchey, Michael Gerard (Inventor); Rash, James Larry (Inventor); Rouff, Christopher A. (Inventor)

2009-01-01

A system and method for deriving a process-based specification for a system is disclosed. The process-based specification is mathematically inferred from a trace-based specification. The trace-based specification is derived from a non-empty set of traces or natural language scenarios. The process-based specification is mathematically equivalent to the trace-based specification. Code is generated, if applicable, from the process-based specification. A process, or phases of a process, using the features disclosed can be reversed and repeated to allow for an interactive development and modification of legacy systems. The process is applicable to any class of system, including, but not limited to, biological and physical systems, electrical and electro-mechanical systems in addition to software, hardware and hybrid hardware-software systems.

A comparison of statistical methods for identifying out-of-date systematic reviews.

Directory of Open Access Journals (Sweden)

Porjai Pattanittum

Full Text Available BACKGROUND: Systematic reviews (SRs can provide accurate and reliable evidence, typically about the effectiveness of health interventions. Evidence is dynamic, and if SRs are out-of-date this information may not be useful; it may even be harmful. This study aimed to compare five statistical methods to identify out-of-date SRs. METHODS: A retrospective cohort of SRs registered in the Cochrane Pregnancy and Childbirth Group (CPCG, published between 2008 and 2010, were considered for inclusion. For each eligible CPCG review, data were extracted and "3-years previous" meta-analyses were assessed for the need to update, given the data from the most recent 3 years. Each of the five statistical methods was used, with random effects analyses throughout the study. RESULTS: Eighty reviews were included in this study; most were in the area of induction of labour. The numbers of reviews identified as being out-of-date using the Ottawa, recursive cumulative meta-analysis (CMA, and Barrowman methods were 34, 7, and 7 respectively. No reviews were identified as being out-of-date using the simulation-based power method, or the CMA for sufficiency and stability method. The overall agreement among the three discriminating statistical methods was slight (Kappa = 0.14; 95% CI 0.05 to 0.23. The recursive cumulative meta-analysis, Ottawa, and Barrowman methods were practical according to the study criteria. CONCLUSION: Our study shows that three practical statistical methods could be applied to examine the need to update SRs.

Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods

Science.gov (United States)

Cubuk, E. D.; Schoenholz, S. S.; Rieser, J. M.; Malone, B. D.; Rottler, J.; Durian, D. J.; Kaxiras, E.; Liu, A. J.

2015-03-01

We use machine-learning methods on local structure to identify flow defects—or particles susceptible to rearrangement—in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.

Why conventional detection methods fail in identifying the existence of contamination events.

Science.gov (United States)

Liu, Shuming; Li, Ruonan; Smith, Kate; Che, Han

2016-04-15

Early warning systems are widely used to safeguard water security, but their effectiveness has raised many questions. To understand why conventional detection methods fail to identify contamination events, this study evaluates the performance of three contamination detection methods using data from a real contamination accident and two artificial datasets constructed using a widely applied contamination data construction approach. Results show that the Pearson correlation Euclidean distance (PE) based detection method performs better for real contamination incidents, while the Euclidean distance method (MED) and linear prediction filter (LPF) method are more suitable for detecting sudden spike-like variation. This analysis revealed why the conventional MED and LPF methods failed to identify existence of contamination events. The analysis also revealed that the widely used contamination data construction approach is misleading. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identifying specific interstellar polycyclic aromatic hydrocarbons

International Nuclear Information System (INIS)

Mulas, Giacomo; Malloci, Giuliano; Porceddu, Ignazio

2005-01-01

Interstellar Polycyclic Aromatic Hydrocarbons (PAHs) have been thought to be ubiquitous for more than twenty years, yet no single species in this class has been identified in the Interstellar Medium (ISM) to date. The unprecedented sensitivity and resolution of present Infrared Space Observatory (ISO) and forthcoming Herschel observations in the far infrared spectral range will offer a unique way out of this embarrassing impasse

Array Manipulation And Matrix-Tree Method To Identify High Concentration Regions HCRs

Directory of Open Access Journals (Sweden)

Rachana Arora

2015-08-01

Full Text Available Abstract-Sequence Alignment and Analysis is one of the most important applications of bioinformatics. It involves alignment a pair or more sequences with each other and identify a common pattern that would ultimately lead to conclusions of homology or dissimilarity. A number of algorithms that make use of dynamic programming to perform alignment between sequences are available. One of their main disadvantages is that they involve complicated computations and backtracking methods that are difficult to implement. This paper describes a much simpler method to identify common regions in 2 sequences and align them based on the density of common sequences identified.

Time-trends in method-specific suicide rates compared with the availability of specific compounds

DEFF Research Database (Denmark)

Nordentoft, Merete; Qin, Ping; Helweg-Larsen, Karin

2006-01-01

Restriction of means for suicide is an important part of suicide preventive strategies in different countries. All suicides in Denmark between 1970 and 2000 were examined with regard to method used for suicide. Overall suicide mortality and method-specific suicide mortality was compared...... in the number of suicides by self-poisoning with these compounds. Restricted access occurred concomittantly with a 55% decrease in suicide rate....

Specific methods on in-pile gammametry

International Nuclear Information System (INIS)

Pointud, M.-L.; Michel, Francois.

1979-01-01

The gammametry technique in nuclear research reactors has evolved by the adequation of its means and the quality of its results since its beginnings in 1972. We do not propose here to make a detailed presentation, nor describe the kinds of well known results that can henceforth be attained with it in a conventional manner; our intention, on the other hand, is to describe a few specific methods developed for using it in the SILOE reactor of the CEN/G [fr

Identifying User Profiles from Statistical Grouping Methods

Directory of Open Access Journals (Sweden)

Francisco Kelsen de Oliveira

2018-02-01

Full Text Available This research aimed to group users into subgroups according to their levels of knowledge about technology. Statistical hierarchical and non-hierarchical clustering methods were studied, compared and used in the creations of the subgroups from the similarities of the skill levels with these users’ technology. The research sample consisted of teachers who answered online questionnaires about their skills with the use of software and hardware with educational bias. The statistical methods of grouping were performed and showed the possibilities of groupings of the users. The analyses of these groups allowed to identify the common characteristics among the individuals of each subgroup. Therefore, it was possible to define two subgroups of users, one with skill in technology and another with skill with technology, so that the partial results of the research showed two main algorithms for grouping with 92% similarity in the formation of groups of users with skill with technology and the other with little skill, confirming the accuracy of the techniques of discrimination against individuals.

A method to identify differential expression profiles of time-course gene data with Fourier transformation.

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Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

2013-10-18

Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be

In vivo conditions to identify Prkci phosphorylation targets using the analog-sensitive kinase method in zebrafish.

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Elena Cibrián Uhalte

Full Text Available Protein kinase C iota is required for various cell biological processes including epithelial tissue polarity and organ morphogenesis. To gain mechanistic insight into different roles of this kinase, it is essential to identify specific substrate proteins in their cellular context. The analog-sensitive kinase method provides a powerful tool for the identification of kinase substrates under in vivo conditions. However, it has remained a major challenge to establish screens based on this method in multicellular model organisms. Here, we report the methodology for in vivo conditions using the analog-sensitive kinase method in a genetically-tractable vertebrate model organism, the zebrafish. With this approach, kinase substrates can uniquely be labeled in the developing zebrafish embryo using bulky ATPγS analogs which results in the thiophosphorylation of substrates. The labeling of kinase substrates with a thiophosphoester epitope differs from phosphoesters that are generated by all other kinases and allows for an enrichment of thiophosphopeptides by immunoaffinity purification. This study provides the foundation for using the analog-sensitive kinase method in the context of complex vertebrate development, physiology, or disease.

A simple negative selection method to identify adenovirus recombinants using colony PCR

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Yongliang Zhao

2014-01-01

Conclusions: The negative selection method to identify AdEasy adenovirus recombinants by colony PCR can identify the recombined colony within a short time-period, and maximally avoid damage to the recombinant plasmid by limiting recombination time, resulting in improved adenovirus packaging.

Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms

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Arehart Eric

2009-03-01

Full Text Available Abstract Background The fidelity of DNA replication serves as the nidus for both genetic evolution and genomic instability fostering disease. Single nucleotide polymorphisms (SNPs constitute greater than 80% of the genetic variation between individuals. A new theory regarding DNA replication fidelity has emerged in which selectivity is governed by base-pair geometry through interactions between the selected nucleotide, the complementary strand, and the polymerase active site. We hypothesize that specific nucleotide combinations in the flanking regions of SNP fragments are associated with mutation. Results We modeled the relationship between DNA sequence and observed polymorphisms using the novel multifactor dimensionality reduction (MDR approach. MDR was originally developed to detect synergistic interactions between multiple SNPs that are predictive of disease susceptibility. We initially assembled data from the Broad Institute as a pilot test for the hypothesis that flanking region patterns associate with mutagenesis (n = 2194. We then confirmed and expanded our inquiry with human SNPs within coding regions and their flanking sequences collected from the National Center for Biotechnology Information (NCBI database (n = 29967 and a control set of sequences (coding region not associated with SNP sites randomly selected from the NCBI database (n = 29967. We discovered seven flanking region pattern associations in the Broad dataset which reached a minimum significance level of p ≤ 0.05. Significant models (p Conclusion The present study represents the first use of this computational methodology for modeling nonlinear patterns in molecular genetics. MDR was able to identify distinct nucleotide patterning around sites of mutations dependent upon the observed nucleotide change. We discovered one flanking region set that included five nucleotides clustered around a specific type of SNP site. Based on the strongly associated patterns identified in

Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer.

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Tang, Yew Chung; Ho, Szu-Chi; Tan, Elisabeth; Ng, Alvin Wei Tian; McPherson, John R; Goh, Germaine Yen Lin; Teh, Bin Tean; Bard, Frederic; Rozen, Steven G

2018-03-22

-SSL patterns of activity in a large proportion of PTEN-deficient breast cancer cell lines and are potential specific vulnerabilities in PTEN-deficient breast cancer. Furthermore, the NUAK1 PTEN-SSL vulnerability identified by RNA interference techniques can be recapitulated and exploited using the small molecule kinase inhibitor HTH-01-015. Thus, NUAK1 inhibition may be an effective strategy for precision treatment of PTEN-deficient breast tumors.

Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior

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Julia Brasch

2018-05-01

Full Text Available Summary: Type II cadherins are cell-cell adhesion proteins critical for tissue patterning and neuronal targeting but whose molecular binding code remains poorly understood. Here, we delineate binding preferences for type II cadherin cell-adhesive regions, revealing extensive heterophilic interactions between specific pairs, in addition to homophilic interactions. Three distinct specificity groups emerge from our analysis with members that share highly similar heterophilic binding patterns and favor binding to one another. Structures of adhesive fragments from each specificity group confirm near-identical dimer topology conserved throughout the family, allowing interface residues whose conservation corresponds to specificity preferences to be identified. We show that targeted mutation of these residues converts binding preferences between specificity groups in biophysical and co-culture assays. Our results provide a detailed understanding of the type II cadherin interaction map and a basis for defining their role in tissue patterning and for the emerging importance of their heterophilic interactions in neural connectivity. : Type II cadherins are a family of vertebrate cell adhesion proteins expressed primarily in the CNS. Brasch et al. measure binding between adhesive fragments, revealing homophilic and extensive selective heterophilic binding with specificities that define groups of similar cadherins. Structures reveal common adhesive dimers, with residues governing cell-adhesive specificity. Keywords: cell adhesion, crystal structure, hemophilic specificity, heterophilic specificity, neural patterning, synaptic targeting, cadherin

The research on business rules classification and specification methods

OpenAIRE

Baltrušaitis, Egidijus

2005-01-01

The work is based on the research of business rules classification and specification methods. The basics of business rules approach are discussed. The most common business rules classification and modeling methods are analyzed. Business rules modeling techniques and tools for supporting them in the information systems are presented. Basing on the analysis results business rules classification method is proposed. Templates for every business rule type are presented. Business rules structuring ...

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

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Tien, Shin-Ming; Hsu, Chih-Yuan; Chen, Bor-Sen

2016-01-01

Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

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Shin-Ming Tien

Full Text Available Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

A Simple Method for Identifying the Acromioclavicular Joint During Arthroscopic Procedures

OpenAIRE

Javed, Saqib; Heasley, Richard; Ravenscroft, Matt

2013-01-01

Arthroscopic acromioclavicular joint excision is performed via an anterior portal and is technically demanding. We present a simple method for identifying the acromioclavicular joint during arthroscopic procedures.

Comparison of methods to identify crop productivity constraints in developing countries. A review

NARCIS (Netherlands)

Kraaijvanger, R.G.M.; Sonneveld, M.P.W.; Almekinders, C.J.M.; Veldkamp, T.

2015-01-01

Selecting a method for identifying actual crop productivity constraints is an important step for triggering innovation processes. Applied methods can be diverse and although such methods have consequences for the design of intervention strategies, documented comparisons between various methods are

Tumor specific glycoproteins and method for detecting tumorigenic cancers

International Nuclear Information System (INIS)

Davidson, E.A.; Bolmer, S.D.

1981-01-01

The detection of tumour specific glycoproteins (TSGP) in human sera often indicates the presence of a malignant tumour in a patient. The distinguishing characteristics of TSGP isolated from the blood sera of cancer patients are described in detail together with methods of TSGP isolation and purification. Details are also given of radioimmunoassay techniques capable of detecting very low levels of serum TSGP with high specificity. (U.K.)

A method for isolating identifying and culturing of rat trachea-bronchia epithelial cells

International Nuclear Information System (INIS)

Cui Fengmei; Su Shibiao; Nie Jihua; Li Bingyan; Tong Jian

2005-01-01

Objective: To explore a method for isolating identifying and culturing the rat trachea-bronchia epithelial cells. Methods: The rat trachea-bronchia epithelial cells were isolated by digestion with pronase and brushing with cell brush, identified using confocul and cultured in entire F12 media with no serum. Results: With this method, cells in high purity and high viability could be obtained, and about 10 6 cells per rat. The cells grow well in entire F12 media with no serum. Conclusion: The method is useful for isolating rate trachea-bronchia epithelial cells and the entire F12 media with no serum is effective for culturing. (authors)

Analytical methods to identify irradiated food

International Nuclear Information System (INIS)

Helle, N.; Schreiber, G.A.; Boegl, K.W.

1992-01-01

During the last years, three promising techniques for the identification of irradiated food were developed: - Studies of luminescence, mainly thermoluminescence measurements, of food containing mineral impurities like spices, dried vegetables: and fresh fuit and vegetables. This technique can probably be applied also to food with crystalline components like shells or bones. - Gaschromatographic/mass-spectrometric investigation of radiation-induced lipid changes. - Electron-spin-resonance measurements of dried products or of products containing dry components like bones, fish bones, shells or seeds. The thermoluminescence technique has been routinely applied for more than one year by several German Food Inspection Laboratories. The results suggest that there are scarcely any irradiated spices and dried vegetables in the German market. Gaschromatography/mass spectrometry of lipid components and electron-spin-resonance spectroscopy will be established in routine food inspections in Germany in the next two years. Further possibilities to identify irradiated food are the analysis of specific changes in amino acids, DNA and carbohydrates. Radiation-induced viscosity changes, and changes in electric properties (impedance) may be helpful in identifiying at least some irradiated products. Also microbiological and biological techniques as e.g. microbial flora shift or embryo development tests in citrus fruit have been considered. All activities concerning the development of identification techniques are now coordinated by the European Communities and by IAEA. (orig.) [de

Identifying and prioritizing customer requirements from tractor production by QFD method

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H Taghizadeh

2017-05-01

Full Text Available Introduction Discovering and understanding customer needs and expectations are considered as important factors on customer satisfaction and play vital role to maintain the current activity among its competitors, proceeding and obtaining customer satisfaction which are critical factors to design a successful production; thus the successful organizations must meet their needs containing the quality of the products or services to customers. Quality Function Deployment (QFD is a technique for studying demands and needs of customers which is going to give more emphasis to the customer's interests in this way. The QFD method in general implemented various tools and methods for reaching qualitative goals; but the most important and the main tool of this method is the house of quality diagrams. The Analytic Hierarchy Process (AHP is a famous and common MADM method based on pair wise comparisons used for determining the priority of understudied factors in various studies until now. With considering effectiveness of QFD method to explicating customer's demands and obtaining customer satisfaction, generally, the researchers followed this question's suite and scientific answer: how can QFD explicate real demands and requirements of customers from tractor final production and what is the prioritization of these demands and requirements in view of customers. Accordingly, the aim of this study was to identify and prioritize the customer requirements of Massey Ferguson (MF 285 tractor production in Iran tractor manufacturing company with t- student statistical test, AHP and QFD methods. Materials and Methods Research method was descriptive and statistical population included all of the tractor customers of Tractor Manufacturing Company in Iran from March 2011 to March 2015. The statistical sample size was 171 which are determined with Cochran index. Moreover, 20 experts' opinion has been considered for determining product's technical requirements. Literature

Increasing organizational energy conservation behaviors: Comparing the theory of planned behavior and reasons theory for identifying specific motivational factors to target for change

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Finlinson, Scott Michael

Social scientists frequently assess factors thought to underlie behavior for the purpose of designing behavioral change interventions. Researchers commonly identify these factors by examining relationships between specific variables and the focal behaviors being investigated. Variables with the strongest relationships to the focal behavior are then assumed to be the most influential determinants of that behavior, and therefore often become the targets for change in a behavioral change intervention. In the current proposal, multiple methods are used to compare the effectiveness of two theoretical frameworks for identifying influential motivational factors. Assessing the relative influence of all factors and sets of factors for driving behavior should clarify which framework and methodology is the most promising for identifying effective change targets. Results indicated each methodology adequately predicted the three focal behaviors examined. However, the reasons theory approach was superior for predicting factor influence ratings compared to the TpB approach. While common method variance contamination had minimal impact on the results or conclusions derived from the present study's findings, there were substantial differences in conclusions depending on the questionnaire design used to collect the data. Examples of applied uses of the present study are discussed.

The use of human factors methods to identify and mitigate safety issues in radiation therapy

International Nuclear Information System (INIS)

Chan, Alvita J.; Islam, Mohammad K.; Rosewall, Tara; Jaffray, David A.; Easty, Anthony C.; Cafazzo, Joseph A.

2010-01-01

Background and purpose: New radiation therapy technologies can enhance the quality of treatment and reduce error. However, the treatment process has become more complex, and radiation dose is not always delivered as intended. Using human factors methods, a radiotherapy treatment delivery process was evaluated, and a redesign was undertaken to determine the effect on system safety. Material and methods: An ethnographic field study and workflow analysis was conducted to identify human factors issues of the treatment delivery process. To address specific issues, components of the user interface were redesigned through a user-centered approach. Sixteen radiation therapy students were then used to experimentally evaluate the redesigned system through a usability test to determine the effectiveness in mitigating use errors. Results: According to findings from the usability test, the redesigned system successfully reduced the error rates of two common errors (p < .04 and p < .01). It also improved the mean task completion time by 5.5% (p < .02) and achieved a higher level of user satisfaction. Conclusions: These findings demonstrated the importance and benefits of applying human factors methods in the design of radiation therapy systems. Many other opportunities still exist to improve patient safety in this area using human factors methods.

A Nondestructive Method to Identify POP Contamination Sources in Omnivorous Seabirds.

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Michielsen, Rosanne J; Shamoun-Baranes, Judy; Parsons, John R; Kraak, Michiel H S

2018-03-13

Persistent organic pollutants (POPs) are present in almost all environments due to their high bioaccumulation potential. Especially species that adapted to human activities, like gulls, might be exposed to harmful concentrations of these chemicals. The nature and degree of the exposure to POPs greatly vary between individual gulls, due to their diverse foraging behavior and specialization in certain foraging tactics. Therefore, in order clarify the effect of POP-contaminated areas on gull populations, it is important to identify the sources of POP contamination in individual gulls. Conventional sampling methods applied when studying POP contamination are destructive and ethically undesired. The aim of this literature review was to evaluate the potential of using feathers as a nondestructive method to determine sources of POP contamination in individual gulls. The reviewed data showed that high concentrations of PCBs and PBDEs in feathers together with a large proportion of less bioaccumulative congeners may indicate that the contamination originates from landfills. Low PCB and PBDE concentrations in feathers and a large proportion of more bioaccumulative congeners could indicate that the contamination originates from marine prey. We propose a nondestructive approach to identify the source of contamination in individual gulls based on individual contamination levels and PCB and PBDE congener profiles in feathers. Despite some uncertainties that might be reduced by future research, we conclude that especially when integrated with other methods like GPS tracking and the analysis of stable isotopic signatures, identifying the source of POP contamination based on congener profiles in feathers could become a powerful nondestructive method.

Football refereeing: Identifying innovative methods

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Reza MohammadKazemi

2014-08-01

Full Text Available The aim of the present study is to identify the potentials innovation in football industry. Data were collected from 10 national and international referees, assistant referees and referees’ supervisors in Iran. In this study, technological innovations are identified that assist better refereeing performances. The analysis revealed a significant relationship between using new technologies and referees ‘performance. The results indicate that elite referees, assistant referees and supervisors agreed to use new technological innovations during the game. According to their comments, this kind of technology causes the referees’ performance development.

Coupling genetics and proteomics to identify aphid proteins associated with vector-specific transmission of polerovirus (luteoviridae).

Science.gov (United States)

Yang, Xiaolong; Thannhauser, T W; Burrows, Mary; Cox-Foster, Diana; Gildow, Fred E; Gray, Stewart M

2008-01-01

Cereal yellow dwarf virus-RPV (CYDV-RPV) is transmitted specifically by the aphids Rhopalosiphum padi and Schizaphis graminum in a circulative nonpropagative manner. The high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. Studies of F(2) progeny from crosses of vector and nonvector genotypes of S. graminum showed that virus transmission efficiency is a heritable trait regulated by multiple genes acting in an additive fashion and that gut- and salivary gland-associated factors are not genetically linked. Utilizing two-dimensional difference gel electrophoresis to compare the proteomes of vector and nonvector parental and F(2) genotypes, four aphid proteins (S4, S8, S29, and S405) were specifically associated with the ability of S. graminum to transmit CYDV-RPV. The four proteins were coimmunoprecipitated with purified RPV, indicating that the aphid proteins are capable of binding to virus. Analysis by mass spectrometry identified S4 as a luciferase and S29 as a cyclophilin, both of which have been implicated in macromolecular transport. Proteins S8 and S405 were not identified from available databases. Study of this unique genetic system coupled with proteomic analysis indicated that these four virus-binding aphid proteins were specifically inherited and conserved in different generations of vector genotypes and suggests that they play a major role in regulating polerovirus transmission.

CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems.

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Lihua J Zhu

Full Text Available CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria that target foreign DNA sequences for cleavage. Derivatives of these complexes have been engineered to cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA and the source of the Cas9 protein. Important considerations for the design of gRNAs are to maximize aimed activity at the desired target site while minimizing off-target cleavage. Because of the rapid advances in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and the development of novel RNA-guided nuclease systems, it is critical to have computational tools that can accommodate a wide range of different parameters for the design of target-specific RNA-guided nuclease systems. We have developed CRISPRseek, a highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will identify potential gRNAs that target a sequence of interest for CRISPR-Cas9 systems from different bacterial species and generate a cleavage score for potential off-target sequences utilizing published or user-supplied weight matrices with position-specific mismatch penalty scores. Identified gRNAs may be further filtered to only include those that occur in paired orientations for increased specificity and/or those that overlap restriction enzyme sites. For applications where gRNAs are desired to discriminate between two related sequences, CRISPRseek can rank gRNAs based on the difference between predicted cleavage scores in each input sequence. CRISPRseek is implemented as a Bioconductor package within the R statistical programming environment, allowing it to be incorporated into computational pipelines to automate the design of gRNAs for target sequences identified in a wide variety of genome-wide analyses. CRISPRseek is available under the GNU General

Identifying Country-Specific Cultures of Physics Education: A differential item functioning approach

Science.gov (United States)

Mesic, Vanes

2012-11-01

In international large-scale assessments of educational outcomes, student achievement is often represented by unidimensional constructs. This approach allows for drawing general conclusions about country rankings with respect to the given achievement measure, but it typically does not provide specific diagnostic information which is necessary for systematic comparisons and improvements of educational systems. Useful information could be obtained by exploring the differences in national profiles of student achievement between low-achieving and high-achieving countries. In this study, we aimed to identify the relative weaknesses and strengths of eighth graders' physics achievement in Bosnia and Herzegovina in comparison to the achievement of their peers from Slovenia. For this purpose, we ran a secondary analysis of Trends in International Mathematics and Science Study (TIMSS) 2007 data. The student sample consisted of 4,220 students from Bosnia and Herzegovina and 4,043 students from Slovenia. After analysing the cognitive demands of TIMSS 2007 physics items, the correspondent differential item functioning (DIF)/differential group functioning contrasts were estimated. Approximately 40% of items exhibited large DIF contrasts, indicating significant differences between cultures of physics education in Bosnia and Herzegovina and Slovenia. The relative strength of students from Bosnia and Herzegovina showed to be mainly associated with the topic area 'Electricity and magnetism'. Classes of items which required the knowledge of experimental method, counterintuitive thinking, proportional reasoning and/or the use of complex knowledge structures proved to be differentially easier for students from Slovenia. In the light of the presented results, the common practice of ranking countries with respect to universally established cognitive categories seems to be potentially misleading.

Performance and specificity of the covalently linked immunomagnetic separation-ATP method for rapid detection and enumeration of enterococci in coastal environments.

Science.gov (United States)

Zimmer-Faust, Amity G; Thulsiraj, Vanessa; Ferguson, Donna; Jay, Jennifer A

2014-05-01

The performance and specificity of the covalently linked immunomagnetic separation-ATP (Cov-IMS/ATP) method for the detection and enumeration of enterococci was evaluated in recreational waters. Cov-IMS/ATP performance was compared with standard methods: defined substrate technology (Enterolert; IDEXX Laboratories), membrane filtration (EPA Method 1600), and an Enterococcus-specific quantitative PCR (qPCR) assay (EPA Method A). We extend previous studies by (i) analyzing the stability of the relationship between the Cov-IMS/ATP method and culture-based methods at different field sites, (ii) evaluating specificity of the assay for seven ATCC Enterococcus species, (iii) identifying cross-reacting organisms binding the antibody-bead complexes with 16S rRNA gene sequencing and evaluating specificity of the assay to five nonenterococcus species, and (iv) conducting preliminary tests of preabsorption as a means of improving the assay. Cov-IMS/ATP was found to perform consistently and with strong agreement rates (based on exceedance/compliance with regulatory limits) of between 83% and 100% compared to the culture-based Enterolert method at a variety of sites with complex inputs. The Cov-IMS/ATP method is specific to five of seven different Enterococcus spp. tested. However, there is potential for nontarget bacteria to bind the antibody, which may be reduced by purification of the IgG serum with preabsorption at problematic sites. The findings of this study help to validate the Cov-IMS/ATP method, suggesting a predictable relationship between the Cov-IMS/ATP method and traditional culture-based methods, which will allow for more widespread application of this rapid and field-portable method for coastal water quality assessment.

An Efficient, Noniterative Method of Identifying the Cost-Effectiveness Frontier.

Science.gov (United States)

Suen, Sze-chuan; Goldhaber-Fiebert, Jeremy D

2016-01-01

Cost-effectiveness analysis aims to identify treatments and policies that maximize benefits subject to resource constraints. However, the conventional process of identifying the efficient frontier (i.e., the set of potentially cost-effective options) can be algorithmically inefficient, especially when considering a policy problem with many alternative options or when performing an extensive suite of sensitivity analyses for which the efficient frontier must be found for each. Here, we describe an alternative one-pass algorithm that is conceptually simple, easier to implement, and potentially faster for situations that challenge the conventional approach. Our algorithm accomplishes this by exploiting the relationship between the net monetary benefit and the cost-effectiveness plane. To facilitate further evaluation and use of this approach, we also provide scripts in R and Matlab that implement our method and can be used to identify efficient frontiers for any decision problem. © The Author(s) 2015.

Nuclear data for specific problems. Part 1: Methods

International Nuclear Information System (INIS)

Leszczynski, Francisco

1999-01-01

The growing volume of basic nuclear data, methods and codes for processing these data, and the wide variety of problems where these data and codes are required, oblige to have an efficient system for managing all this information. In this work we present a new methodology for nuclear data processing, applied to neutron and photon transport calculations for specific problems. The base of the new methodology is the analysis of the requirements, following the chain: Problem-Components-Materials-Elements-Isotopes-Process-Tests-Final product (a library with processed data). This order is the inverse of the normal order followed up to date where, for performing a specific calculation, the first step is the choice of an existing data library for general purposes, without the previous steps of pre-processing data, and tests of the final library. Then, the used data are limited to the isotope content of this library, and the adaptation of material compositions and components to the data availability is necessary , performing finally the required calculations in a rather approximated form, depending on the available data. An interactive computer program for PC , is developed, for managing all the information generated by nuclear data processing, with the additional advantage of having a help tool for performing the needed analysis, before processing data calculations for specific applications. These analyses are based on the particular characteristics of each application, and the processed information of previous cases, is stored in conveniently designed data bases for an easy inspection of its contents. By means of an example of application of the new method, in this paper the methods of analysis and calculations and the tools used (computer programs, data bases and documents) are describes. (author)

Metabolic labeling of sialic acids in tissue culture cell lines: methods to identify substituted and modified radioactive neuraminic acids

International Nuclear Information System (INIS)

Diaz, S.; Varki, A.

1985-01-01

The parent sialic acid N-acetylneuraminic acid can be modified or substituted in various ways, giving rise to a family of more than 25 compounds. The definitive identification of these compounds has previously required isolation of nanomole amounts for mass spectrometry or NMR. We have explored the possibility of using the known metabolic precursors of the sialic acids, particularly N-acetyl-[6-3H]mannosamine, to label and identify various forms of sialic acids in tissue culture cells. Firstly, we defined several variables that affect the labeling of sialic acids with N-acetyl-[6-3H]mannosamine. Secondly, we have devised a simple screening method to identify cell lines that synthesize substituted or modified sialic acids. We next demonstrate that it is possible to definitively identify the natures of the various labeled sialic acids without the use of mass spectrometry, even though they are present only in tracer amounts. The methods used include paper chromatography, analytical de-O-acetylation, periodate release of the 9-3H as [3H]formaldehyde (which is subsequently converted to a specific 3H-labeled chromophore), acylneuraminate pyruvate lyase treatment with identification of [3H]acylmannosamines, gas-liquid chromatography with radioactive detection, and two new high-pressure liquid chromatography methods utilizing the amine-adsorption:ion suppression and ion-pair principles. The use of an internal N-acetyl-[4-14C]neuraminic acid standard in each of these methods assures precision and accuracy. The combined use of these methods now allows the identification of radioactive tracer amounts of the various types of sialic acids in well-defined populations of tissue culture cells; it may also allow the identification of hitherto unknown forms of sialic acids

Ready for goal setting? Process evaluation of a patient-specific goal-setting method in physiotherapy.

Science.gov (United States)

Stevens, Anita; Köke, Albère; van der Weijden, Trudy; Beurskens, Anna

2017-08-31

Patient participation and goal setting appear to be difficult in daily physiotherapy practice, and practical methods are lacking. An existing patient-specific instrument, Patient-Specific Complaints (PSC), was therefore optimized into a new Patient Specific Goal-setting method (PSG). The aims of this study were to examine the feasibility of the PSG in daily physiotherapy practice, and to explore the potential impact of the new method. We conducted a process evaluation within a non-controlled intervention study. Community-based physiotherapists were instructed on how to work with the PSG in three group training sessions. The PSG is a six-step method embedded across the physiotherapy process, in which patients are stimulated to participate in the goal-setting process by: identifying problematic activities, prioritizing them, scoring their abilities, setting goals, planning and evaluating. Quantitative and qualitative data were collected among patients and physiotherapists by recording consultations and assessing patient files, questionnaires and written reflection reports. Data were collected from 51 physiotherapists and 218 patients, and 38 recordings and 219 patient files were analysed. The PSG steps were performed as intended, but the 'setting goals' and 'planning treatment' steps were not performed in detail. The patients and physiotherapists were positive about the method, and the physiotherapists perceived increased patient participation. They became aware of the importance of engaging patients in a dialogue, instead of focusing on gathering information. The lack of integration in the electronic patient system was a major barrier for optimal use in practice. Although the self-reported actual use of the PSG, i.e. informing and involving patients, and client-centred competences had improved, this was not completely confirmed by the objectively observed behaviour. The PSG is a feasible method and tends to have impact on increasing patient participation in the goal

The Contribution of Qualitative Methods for Identifying the Educational Needs of Adults

Science.gov (United States)

Boz, Hayat; Dagli, Yakup

2017-01-01

This study addresses the contribution of applying qualitative research methods for identifying the educational activities planned for adults. The paper is based on the experience gained during in-depth interviews with 39 elderly and 33 middle-aged participants, by purposive sampling method and maximum variation technique, within a needs analysis…

Identifying critical constraints for the maximum loadability of electric power systems - analysis via interior point method

Energy Technology Data Exchange (ETDEWEB)

Barboza, Luciano Vitoria [Sul-riograndense Federal Institute for Education, Science and Technology (IFSul), Pelotas, RS (Brazil)], E-mail: luciano@pelotas.ifsul.edu.br

2009-07-01

This paper presents an overview about the maximum load ability problem and aims to study the main factors that limit this load ability. Specifically this study focuses its attention on determining which electric system buses influence directly on the power demand supply. The proposed approach uses the conventional maximum load ability method modelled by an optimization problem. The solution of this model is performed using the Interior Point methodology. As consequence of this solution method, the Lagrange multipliers are used as parameters that identify the probable 'bottlenecks' in the electric power system. The study also shows the relationship between the Lagrange multipliers and the cost function in the Interior Point optimization interpreted like sensitivity parameters. In order to illustrate the proposed methodology, the approach was applied to an IEEE test system and to assess its performance, a real equivalent electric system from the South- Southeast region of Brazil was simulated. (author)

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

Science.gov (United States)

Johnston, Iain G; Williams, Ben P

2016-02-24

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

A comparison of visual and quantitative methods to identify interstitial lung abnormalities

OpenAIRE

Kliment, Corrine R.; Araki, Tetsuro; Doyle, Tracy J.; Gao, Wei; Dupuis, Jos?e; Latourelle, Jeanne C.; Zazueta, Oscar E.; Fernandez, Isis E.; Nishino, Mizuki; Okajima, Yuka; Ross, James C.; Est?par, Ra?l San Jos?; Diaz, Alejandro A.; Lederer, David J.; Schwartz, David A.

2015-01-01

Background: Evidence suggests that individuals with interstitial lung abnormalities (ILA) on a chest computed tomogram (CT) may have an increased risk to develop a clinically significant interstitial lung disease (ILD). Although methods used to identify individuals with ILA on chest CT have included both automated quantitative and qualitative visual inspection methods, there has been not direct comparison between these two methods. To investigate this relationship, we created lung density met...

From user needs to system specifications: multi-disciplinary thematic seminars as a collaborative design method for development of health information systems.

Science.gov (United States)

Scandurra, I; Hägglund, M; Koch, S

2008-08-01

This paper presents a new multi-disciplinary method for user needs analysis and requirements specification in the context of health information systems based on established theories from the fields of participatory design and computer supported cooperative work (CSCW). Whereas conventional methods imply a separate, sequential needs analysis for each profession, the "multi-disciplinary thematic seminar" (MdTS) method uses a collaborative design process. Application of the method in elderly homecare resulted in prototypes that were well adapted to the intended user groups. Vital information in the points of intersection between different care professions was elicited and a holistic view of the entire care process was obtained. Health informatics-usability specialists and clinical domain experts are necessary to apply the method. Although user needs acquisition can be time-consuming, MdTS was perceived to efficiently identify in-context user needs, and transformed these directly into requirements specifications. Consequently the method was perceived to expedite the entire ICT implementation process.

Specific and Class Object Recognition for Service Robots through Autonomous and Interactive Methods

Science.gov (United States)

Mansur, Al; Kuno, Yoshinori

Service robots need to be able to recognize and identify objects located within complex backgrounds. Since no single method may work in every situation, several methods need to be combined and robots have to select the appropriate one automatically. In this paper we propose a scheme to classify situations depending on the characteristics of the object of interest and user demand. We classify situations into four groups and employ different techniques for each. We use Scale-invariant feature transform (SIFT), Kernel Principal Components Analysis (KPCA) in conjunction with Support Vector Machine (SVM) using intensity, color, and Gabor features for five object categories. We show that the use of appropriate features is important for the use of KPCA and SVM based techniques on different kinds of objects. Through experiments we show that by using our categorization scheme a service robot can select an appropriate feature and method, and considerably improve its recognition performance. Yet, recognition is not perfect. Thus, we propose to combine the autonomous method with an interactive method that allows the robot to recognize the user request for a specific object and class when the robot fails to recognize the object. We also propose an interactive way to update the object model that is used to recognize an object upon failure in conjunction with the user's feedback.

Methods for Specific Electrode Resistance Measurement during Transcranial Direct Current Stimulation

Science.gov (United States)

Khadka, Niranjan; Rahman, Asif; Sarantos, Chris; Truong, Dennis Q.; Bikson, Marom

2014-01-01

Background Transcranial Direct Current Stimulation (tDCS) is investigated to treat a wide range of neuropsychiatric disorders, for rehabilitation, and for enhancing cognitive performance. The monitoring of electrode resistance before and during tDCS is considered important for tolerability and safety, where an unusually high resistance is indicative of undesired electrode or poor skin contact conditions. Conventional resistance measurement methods do not isolate individual electrode resistance but rather measures overall voltage. Moreover, for HD-tDCS devices, cross talk across electrodes makes concurrent resistance monitoring unreliable. Objective We propose a novel method for monitoring of the individual electrode resistance during tDCS, using a super-position of direct current with a test-signal (low-intensity and low-frequency sinusoids with electrode– specific frequencies) and a single sentinel electrode (not used for DC). Methods To validate this methodology, we developed lumped-parameter models of two and multi-electrode tDCS. Approaches with and without a sentinel electrode were solved and underlying assumptions identified. Assumptions were tested and parameterized in healthy participants using forearm stimulation combining tDCS (2 mA) and sinusoidal test-signals (38 μA and 76 μA peak to peak at 1 Hz, 10 Hz, and 100 Hz) and an in vitro test (where varied electrode failure modes were created). DC and AC component voltages across the electrodes were compared and participants were asked to rate subjective pain. Results A sentinel electrode is required to isolate electrode resistance in a two-electrode tDCS system. For multi-electrode resistance tracking, cross talk was aggravated with electrode proximity and current/resistance mismatches, but could be corrected using proposed approaches. Average voltage and average pain scores were not significantly different across test current intensities and frequencies (two-way repeated measures ANOVA) indicating the

Alu polymerase chain reaction: A method for rapid isolation of human-specific sequences from complex DNA sources

International Nuclear Information System (INIS)

Nelson, D.L.; Ledbetter, S.A.; Corbo, L.; Victoria, M.F.; Ramirez-Solis, R.; Webster, T.D.; Ledbetter, D.H.; Caskey, C.T.

1989-01-01

Current efforts to map the human genome are focused on individual chromosomes or smaller regions and frequently rely on the use of somatic cell hybrids. The authors report the application of the polymerase chain reaction to direct amplification of human DNA from hybrid cells containing regions of the human genome in rodent cell backgrounds using primers directed to the human Alu repeat element. They demonstrate Alu-directed amplification of a fragment of the human HPRT gene from both hybrid cell and cloned DNA and identify through sequence analysis the Alu repeats involved in this amplification. They also demonstrate the application of this technique to identify the chromosomal locations of large fragments of the human X chromosome cloned in a yeast artificial chromosome and the general applicability of the method to the preparation of DNA probes from cloned human sequences. The technique allows rapid gene mapping and provides a simple method for the isolation and analysis of specific chromosomal regions

A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.

Directory of Open Access Journals (Sweden)

Warren D Anderson

2017-07-01

Full Text Available Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension. We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences. We obtained experimental data on the expression of 22 genes across five organs, over a time span that encompassed the development of autonomic nervous system dysfunction and hypertension. We pursued a unique approach for identification of continuous-time models that jointly described the dynamics and structure of multi-organ networks by estimating a sparse subset of ∼12,000 possible gene regulatory interactions. Our analyses revealed that an autonomic dysfunction-specific multi-organ sequence of gene expression activation patterns was associated with a distinct gene regulatory network. We analyzed the model structures for adaptation motifs, and identified disease-specific network motifs involving genes that exhibited aberrant temporal dynamics. Bioinformatic analyses identified disease-specific single nucleotide variants within or near transcription factor binding sites upstream of key genes implicated in maintaining physiological homeostasis. Our approach illustrates a novel framework for investigating the pathogenesis through model-based analysis of multi-organ system dynamics and network properties. Our results yielded novel candidate molecular targets driving the development of cardiovascular disease, metabolic syndrome, and immune dysfunction.

Determination of the species specificity of the primers for the detection of chicken and turkey meat by realtime PCR method

Directory of Open Access Journals (Sweden)

Lenka Maršálková

2014-07-01

Full Text Available The aim of this work was to use TaqMan Real-Time PCR for quantitative authentication of chicken and turkey meat. To meet this purpose, a specific pair of primers and TaqMan probe was used. The test was aimed at identifying the reaction cycle of turkey and chicken meat using by two sets of primers. With first set of primer designed for chicken we obtained the following results: Cp = 16.18 for 100% chicken DNA Cp = 29, 18 100% turkey DNA It was also amplified DNA of pig that exceeded the detection threshold fluorescence intensities in the 31.07 cycle (Cp = 31.07. Using primers designed for turkey we obtained the following results Cp = 31.16 for 100% CHDNA, Cp =16.18 100% TDNA. It was also amplified the 100% DNA of rabbit in 31.63 cycle (Cp = 31.63 and deer in cycle 32 (Cp = 32. The DNA of all other animal species was amplificated after more than 35 cycles (Cp >35. It follows that the second detection primer pair is specific enough to unrelated species of animals by 30 cycles of the reaction. Species authentication based on DNA analysis from this perspective overcomes all the shortcomings of proteins. At present, DNA analysis use different types of PCR. Is the most progressive Real-time PCR, which is suitable for the specific use of detection (primers and TaqMan probe. The TaqMan Real-time PCR is within the sensitivity and specificity, clearly one of the best methods for identifying the species of chicken and turkey meat. The specificity of this method, however, depends primarily on the specificity of the primers and TaqMan probe. The 30 cycle reaction was chosen by us as the threshold for specificity using primers for authentication chicken and turkey meat.

Machine-learning identifies substance-specific behavioral markers for opiate and stimulant dependence.

Science.gov (United States)

Ahn, Woo-Young; Vassileva, Jasmin

2016-04-01

Recent animal and human studies reveal distinct cognitive and neurobiological differences between opiate and stimulant addictions; however, our understanding of the common and specific effects of these two classes of drugs remains limited due to the high rates of polysubstance-dependence among drug users. The goal of the current study was to identify multivariate substance-specific markers classifying heroin dependence (HD) and amphetamine dependence (AD), by using machine-learning approaches. Participants included 39 amphetamine mono-dependent, 44 heroin mono-dependent, 58 polysubstance dependent, and 81 non-substance dependent individuals. The majority of substance dependent participants were in protracted abstinence. We used demographic, personality (trait impulsivity, trait psychopathy, aggression, sensation seeking), psychiatric (attention deficit hyperactivity disorder, conduct disorder, antisocial personality disorder, psychopathy, anxiety, depression), and neurocognitive impulsivity measures (Delay Discounting, Go/No-Go, Stop Signal, Immediate Memory, Balloon Analogue Risk, Cambridge Gambling, and Iowa Gambling tasks) as predictors in a machine-learning algorithm. The machine-learning approach revealed substance-specific multivariate profiles that classified HD and AD in new samples with high degree of accuracy. Out of 54 predictors, psychopathy was the only classifier common to both types of addiction. Important dissociations emerged between factors classifying HD and AD, which often showed opposite patterns among individuals with HD and AD. These results suggest that different mechanisms may underlie HD and AD, challenging the unitary account of drug addiction. This line of work may shed light on the development of standardized and cost-efficient clinical diagnostic tests and facilitate the development of individualized prevention and intervention programs for HD and AD. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Identifying context-specific competencies required by community Australian Football sports trainers.

Science.gov (United States)

Donaldson, Alex; Finch, Caroline F

2012-08-01

First-aid is a recommended injury prevention and risk management strategy in community sport; however, little is known about the sport-specific competencies required by first-aid providers. To achieve expert consensus on the competencies required by community Australian Football (community-AF) sports trainers. A three-round online Delphi process. Community-AF. 16 Australian sports first-aid and community-AF experts. Rating of competencies as either 'essential', 'expected', 'ideal' or 'not required'. Results After Round 3, 47 of the 77 (61%) competencies were endorsed as 'essential' or 'expected' for a sports trainer to effectively perform the activities required to the standards expected at a community-AF club by ≥75% of experts. These competencies covered: the role of the sports trainer; the responsibilities of the sports trainer; emergency management; injury and illness assessment and immediate management; taping; and injury prevention and risk management. Four competencies (5%) were endorsed as 'ideal' or 'not required' by ≥85% of experts and were excluded from further consideration. The 26 competencies where consensus was not reached were retained as second-tier, optional competencies. Sports trainers are important members of on-field first-aid teams, providing support to both injured players and other sports medicine professionals. The competencies identified in this study provide the basis of a proposed two-tiered community-AF-specific sports trainer education structure that can be implemented by the peak sports body. This includes six mandatory modules, relating to the 'required' competencies, and a further six optional modules covering competencies on which consensus was not reached.

A method for identifying compromised clients based on DNS traffic analysis

DEFF Research Database (Denmark)

Stevanovic, Matija; Pedersen, Jens Myrup; D’Alconzo, Alessandro

2017-01-01

DNS is widely abused by Internet criminals in order to provide reliable communication within malicious network infrastructure as well as flexible and resilient hosting of malicious content. This paper presents a novel detection method that can be used for identifying potentially compromised clien...

Identifying plant cell-surface receptors: combining 'classical' techniques with novel methods.

Science.gov (United States)

Uebler, Susanne; Dresselhaus, Thomas

2014-04-01

Cell-cell communication during development and reproduction in plants depends largely on a few phytohormones and many diverse classes of polymorphic secreted peptides. The peptide ligands are bound at the cell surface of target cells by their membranous interaction partners representing, in most cases, either receptor-like kinases or ion channels. Although knowledge of both the extracellular ligand and its corresponding receptor(s) is necessary to describe the downstream signalling pathway(s), to date only a few ligand-receptor pairs have been identified. Several methods, such as affinity purification and yeast two-hybrid screens, have been used very successfully to elucidate interactions between soluble proteins, but most of these methods cannot be applied to membranous proteins. Experimental obstacles such as low concentration and poor solubility of membrane receptors, as well as instable transient interactions, often hamper the use of these 'classical' approaches. However, over the last few years, a lot of progress has been made to overcome these problems by combining classical techniques with new methodologies. In the present article, we review the most promising recent methods in identifying cell-surface receptor interactions, with an emphasis on success stories outside the field of plant research.

A general method for identifying major hybrid male sterility genes in Drosophila.

Science.gov (United States)

Zeng, L W; Singh, R S

1995-10-01

The genes responsible for hybrid male sterility in species crosses are usually identified by introgressing chromosome segments, monitored by visible markers, between closely related species by continuous backcrosses. This commonly used method, however, suffers from two problems. First, it relies on the availability of markers to monitor the introgressed regions and so the portion of the genome examined is limited to the marked regions. Secondly, the introgressed regions are usually large and it is impossible to tell if the effects of the introgressed regions are the result of single (or few) major genes or many minor genes (polygenes). Here we introduce a simple and general method for identifying putative major hybrid male sterility genes which is free of these problems. In this method, the actual hybrid male sterility genes (rather than markers), or tightly linked gene complexes with large effects, are selectively introgressed from one species into the background of another species by repeated backcrosses. This is performed by selectively backcrossing heterozygous (for hybrid male sterility gene or genes) females producing fertile and sterile sons in roughly equal proportions to males of either parental species. As no marker gene is required for this procedure, this method can be used with any species pairs that produce unisexual sterility. With the application of this method, a small X chromosome region of Drosophila mauritiana which produces complete hybrid male sterility (aspermic testes) in the background of D. simulans was identified. Recombination analysis reveals that this region contains a second major hybrid male sterility gene linked to the forked locus located at either 62.7 +/- 0.66 map units or at the centromere region of the X chromosome of D. mauritiana.

Women-specific HIV/AIDS services: identifying and defining the components of holistic service delivery for women living with HIV/AIDS

Science.gov (United States)

Carter, Allison J; Bourgeois, Sonya; O'Brien, Nadia; Abelsohn, Kira; Tharao, Wangari; Greene, Saara; Margolese, Shari; Kaida, Angela; Sanchez, Margarite; Palmer, Alexis K; Cescon, Angela; de Pokomandy, Alexandra; Loutfy, Mona R

2013-01-01

Introduction The increasing proportion of women living with HIV has evoked calls for tailored services that respond to women's specific needs. The objective of this investigation was to explore the concept of women-specific HIV/AIDS services to identify and define what key elements underlie this approach to care. Methods A comprehensive review was conducted using online databases (CSA Social Service Abstracts, OvidSP, Proquest, Psycinfo, PubMed, CINAHL), augmented with a search for grey literature. In total, 84 articles were retrieved and 30 were included for a full review. Of these 30, 15 were specific to HIV/AIDS, 11 for mental health and addictions and four stemmed from other disciplines. Results and discussion The review demonstrated the absence of a consensual definition of women-specific HIV/AIDS services in the literature. We distilled this concept into its defining features and 12 additional dimensions (1) creating an atmosphere of safety, respect and acceptance; (2) facilitating communication and interaction among peers; (3) involving women in the planning, delivery and evaluation of services; (4) providing self-determination opportunities; (5) providing tailored programming for women; (6) facilitating meaningful access to care through the provision of social and supportive services; (7) facilitating access to women-specific and culturally sensitive information; (8) considering family as the unit of intervention; (9) providing multidisciplinary integration and coordination of a comprehensive array of services; (10) meeting women “where they are”; (11) providing gender-, culture- and HIV-sensitive training to health and social care providers; and (12) conducting gendered HIV/AIDS research. Conclusions This review highlights that the concept of women-specific HIV/AIDS services is a complex and multidimensional one that has been shaped by diverse theoretical perspectives. Further research is needed to better understand this emerging concept and ultimately

New Method for Simultaneous Species-Specific Identification of Equine Strongyles (Nematoda, Strongylida) by Reverse Line Blot Hybridization▿

Science.gov (United States)

Traversa, Donato; Iorio, Raffaella; Klei, Thomas R.; Kharchenko, Vitaliy A.; Gawor, Jakub; Otranto, Domenico; Sparagano, Olivier A. E.

2007-01-01

The ability of a reverse line blot (RLB) assay to identify 13 common species of equine small strongyles (cyathostomins) and to discriminate them from three Strongylus spp. (large strongyles) was demonstrated. The assay relied on the specific hybridization of PCR-amplified intergenic spacer DNA fragments of the nuclear ribosomal DNA to membrane-bound species-specific probes. All cyathostomins examined were unequivocally identified and simultaneously discriminated from each other and from three large strongyles (Strongylus edentatus, Strongylus equinus, and Strongylus vulgaris). This assay will enable the accurate and rapid identification of equine cyathostomins irrespective of their life cycle stage, opening important avenues for a better understanding of their biology and epidemiology and of the pathogenesis of cyathostomin-associated disease. In particular, this RLB method promises to be a powerful diagnostic tool to determine the roles of individual species in the pathogenesis of mixed infections and to elucidate some aspects of cyathostominosis. Also, it could represent a basic step toward the development of a rapid and simple molecular test for the early detection of drug-resistant genotypes of horse strongyle species. PMID:17626168

Formal specification of open distributed systems - overview and evaluation of existing methods

International Nuclear Information System (INIS)

Stoelen, Ketil

1998-02-01

This report classifies, compares and evaluates eleven specification languages for distributed systems. The eleven specification languages have been picked from a wide spectrum of areas embracing both industry and research. We have selected languages that we see as important; either because they have proved useful within the commercial software industry, or because they play or we expect them to play an important role within research. Based on literature studies, we investigate the suitability of these specification languages to describe open distributed systems. The languages are also evaluated with respect to support for refinement and the characterization of proof-obligations. The report consists of five main parts: Part 1 gives the background and motivation for the evaluation; it also introduces the basic terminology; Part 2 motivates, identifies and formulates the concrete evaluation criterions; Part 3 evaluates the specification languages with respect to the evaluation criterions formulated in Part 2; Part 4 sums up the results from the evaluation in the form of tables; it also draws some conclusions and identifies some directions for further studies; Part 5 consists of two appendices, namely a bibliography and a list of abbreviations. (author)

Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei

OpenAIRE

Zirlinger, M.; Kreiman, Gabriel; Anderson, D. J.

2001-01-01

Microarray technology represents a potentially powerful method for identifying cell type- and regionally restricted genes expressed in the brain. Here we have combined a microarray analysis of differential gene expression among five selected brain regions, including the amygdala, cerebellum, hippocampus, olfactory bulb, and periaqueductal gray, with in situ hybridization. On average, 0.3% of the 34,000 genes interrogated were highly enriched in each of the five regions...

An Entry Point for Formal Methods: Specification and Analysis of Event Logs

Directory of Open Access Journals (Sweden)

Howard Barringer

2010-03-01

Full Text Available Formal specification languages have long languished, due to the grave scalability problems faced by complete verification methods. Runtime verification promises to use formal specifications to automate part of the more scalable art of testing, but has not been widely applied to real systems, and often falters due to the cost and complexity of instrumentation for online monitoring. In this paper we discuss work in progress to apply an event-based specification system to the logging mechanism of the Mars Science Laboratory mission at JPL. By focusing on log analysis, we exploit the "instrumentation" already implemented and required for communicating with the spacecraft. We argue that this work both shows a practical method for using formal specifications in testing and opens interesting research avenues, including a challenging specification learning problem.

The Comparison of Biochemical and Sequencing 16S rDNA Gene Methods to Identify Nontuberculous Mycobacteria

Directory of Open Access Journals (Sweden)

Shafipour1, M.

2014-11-01

Full Text Available The identification of Mycobacteria in the species level has great medical importance. Biochemical tests are laborious and time-consuming, so new techniques could be used to identify the species. This research aimed to the comparison of biochemical and sequencing 16S rDNA gene methods to identify nontuberculous Mycobacteria in patients suspected to tuberculosis in Golestan province which is the most prevalent region of tuberculosis in Iran. Among 3336 patients suspected to tuberculosis referred to hospitals and health care centres in Golestan province during 2010-2011, 319 (9.56% culture positive cases were collected. Identification of species by using biochemical tests was done. On the samples recognized as nontuberculous Mycobacteria, after DNA extraction by boiling, 16S rDNA PCR was done and their sequencing were identified by NCBI BLAST. Of the 319 positive samples in Golestan Province, 300 cases were M.tuberculosis and 19 cases (5.01% were identified as nontuberculous Mycobacteria by biochemical tests. 15 out of 19 nontuberculous Mycobacteria were identified by PCR and sequencing method as similar by biochemical methods (similarity rate: 78.9%. But after PCR, 1 case known as M.simiae by biochemical test was identified as M. lentiflavum and 3 other cases were identified as Nocardia. Biochemical methods corresponded to the 16S rDNA PCR and sequencing in 78.9% of cases. However, in identification of M. lentiflavum and Nocaria sp. the molecular method is better than biochemical methods.

A method of identifying and weighting indicators of energy efficiency assessment in Chinese residential buildings

International Nuclear Information System (INIS)

Yang Yulan; Li Baizhan; Yao Runming

2010-01-01

This paper describes a method of identifying and weighting indicators for assessing the energy efficiency of residential buildings in China. A list of indicators of energy efficiency assessment in residential buildings in the hot summer and cold winter zone in China has been proposed, which supplies an important reference for policy makings in energy efficiency assessment in buildings. The research method applies a wide-ranging literature review and a questionnaire survey involving experts in the field. The group analytic hierarchy process (group AHP) has been used to weight the identified indicators. The size of survey samples are sufficient to support the results, which has been validated by consistency estimation. The proposed method could also be extended to develop the weighted indicators for other climate zones in China. - Research highlights: →Method of identifying indicators of building energy efficiency assessment. →The group AHP method for weighting indicators. →Method of solving multi-criteria decision making problems of choice and prioritisation in policy makings.

A method of identifying and weighting indicators of energy efficiency assessment in Chinese residential buildings

Energy Technology Data Exchange (ETDEWEB)

Yang Yulan [Key Laboratory of the Three Gorges Reservoir Region' s Eco-Environment under Ministry of Education, Chongqing University, Chongqing (China); College of Civil Engineering and Architecture, Zhejiang University of Technology, Hangzhou (China); Li Baizhan [Key Laboratory of the Three Gorges Reservoir Region' s Eco-Environment under the Ministry of Education, Chongqing University, Chongqing (China); Yao Runming, E-mail: r.yao@reading.ac.u [School of Construction Management and Engineering, University of Reading, Reading (United Kingdom); Key Laboratory of the Three Gorges Reservoir Region' s Eco-Environment under Ministry of Education, Chongqing University, Chongqing (China)

2010-12-15

This paper describes a method of identifying and weighting indicators for assessing the energy efficiency of residential buildings in China. A list of indicators of energy efficiency assessment in residential buildings in the hot summer and cold winter zone in China has been proposed, which supplies an important reference for policy makings in energy efficiency assessment in buildings. The research method applies a wide-ranging literature review and a questionnaire survey involving experts in the field. The group analytic hierarchy process (group AHP) has been used to weight the identified indicators. The size of survey samples are sufficient to support the results, which has been validated by consistency estimation. The proposed method could also be extended to develop the weighted indicators for other climate zones in China. - Research highlights: {yields}Method of identifying indicators of building energy efficiency assessment. {yields}The group AHP method for weighting indicators. {yields}Method of solving multi-criteria decision making problems of choice and prioritisation in policy makings.

An Alternative Method for Identifying Interplanetary Magnetic Cloud Regions

Energy Technology Data Exchange (ETDEWEB)

Ojeda-Gonzalez, A.; Prestes, A.; Klausner, V. [Laboratory of Physics and Astronomy, IP and D/Universidade do Vale do Paraíba—UNIVAP, São José dos Campos, SP (Brazil); Mendes, O. [Division of Space Geophysics, National Institute for Space Research, São José dos Campos, SP (Brazil); Calzadilla, A. [Department of Space Geophysics, Institute of Geophysics and Astronomy, Havana (Cuba); Domingues, M. O., E-mail: ojeda.gonzalez.a@gmail.com [Associate Laboratory of Applied Computing and Mathematics, National Institute for Space Research, São José dos Campos, SP (Brazil)

2017-03-10

Spatio-temporal entropy (STE) analysis is used as an alternative mathematical tool to identify possible magnetic cloud (MC) candidates. We analyze Interplanetary Magnetic Field (IMF) data using a time interval of only 10 days. We select a convenient data interval of 2500 records moving forward by 200 record steps until the end of the time series. For every data segment, the STE is calculated at each step. During an MC event, the STE reaches values close to zero. This extremely low value of STE is due to MC structure features. However, not all of the magnetic components in MCs have STE values close to zero at the same time. For this reason, we create a standardization index (the so-called Interplanetary Entropy, IE, index). This index is a worthwhile effort to develop new tools to help diagnose ICME structures. The IE was calculated using a time window of one year (1999), and it has a success rate of 70% over other identifiers of MCs. The unsuccessful cases (30%) are caused by small and weak MCs. The results show that the IE methodology identified 9 of 13 MCs, and emitted nine false alarm cases. In 1999, a total of 788 windows of 2500 values existed, meaning that the percentage of false alarms was 1.14%, which can be considered a good result. In addition, four time windows, each of 10 days, are studied, where the IE method was effective in finding MC candidates. As a novel result, two new MCs are identified in these time windows.

A convenient method to synthesize specifically labelled cholesterol with tritium

International Nuclear Information System (INIS)

Malik, S.; Kenny, M.; Ahmad, S.; Washington Univ., Seattle, WA

1992-01-01

A simple method is described to label cholesterol with tritium. Cholesterol was first oxidized to 5-cholesten-3-one which was then purified by HPLC. Its structure was established by electron impact (EI) mass spectrometry and 1 H-NMR spectroscopy. The ketone was reduced with NaB 3 H 4 to give specifically labelled cholesterol (C-3 3 H) at low specific activity. (author)

How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods.

Science.gov (United States)

May, Michael R; Moore, Brian R

2016-11-01

Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree of Life. This has motivated the development of statistical methods for detecting shifts in the rate of lineage diversification across the branches of phylogenic trees. One of the most frequently used methods, MEDUSA, explores a set of diversification-rate models, where each model assigns branches of the phylogeny to a set of diversification-rate categories. Each model is first fit to the data, and the Akaike information criterion (AIC) is then used to identify the optimal diversification model. Surprisingly, the statistical behavior of this popular method is uncharacterized, which is a concern in light of: (1) the poor performance of the AIC as a means of choosing among models in other phylogenetic contexts; (2) the ad hoc algorithm used to visit diversification models, and; (3) errors that we reveal in the likelihood function used to fit diversification models to the phylogenetic data. Here, we perform an extensive simulation study demonstrating that MEDUSA (1) has a high false-discovery rate (on average, spurious diversification-rate shifts are identified [Formula: see text] of the time), and (2) provides biased estimates of diversification-rate parameters. Understanding the statistical behavior of MEDUSA is critical both to empirical researchers-in order to clarify whether these methods can make reliable inferences from empirical datasets-and to theoretical biologists-in order to clarify the specific problems that need to be solved in order to develop more reliable approaches for detecting shifts in the rate of lineage diversification. [Akaike information criterion; extinction; lineage-specific diversification rates; phylogenetic model selection; speciation.]. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Handbook of methods for risk-based analysis of technical specifications

International Nuclear Information System (INIS)

Samanta, P.K.; Kim, I.S.; Mankamo, T.; Vesely, W.E.

1996-01-01

Technical Specifications (TS) requirements for nuclear power plants define the Limiting Conditions for Operations (LCOs) and Surveillance Requirements (SRs) to assure safety during operation. In general, these requirements are based on deterministic analyses and engineering judgments. Improvements in these requirements are facilitated by the availability of plant-specific Probabilistic Risk Assessments (PRAs). The US Nuclear Regulatory Commission (USNRC) Office of Research sponsored research to develop systematic, risk-based methods to improve various aspects of TS requirements. A handbook of methods summarizing such risk-based approaches has been completed in 1994. It is expected that this handbook will provide valuable input to NRC's present work in developing guidance for using PRA in risk-informed regulation. The handbook addresses reliability and risk-based methods for evaluating allowed outage times (AOTs), action statements requiring shutdown where shutdown risk may be substantial, surveillance test intervals (STIs), managing plant configurations, and scheduling maintenance

Coupling Genetics and Proteomics To Identify Aphid Proteins Associated with Vector-Specific Transmission of Polerovirus (Luteoviridae)▿

Science.gov (United States)

Yang, Xiaolong; Thannhauser, T. W.; Burrows, Mary; Cox-Foster, Diana; Gildow, Fred E.; Gray, Stewart M.

2008-01-01

Cereal yellow dwarf virus-RPV (CYDV-RPV) is transmitted specifically by the aphids Rhopalosiphum padi and Schizaphis graminum in a circulative nonpropagative manner. The high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. Studies of F2 progeny from crosses of vector and nonvector genotypes of S. graminum showed that virus transmission efficiency is a heritable trait regulated by multiple genes acting in an additive fashion and that gut- and salivary gland-associated factors are not genetically linked. Utilizing two-dimensional difference gel electrophoresis to compare the proteomes of vector and nonvector parental and F2 genotypes, four aphid proteins (S4, S8, S29, and S405) were specifically associated with the ability of S. graminum to transmit CYDV-RPV. The four proteins were coimmunoprecipitated with purified RPV, indicating that the aphid proteins are capable of binding to virus. Analysis by mass spectrometry identified S4 as a luciferase and S29 as a cyclophilin, both of which have been implicated in macromolecular transport. Proteins S8 and S405 were not identified from available databases. Study of this unique genetic system coupled with proteomic analysis indicated that these four virus-binding aphid proteins were specifically inherited and conserved in different generations of vector genotypes and suggests that they play a major role in regulating polerovirus transmission. PMID:17959668

Seismic Methods of Identifying Explosions and Estimating Their Yield

Science.gov (United States)

Walter, W. R.; Ford, S. R.; Pasyanos, M.; Pyle, M. L.; Myers, S. C.; Mellors, R. J.; Pitarka, A.; Rodgers, A. J.; Hauk, T. F.

2014-12-01

Seismology plays a key national security role in detecting, locating, identifying and determining the yield of explosions from a variety of causes, including accidents, terrorist attacks and nuclear testing treaty violations (e.g. Koper et al., 2003, 1999; Walter et al. 1995). A collection of mainly empirical forensic techniques has been successfully developed over many years to obtain source information on explosions from their seismic signatures (e.g. Bowers and Selby, 2009). However a lesson from the three DPRK declared nuclear explosions since 2006, is that our historic collection of data may not be representative of future nuclear test signatures (e.g. Selby et al., 2012). To have confidence in identifying future explosions amongst the background of other seismic signals, and accurately estimate their yield, we need to put our empirical methods on a firmer physical footing. Goals of current research are to improve our physical understanding of the mechanisms of explosion generation of S- and surface-waves, and to advance our ability to numerically model and predict them. As part of that process we are re-examining regional seismic data from a variety of nuclear test sites including the DPRK and the former Nevada Test Site (now the Nevada National Security Site (NNSS)). Newer relative location and amplitude techniques can be employed to better quantify differences between explosions and used to understand those differences in term of depth, media and other properties. We are also making use of the Source Physics Experiments (SPE) at NNSS. The SPE chemical explosions are explicitly designed to improve our understanding of emplacement and source material effects on the generation of shear and surface waves (e.g. Snelson et al., 2013). Finally we are also exploring the value of combining seismic information with other technologies including acoustic and InSAR techniques to better understand the source characteristics. Our goal is to improve our explosion models

Interlaboratory diagnostic accuracy of a Salmonella specific PCR-based method

DEFF Research Database (Denmark)

Malorny, B.; Hoorfar, Jeffrey; Hugas, M.

2003-01-01

A collaborative study involving four European laboratories was conducted to investigate the diagnostic accuracy of a Salmonella specific PCR-based method, which was evaluated within the European FOOD-PCR project (http://www.pcr.dk). Each laboratory analysed by the PCR a set of independent obtained...... presumably naturally contaminated samples and compared the results with the microbiological culture method. The PCR-based method comprised a preenrichment step in buffered peptone water followed by a thermal cell lysis using a closed tube resin-based method. Artificially contaminated minced beef and whole......-based diagnostic methods and is currently proposed as international standard document....

Application of a path sensitizing method on automated generation of test specifications for control software

International Nuclear Information System (INIS)

Morimoto, Yuuichi; Fukuda, Mitsuko

1995-01-01

An automated generation method for test specifications has been developed for sequential control software in plant control equipment. Sequential control software can be represented as sequential circuits. The control software implemented in a control equipment is designed from these circuit diagrams. In logic tests of VLSI's, path sensitizing methods are widely used to generate test specifications. But the method generates test specifications at a single time only, and can not be directly applied to sequential control software. The basic idea of the proposed method is as follows. Specifications of each logic operator in the diagrams are defined in the software design process. Therefore, test specifications of each operator in the control software can be determined from these specifications, and validity of software can be judged by inspecting all of the operators in the logic circuit diagrams. Candidates for sensitized paths, on which test data for each operator propagates, can be generated by the path sensitizing method. To confirm feasibility of the method, it was experimentally applied to control software in digital control equipment. The program could generate test specifications exactly, and feasibility of the method was confirmed. (orig.) (3 refs., 7 figs.)

Risk-based analysis methods applied to nuclear power plant technical specifications

International Nuclear Information System (INIS)

Wagner, D.P.; Minton, L.A.; Gaertner, J.P.

1989-01-01

A computer-aided methodology and practical applications of risk-based evaluation of technical specifications are described. The methodology, developed for use by the utility industry, is a part of the overall process of improving nuclear power plant technical specifications. The SOCRATES computer program uses the results of a probabilistic risk assessment or a system-level risk analysis to calculate changes in risk due to changes in the surveillance test interval and/or the allowed outage time stated in the technical specification. The computer program can accommodate various testing strategies (such as staggered or simultaneous testing) to allow modeling of component testing as it is carried out at the plant. The methods and computer program are an integral part of a larger decision process aimed at determining benefits from technical specification changes. These benefits can include cost savings to the utilities by reducing forced shutdowns and decreasing labor requirements for test and maintenance activities, with no adverse impacts on risk. The methodology and the SOCRATES computer program have been used extensively toe valuate several actual technical specifications in case studies demonstrating the methods. Summaries of these applications demonstrate the types of results achieved and the usefulness of the risk-based evaluation in improving the technical specifications

A simple field method to identify foot strike pattern during running.

Science.gov (United States)

Giandolini, Marlène; Poupard, Thibaut; Gimenez, Philippe; Horvais, Nicolas; Millet, Guillaume Y; Morin, Jean-Benoît; Samozino, Pierre

2014-05-07

Identifying foot strike patterns in running is an important issue for sport clinicians, coaches and footwear industrials. Current methods allow the monitoring of either many steps in laboratory conditions or only a few steps in the field. Because measuring running biomechanics during actual practice is critical, our purpose is to validate a method aiming at identifying foot strike patterns during continuous field measurements. Based on heel and metatarsal accelerations, this method requires two uniaxial accelerometers. The time between heel and metatarsal acceleration peaks (THM) was compared to the foot strike angle in the sagittal plane (αfoot) obtained by 2D video analysis for various conditions of speed, slope, footwear, foot strike and state of fatigue. Acceleration and kinematic measurements were performed at 1000Hz and 120Hz, respectively, during 2-min treadmill running bouts. Significant correlations were observed between THM and αfoot for 14 out of 15 conditions. The overall correlation coefficient was r=0.916 (Pstrike except for extreme forefoot strike during which the heel rarely or never strikes the ground, and for different footwears and states of fatigue. We proposed a classification based on THM: FFS<-5.49msmethod, it is reliable for distinguishing rearfoot and non-rearfoot strikers in situ. Copyright © 2014 Elsevier Ltd. All rights reserved.

Generating method-specific Reference Ranges - A harmonious outcome?

Science.gov (United States)

Lee, Graham R; Griffin, Alison; Halton, Kieran; Fitzgibbon, Maria C

2017-12-01

When laboratory Reference Ranges (RR) do not reflect analytical methodology, result interpretation can cause misclassification of patients and inappropriate management. This can be mitigated by determining and implementing method-specific RRs, which was the main objective of this study. Serum was obtained from healthy volunteers (Male + Female, n > 120) attending hospital health-check sessions during June and July 2011. Pseudo-anonymised aliquots were stored (at - 70 °C) prior t° analysis on Abbott ARCHITECT c16000 chemistry and i 2000SR immunoassay analysers. Data were stratified by gender where appropriate. Outliers were excluded statistically (Tukey method) to generate non-parametric RRs (2.5th + 97.5th percentiles). RRs were compared to those quoted by Abbott and UK Pathology Harmony (PH) where possible. For 7 selected tests, RRs were verified using a data mining approach. For chemistry tests (n = 23), Upper or Lower Reference Limits (LRL or URL) were > 20% different from Abbott ranges in 25% of tests (11% from PH ranges) but in 38% for immunoassay tests (n = 13). RRs (mmol/L) for sodium (138-144), potassium (3.8-4.9) and chloride (102-110) were considerably narrower than PH ranges (133-146, 3.5-5.0 and 95-108, respectively). The gender difference for ferritin (M: 29-441, F: 8-193 ng/mL) was more pronounced than reported by Abbott (M: 22-275, F: 5-204 ng/mL). Verification studies showed good agreement for chemistry tests (mean [SD] difference = 0.4% [1.2%]) but less so for immunoassay tests (27% [29%]), particularly for TSH (LRL). Where resource permits, we advocate using method-specific RRs in preference to other sources, particularly where method bias and lack of standardisation limits RR transferability and harmonisation.

Simplified LCA and matrix methods in identifying the environmental aspects of a product system.

Science.gov (United States)

Hur, Tak; Lee, Jiyong; Ryu, Jiyeon; Kwon, Eunsun

2005-05-01

In order to effectively integrate environmental attributes into the product design and development processes, it is crucial to identify the significant environmental aspects related to a product system within a relatively short period of time. In this study, the usefulness of life cycle assessment (LCA) and a matrix method as tools for identifying the key environmental issues of a product system were examined. For this, a simplified LCA (SLCA) method that can be applied to Electrical and Electronic Equipment (EEE) was developed to efficiently identify their significant environmental aspects for eco-design, since a full scale LCA study is usually very detailed, expensive and time-consuming. The environmentally responsible product assessment (ERPA) method, which is one of the matrix methods, was also analyzed. Then, the usefulness of each method in eco-design processes was evaluated and compared using the case studies of the cellular phone and vacuum cleaner systems. It was found that the SLCA and the ERPA methods provided different information but they complemented each other to some extent. The SLCA method generated more information on the inherent environmental characteristics of a product system so that it might be useful for new design/eco-innovation when developing a completely new product or method where environmental considerations play a major role from the beginning. On the other hand, the ERPA method gave more information on the potential for improving a product so that it could be effectively used in eco-redesign which intends to alleviate environmental impacts of an existing product or process.

Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

Science.gov (United States)

van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Deelen, Joris; Isaacs, Aaron; Medina-Gomez, Carolina; Mbarek, Hamdi; Kanterakis, Alexandros; Trompet, Stella; Postmus, Iris; Verweij, Niek; van Enckevort, David J.; Huffman, Jennifer E.; White, Charles C.; Feitosa, Mary F.; Bartz, Traci M.; Manichaikul, Ani; Joshi, Peter K.; Peloso, Gina M.; Deelen, Patrick; van Dijk, Freerk; Willemsen, Gonneke; de Geus, Eco J.; Milaneschi, Yuri; Penninx, Brenda W.J.H.; Francioli, Laurent C.; Menelaou, Androniki; Pulit, Sara L.; Rivadeneira, Fernando; Hofman, Albert; Oostra, Ben A.; Franco, Oscar H.; Leach, Irene Mateo; Beekman, Marian; de Craen, Anton J.M.; Uh, Hae-Won; Trochet, Holly; Hocking, Lynne J.; Porteous, David J.; Sattar, Naveed; Packard, Chris J.; Buckley, Brendan M.; Brody, Jennifer A.; Bis, Joshua C.; Rotter, Jerome I.; Mychaleckyj, Josyf C.; Campbell, Harry; Duan, Qing; Lange, Leslie A.; Wilson, James F.; Hayward, Caroline; Polasek, Ozren; Vitart, Veronique; Rudan, Igor; Wright, Alan F.; Rich, Stephen S.; Psaty, Bruce M.; Borecki, Ingrid B.; Kearney, Patricia M.; Stott, David J.; Adrienne Cupples, L.; Neerincx, Pieter B.T.; Elbers, Clara C.; Francesco Palamara, Pier; Pe'er, Itsik; Abdellaoui, Abdel; Kloosterman, Wigard P.; van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen F.J.; Stoneking, Mark; de Knijff, Peter; Kayser, Manfred; Veldink, Jan H.; van den Berg, Leonard H.; Byelas, Heorhiy; den Dunnen, Johan T.; Dijkstra, Martijn; Amin, Najaf; Joeri van der Velde, K.; van Setten, Jessica; Kattenberg, Mathijs; van Schaik, Barbera D.C.; Bot, Jan; Nijman, Isaäc J.; Mei, Hailiang; Koval, Vyacheslav; Ye, Kai; Lameijer, Eric-Wubbo; Moed, Matthijs H.; Hehir-Kwa, Jayne Y.; Handsaker, Robert E.; Sunyaev, Shamil R.; Sohail, Mashaal; Hormozdiari, Fereydoun; Marschall, Tobias; Schönhuth, Alexander; Guryev, Victor; Suchiman, H. Eka D.; Wolffenbuttel, Bruce H.; Platteel, Mathieu; Pitts, Steven J.; Potluri, Shobha; Cox, David R.; Li, Qibin; Li, Yingrui; Du, Yuanping; Chen, Ruoyan; Cao, Hongzhi; Li, Ning; Cao, Sujie; Wang, Jun; Bovenberg, Jasper A.; Jukema, J. Wouter; van der Harst, Pim; Sijbrands, Eric J.; Hottenga, Jouke-Jan; Uitterlinden, Andre G.; Swertz, Morris A.; van Ommen, Gert-Jan B.; de Bakker, Paul I.W.; Eline Slagboom, P.; Boomsma, Dorret I.; Wijmenga, Cisca; van Duijn, Cornelia M.

2015-01-01

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value <6.61 × 10−4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C=0.135, βTC=0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR. PMID:25751400

A molecular method to detect and identify the native species of southwestern Atlantic Crassostrea (Mollusca: Ostreidae

Directory of Open Access Journals (Sweden)

Sandra Ludwig

2011-08-01

Full Text Available Among oysters, species of Crassostrea (Sacco, 1897 are the most attractive to aquaculture. In Brazil, the genus is represented by C. rhizophorae (Guilding, 1828 and C. brasiliana (Lamarck, 1819. Because the maturation and breeding technology is not well developed for these species, aquaculturists need a reliable method to decide the correct time to place spat collectors in the field, and to identify both species, which are morphologically similar. In this study a specific Multiplex PCR protocol was developed, using one pair of universal primers from 18S rDNA as a positive control and a pair of specific primers for each target species. The sensitivity and specificity of the protocol was evaluated. It detected C. rhizophorae DNA in low concentrations, and C. brasiliana DNA in even lower concentrations. Further, the Multiplex PCR proved efficient in detecting DNA in concentrations equivalent to that of a single larva of each species, either separated or combined, when mixed with total DNA extract of a plankton sample representing 1000 L of filtered water. Field tests confirmed the applicability of the protocol, which holds the promise to become an important tool for aquaculture or conservation programs, allowing for the continuous monitoring of the life cycle of C. brasiliana and C. rhizophorae, by detecting the right periods of larval release and settlement.

Towards a theory of product design specifications

DEFF Research Database (Denmark)

Hansen, Claus Thorp; Andreasen, Mogens Myrup

2004-01-01

, which express the customers¿ need and perception of value. In this paper we will scrutinize this assumption. We outline the roles and tasks of the product design specification in order to identify the requirements on a theory of product design specifications and we identify existing theory elements....... In the design methodology literature we find guidelines and methods to compile a product design specification. The contributions are based on the common underlying assumption that it is meaningful and the only feasible approach to interpret the result of a need analysis into a set of technical specifications...... to build such a theory of product design specifications upon....

Internally readable identifying tag

International Nuclear Information System (INIS)

Jefferts, K.B.; Jefferts, E.R.

1980-01-01

A method of identifying non-metallic objects by means of X-ray equipment is described in detail. A small metal pin with a number of grooves cut in a pre-determined equi-spaced pattern is implanted into the non-metallic object and by decoding the groove patterns using X-ray equipment, the object is uniquely identified. A specific example of such an application is in studying the migratory habits of fish. The pin inserted into the snout of the fish is 0.010 inch in diameter, 0.040 inch in length with 8 possible positions for grooves if spaced 0.005 inch apart. With 6 of the groove positions available for data, the capacity is 2 6 or 64 combinations; clearly longer pins would increase the data capacity. This method of identification is a major advance over previous techniques which necessitated destruction of the fish in order to recover the identification tag. (UK)

A comparison between brand-specific and traditional alcohol surveillance methods to assess underage drinkers' reported alcohol use.

Science.gov (United States)

Roberts, Sarah P; Siegel, Michael B; DeJong, William; Jernigan, David H

2014-11-01

Adolescent alcohol consumption remains common and is associated with many negative health outcomes. Unfortunately, common alcohol surveillance methods often underestimate consumption. Improved alcohol use measures are needed to characterize the landscape of youth drinking. We aimed to compare a standard quantity-frequency measure of youth alcohol consumption to a novel brand-specific measure. We recruited a sample of 1031 respondents across the United States to complete an online survey. Analyses included 833 male and female underage drinkers ages 13-20. Respondents reported on how many of the past 30 days they consumed alcohol, and the number of drinks consumed on an average drinking day. Using our brand-specific measure, respondents identified which brands they consumed, how many days they consumed each brand, and how many drinks per brand they usually had. Youth reported consuming significantly more alcohol (on average, 11 drinks more per month) when responding to the brand-specific versus the standard measure (p brands consumed (p brand preferences and consumption.

Specific Methods of Information Security for Nuclear Materials Control and Accounting Automate Systems

Directory of Open Access Journals (Sweden)

Konstantin Vyacheslavovich Ivanov

2013-02-01

Full Text Available The paper is devoted to specific methods of information security for nuclear materials control and accounting automate systems which is not required of OS and DBMS certifications and allowed to programs modification for clients specific without defenses modification. System ACCORD-2005 demonstrates the realization of this method.

Differences in health insurance and health service utilization among Asian Americans: method for using the NHIS to identify unique patterns between ethnic groups.

Science.gov (United States)

Ruy, Hosihn; Young, Wendy B; Kwak, Hoil

2002-01-01

The purpose of this study is to outline a method to identify the characteristics of socioeconomic variables in determining the differences in health insurance coverage and health services utilization patterns for different ethnic groups, using the behavioural model of health service utilization. A sample drawn from Asian American adult respondents to the 1992, 1993, and 1994 National Health Interview Surveys (NHIS) in the USA formed the data set. The results showed Asian Americans as not being homogeneous. There were distinctly different demographic and socioeconomic characteristics between six Asian American ethnic groups that affect health insurance coverage and health service utilization. The study method is useful for constructing health policy and services to address the general public need without adversely affecting smaller minority groups. Secondary analysis of well-constructed national data sets such as the specific Asian ethnic groups in NHIS, offers a rich method for predicting the differential impact of specific health policies on various ethnic groups.

Methods for identifying surgical wound infection after discharge from hospital: a systematic review

Directory of Open Access Journals (Sweden)

Moore Peter J

2006-11-01

Full Text Available Abstract Background Wound infections are a common complication of surgery that add significantly to the morbidity of patients and costs of treatment. The global trend towards reducing length of hospital stay post-surgery and the increase in day case surgery means that surgical site infections (SSI will increasingly occur after hospital discharge. Surveillance of SSIs is important because rates of SSI are viewed as a measure of hospital performance, however accurate detection of SSIs post-hospital discharge is not straightforward. Methods We conducted a systematic review of methods of post discharge surveillance for surgical wound infection and undertook a national audit of methods of post-discharge surveillance for surgical site infection currently used within United Kingdom NHS Trusts. Results Seven reports of six comparative studies which examined the validity of post-discharge surveillance methods were located; these involved different comparisons and some had methodological limitations, making it difficult to identify an optimal method. Several studies evaluated automated screening of electronic records and found this to be a useful strategy for the identification of SSIs that occurred post discharge. The audit identified a wide range of relevant post-discharge surveillance programmes in England, Scotland and Wales and Northern Ireland; however, these programmes used varying approaches for which there is little supporting evidence of validity and/or reliability. Conclusion In order to establish robust methods of surveillance for those surgical site infections that occur post discharge, there is a need to develop a method of case ascertainment that is valid and reliable post discharge. Existing research has not identified a valid and reliable method. A standardised definition of wound infection (e.g. that of the Centres for Disease Control should be used as a basis for developing a feasible, valid and reliable approach to defining post

Prognostic factors for specific lower extremity and spinal musculoskeletal injuries identified through medical screening and training load monitoring in professional football (soccer): a systematic review

Science.gov (United States)

Sergeant, Jamie C; Parkes, Matthew J; Callaghan, Michael J

2017-01-01

Background Medical screening and load monitoring procedures are commonly used in professional football to assess factors perceived to be associated with injury. Objectives To identify prognostic factors (PFs) and models for lower extremity and spinal musculoskeletal injuries in professional/elite football players from medical screening and training load monitoring processes. Methods The MEDLINE, AMED, EMBASE, CINAHL Plus, SPORTDiscus and PubMed electronic bibliographic databases were searched (from inception to January 2017). Prospective and retrospective cohort studies of lower extremity and spinal musculoskeletal injury incidence in professional/elite football players aged between 16 and 40 years were included. The Quality in Prognostic Studies appraisal tool and the modified Grading of Recommendations Assessment, Development and Evaluation synthesis approach was used to assess the quality of the evidence. Results Fourteen studies were included. 16 specific lower extremity injury outcomes were identified. No spinal injury outcomes were identified. Meta-analysis was not possible due to heterogeneity and study quality. All evidence related to PFs and specific lower extremity injury outcomes was of very low to low quality. On the few occasions where multiple studies could be used to compare PFs and outcomes, only two factors demonstrated consensus. A history of previous hamstring injuries (HSI) and increasing age may be prognostic for future HSI in male players. Conclusions The assumed ability of medical screening tests to predict specific musculoskeletal injuries is not supported by the current evidence. Screening procedures should currently be considered as benchmarks of function or performance only. The prognostic value of load monitoring modalities is unknown. PMID:29177074

An automatic method to generate domain-specific investigator networks using PubMed abstracts

Directory of Open Access Journals (Sweden)

Gwinn Marta

2007-06-01

Full Text Available Abstract Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8% and from 94.2% of HuGE PubMed records (accuracy 87.0. We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit, indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a

An automatic method to generate domain-specific investigator networks using PubMed abstracts

Science.gov (United States)

Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

2007-01-01

Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a web-based prototype

Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer.

Directory of Open Access Journals (Sweden)

Philip Stegmaier

Full Text Available The molecular causes by which the epidermal growth factor receptor tyrosine kinase induces malignant transformation are largely unknown. To better understand EGFs' transforming capacity whole genome scans were applied to a transgenic mouse model of liver cancer and subjected to advanced methods of computational analysis to construct de novo gene regulatory networks based on a combination of sequence analysis and entrained graph-topological algorithms. Here we identified transcription factors, processes, key nodes and molecules to connect as yet unknown interacting partners at the level of protein-DNA interaction. Many of those could be confirmed by electromobility band shift assay at recognition sites of gene specific promoters and by western blotting of nuclear proteins. A novel cellular regulatory circuitry could therefore be proposed that connects cell cycle regulated genes with components of the EGF signaling pathway. Promoter analysis of differentially expressed genes suggested the majority of regulated transcription factors to display specificity to either the pre-tumor or the tumor state. Subsequent search for signal transduction key nodes upstream of the identified transcription factors and their targets suggested the insulin-like growth factor pathway to render the tumor cells independent of EGF receptor activity. Notably, expression of IGF2 in addition to many components of this pathway was highly upregulated in tumors. Together, we propose a switch in autocrine signaling to foster tumor growth that was initially triggered by EGF and demonstrate the knowledge gain form promoter analysis combined with upstream key node identification.

Genome-wide association studies identify four ER negative-specific breast cancer risk loci

DEFF Research Database (Denmark)

Garcia-Closas, Montserrat; Couch, Fergus J; Lindstrom, Sara

2013-01-01

differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls......), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER...

Structural correlation method for model reduction and practical estimation of patient specific parameters illustrated on heart rate regulation

DEFF Research Database (Denmark)

Ottesen, Johnny T.; Mehlsen, Jesper; Olufsen, Mette

2014-01-01

We consider the inverse and patient specific problem of short term (seconds to minutes) heart rate regulation specified by a system of nonlinear ODEs and corresponding data. We show how a recent method termed the structural correlation method (SCM) can be used for model reduction and for obtaining...... a set of practically identifiable parameters. The structural correlation method includes two steps: sensitivity and correlation analysis. When combined with an optimization step, it is possible to estimate model parameters, enabling the model to fit dynamics observed in data. This method is illustrated...... in detail on a model predicting baroreflex regulation of heart rate and applied to analysis of data from a rat and healthy humans. Numerous mathematical models have been proposed for prediction of baroreflex regulation of heart rate, yet most of these have been designed to provide qualitative predictions...

Time-trends in method-specific suicide rates compared with the availability of specific compounds. The Danish experience

DEFF Research Database (Denmark)

Nordentoft, Merete; Qin, Ping; Helweg-Larsen, Karin

2006-01-01

Restriction of means for suicide is an important part of suicide preventive strategies in different countries. All suicides in Denmark between 1970 and 2000 were examined with regard to method used for suicide. Overall suicide mortality and method-specific suicide mortality was compared...... in the number of suicides by self-poisoning with these compounds. Restricted access occurred concomittantly with a 55% decrease in suicide rate...

msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks

Directory of Open Access Journals (Sweden)

Yuan Zhang

2014-01-01

Full Text Available Dynamics of protein-protein interactions (PPIs reveals the recondite principles of biological processes inside a cell. Shown in a wealth of study, just a small group of proteins, rather than the majority, play more essential roles at crucial points of biological processes. This present work focuses on identifying these critical proteins exhibiting dramatic structural changes in dynamic PPI networks. First, a comprehensive way of modeling the dynamic PPIs is presented which simultaneously analyzes the activity of proteins and assembles the dynamic coregulation correlation between proteins at each time point. Second, a novel method is proposed, named msiDBN, which models a common representation of multiple PPI networks using a deep belief network framework and analyzes the reconstruction errors and the variabilities across the time courses in the biological process. Experiments were implemented on data of yeast cell cycles. We evaluated our network construction method by comparing the functional representations of the derived networks with two other traditional construction methods. The ranking results of critical proteins in msiDBN were compared with the results from the baseline methods. The results of comparison showed that msiDBN had better reconstruction rate and identified more proteins of critical value to yeast cell cycle process.

SABER: a computational method for identifying active sites for new reactions.

Science.gov (United States)

Nosrati, Geoffrey R; Houk, K N

2012-05-01

A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. Copyright © 2012 The Protein Society.

An Efficient, Non-iterative Method of Identifying the Cost-Effectiveness Frontier

Science.gov (United States)

Suen, Sze-chuan; Goldhaber-Fiebert, Jeremy D.

2015-01-01

Cost-effectiveness analysis aims to identify treatments and policies that maximize benefits subject to resource constraints. However, the conventional process of identifying the efficient frontier (i.e., the set of potentially cost-effective options) can be algorithmically inefficient, especially when considering a policy problem with many alternative options or when performing an extensive suite of sensitivity analyses for which the efficient frontier must be found for each. Here, we describe an alternative one-pass algorithm that is conceptually simple, easier to implement, and potentially faster for situations that challenge the conventional approach. Our algorithm accomplishes this by exploiting the relationship between the net monetary benefit and the cost-effectiveness plane. To facilitate further evaluation and use of this approach, we additionally provide scripts in R and Matlab that implement our method and can be used to identify efficient frontiers for any decision problem. PMID:25926282

Methods and Techniques of Sampling, Culturing and Identifying of Subsurface Bacteria

International Nuclear Information System (INIS)

Lee, Seung Yeop; Baik, Min Hoon

2010-11-01

This report described sampling, culturing and identifying of KURT underground bacteria, which existed as iron-, manganese-, and sulfate-reducing bacteria. The methods of culturing and media preparation were different by bacteria species affecting bacteria growth-rates. It will be possible for the cultured bacteria to be used for various applied experiments and researches in the future

Identifying research priorities for public health research to address health inequalities: use of Delphi-like survey methods.

Science.gov (United States)

Turner, S; Ollerhead, E; Cook, A

2017-10-09

In the funding of health research and public health research it is vital that research questions posed are important and that funded research meets a research need or a gap in evidence. Many methods are used in the identification of research priorities, however, these can be resource intensive, costly and logistically challenging. Identifying such research priorities can be particularly challenging for complex public health problems as there is a need to consult a number of experts across disciplines and with a range of expertise. This study investigated the use of Delphi-like survey methods in identifying important research priorities relating to health inequalities and framing tractable research questions for topic areas identified. The study was conducted in two phases, both using Delphi-like survey methods. Firstly, public health professionals with an interest in health inequalities were asked to identify research priorities. Secondly academic researchers were asked to frame tractable research questions relating to the priorities identified. These research priorities identified using Delphi-like survey methods were subsequently compared to those identified using different methods. A total of 52 public health professionals and 21 academics across the United Kingdom agreed to take part. The response rates were high, from public health professionals across three survey rounds (69%, 50% and 40%) and from academics across one round (52%), indicating that participants were receptive to the method and motivated to respond. The themes identified as encompassing the most important research priorities were mental health, healthy environment and health behaviours. Within these themes, the topic areas that emerged most strongly included community interventions for prevention of mental health problems and the food and alcohol environment. Some responses received from academic researchers were (as requested) in the form of tractable research questions, whereas others

A new method for discovering disease-specific MiRNA-target regulatory networks.

Directory of Open Access Journals (Sweden)

Miriam Baglioni

Full Text Available Genes and their expression regulation are among the key factors in the comprehension of the genesis and development of complex diseases. In this context, microRNAs (miRNAs are post-transcriptional regulators that play an important role in gene expression since they are frequently deregulated in pathologies like cardiovascular disease and cancer. In vitro validation of miRNA--targets regulation is often too expensive and time consuming to be carried out for every possible alternative. As a result, a tool able to provide some criteria to prioritize trials is becoming a pressing need. Moreover, before planning in vitro experiments, the scientist needs to evaluate the miRNA-target genes interaction network. In this paper we describe the miRable method whose purpose is to identify new potentially relevant genes and their interaction networks associate to a specific pathology. To achieve this goal miRable follows a system biology approach integrating together general-purpose medical knowledge (literature, Protein-Protein Interaction networks, prediction tools and pathology specific data (gene expression data. A case study on Prostate Cancer has shown that miRable is able to: 1 find new potential miRNA-targets pairs, 2 highlight novel genes potentially involved in a disease but never or little studied before, 3 reconstruct all possible regulatory subnetworks starting from the literature to expand the knowledge on the regulation of miRNA regulatory mechanisms.

Screening DNA chip and event-specific multiplex PCR detection methods for biotech crops.

Science.gov (United States)

Lee, Seong-Hun

2014-11-01

There are about 80 biotech crop events that have been approved by safety assessment in Korea. They have been controlled by genetically modified organism (GMO) and living modified organism (LMO) labeling systems. The DNA-based detection method has been used as an efficient scientific management tool. Recently, the multiplex polymerase chain reaction (PCR) and DNA chip have been developed as simultaneous detection methods for several biotech crops' events. The event-specific multiplex PCR method was developed to detect five biotech maize events: MIR604, Event 3272, LY 038, MON 88017 and DAS-59122-7. The specificity was confirmed and the sensitivity was 0.5%. The screening DNA chip was developed from four endogenous genes of soybean, maize, cotton and canola respectively along with two regulatory elements and seven genes: P35S, tNOS, pat, bar, epsps1, epsps2, pmi, cry1Ac and cry3B. The specificity was confirmed and the sensitivity was 0.5% for four crops' 12 events: one soybean, six maize, three cotton and two canola events. The multiplex PCR and DNA chip can be available for screening, gene-specific and event-specific analysis of biotech crops as efficient detection methods by saving on workload and time. © 2014 Society of Chemical Industry. © 2014 Society of Chemical Industry.

Identifying risk factors for exposure to culturable allergenic moulds in energy efficient homes by using highly specific monoclonal antibodies

Energy Technology Data Exchange (ETDEWEB)

Sharpe, Richard A. [European Centre for Environment and Human Health, University of Exeter Medical School, Truro TR1 3HD (United Kingdom); Cocq, Kate Le [Rothamsted Research, North Wyke, Okehampton EX20 2SB (United Kingdom); Nikolaou, Vasilis [University of Exeter Medical School, The Veysey Building, Salmon Pool Lane, Exeter EX2 4SG (United Kingdom); Osborne, Nicholas J. [European Centre for Environment and Human Health, University of Exeter Medical School, Truro TR1 3HD (United Kingdom); Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Sydney Medical School, The University of Sydney, NSW (Australia); Thornton, Christopher R., E-mail: c.r.thornton@exeter.ac.uk [Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD (United Kingdom)

2016-01-15

The aim of this study was to determine the accuracy of monoclonal antibodies (mAbs) in identifying culturable allergenic fungi present in visible mould growth in energy efficient homes, and to identify risk factors for exposure to these known allergenic fungi. Swabs were taken from fungal contaminated surfaces and culturable yeasts and moulds isolated by using mycological culture. Soluble antigens from cultures were tested by ELISA using mAbs specific to the culturable allergenic fungi Aspergillus and Penicillium spp., Ulocladium, Alternaria, and Epicoccum spp., Cladosporium spp., Fusarium spp., and Trichoderma spp. Diagnostic accuracies of the ELISA tests were determined by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2-encoding regions of recovered fungi following ELISA. There was 100% concordance between the two methods, with ELISAs providing genus-level identity and ITS sequencing providing species-level identities (210 out of 210 tested). Species of Aspergillus/Penicillium, Cladosporium, Ulocladium/Alternaria/Epicoccum, Fusarium and Trichoderma were detected in 82% of the samples. The presence of condensation was associated with an increased risk of surfaces being contaminated by Aspergillus/Penicillium spp. and Cladosporium spp., whereas moisture within the building fabric (water ingress/rising damp) was only associated with increased risk of Aspergillus/Penicillium spp. Property type and energy efficiency levels were found to moderate the risk of indoor surfaces becoming contaminated with Aspergillus/Penicillium and Cladosporium which in turn was modified by the presence of condensation, water ingress and rising damp, consistent with previous literature. - Highlights: • Monoclonal antibodies were used to track culturable allergenic moulds in homes. • Allergenic moulds were recovered from 82% of swabs from contaminated surfaces. • The mAbs were highly specific with 100% agreement to PCR of recovered fungi. • Improvements to energy

Identifying risk factors for exposure to culturable allergenic moulds in energy efficient homes by using highly specific monoclonal antibodies

International Nuclear Information System (INIS)

Sharpe, Richard A.; Cocq, Kate Le; Nikolaou, Vasilis; Osborne, Nicholas J.; Thornton, Christopher R.

2016-01-01

The aim of this study was to determine the accuracy of monoclonal antibodies (mAbs) in identifying culturable allergenic fungi present in visible mould growth in energy efficient homes, and to identify risk factors for exposure to these known allergenic fungi. Swabs were taken from fungal contaminated surfaces and culturable yeasts and moulds isolated by using mycological culture. Soluble antigens from cultures were tested by ELISA using mAbs specific to the culturable allergenic fungi Aspergillus and Penicillium spp., Ulocladium, Alternaria, and Epicoccum spp., Cladosporium spp., Fusarium spp., and Trichoderma spp. Diagnostic accuracies of the ELISA tests were determined by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2-encoding regions of recovered fungi following ELISA. There was 100% concordance between the two methods, with ELISAs providing genus-level identity and ITS sequencing providing species-level identities (210 out of 210 tested). Species of Aspergillus/Penicillium, Cladosporium, Ulocladium/Alternaria/Epicoccum, Fusarium and Trichoderma were detected in 82% of the samples. The presence of condensation was associated with an increased risk of surfaces being contaminated by Aspergillus/Penicillium spp. and Cladosporium spp., whereas moisture within the building fabric (water ingress/rising damp) was only associated with increased risk of Aspergillus/Penicillium spp. Property type and energy efficiency levels were found to moderate the risk of indoor surfaces becoming contaminated with Aspergillus/Penicillium and Cladosporium which in turn was modified by the presence of condensation, water ingress and rising damp, consistent with previous literature. - Highlights: • Monoclonal antibodies were used to track culturable allergenic moulds in homes. • Allergenic moulds were recovered from 82% of swabs from contaminated surfaces. • The mAbs were highly specific with 100% agreement to PCR of recovered fungi. • Improvements to energy

Terahertz spectral unmixing based method for identifying gastric cancer

Science.gov (United States)

Cao, Yuqi; Huang, Pingjie; Li, Xian; Ge, Weiting; Hou, Dibo; Zhang, Guangxin

2018-02-01

At present, many researchers are exploring biological tissue inspection using terahertz time-domain spectroscopy (THz-TDS) techniques. In this study, based on a modified hard modeling factor analysis method, terahertz spectral unmixing was applied to investigate the relationships between the absorption spectra in THz-TDS and certain biomarkers of gastric cancer in order to systematically identify gastric cancer. A probability distribution and box plot were used to extract the distinctive peaks that indicate carcinogenesis, and the corresponding weight distributions were used to discriminate the tissue types. The results of this work indicate that terahertz techniques have the potential to detect different levels of cancer, including benign tumors and polyps.

Periodic local MP2 method employing orbital specific virtuals

International Nuclear Information System (INIS)

Usvyat, Denis; Schütz, Martin; Maschio, Lorenzo

2015-01-01

We introduce orbital specific virtuals (OSVs) to represent the truncated pair-specific virtual space in periodic local Møller-Plesset perturbation theory of second order (LMP2). The OSVs are constructed by diagonalization of the LMP2 amplitude matrices which correspond to diagonal Wannier-function (WF) pairs. Only a subset of these OSVs is adopted for the subsequent OSV-LMP2 calculation, namely, those with largest contribution to the diagonal pair correlation energy and with the accumulated value of these contributions reaching a certain accuracy. The virtual space for a general (non diagonal) pair is spanned by the union of the two OSV sets related to the individual WFs of the pair. In the periodic LMP2 method, the diagonal LMP2 amplitude matrices needed for the construction of the OSVs are calculated in the basis of projected atomic orbitals (PAOs), employing very large PAO domains. It turns out that the OSVs are excellent to describe short range correlation, yet less appropriate for long range van der Waals correlation. In order to compensate for this bias towards short range correlation, we augment the virtual space spanned by the OSVs by the most diffuse PAOs of the corresponding minimal PAO domain. The Fock and overlap matrices in OSV basis are constructed in the reciprocal space. The 4-index electron repulsion integrals are calculated by local density fitting and, for distant pairs, via multipole approximation. New procedures for determining the fit-domains and the distant-pair lists, leading to higher efficiency in the 4-index integral evaluation, have been implemented. Generally, and in contrast to our previous PAO based periodic LMP2 method, the OSV-LMP2 method does not require anymore great care in the specification of the individual domains (to get a balanced description when calculating energy differences) and is in that sense a black box procedure. Discontinuities in potential energy surfaces, which may occur for PAO-based calculations if one is not

Periodic local MP2 method employing orbital specific virtuals

Energy Technology Data Exchange (ETDEWEB)

Usvyat, Denis, E-mail: denis.usvyat@chemie.uni-regensburg.de; Schütz, Martin, E-mail: martin.schuetz@chemie.uni-regensburg.de [Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstraße 31, D-93040 Regensburg (Germany); Maschio, Lorenzo, E-mail: lorenzo.maschio@unito.it [Dipartimento di Chimica, and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, I-10125 Torino (Italy)

2015-09-14

We introduce orbital specific virtuals (OSVs) to represent the truncated pair-specific virtual space in periodic local Møller-Plesset perturbation theory of second order (LMP2). The OSVs are constructed by diagonalization of the LMP2 amplitude matrices which correspond to diagonal Wannier-function (WF) pairs. Only a subset of these OSVs is adopted for the subsequent OSV-LMP2 calculation, namely, those with largest contribution to the diagonal pair correlation energy and with the accumulated value of these contributions reaching a certain accuracy. The virtual space for a general (non diagonal) pair is spanned by the union of the two OSV sets related to the individual WFs of the pair. In the periodic LMP2 method, the diagonal LMP2 amplitude matrices needed for the construction of the OSVs are calculated in the basis of projected atomic orbitals (PAOs), employing very large PAO domains. It turns out that the OSVs are excellent to describe short range correlation, yet less appropriate for long range van der Waals correlation. In order to compensate for this bias towards short range correlation, we augment the virtual space spanned by the OSVs by the most diffuse PAOs of the corresponding minimal PAO domain. The Fock and overlap matrices in OSV basis are constructed in the reciprocal space. The 4-index electron repulsion integrals are calculated by local density fitting and, for distant pairs, via multipole approximation. New procedures for determining the fit-domains and the distant-pair lists, leading to higher efficiency in the 4-index integral evaluation, have been implemented. Generally, and in contrast to our previous PAO based periodic LMP2 method, the OSV-LMP2 method does not require anymore great care in the specification of the individual domains (to get a balanced description when calculating energy differences) and is in that sense a black box procedure. Discontinuities in potential energy surfaces, which may occur for PAO-based calculations if one is not

Combined gene expression analysis of whole-tissue and microdissected pancreatic ductal adenocarcinoma identifies genes specifically overexpressed in tumor epithelia.

Science.gov (United States)

Badea, Liviu; Herlea, Vlad; Dima, Simona Olimpia; Dumitrascu, Traian; Popescu, Irinel

2008-01-01

The precise details of pancreatic ductal adenocarcinoma (PDAC) pathogenesis are still insufficiently known, requiring the use of high-throughput methods. However, PDAC is especially difficult to study using microarrays due to its strong desmoplastic reaction, which involves a hyperproliferating stroma that effectively "masks" the contribution of the minoritary neoplastic epithelial cells. Thus it is not clear which of the genes that have been found differentially expressed between normal and whole tumor tissues are due to the tumor epithelia and which simply reflect the differences in cellular composition. To address this problem, laser microdissection studies have been performed, but these have to deal with much smaller tissue sample quantities and therefore have significantly higher experimental noise. In this paper we combine our own large sample whole-tissue study with a previously published smaller sample microdissection study by Grützmann et al. to identify the genes that are specifically overexpressed in PDAC tumor epithelia. The overlap of this list of genes with other microarray studies of pancreatic cancer as well as with the published literature is impressive. Moreover, we find a number of genes whose over-expression appears to be inversely correlated with patient survival: keratin 7, laminin gamma 2, stratifin, platelet phosphofructokinase, annexin A2, MAP4K4 and OACT2 (MBOAT2), which are all specifically upregulated in the neoplastic epithelia, rather than the tumor stroma. We improve on other microarray studies of PDAC by putting together the higher statistical power due to a larger number of samples with information about cell-type specific expression and patient survival.

Methods and Measures: Growth Mixture Modeling--A Method for Identifying Differences in Longitudinal Change among Unobserved Groups

Science.gov (United States)

Ram, Nilam; Grimm, Kevin J.

2009-01-01

Growth mixture modeling (GMM) is a method for identifying multiple unobserved sub-populations, describing longitudinal change within each unobserved sub-population, and examining differences in change among unobserved sub-populations. We provide a practical primer that may be useful for researchers beginning to incorporate GMM analysis into their…

DEVELOPMENT OF A MOLECULAR METHOD TO IDENTIFY HEPATITIS E VIRUS IN WATER

Science.gov (United States)

Hepatitis E virus (HEV) causes an infectious form of hepatitis associated with contaminated water. By analyzing the sequence of several HEV isolates, a reverse transciption-polymerase chain reaction method was developed and optimized that should be able to identify all of the kn...

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

Science.gov (United States)

Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

2015-04-01

To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

Application of multi-locus analytical methods to identify interacting loci in case-control studies.

NARCIS (Netherlands)

Vermeulen, S.; Heijer, M. den; Sham, P.; Knight, J.

2007-01-01

To identify interacting loci in genetic epidemiological studies the application of multi-locus methods of analysis is warranted. Several more advanced classification methods have been developed in the past years, including multiple logistic regression, sum statistics, logic regression, and the

Rapid analysis method for the determination of 14C specific activity in irradiated graphite.

Science.gov (United States)

Remeikis, Vidmantas; Lagzdina, Elena; Garbaras, Andrius; Gudelis, Arūnas; Garankin, Jevgenij; Plukienė, Rita; Juodis, Laurynas; Duškesas, Grigorijus; Lingis, Danielius; Abdulajev, Vladimir; Plukis, Artūras

2018-01-01

14C is one of the limiting radionuclides used in the categorization of radioactive graphite waste; this categorization is crucial in selecting the appropriate graphite treatment/disposal method. We propose a rapid analysis method for 14C specific activity determination in small graphite samples in the 1-100 μg range. The method applies an oxidation procedure to the sample, which extracts 14C from the different carbonaceous matrices in a controlled manner. Because this method enables fast online measurement and 14C specific activity evaluation, it can be especially useful for characterizing 14C in irradiated graphite when dismantling graphite moderator and reflector parts, or when sorting radioactive graphite waste from decommissioned nuclear power plants. The proposed rapid method is based on graphite combustion and the subsequent measurement of both CO2 and 14C, using a commercial elemental analyser and the semiconductor detector, respectively. The method was verified using the liquid scintillation counting (LSC) technique. The uncertainty of this rapid method is within the acceptable range for radioactive waste characterization purposes. The 14C specific activity determination procedure proposed in this study takes approximately ten minutes, comparing favorably to the more complicated and time consuming LSC method. This method can be potentially used to radiologically characterize radioactive waste or used in biomedical applications when dealing with the specific activity determination of 14C in the sample.

Rapid analysis method for the determination of 14C specific activity in irradiated graphite.

Directory of Open Access Journals (Sweden)

Vidmantas Remeikis

Full Text Available 14C is one of the limiting radionuclides used in the categorization of radioactive graphite waste; this categorization is crucial in selecting the appropriate graphite treatment/disposal method. We propose a rapid analysis method for 14C specific activity determination in small graphite samples in the 1-100 μg range. The method applies an oxidation procedure to the sample, which extracts 14C from the different carbonaceous matrices in a controlled manner. Because this method enables fast online measurement and 14C specific activity evaluation, it can be especially useful for characterizing 14C in irradiated graphite when dismantling graphite moderator and reflector parts, or when sorting radioactive graphite waste from decommissioned nuclear power plants. The proposed rapid method is based on graphite combustion and the subsequent measurement of both CO2 and 14C, using a commercial elemental analyser and the semiconductor detector, respectively. The method was verified using the liquid scintillation counting (LSC technique. The uncertainty of this rapid method is within the acceptable range for radioactive waste characterization purposes. The 14C specific activity determination procedure proposed in this study takes approximately ten minutes, comparing favorably to the more complicated and time consuming LSC method. This method can be potentially used to radiologically characterize radioactive waste or used in biomedical applications when dealing with the specific activity determination of 14C in the sample.

A method to determine site-specific, anisotropic fracture toughness in biological materials

International Nuclear Information System (INIS)

Bechtle, Sabine; Özcoban, Hüseyin; Yilmaz, Ezgi D.; Fett, Theo; Rizzi, Gabriele; Lilleodden, Erica T.; Huber, Norbert; Schreyer, Andreas; Swain, Michael V.; Schneider, Gerold A.

2012-01-01

Many biological materials are hierarchically structured, with highly anisotropic structures and properties on several length scales. To characterize the mechanical properties of such materials, detailed testing methods are required that allow precise and site-specific measurements on several length scales. We propose a fracture toughness measurement technique based on notched focused ion beam prepared cantilevers of lower and medium micron size scales. Using this approach, site-specific fracture toughness values in dental enamel were determined. The usefulness and challenges of the method are discussed.

Preference-based disease-specific health-related quality of life instrument for glaucoma: a mixed methods study protocol

Science.gov (United States)

Muratov, Sergei; Podbielski, Dominik W; Jack, Susan M; Ahmed, Iqbal Ike K; Mitchell, Levine A H; Baltaziak, Monika; Xie, Feng

2016-01-01

Introduction A primary objective of healthcare services is to improve patients' health and health-related quality of life (HRQoL). Glaucoma, which affects a substantial proportion of the world population, has a significant detrimental impact on HRQoL. Although there are a number of glaucoma-specific questionnaires to measure HRQoL, none is preference-based which prevent them from being used in health economic evaluation. The proposed study is aimed to develop a preference-based instrument that is capable of capturing important effects specific to glaucoma and treatments on HRQoL and is scored based on the patients' preferences. Methods A sequential, exploratory mixed methods design will be used to guide the development and evaluation of the HRQoL instrument. The study consists of several stages to be implemented sequentially: item identification, item selection, validation and valuation. The instrument items will be identified and selected through a literature review and the conduct of a qualitative study. Validation will be conducted to establish psychometric properties of the instrument followed by a valuation exercise to derive utility scores for the health states described. Ethics and dissemination This study has been approved by the Trillium Health Partners Research Ethics Board (ID number 753). All personal information will be de-identified with the identification code kept in a secured location including the rest of the study data. Only qualified and study-related personnel will be allowed to access the data. The results of the study will be distributed widely through peer-reviewed journals, conferences and internal meetings. PMID:28186941

Development of a new method to identify aminoacylated RNA

Directory of Open Access Journals (Sweden)

Wang Ji

2014-02-01

Full Text Available A RT-PCR method is developed to isolate RNA aminoacylated on their 3’ end from large pools of RNA. The method is being applied in two separate projects. We are interested in isolating a new class of ribozymes that could successively catalyze the two chemical reactions leading to their own 3’ aminoacylation (ATP activation of an amino acid followed by 3' esterification of the RNA. The catalysis of each of the two reactions has independently been demonstrated for some RNA isolated with the SELEX methodology [1-2]. However, the coupling of both reactions on a same molecule has not been achieved yet. The identification of these still hypothetical ribozymes may help understand how the former translation system started in the absence of the aminoacyltRNA Synthetase, which catalyzes the above two reactions on tRNA in modern cells. In another project, we would like to identify the whole repertoire of aminoacylated RNA (the “aminoacylome” in cells. There are strong indications that other RNA besides tRNA and tmRNA may be aminoacylated for biological purposes [3-4].

Optimization method for identifying the source term in an inverse wave equation

Directory of Open Access Journals (Sweden)

Arumugam Deiveegan

2017-08-01

Full Text Available In this work, we investigate the inverse problem of identifying a space-wise dependent source term of wave equation from the measurement on the boundary. On the basis of the optimal control framework, the inverse problem is transformed into an optimization problem. The existence and necessary condition of the minimizer for the cost functional are obtained. The projected gradient method and two-parameter model function method are applied to the minimization problem and numerical results are illustrated.

Handbook of methods for risk-based analysis of technical specification requirements

International Nuclear Information System (INIS)

Samanta, P.K.; Vesely, W.E.

1994-01-01

Technical Specifications (TS) requirements for nuclear power plants define the Limiting Conditions for Operation (LCOs) and Surveillance Requirements (SRs) to assure safety during operation. In general, these requirements were based on deterministic analysis and engineering judgments. Experiences with plant operation indicate that some elements of the requirements are unnecessarily restrictive, while others may not be conducive to safety. Improvements in these requirements are facilitated by the availability of plant specific Probabilistic Safety Assessments (PSAs). The use of risk and reliability-based methods to improve TS requirements has gained wide interest because these methods can: Quantitatively evaluate the risk and justify changes based on objective risk arguments; Provide a defensible basis for these requirements for regulatory applications. The US NRC Office of Research is sponsoring research to develop systematic risk-based methods to improve various aspects of TS requirements. The handbook of methods, which is being prepared, summarizes such risk-based methods. The scope of the handbook includes reliability and risk-based methods for evaluating allowed outage times (AOTs), action statements requiring shutdown where shutdown risk may be substantial, surveillance test intervals (STIs), defenses against common-cause failures, managing plant configurations, and scheduling maintenances. For each topic, the handbook summarizes methods of analysis and data needs, outlines the insights to be gained, lists additional references, and presents examples of evaluations

Handbook of methods for risk-based analysis of Technical Specification requirements

International Nuclear Information System (INIS)

Samanta, P.K.; Vesely, W.E.

1993-01-01

Technical Specifications (TS) requirements for nuclear power plants define the Limiting Conditions for Operation (LCOs) and Surveillance Requirements (SRs) to assure safety during operation. In general, these requirements were based on deterministic analysis and engineering judgments. Experiences with plant operation indicate that some elements of the requirements are unnecessarily restrictive, while others may not be conducive to safety. Improvements in these requirements are facilitated by the availability of plant specific Probabilistic Safety Assessments (PSAs). The use of risk and reliability-based methods to improve TS requirements has gained wide interest because these methods can: quantitatively evaluate the risk impact and justify changes based on objective risk arguments. Provide a defensible basis for these requirements for regulatory applications. The United States Nuclear Regulatory Commission (USNRC) Office of Research is sponsoring research to develop systematic risk-based methods to improve various aspects of TS requirements. The handbook of methods, which is being prepared, summarizes such risk-based methods. The scope of the handbook includes reliability and risk-based methods for evaluating allowed outage times (AOTs), action statements requiring shutdown where shutdown risk may be substantial, surveillance test intervals (STIs), defenses against common-cause failures, managing plant configurations, and scheduling maintenances. For each topic, the handbook summarizes methods of analysis and data needs, outlines the insights to be gained, lists additional references, and presents examples of evaluations

Specific activity measurement of 64Cu: A comparison of methods

International Nuclear Information System (INIS)

Mastren, Tara; Guthrie, James; Eisenbeis, Paul; Voller, Tom; Mebrahtu, Efrem; Robertson, J. David; Lapi, Suzanne E.

2014-01-01

Effective specific activity of 64 Cu (amount of radioactivity per µmol metal) is important in order to determine purity of a particular 64 Cu lot and to assist in optimization of the purification process. Metal impurities can affect effective specific activity and therefore it is important to have a simple method that can measure trace amounts of metals. This work shows that ion chromatography (IC) yields similar results to ICP mass spectrometry for copper, nickel and iron contaminants in 64 Cu production solutions. - Highlights: • Comparison of TETA titration, ICP mass spectrometry, and ion chromatography to measure specific activity. • Validates ion chromatography by using ICP mass spectrometry as the “gold standard”. • Shows different types and amounts of metal impurities present in 64 Cu

BDA: A novel method for identifying defects in body-centered cubic crystals.

Science.gov (United States)

Möller, Johannes J; Bitzek, Erik

2016-01-01

The accurate and fast identification of crystallographic defects plays a key role for the analysis of atomistic simulation output data. For face-centered cubic (fcc) metals, most existing structure analysis tools allow for the direct distinction of common defects, such as stacking faults or certain low-index surfaces. For body-centered cubic (bcc) metals, on the other hand, a robust way to identify such defects is currently not easily available. We therefore introduce a new method for analyzing atomistic configurations of bcc metals, the BCC Defect Analysis (BDA). It uses existing structure analysis algorithms and combines their results to uniquely distinguish between typical defects in bcc metals. In essence, the BDA method offers the following features:•Identification of typical defect structures in bcc metals.•Reduction of erroneously identified defects by iterative comparison to the defects in the atom's neighborhood.•Availability as ready-to-use Python script for the widespread visualization tool OVITO [http://ovito.org].

Generalized framework for context-specific metabolic model extraction methods

Directory of Open Access Journals (Sweden)

Semidán eRobaina Estévez

2014-09-01

Full Text Available Genome-scale metabolic models are increasingly applied to investigate the physiology not only of simple prokaryotes, but also eukaryotes, such as plants, characterized with compartmentalized cells of multiple types. While genome-scale models aim at including the entirety of known metabolic reactions, mounting evidence has indicated that only a subset of these reactions is active in a given context, including: developmental stage, cell type, or environment. As a result, several methods have been proposed to reconstruct context-specific models from existing genome-scale models by integrating various types of high-throughput data. Here we present a mathematical framework that puts all existing methods under one umbrella and provides the means to better understand their functioning, highlight similarities and differences, and to help users in selecting a most suitable method for an application.

Technical specification improvement through safety margin considerations

International Nuclear Information System (INIS)

Howard, R.C.; Jansen, R.L.

1986-01-01

Westinghouse has developed an approach for utilizing safety analysis margin considerations to improve plant operability through technical specification revision. This approach relies on the identification and use of parameter interrelations and sensitivities to identify acceptable operating envelopes. This paper summarizes technical specification activities to date and presents the use of safety margin considerations as another viable method to obtain technical specification improvement

Specific binding-adsorbent assay method and test means

International Nuclear Information System (INIS)

1981-01-01

A description is given of an improved specific binding assay method and test means employing a nonspecific adsorbent for the substance to be determined, particularly hepatitis B surface (HBsub(s)) antigen, in its free state or additionally in the form of its immune complex. The invention is illustrated by 1) the radioimmunoadsorbent assay for HBsub(s) antigen, 2) the radioimmunoadsorbent assay for HBsub(s) antigen in the form of immune complex with antibody, 3) a study of adsorption characteristics of various anion exchange materials for HBsub(s) antigen, 4) the use of hydrophobic adsorbents in a radioimmunoadsorbent assay for HBsub(s) antigen and 5) the radioimmunoadsorbent assay for antibody to HBsub(s) antigen. The advantages of the present method for detecting HBsub(s) antigen compared to previous methods include the manufacturing advantages of eliminating the need for insolubilised anti-HBsub(s) and the advantages of a single incubation step, fewer manipulations, storability of adsorbent materials, increased sensitivity and versatility of detecting HBsub(s) antigen in the form of its immune complex if desired. (U.K.)

Identifying Domain-General and Domain-Specific Predictors of Low Mathematics Performance: A Classification and Regression Tree Analysis

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David J. Purpura

2017-12-01

Full Text Available Many children struggle to successfully acquire early mathematics skills. Theoretical and empirical evidence has pointed to deficits in domain-specific skills (e.g., non-symbolic mathematics skills or domain-general skills (e.g., executive functioning and language as underlying low mathematical performance. In the current study, we assessed a sample of 113 three- to five-year old preschool children on a battery of domain-specific and domain-general factors in the fall and spring of their preschool year to identify Time 1 (fall factors associated with low performance in mathematics knowledge at Time 2 (spring. We used the exploratory approach of classification and regression tree analyses, a strategy that uses step-wise partitioning to create subgroups from a larger sample using multiple predictors, to identify the factors that were the strongest classifiers of low performance for younger and older preschool children. Results indicated that the most consistent classifier of low mathematics performance at Time 2 was children’s Time 1 mathematical language skills. Further, other distinct classifiers of low performance emerged for younger and older children. These findings suggest that risk classification for low mathematics performance may differ depending on children’s age.

Structural identifiability of systems biology models: a critical comparison of methods.

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Oana-Teodora Chis

Full Text Available Analysing the properties of a biological system through in silico experimentation requires a satisfactory mathematical representation of the system including accurate values of the model parameters. Fortunately, modern experimental techniques allow obtaining time-series data of appropriate quality which may then be used to estimate unknown parameters. However, in many cases, a subset of those parameters may not be uniquely estimated, independently of the experimental data available or the numerical techniques used for estimation. This lack of identifiability is related to the structure of the model, i.e. the system dynamics plus the observation function. Despite the interest in knowing a priori whether there is any chance of uniquely estimating all model unknown parameters, the structural identifiability analysis for general non-linear dynamic models is still an open question. There is no method amenable to every model, thus at some point we have to face the selection of one of the possibilities. This work presents a critical comparison of the currently available techniques. To this end, we perform the structural identifiability analysis of a collection of biological models. The results reveal that the generating series approach, in combination with identifiability tableaus, offers the most advantageous compromise among range of applicability, computational complexity and information provided.

Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset

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Yamada Yoichi

2012-12-01

Full Text Available Abstract Background We previously proposed an algorithm for the identification of GO terms that commonly annotate genes whose expression is upregulated or downregulated in some microarray data compared with in other microarray data. We call these “differentially expressed GO terms” and have named the algorithm “matrix-assisted identification method of differentially expressed GO terms” (MIMGO. MIMGO can also identify microarray data in which genes annotated with a differentially expressed GO term are upregulated or downregulated. However, MIMGO has not yet been validated on a real microarray dataset using all available GO terms. Findings We combined Gene Set Enrichment Analysis (GSEA with MIMGO to identify differentially expressed GO terms in a yeast cell cycle microarray dataset. GSEA followed by MIMGO (GSEA + MIMGO correctly identified (p Conclusions MIMGO is a reliable method to identify differentially expressed GO terms comprehensively.

Identifying complications of interventional procedures from UK routine healthcare databases: a systematic search for methods using clinical codes.

Science.gov (United States)

Keltie, Kim; Cole, Helen; Arber, Mick; Patrick, Hannah; Powell, John; Campbell, Bruce; Sims, Andrew

2014-11-28

Several authors have developed and applied methods to routine data sets to identify the nature and rate of complications following interventional procedures. But, to date, there has been no systematic search for such methods. The objective of this article was to find, classify and appraise published methods, based on analysis of clinical codes, which used routine healthcare databases in a United Kingdom setting to identify complications resulting from interventional procedures. A literature search strategy was developed to identify published studies that referred, in the title or abstract, to the name or acronym of a known routine healthcare database and to complications from procedures or devices. The following data sources were searched in February and March 2013: Cochrane Methods Register, Conference Proceedings Citation Index - Science, Econlit, EMBASE, Health Management Information Consortium, Health Technology Assessment database, MathSciNet, MEDLINE, MEDLINE in-process, OAIster, OpenGrey, Science Citation Index Expanded and ScienceDirect. Of the eligible papers, those which reported methods using clinical coding were classified and summarised in tabular form using the following headings: routine healthcare database; medical speciality; method for identifying complications; length of follow-up; method of recording comorbidity. The benefits and limitations of each approach were assessed. From 3688 papers identified from the literature search, 44 reported the use of clinical codes to identify complications, from which four distinct methods were identified: 1) searching the index admission for specified clinical codes, 2) searching a sequence of admissions for specified clinical codes, 3) searching for specified clinical codes for complications from procedures and devices within the International Classification of Diseases 10th revision (ICD-10) coding scheme which is the methodology recommended by NHS Classification Service, and 4) conducting manual clinical

Novel Application of Statistical Methods to Identify New Urinary Incontinence Risk Factors

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Theophilus O. Ogunyemi

2012-01-01

Full Text Available Longitudinal data for studying urinary incontinence (UI risk factors are rare. Data from one study, the hallmark Medical, Epidemiological, and Social Aspects of Aging (MESA, have been analyzed in the past; however, repeated measures analyses that are crucial for analyzing longitudinal data have not been applied. We tested a novel application of statistical methods to identify UI risk factors in older women. MESA data were collected at baseline and yearly from a sample of 1955 men and women in the community. Only women responding to the 762 baseline and 559 follow-up questions at one year in each respective survey were examined. To test their utility in mining large data sets, and as a preliminary step to creating a predictive index for developing UI, logistic regression, generalized estimating equations (GEEs, and proportional hazard regression (PHREG methods were used on the existing MESA data. The GEE and PHREG combination identified 15 significant risk factors associated with developing UI out of which six of them, namely, urinary frequency, urgency, any urine loss, urine loss after emptying, subject’s anticipation, and doctor’s proactivity, are found most highly significant by both methods. These six factors are potential candidates for constructing a future UI predictive index.

A Nested-Splicing by Overlap Extension PCR Improves Specificity of this Standard Method.

Science.gov (United States)

Karkhane, Ali Asghar; Yakhchali, Bagher; Rastgar Jazii, Ferdous; Bambai, Bijan; Aminzadeh, Saeed; Rahimi, Fatemeh

2015-06-01

Splicing by overlap extension (SOE) PCR is used to create mutation in the coding sequence of an enzyme in order to study the role of specific residues in protein's structure and function. We introduced a nested-SOE-PCR (N -SOE-PCR) in order to increase the specificity and generating mutations in a gene by SOE-PCR. Genomic DNA from Bacillus thermocatenulatus was extracted. Nested PCR was used to amplify B. thermocatenulatus lipase gene variants, namely wild type and mutant, using gene specific and mutagenic specific primers, followed by cloning in a suitable vector. Briefly in N-SOE-PCR method, instead of two pairs of primers, three pairs of primers are used to amplify a mutagenic fragment. Moreover, the first and second PCR products are slightly longer than PCR products in a conventional SOE. PCR products obtained from the first round of PCR are used for the second PCR by applying the nested and mutated primers. Following to the purification of the amplified fragments, they will be subject of the further purification and will be used as template to perform the third round of PCR using gene specific primers. In the end, the products will be cloned into a suitable vector for subsequent application. In comparison to the conventional SOE-PCR, the improved method (i.e. N-SOE-PCR) increases the yield and specificity of the products. In addition, the proposed method shows a large reduction in the non-specific products. By applying two more primers in the conventional SOE, the specificity of the method will be improved. This would be in part due to annealing of the primers further inside the amplicon that increases both the efficiency and a better attachment of the primers. Positioning of the primer far from both ends of an amplicon leads to an enhanced binding as well as increased affinity in the third round of amplification in SOE.

A Method for Identifying Contours in Processing Digital Images from Computer Tomograph

Science.gov (United States)

Roşu, Şerban; Pater, Flavius; Costea, Dan; Munteanu, Mihnea; Roşu, Doina; Fratila, Mihaela

2011-09-01

The first step in digital processing of two-dimensional computed tomography images is to identify the contour of component elements. This paper deals with the collective work of specialists in medicine and applied mathematics in computer science on elaborating new algorithms and methods in medical 2D and 3D imagery.

Using natural language processing and machine learning to identify gout flares from electronic clinical notes.

Science.gov (United States)

Zheng, Chengyi; Rashid, Nazia; Wu, Yi-Lin; Koblick, River; Lin, Antony T; Levy, Gerald D; Cheetham, T Craig

2014-11-01

Gout flares are not well documented by diagnosis codes, making it difficult to conduct accurate database studies. We implemented a computer-based method to automatically identify gout flares using natural language processing (NLP) and machine learning (ML) from electronic clinical notes. Of 16,519 patients, 1,264 and 1,192 clinical notes from 2 separate sets of 100 patients were selected as the training and evaluation data sets, respectively, which were reviewed by rheumatologists. We created separate NLP searches to capture different aspects of gout flares. For each note, the NLP search outputs became the ML system inputs, which provided the final classification decisions. The note-level classifications were grouped into patient-level gout flares. Our NLP+ML results were validated using a gold standard data set and compared with the claims-based method used by prior literatures. For 16,519 patients with a diagnosis of gout and a prescription for a urate-lowering therapy, we identified 18,869 clinical notes as gout flare positive (sensitivity 82.1%, specificity 91.5%): 1,402 patients with ≥3 flares (sensitivity 93.5%, specificity 84.6%), 5,954 with 1 or 2 flares, and 9,163 with no flare (sensitivity 98.5%, specificity 96.4%). Our method identified more flare cases (18,869 versus 7,861) and patients with ≥3 flares (1,402 versus 516) when compared to the claims-based method. We developed a computer-based method (NLP and ML) to identify gout flares from the clinical notes. Our method was validated as an accurate tool for identifying gout flares with higher sensitivity and specificity compared to previous studies. Copyright © 2014 by the American College of Rheumatology.

On the Use of Biomineral Oxygen Isotope Data to Identify Human Migrants in the Archaeological Record: Intra-Sample Variation, Statistical Methods and Geographical Considerations.

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Emma Lightfoot

Full Text Available Oxygen isotope analysis of archaeological skeletal remains is an increasingly popular tool to study past human migrations. It is based on the assumption that human body chemistry preserves the δ18O of precipitation in such a way as to be a useful technique for identifying migrants and, potentially, their homelands. In this study, the first such global survey, we draw on published human tooth enamel and bone bioapatite data to explore the validity of using oxygen isotope analyses to identify migrants in the archaeological record. We use human δ18O results to show that there are large variations in human oxygen isotope values within a population sample. This may relate to physiological factors influencing the preservation of the primary isotope signal, or due to human activities (such as brewing, boiling, stewing, differential access to water sources and so on causing variation in ingested water and food isotope values. We compare the number of outliers identified using various statistical methods. We determine that the most appropriate method for identifying migrants is dependent on the data but is likely to be the IQR or median absolute deviation from the median under most archaeological circumstances. Finally, through a spatial assessment of the dataset, we show that the degree of overlap in human isotope values from different locations across Europe is such that identifying individuals' homelands on the basis of oxygen isotope analysis alone is not possible for the regions analysed to date. Oxygen isotope analysis is a valid method for identifying first-generation migrants from an archaeological site when used appropriately, however it is difficult to identify migrants using statistical methods for a sample size of less than c. 25 individuals. In the absence of local previous analyses, each sample should be treated as an individual dataset and statistical techniques can be used to identify migrants, but in most cases pinpointing a specific

A systematic method for identifying vital areas at complex nuclear facilities.

Energy Technology Data Exchange (ETDEWEB)

Beck, David Franklin; Hockert, John

2005-05-01

Identifying the areas to be protected is an important part of the development of measures for physical protection against sabotage at complex nuclear facilities. In June 1999, the International Atomic Energy Agency published INFCIRC/225/Rev.4, 'The Physical Protection of Nuclear Material and Nuclear Facilities.' This guidance recommends that 'Safety specialists, in close cooperation with physical protection specialists, should evaluate the consequences of malevolent acts, considered in the context of the State's design basis threat, to identify nuclear material, or the minimum complement of equipment, systems or devices to be protected against sabotage.' This report presents a structured, transparent approach for identifying the areas that contain this minimum complement of equipment, systems, and devices to be protected against sabotage that is applicable to complex nuclear facilities. The method builds upon safety analyses to develop sabotage fault trees that reflect sabotage scenarios that could cause unacceptable radiological consequences. The sabotage actions represented in the fault trees are linked to the areas from which they can be accomplished. The fault tree is then transformed (by negation) into its dual, the protection location tree, which reflects the sabotage actions that must be prevented in order to prevent unacceptable radiological consequences. The minimum path sets of this fault tree dual yield, through the area linkage, sets of areas, each of which contains nuclear material, or a minimum complement of equipment, systems or devices that, if protected, will prevent sabotage. This method also provides guidance for the selection of the minimum path set that permits optimization of the trade-offs among physical protection effectiveness, safety impact, cost and operational impact.

A side-effect free method for identifying cancer drug targets.

Science.gov (United States)

Ashraf, Md Izhar; Ong, Seng-Kai; Mujawar, Shama; Pawar, Shrikant; More, Pallavi; Paul, Somnath; Lahiri, Chandrajit

2018-04-27

Identifying effective drug targets, with little or no side effects, remains an ever challenging task. A potential pitfall of failing to uncover the correct drug targets, due to side effect of pleiotropic genes, might lead the potential drugs to be illicit and withdrawn. Simplifying disease complexity, for the investigation of the mechanistic aspects and identification of effective drug targets, have been done through several approaches of protein interactome analysis. Of these, centrality measures have always gained importance in identifying candidate drug targets. Here, we put forward an integrated method of analysing a complex network of cancer and depict the importance of k-core, functional connectivity and centrality (KFC) for identifying effective drug targets. Essentially, we have extracted the proteins involved in the pathways leading to cancer from the pathway databases which enlist real experimental datasets. The interactions between these proteins were mapped to build an interactome. Integrative analyses of the interactome enabled us to unearth plausible reasons for drugs being rendered withdrawn, thereby giving future scope to pharmaceutical industries to potentially avoid them (e.g. ESR1, HDAC2, F2, PLG, PPARA, RXRA, etc). Based upon our KFC criteria, we have shortlisted ten proteins (GRB2, FYN, PIK3R1, CBL, JAK2, LCK, LYN, SYK, JAK1 and SOCS3) as effective candidates for drug development.

Formal Methods for Abstract Specifications – A Comparison of Concepts

DEFF Research Database (Denmark)

Instenberg, Martin; Schneider, Axel; Schnetter, Sabine

2006-01-01

In industry formal methods are becoming increasingly important for the verification of hardware and software designs. However current practice for specification of system and protocol functionality on high level of abstraction is textual description. For verification of the system behavior manual...... inspections and tests are usual means. To facilitate the introduction of formal methods in the development process of complex systems and protocols, two different tools evolved from research activities – UPPAAL and SpecEdit – have been investigated and compared regarding their concepts and functionality...

A structured elicitation method to identify key direct risk factors for the management of natural resources

Directory of Open Access Journals (Sweden)

Michael Smith

2015-11-01

Full Text Available The high level of uncertainty inherent in natural resource management requires planners to apply comprehensive risk analyses, often in situations where there are few resources. In this paper, we demonstrate a broadly applicable, novel and structured elicitation approach to identify important direct risk factors. This new approach combines expert calibration and fuzzy based mathematics to capture and aggregate subjective expert estimates of the likelihood that a set of direct risk factors will cause management failure. A specific case study is used to demonstrate the approach; however, the described methods are widely applicable in risk analysis. For the case study, the management target was to retain all species that characterise a set of natural biological elements. The analysis was bounded by the spatial distribution of the biological elements under consideration and a 20-year time frame. Fourteen biological elements were expected to be at risk. Eleven important direct risk factors were identified that related to surrounding land use practices, climate change, problem species (e.g., feral predators, fire and hydrological change. In terms of their overall influence, the two most important risk factors were salinisation and a lack of water which together pose a considerable threat to the survival of nine biological elements. The described approach successfully overcame two concerns arising from previous risk analysis work: (1 the lack of an intuitive, yet comprehensive scoring method enabling the detection and clarification of expert agreement and associated levels of uncertainty; and (2 the ease with which results can be interpreted and communicated while preserving a rich level of detail essential for informed decision making.

Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

Science.gov (United States)

Condie, Brian G; Urbanski, William M

2014-01-01

Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

Global Transcriptome Sequencing Identifies Chlamydospore Specific Markers in Candida albicans and Candida dubliniensis

LENUS (Irish Health Repository)

Palige, Katja

2013-04-15

Candida albicans and Candida dubliniensis are pathogenic fungi that are highly related but differ in virulence and in some phenotypic traits. During in vitro growth on certain nutrient-poor media, C. albicans and C. dubliniensis are the only yeast species which are able to produce chlamydospores, large thick-walled cells of unknown function. Interestingly, only C. dubliniensis forms pseudohyphae with abundant chlamydospores when grown on Staib medium, while C. albicans grows exclusively as a budding yeast. In order to further our understanding of chlamydospore development and assembly, we compared the global transcriptional profile of both species during growth in liquid Staib medium by RNA sequencing. We also included a C. albicans mutant in our study which lacks the morphogenetic transcriptional repressor Nrg1. This strain, which is characterized by its constitutive pseudohyphal growth, specifically produces masses of chlamydospores in Staib medium, similar to C. dubliniensis. This comparative approach identified a set of putatively chlamydospore-related genes. Two of the homologous C. albicans and C. dubliniensis genes (CSP1 and CSP2) which were most strongly upregulated during chlamydospore development were analysed in more detail. By use of the green fluorescent protein as a reporter, the encoded putative cell wall related proteins were found to exclusively localize to C. albicans and C. dubliniensis chlamydospores. Our findings uncover the first chlamydospore specific markers in Candida species and provide novel insights in the complex morphogenetic development of these important fungal pathogens.

A novel affinity purification method to isolate peptide specific antibodies

DEFF Research Database (Denmark)

Karlsen, Alan E; Lernmark, A; Kofod, Hans

1990-01-01

Site-specific, high affinity polyclonal antisera are effectively and successfully produced by immunizing rabbits with synthetic peptides. The use of these antisera in subsequent immune analysis is often limited because of non-specific binding. We describe a new and simple method to effectively...... affinity-purify anti-peptide antibodies. To test our system, rabbits were immunized with model peptides representing sequences of the putative rabbit growth hormone receptor and several HLA-DQ beta-chain molecules. Polystyrene plastic beads were coated with peptides. Immune serum was incubated...... with the beads and after a wash step the bound antibodies were eluted in 1 M acetic acid. The eluted material was composed predominantly of intact immunoglobulin as evidenced by the presence of heavy and light chain bands in SDS-PAGE. The eluted antibodies were peptide specific in ELISA and bound only to intact...

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

Directory of Open Access Journals (Sweden)

Andrew Williams

2015-12-01

Full Text Available Background: The presence of diverse types of nanomaterials (NMs in commerce is growing at an exponential pace. As a result, human exposure to these materials in the environment is inevitable, necessitating the need for rapid and reliable toxicity testing methods to accurately assess the potential hazards associated with NMs. In this study, we applied biclustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related biclusters of genes showing similar expression profiles were identified. The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO2, carbon black (CB or carbon nanotubes (CNTs to determine the disease significance of these data-driven gene sets.Results: Biclusters representing inflammation (chemokine activity, DNA binding, cell cycle, apoptosis, reactive oxygen species (ROS and fibrosis processes were identified. All of the NM studies were significant with respect to the bicluster related to chemokine activity (DAVID; FDR p-value = 0.032. The bicluster related to pulmonary fibrosis was enriched in studies where toxicity induced by CNT and CB studies was investigated, suggesting the potential for these materials to induce lung fibrosis. The pro-fibrogenic potential of CNTs is well established. Although CB has not been shown to induce fibrosis, it induces stronger inflammatory, oxidative stress and DNA damage responses than nano-TiO2 particles.Conclusion: The results of the analysis correctly identified all NMs to be inflammogenic and only CB and CNTs as potentially fibrogenic. In addition to identifying several

Phonon spectrum of YBCO obtained by specific heat inversion method for real data

CERN Document Server

Tao Wen; Dai Xian Xi; Dai Ji Xin; Evenson, W E

2003-01-01

In this paper, the phonon spectrum of YBCO is obtained from experimental specific heat data by an exact inversion formula with a parameter for eliminating divergences. The results can be compared to those of neutron inelastic scattering, which can only be carried out in a few laboratories. Some key points of specific heat-phonon spectrum inversion (SPI) theory and a method of asymptotic behaviour control are discussed. An improved unique existence theorem is presented, and a universal function set for numerical calculation of SPI is calculated with high accuracy, which makes the inversion method applicable and convenient in practice. This is the first time specific heat-phonon SPI has been realized for a concrete system.

Analysis of Formal Methods for Specification of E-Commerce Applications

Directory of Open Access Journals (Sweden)

Sadiq Ali Khan

2016-01-01

Full Text Available E-commerce based application characteristics portray elevated dynamics while incorporating decentralized nature. Extreme emphasis influencing structural design plus implementation, positions such applications highly appreciated. Significant research articles reveal that, applying formal methods addressing challenges incumbent with E-commerce based applications, contribute towards reliability and robustness obliging the system. Anticipating and designing sturdy e-process and concurrent implementation, allows application behavior extra strength against errors, frauds and hacking, minimizing program faults during application operations. Programmers find extreme difficulty guaranteeing correct processing under all circumstances, however, not impossible. Concealed flaws and errors, triggered only under unexpected and unanticipated scenarios, pilot subtle mistakes and appalling failures. Code authors utilize various formal methods for reducing these flaws. Mentioning prominent methods would include, ASM (Abstract State Machines, B-Method, z-Language, UML (Unified Modelling Language etc. This paper primarily focuses different formal methods applied while deliberating specification and verification techniques for cost effective.

Using mixed methods to identify and answer clinically relevant research questions.

Science.gov (United States)

Shneerson, Catherine L; Gale, Nicola K

2015-06-01

The need for mixed methods research in answering health care questions is becoming increasingly recognized because of the complexity of factors that affect health outcomes. In this article, we argue for the value of using a qualitatively driven mixed method approach for identifying and answering clinically relevant research questions. This argument is illustrated by findings from a study on the self-management practices of cancer survivors and the exploration of one particular clinically relevant finding about higher uptake of self-management in cancer survivors who had received chemotherapy treatment compared with those who have not. A cross-sectional study generated findings that formed the basis for the qualitative study, by informing the purposive sampling strategy and generating new qualitative research questions. Using a quantitative research component to supplement a qualitative study can enhance the generalizability and clinical relevance of the findings and produce detailed, contextualized, and rich answers to research questions that would be unachievable through quantitative or qualitative methods alone. © The Author(s) 2015.

Comparing hair-morphology and molecular methods to identify fecal samples from Neotropical felids.

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Carlos C Alberts

Full Text Available To avoid certain problems encountered with more-traditional and invasive methods in behavioral-ecology studies of mammalian predators, such as felids, molecular approaches have been employed to identify feces found in the field. However, this method requires a complete molecular biology laboratory, and usually also requires very fresh fecal samples to avoid DNA degradation. Both conditions are normally absent in the field. To address these difficulties, identification based on morphological characters (length, color, banding, scales and medullar patterns of hairs found in feces could be employed as an alternative. In this study we constructed a morphological identification key for guard hairs of eight Neotropical felids (jaguar, oncilla, Geoffroy's cat, margay, ocelot, Pampas cat, puma and jaguarundi and compared its efficiency to that of a molecular identification method, using the ATP6 region as a marker. For this molecular approach, we simulated some field conditions by postponing sample-conservation procedures. A blind test of the identification key obtained a nearly 70% overall success rate, which we considered equivalent to or better than the results of some molecular methods (probably due to DNA degradation found in other studies. The jaguar, puma and jaguarundi could be unequivocally discriminated from any other Neotropical felid. On a scale ranging from inadequate to excellent, the key proved poor only for the margay, with only 30% of its hairs successfully identified using this key; and have intermediate success rates for the remaining species, the oncilla, Geoffroy's cat, ocelot and Pampas cat, were intermediate. Complementary information about the known distributions of felid populations may be necessary to substantially improve the results obtained with the key. Our own molecular results were even better, since all blind-tested samples were correctly identified. Part of these identifications were made from samples kept in suboptimal

Identifying usability issues for personalization during formative evaluations: a comparisons of three methods

NARCIS (Netherlands)

van Velsen, Lex Stefan; van der Geest, Thea; Klaassen, R.F.

2011-01-01

A personalized system is one that generates unique output for each individual. As a result, personalization has transformed the interaction between the user and the system, and specific new usability issues have arisen. Methods used for evaluating personalized systems should be able to reveal the

Identifying Copy Number Variants under Selection in Geographically Structured Populations Based on -statistics

Directory of Open Access Journals (Sweden)

Hae-Hiang Song

2012-06-01

Full Text Available Large-scale copy number variants (CNVs in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional FST measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the FST estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific FST and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.

Comparison of methods applicable to evaluation of nuclear power plant technical specifications

International Nuclear Information System (INIS)

Cho, N.Z.; Bozoki, G.E.; Youngblood, R.W.

1986-01-01

This study compares three probabilistic methods based on the static fault tree analysis, time-dependent unavailability analysis, and Markov analysis, which can be used to evaluate technical specifications in nuclear power plants. They are tested on a sample problem which was devised to closely represent the important and essential characteristics that should be addressed in determination and evaluation of the technical specifications

[Development and validation of event-specific quantitative PCR method for genetically modified maize LY038].

Science.gov (United States)

Mano, Junichi; Masubuchi, Tomoko; Hatano, Shuko; Futo, Satoshi; Koiwa, Tomohiro; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Akiyama, Hiroshi; Teshima, Reiko; Kurashima, Takeyo; Takabatake, Reona; Kitta, Kazumi

2013-01-01

In this article, we report a novel real-time PCR-based analytical method for quantitation of the GM maize event LY038. We designed LY038-specific and maize endogenous reference DNA-specific PCR amplifications. After confirming the specificity and linearity of the LY038-specific PCR amplification, we determined the conversion factor required to calculate the weight-based content of GM organism (GMO) in a multilaboratory evaluation. Finally, in order to validate the developed method, an interlaboratory collaborative trial according to the internationally harmonized guidelines was performed with blind DNA samples containing LY038 at the mixing levels of 0, 0.5, 1.0, 5.0 and 10.0%. The precision of the method was evaluated as the RSD of reproducibility (RSDR), and the values obtained were all less than 25%. The limit of quantitation of the method was judged to be 0.5% based on the definition of ISO 24276 guideline. The results from the collaborative trial suggested that the developed quantitative method would be suitable for practical testing of LY038 maize.

Postural Response Signal Characteristics Identified by Method of Developed Statokinesigram

Directory of Open Access Journals (Sweden)

Barbolyas Boris

2015-12-01

Full Text Available Human postural system is taken as complex biological system with specific input and output time characteristics, in this study. Evaluation of measured output characteristics is useful in medical diagnostics or in describing postural system disorders. System theory principle provide suitable basis for postural signals analysis. Participating volunteers were instructed to maintain quiet upright stance posture on firm support surface of stabilometric platform for 60s. Postural system actuation was realized by vibration stimuli applied bilaterally on Achilles tendons for 20s. Postural reaction signal, its time profile and static and dynamic characteristics were evaluated by Method of Developed Statokinesigram Trajectory (MDST.

Using budget-friendly methods to analyze sport specific movements

Science.gov (United States)

Jackson, Lindsay; Williams, Sarah; Ferrara, Davon

2015-03-01

When breaking down the physics behind sport specific movements, athletes, usually professional, are often assessed in multimillion-dollar laboratories and facilities. Budget-friendly methods, such as video analysis using low-cost cameras, iPhone sensors, or inexpensive force sensors can make this process more accessible to amateur athletes, which in-turn can give insight into injury mechanisms. Here we present a comparison of two methods of determining the forces experienced by a cheerleader during co-education stunting and soccer goalies while side-diving. For the cheerleader, accelerometer measurements were taken by an iPhone 5 and compared to video analysis. The measurements done on the soccer players were taken using FlexiForce force sensors and again compared to video analysis. While these budget-friendly methods could use some refining, they show promise for producing usable measurements for possibly increasing our understanding of injury in amateur players. Furthermore, low-cost physics experiments with sports can foster an active learning environment for students with minimum physics and mathematical background.

Utilization of genomic signatures to identify phenotype-specific drugs.

Directory of Open Access Journals (Sweden)

Seiichi Mori

2009-08-01

Full Text Available Genetic and genomic studies highlight the substantial complexity and heterogeneity of human cancers and emphasize the general lack of therapeutics that can match this complexity. With the goal of expanding opportunities for drug discovery, we describe an approach that makes use of a phenotype-based screen combined with the use of multiple cancer cell lines. In particular, we have used the NCI-60 cancer cell line panel that includes drug sensitivity measures for over 40,000 compounds assayed on 59 independent cells lines. Targets are cancer-relevant phenotypes represented as gene expression signatures that are used to identify cells within the NCI-60 panel reflecting the signature phenotype and then connect to compounds that are selectively active against those cells. As a proof-of-concept, we show that this strategy effectively identifies compounds with selectivity to the RAS or PI3K pathways. We have then extended this strategy to identify compounds that have activity towards cells exhibiting the basal phenotype of breast cancer, a clinically-important breast cancer characterized as ER-, PR-, and Her2- that lacks viable therapeutic options. One of these compounds, Simvastatin, has previously been shown to inhibit breast cancer cell growth in vitro and importantly, has been associated with a reduction in ER-, PR- breast cancer in a clinical study. We suggest that this approach provides a novel strategy towards identification of therapeutic agents based on clinically relevant phenotypes that can augment the conventional strategies of target-based screens.

An exploratory GIS-based method to identify and characterise landscapes with an elevated epidemiological risk of Rhodesian human African trypanosomiasis

Directory of Open Access Journals (Sweden)

Wardrop Nicola A

2012-11-01

Full Text Available Abstract Background Specific land cover types and activities have been correlated with Trypanosoma brucei rhodesiense distributions, indicating the importance of landscape for epidemiological risk. However, methods proposed to identify specific areas with elevated epidemiological risk (i.e. where transmission is more likely to occur tend to be costly and time consuming. This paper proposes an exploratory spatial analysis using geo-referenced human African trypanosomiasis (HAT cases and matched controls from Serere hospital, Uganda (December 1998 to November 2002 to identify areas with an elevated epidemiological risk of HAT. Methods Buffers 3 km from each case and control were used to represent areas in which village inhabitants would carry out their daily activities. It was hypothesised that the selection of areas where several case village buffers overlapped would enable the identification of locations with increased risk of HAT transmission, as these areas were more likely to be frequented by HAT cases in several surrounding villages. The landscape within these overlap areas should more closely relate to the environment in which transmission occurs as opposed to using the full buffer areas. The analysis was carried out for each of four annual periods, for both cases and controls, using a series of threshold values (number of overlapping buffers, including a threshold of one, which represented the benchmark (e.g. use of the full buffer area as opposed to the overlap areas. Results A greater proportion of the overlap areas for cases consisted of seasonally flooding grassland and lake fringe swamp, than the control overlap areas, correlating well with the preferred habitat of the predominant tsetse species within the study area (Glossina fuscipes fuscipes. The use of overlap areas also resulted in a greater difference between case and control landscapes, when compared with the benchmark (using the full buffer area. Conclusions These results

Common genetic variants associated with cognitive performance identified using the proxy-phenotype method

NARCIS (Netherlands)

C.A. Rietveld (Niels); T. Esko (Tõnu); G. Davies (Gail); T.H. Pers (Tune); P. Turley (Patrick); B. Benyamin (Beben); C.F. Chabris (Christopher F.); V. Emilsson (Valur); A.D. Johnson (Andrew); J.J. Lee (James J.); C. de Leeuw (Christiaan); R.E. Marioni (Riccardo); S.E. Medland (Sarah Elizabeth); M. Miller (Mike); O. Rostapshova (Olga); S.J. van der Lee (Sven); A.A.E. Vinkhuyzen (Anna A.); N. Amin (Najaf); D. Conley (Dalton); J. Derringer; C.M. van Duijn (Cornelia); R.S.N. Fehrmann (Rudolf); L. Franke (Lude); E.L. Glaeser (Edward L.); N.K. Hansell (Narelle); C. Hayward (Caroline); W.G. Iacono (William); C.A. Ibrahim-Verbaas (Carla); V.W.V. Jaddoe (Vincent); J. Karjalainen (Juha); D. Laibson (David); P. Lichtenstein (Paul); D.C. Liewald (David C.); P.K. Magnusson (Patrik); N.G. Martin (Nicholas); M. McGue (Matt); G. Mcmahon (George); N.L. Pedersen (Nancy); S. Pinker (Steven); D.J. Porteous (David J.); D. Posthuma (Danielle); F. Rivadeneira Ramirez (Fernando); B.H. Smithk (Blair H.); J.M. Starr (John); H.W. Tiemeier (Henning); N.J. Timpsonm (Nicholas J.); M. Trzaskowskin (Maciej); A.G. Uitterlinden (André); F.C. Verhulst (Frank); M.E. Ward (Mary); M.J. Wright (Margaret); G.D. Smith; I.J. Deary (Ian J.); M. Johannesson (Magnus); R. Plomin (Robert); P.M. Visscher (Peter); D.J. Benjamin (Daniel J.); D. Cesarini (David); Ph.D. Koellinger (Philipp)

2014-01-01

textabstractWe identify common genetic variants associated with cognitive performance using a two-stage approach, which we call the proxyphenotype method. First, we conduct a genome-wide association study of educational attainment in a large sample (n = 106,736), which produces a set of 69

METHOD FOR THE MEASUREMENT OF SITE-SPECIFIC TAUTOMERIC AND ZWITTERIONIC MICROSPECIES EQUILIBRIUM CONSTANTS

Science.gov (United States)

We describe a method for the individual measurement of simultaneously occurring, unimolecular, site-specific “microequilibrium” constants as in, for example, prototropic tautomerism and zwitterionic equilibria. Our method represents an elaboration of that of Nygren et al. (Anal. ...

Identifying bottlenecks in the iron and folic acid supply chain in Bihar, India: a mixed-methods study.

Science.gov (United States)

Wendt, Amanda S; Stephenson, Rob; Young, Melissa F; Verma, Pankaj; Srikantiah, Sridhar; Webb-Girard, Amy; Hogue, Carol J; Ramakrishnan, Usha; Martorell, Reynaldo

2018-04-12

Maternal anaemia prevalence in Bihar, India remains high despite government mandated iron supplementation targeting pregnant women. Inadequate supply has been identified as a potential barrier to iron and folic acid (IFA) receipt. Our study objective was to examine the government health system's IFA supply and distribution system and identify bottlenecks contributing to insufficient IFA supply. Primary data collection was conducted in November 2011 and July 2012 across 8 districts in Bihar, India. A cross-sectional, observational, mixed methods approach was utilized. Auxiliary Nurse Midwives were surveyed on current IFA supply and practices. In-depth interviews (n = 59) were conducted with health workers at state, district, block, health sub-centre, and village levels. Overall, 44% of Auxiliary Nurse Midwives were out of IFA stock. Stock levels and supply chain practices varied greatly across districts. Qualitative data revealed specific bottlenecks impacting IFA forecasting, procurement, storage, disposal, lack of personnel, and few training opportunities for key players in the supply chain. Inadequate IFA supply is a major constraint to the IFA supplementation program, the extent of which varies widely across districts. Improvements at all levels of infrastructure, practices, and effective monitoring will be critical to strengthen the IFA supply chain in Bihar.

Use of epitope libraries to identify exon-specific monoclonal antibodies for characterization of altered dystrophins in muscular dystrophy

Energy Technology Data Exchange (ETDEWEB)

Nguyen thi Man; Morris, G.E. (North East Wales Inst., Clwyd (United Kingdom))

1993-06-01

The majority of mutations in Xp21-linked muscular dystrophy (MD) can be identified by PCR or Southern blotting, as deletions or duplications of groups of exons in the dystrophin gene, but it is not always possible to predict how much altered dystrophin, if any, will be produced. Use of exon-specific monoclonal antibodies (mAbs) on muscle biopsies from MD patients can, in principle, provide information on both the amount of altered dystrophin produced and, when dystrophin is present, the nature of the genetic deletion or point mutation. For this purpose, mAbs which recognize regions of dystrophin encoded by known exons and whose binding is unaffected by the absence of adjacent exons are required. To map mAbs to specific exons, random [open quotes]libraries[close quotes] of expressed dystrophin fragments were created by cloning DNAseI digestion fragments of a 4.3-kb dystrophin cDNA into a pTEX expression vector. The libraries were then used to locate the epitopes recognized by 48 mAbs to fragments of 25--60 amino acids within the 1,434-amino-acid dystrophin fragment used to produce the antibodies. This is sufficiently detailed to allow further refinement by using synthetic peptides and, in many cases, to identify the exon in the DMD (Duchenne MD) gene which encodes the epitope. To illustrate their use in dystrophin analysis, a Duchenne patient with a frameshift deletion of exons 42 and 43 makes a truncated dystrophin encoded by exons 1--41, and the authors now show that this can be detected in the sarcolemma by mAbs up to and including those specific for exon 41 epitopes but not by mAbs specific for exon 43 or later epitopes. 38 refs., 2 figs., 4 tabs.

Compositions and methods for xylem-specific expression in plant cells

Energy Technology Data Exchange (ETDEWEB)

Han, Kyung-Hwan; Ko, Jae-Heung

2017-12-19

The invention provides promoter sequences that regulate specific expression of operably linked sequences in developing xylem cells and/or in developing xylem tissue. The developing xylem-specific sequences are exemplified by the DX5, DX8, DX11, and DX15 promoters, portions thereof, and homologs thereof. The invention further provides expression vectors, cells, tissues and plants that contain the invention's sequences. The compositions of the invention and methods of using them are useful in, for example, improving the quantity (biomass) and/or the quality (wood density, lignin content, sugar content etc.) of expressed biomass feedstock products that may be used for bioenergy, biorefinary, and generating wood products such as pulp, paper, and solid wood.

Application of specific gravity method for normalization of urinary excretion rates of radionuclides

International Nuclear Information System (INIS)

Thakur, Smita S.; Yadav, J.R.; Rao, D.D.

2015-01-01

In vitro bioassay monitoring is based on the determination of activity concentration in biological samples excreted from the body and is most suitable for alpha and beta emitters. For occupational workers handling actinides in reprocessing facilities possibility of internal exposure exists and urine assay is preferred method for monitoring such exposure. Urine samples collected for 24 h duration, is the true representative of bioassay sample and hence in the case of insufficient collection time, specific gravity applied method of normalization of urine sample is used. The present study reports the data of specific gravity generated for controlled group of Indian population by the use of densitometer and its application in urinary sample activity normalization. The average specific gravity value obtained for the controlled group was 1.008±0.005 gm/ml. (author)

New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Yesylevskyy S. O.

2010-04-01

Full Text Available Aim. Despite a large number of existing domain identification techniques there is no universally accepted method, which identifies the hierarchy of dynamic domains using the data of molecular dynamics (MD simulations. The goal of this work is to develop such technique. Methods. The dynamic domains are identified by eliminating systematic motions from MD trajectories recursively in a model-free manner. Results. The technique called the Hierarchical Domain-Wise Alignment (HDWA to identify hierarchically organized dynamic domains in proteins using the MD trajectories has been developed. Conclusion. A new method of domain identification in proteins is proposed

Identified adjustability dimensions when generating a product specific requirements specification by requirements reuse

DEFF Research Database (Denmark)

Hauksdóttir, Dagný; Mortensen, Niels Henrik; Nielsen, Poul Erik

2014-01-01

. An extensive state of the art is included to introduce the presented methods related to each adjustability dimensions. The options for implementing each adjustability dimensions in a requirement reuse approach are illustrated along with a discussion regarding the benefits and issues resulting from each option....... This discussion should help practitioners to better understand the possible methods that can be implemented and to design a user friendly and sustainable approach. A case study, describing how the dimensions are incorporated in two requirements reuse approaches, for Danfoss Solar Inverters (SI) and Danfoss...

Clinimetric evaluation of methods to measure muscle functioning in patients with non-specific neck pain: a systematic review

Directory of Open Access Journals (Sweden)

Smits-Engelsman Bouwien CM

2008-10-01

Full Text Available Abstract Background Neck pain is a significant health problem in modern society. There is evidence to suggest that neck muscle strength is reduced in patients with neck pain. This article provides a critical analysis of the research literature on the clinimetric properties of tests to measure neck muscle strength or endurance in patients with non-specific neck pain, which can be used in daily practice. Methods A computerised literature search was performed in the Medline, CINAHL and Embase databases from 1980 to January 2007. Two reviewers independently assessed the clinimetric properties of identified measurement methods, using a checklist of generally accepted criteria for reproducibility (inter- and intra-observer reliability and agreement, construct validity, responsiveness and feasibility. Results The search identified a total of 16 studies. The instruments or tests included were: muscle endurance tests for short neck flexors, craniocervical flexion test with an inflatable pressure biofeedback unit, manual muscle testing of neck musculature, dynamometry and functional lifting tests (the cervical progressive iso-inertial lifting evaluation (PILE test and the timed weighted overhead test. All the articles included report information on the reproducibility of the tests. Acceptable intra- and inter-observer reliability was demonstrated for t enduranctest for short neck flexors and the cervical PILE test. Construct validity and responsiveness have hardly been documented for tests on muscle functioning. Conclusion The endurance test of the short neck flexors and the cervical PILE test can be regarded as appropriate instruments for measuring different aspects of neck muscle function in patients with non-specific neck pain. Common methodological flaws in the studies were their small sample size and an inappropriate description of the study design.

Software specification methods

CERN Document Server

Habrias, Henri

2010-01-01

This title provides a clear overview of the main methods, and has a practical focus that allows the reader to apply their knowledge to real-life situations. The following are just some of the techniques covered: UML, Z, TLA+, SAZ, B, OMT, VHDL, Estelle, SDL and LOTOS.

An integrated chemical biology approach identifies specific vulnerability of Ewing's sarcoma to combined inhibition of Aurora kinases A and B.

Science.gov (United States)

Winter, Georg E; Rix, Uwe; Lissat, Andrej; Stukalov, Alexey; Müllner, Markus K; Bennett, Keiryn L; Colinge, Jacques; Nijman, Sebastian M; Kubicek, Stefan; Kovar, Heinrich; Kontny, Udo; Superti-Furga, Giulio

2011-10-01

Ewing's sarcoma is a pediatric cancer of the bone that is characterized by the expression of the chimeric transcription factor EWS-FLI1 that confers a highly malignant phenotype and results from the chromosomal translocation t(11;22)(q24;q12). Poor overall survival and pronounced long-term side effects associated with traditional chemotherapy necessitate the development of novel, targeted, therapeutic strategies. We therefore conducted a focused viability screen with 200 small molecule kinase inhibitors in 2 different Ewing's sarcoma cell lines. This resulted in the identification of several potential molecular intervention points. Most notably, tozasertib (VX-680, MK-0457) displayed unique nanomolar efficacy, which extended to other cell lines, but was specific for Ewing's sarcoma. Furthermore, tozasertib showed strong synergies with the chemotherapeutic drugs etoposide and doxorubicin, the current standard agents for Ewing's sarcoma. To identify the relevant targets underlying the specific vulnerability toward tozasertib, we determined its cellular target profile by chemical proteomics. We identified 20 known and unknown serine/threonine and tyrosine protein kinase targets. Additional target deconvolution and functional validation by RNAi showed simultaneous inhibition of Aurora kinases A and B to be responsible for the observed tozasertib sensitivity, thereby revealing a new mechanism for targeting Ewing's sarcoma. We further corroborated our cellular observations with xenograft mouse models. In summary, the multilayered chemical biology approach presented here identified a specific vulnerability of Ewing's sarcoma to concomitant inhibition of Aurora kinases A and B by tozasertib and danusertib, which has the potential to become a new therapeutic option.

A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.

Directory of Open Access Journals (Sweden)

Marc W Schmid

Full Text Available The acquisition of distinct cell fates is central to the development of multicellular organisms and is largely mediated by gene expression patterns specific to individual cells and tissues. A spatially and temporally resolved analysis of gene expression facilitates the elucidation of transcriptional networks linked to cellular identity and function. We present an approach that allows cell type-specific transcriptional profiling of distinct target cells, which are rare and difficult to access, with unprecedented sensitivity and resolution. We combined laser-assisted microdissection (LAM, linear amplification starting from <1 ng of total RNA, and RNA-sequencing (RNA-Seq. As a model we used the central cell of the Arabidopsis thaliana female gametophyte, one of the female gametes harbored in the reproductive organs of the flower. We estimated the number of expressed genes to be more than twice the number reported previously in a study using LAM and ATH1 microarrays, and identified several classes of genes that were systematically underrepresented in the transcriptome measured with the ATH1 microarray. Among them are many genes that are likely to be important for developmental processes and specific cellular functions. In addition, we identified several intergenic regions, which are likely to be transcribed, and describe a considerable fraction of reads mapping to introns and regions flanking annotated loci, which may represent alternative transcript isoforms. Finally, we performed a de novo assembly of the transcriptome and show that the method is suitable for studying individual cell types of organisms lacking reference sequence information, demonstrating that this approach can be applied to most eukaryotic organisms.

A task specific uncertainty analysis method for least-squares-based form characterization of ultra-precision freeform surfaces

International Nuclear Information System (INIS)

Ren, M J; Cheung, C F; Kong, L B

2012-01-01

In the measurement of ultra-precision freeform surfaces, least-squares-based form characterization methods are widely used to evaluate the form error of the measured surfaces. Although many methodologies have been proposed in recent years to improve the efficiency of the characterization process, relatively little research has been conducted on the analysis of associated uncertainty in the characterization results which may result from those characterization methods being used. As a result, this paper presents a task specific uncertainty analysis method with application in the least-squares-based form characterization of ultra-precision freeform surfaces. That is, the associated uncertainty in the form characterization results is estimated when the measured data are extracted from a specific surface with specific sampling strategy. Three factors are considered in this study which include measurement error, surface form error and sample size. The task specific uncertainty analysis method has been evaluated through a series of experiments. The results show that the task specific uncertainty analysis method can effectively estimate the uncertainty of the form characterization results for a specific freeform surface measurement

Use of species-specific PCR for the identification of 10 sea cucumber species

Science.gov (United States)

Wen, Jing; Zeng, Ling

2014-11-01

We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

A scalable method for identifying frequent subtrees in sets of large phylogenetic trees.

Science.gov (United States)

Ramu, Avinash; Kahveci, Tamer; Burleigh, J Gordon

2012-10-03

We consider the problem of finding the maximum frequent agreement subtrees (MFASTs) in a collection of phylogenetic trees. Existing methods for this problem often do not scale beyond datasets with around 100 taxa. Our goal is to address this problem for datasets with over a thousand taxa and hundreds of trees. We develop a heuristic solution that aims to find MFASTs in sets of many, large phylogenetic trees. Our method works in multiple phases. In the first phase, it identifies small candidate subtrees from the set of input trees which serve as the seeds of larger subtrees. In the second phase, it combines these small seeds to build larger candidate MFASTs. In the final phase, it performs a post-processing step that ensures that we find a frequent agreement subtree that is not contained in a larger frequent agreement subtree. We demonstrate that this heuristic can easily handle data sets with 1000 taxa, greatly extending the estimation of MFASTs beyond current methods. Although this heuristic does not guarantee to find all MFASTs or the largest MFAST, it found the MFAST in all of our synthetic datasets where we could verify the correctness of the result. It also performed well on large empirical data sets. Its performance is robust to the number and size of the input trees. Overall, this method provides a simple and fast way to identify strongly supported subtrees within large phylogenetic hypotheses.

Handbook of methods for risk-based analyses of technical specifications

International Nuclear Information System (INIS)

Samanta, P.K.; Kim, I.S.; Mankamo, T.; Vesely, W.E.

1994-12-01

Technical Specifications (TS) requirements for nuclear power plants define the Limiting Conditions for Operation (LCOs) and Surveillance Requirements (SRs) to assure safety during operation. In general, these requirements are based on deterministic analysis and engineering judgments. Experiences with plant operation indicate that some elements of the requirements are unnecessarily restrictive, while a few may not be conducive to safety. The US Nuclear Regulatory Commission (USNRC) Office of Research has sponsored research to develop systematic risk-based methods to improve various aspects of TS requirements. This handbook summarizes these risk-based methods. The scope of the handbook includes reliability and risk-based methods for evaluating allowed outage times (AOTs), scheduled or preventive maintenance, action statements requiring shutdown where shutdown risk may be substantial, surveillance test intervals (STIs), and management of plant configurations resulting from outages of systems, or components. For each topic, the handbook summarizes analytic methods with data needs, outlines the insights to be gained, lists additional references, and gives examples of evaluations

Handbook of methods for risk-based analyses of technical specifications

Energy Technology Data Exchange (ETDEWEB)

Samanta, P.K.; Kim, I.S. [Brookhaven National Lab., Upton, NY (United States); Mankamo, T. [Avaplan Oy, Espoo (Finland); Vesely, W.E. [Science Applications International Corp., Dublin, OH (United States)

1994-12-01

Technical Specifications (TS) requirements for nuclear power plants define the Limiting Conditions for Operation (LCOs) and Surveillance Requirements (SRs) to assure safety during operation. In general, these requirements are based on deterministic analysis and engineering judgments. Experiences with plant operation indicate that some elements of the requirements are unnecessarily restrictive, while a few may not be conducive to safety. The US Nuclear Regulatory Commission (USNRC) Office of Research has sponsored research to develop systematic risk-based methods to improve various aspects of TS requirements. This handbook summarizes these risk-based methods. The scope of the handbook includes reliability and risk-based methods for evaluating allowed outage times (AOTs), scheduled or preventive maintenance, action statements requiring shutdown where shutdown risk may be substantial, surveillance test intervals (STIs), and management of plant configurations resulting from outages of systems, or components. For each topic, the handbook summarizes analytic methods with data needs, outlines the insights to be gained, lists additional references, and gives examples of evaluations.

MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets.

Science.gov (United States)

Kim, Taehyung; Tyndel, Marc S; Huang, Haiming; Sidhu, Sachdev S; Bader, Gary D; Gfeller, David; Kim, Philip M

2012-03-01

Peptide recognition domains and transcription factors play crucial roles in cellular signaling. They bind linear stretches of amino acids or nucleotides, respectively, with high specificity. Experimental techniques that assess the binding specificity of these domains, such as microarrays or phage display, can retrieve thousands of distinct ligands, providing detailed insight into binding specificity. In particular, the advent of next-generation sequencing has recently increased the throughput of such methods by several orders of magnitude. These advances have helped reveal the presence of distinct binding specificity classes that co-exist within a set of ligands interacting with the same target. Here, we introduce a software system called MUSI that can rapidly analyze very large data sets of binding sequences to determine the relevant binding specificity patterns. Our pipeline provides two major advances. First, it can detect previously unrecognized multiple specificity patterns in any data set. Second, it offers integrated processing of very large data sets from next-generation sequencing machines. The results are visualized as multiple sequence logos describing the different binding preferences of the protein under investigation. We demonstrate the performance of MUSI by analyzing recent phage display data for human SH3 domains as well as microarray data for mouse transcription factors.

Characterization of a monoclonal antibody with specificity for holo-transcobalamin

Directory of Open Access Journals (Sweden)

Fedosov Sergey N

2006-01-01

Full Text Available Abstract Background Holotranscobalamin, cobalamin-saturated transcobalamin, is the minor fraction of circulating cobalamin (vitamin B12, which is available for cellular uptake and hence is physiologically relevant. Currently, no method allows simple, direct quantification of holotranscobalamin. We now report on the identification and characterization of a monoclonal antibody with a unique specificity for holotranscobalamin. Methods The specificity and affinity of the monoclonal antibodies were determined using surface plasmon resonance and recombinant transcobalamin as well as by immobilizing the antibodies on magnetic microspheres and using native transcobalamin in serum. The epitope of the holotranscobalamin specific antibody was identified using phage display and comparison to a de novo generated three-dimensional model of transcobalamin using the program Rosetta. A direct assay for holotrnscobalamin in the ELISA format was developed using the specific antibody and compared to the commercial assay HoloTC RIA. Results An antibody exhibiting >100-fold specificity for holotranscobalamin over apotranscobalamin was identified. The affinity but not the specificity varied inversely with ionic strength and pH, indicating importance of electrostatic interactions. The epitope was discontinuous and epitope mapping of the antibody by phage display identified two similar motifs with no direct sequence similarity to transcobalamin. A comparison of the motifs with a de novo generated three-dimensional model of transcobalamin identified two structures in the N-terminal part of transcobalamin that resembled the motif. Using this antibody an ELISA based prototype assay was developed and compared to the only available commercial assay for measuring holotranscobalamin, HoloTC RIA. Conclusion The identified antibody possesses a unique specificity for holotranscobalamin and can be used to develop a direct assay for the quantification of holotranscobalamin.

Structural parameter identifiability analysis for dynamic reaction networks

DEFF Research Database (Denmark)

Davidescu, Florin Paul; Jørgensen, Sten Bay

2008-01-01

method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...... where for a given set of measured variables it is desirable to investigate which parameters may be estimated prior to spending computational effort on the actual estimation. This contribution addresses the structural parameter identifiability problem for the typical case of reaction network models....... The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...

Technical evaluation of methods for identifying chemotherapy-induced febrile neutropenia in healthcare claims databases

OpenAIRE

Weycker Derek; Sofrygin Oleg; Seefeld Kim; Deeter Robert G; Legg Jason; Edelsberg John

2013-01-01

Abstract Background Healthcare claims databases have been used in several studies to characterize the risk and burden of chemotherapy-induced febrile neutropenia (FN) and effectiveness of colony-stimulating factors against FN. The accuracy of methods previously used to identify FN in such databases has not been formally evaluated. Methods Data comprised linked electronic medical records from Geisinger Health System and healthcare claims data from Geisinger Health Plan. Subjects were classifie...

Estimation of the specific activity of radioiodinated gonadotrophins: comparison of three methods

Energy Technology Data Exchange (ETDEWEB)

Englebienne, P [Centre for Research and Diagnosis in Endocrinology, Kain (Belgium); Slegers, G [Akademisch Ziekenhuis, Ghent (Belgium). Lab. voor Analytische Chemie

1983-01-14

The authors compared 3 methods for estimating the specific activity of radioiodinated gonadotrophins. Two of the methods (column recovery and isotopic dilution) gave similar results, while the third (autodisplacement) gave significantly higher estimations. In the autodisplacement method, B/T ratios, obtained when either labelled hormone alone, or labelled and unlabelled hormone, are added to the antibody, were compared as estimates of the mass of hormone iodinated. It is likely that immunologically unreactive impurities present in the labelled hormone solution invalidate such comparison.

Control-based method to identify underlying delays of a nonlinear dynamical system.

Science.gov (United States)

Yu, Dongchuan; Frasca, Mattia; Liu, Fang

2008-10-01

We suggest several stationary state control-based delay identification methods which do not require any structural information about the controlled systems and are applicable to systems described by delayed ordinary differential equations. This proposed technique includes three steps: (i) driving a system to a steady state; (ii) perturbing the control signal for shifting the steady state; and (iii) identifying all delays by detecting the time that the system is abruptly drawn out of stationarity. Some aspects especially important for applications are discussed as well, including interaction delay identification, stationary state convergence speed, performance comparison, and the influence of noise on delay identification. Several examples are presented to illustrate the reliability and robustness of all delay identification methods suggested.

Identifying risk factors for exposure to culturable allergenic moulds in energy efficient homes by using highly specific monoclonal antibodies.

Science.gov (United States)

Sharpe, Richard A; Cocq, Kate Le; Nikolaou, Vasilis; Osborne, Nicholas J; Thornton, Christopher R

2016-01-01

The aim of this study was to determine the accuracy of monoclonal antibodies (mAbs) in identifying culturable allergenic fungi present in visible mould growth in energy efficient homes, and to identify risk factors for exposure to these known allergenic fungi. Swabs were taken from fungal contaminated surfaces and culturable yeasts and moulds isolated by using mycological culture. Soluble antigens from cultures were tested by ELISA using mAbs specific to the culturable allergenic fungi Aspergillus and Penicillium spp., Ulocladium, Alternaria, and Epicoccum spp., Cladosporium spp., Fusarium spp., and Trichoderma spp. Diagnostic accuracies of the ELISA tests were determined by sequencing of the internally transcribed spacer 1 (ITS1)-5.8S-ITS2-encoding regions of recovered fungi following ELISA. There was 100% concordance between the two methods, with ELISAs providing genus-level identity and ITS sequencing providing species-level identities (210 out of 210 tested). Species of Aspergillus/Penicillium, Cladosporium, Ulocladium/Alternaria/Epicoccum, Fusarium and Trichoderma were detected in 82% of the samples. The presence of condensation was associated with an increased risk of surfaces being contaminated by Aspergillus/Penicillium spp. and Cladosporium spp., whereas moisture within the building fabric (water ingress/rising damp) was only associated with increased risk of Aspergillus/Penicillium spp. Property type and energy efficiency levels were found to moderate the risk of indoor surfaces becoming contaminated with Aspergillus/Penicillium and Cladosporium which in turn was modified by the presence of condensation, water ingress and rising damp, consistent with previous literature. Copyright © 2015 Elsevier Inc. All rights reserved.

Identifying Effective Methods of Instruction for Adult Emergent Readers through Community-Based Research

Science.gov (United States)

Blackmer, Rachel; Hayes-Harb, Rachel

2016-01-01

We present a community-based research project aimed at identifying effective methods and materials for teaching English literacy skills to adult English as a second language emergent readers. We conducted a quasi-experimental study whereby we evaluated the efficacy of two approaches, one based on current practices at the English Skills Learning…

Whole genome DNA copy number changes identified by high density oligonucleotide arrays

Directory of Open Access Journals (Sweden)

Huang Jing

2004-05-01

Full Text Available Abstract Changes in DNA copy number are one of the hallmarks of the genetic instability common to most human cancers. Previous micro-array-based methods have been used to identify chromosomal gains and losses; however, they are unable to genotype alleles at the level of single nucleotide polymorphisms (SNPs. Here we describe a novel algorithm that uses a recently developed high-density oligonucleotide array-based SNP genotyping method, whole genome sampling analysis (WGSA, to identify genome-wide chromosomal gains and losses at high resolution. WGSA simultaneously genotypes over 10,000 SNPs by allele-specific hybridisation to perfect match (PM and mismatch (MM probes synthesised on a single array. The copy number algorithm jointly uses PM intensity and discrimination ratios between paired PM and MM intensity values to identify and estimate genetic copy number changes. Values from an experimental sample are compared with SNP-specific distributions derived from a reference set containing over 100 normal individuals to gain statistical power. Genomic regions with statistically significant copy number changes can be identified using both single point analysis and contiguous point analysis of SNP intensities. We identified multiple regions of amplification and deletion using a panel of human breast cancer cell lines. We verified these results using an independent method based on quantitative polymerase chain reaction and found that our approach is both sensitive and specific and can tolerate samples which contain a mixture of both tumour and normal DNA. In addition, by using known allele frequencies from the reference set, statistically significant genomic intervals can be identified containing contiguous stretches of homozygous markers, potentially allowing the detection of regions undergoing loss of heterozygosity (LOH without the need for a matched normal control sample. The coupling of LOH analysis, via SNP genotyping, with copy number

ASPECTS REGARDING NEUROMARKETING SPECIFIC RESEARCH METHODS

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MIRELA-CRISTINA VOICU

2012-05-01

Full Text Available Information is one of the most important resources that a company must posses. Some informations are hidden deep in the black box - the mind of the consumer. Neuromarketing helps us find what is inside of the black box without troubling the consumer with questions that he doesn’t want to answer or that he can’t answer. Today because of an extensive research in mapping cortical and subcortical activity in association with behaviors and thoughts, the confidence in neurological data is growing. Thanks to discoveries in perceptual sciences we can identify the parts of the brain that are responsible for the phenomena that we experience daily. For all those interested in information obtained through neuromarketing techniques it becomes evident that there are corresponding neural substrates of consumer decision making process and these substrates can be observed, measured, and possibly manipulated. The following paper reveals some important aspects of the use of neuromarketing in studying consumer behavior by presenting the concepts, methods and techniques used under this sophisticated name, the limitations and advantages of using neuromarketing techniques and the importance of this type of information in decision making process at a company level.

Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci

DEFF Research Database (Denmark)

Jones, Gregory T; Tromp, Gerard; Kuivaniemi, Helena

2017-01-01

studies (GWAS). Through a meta-analysis of 6 GWAS datasets and a validation study totalling 10,204 cases and 107,766 controls we identified 4 new AAA risk loci: 1q32.3 (SMYD2), 13q12.11 (LINC00540), 20q13.12 (near PCIF1/MMP9/ZNF335), and 21q22.2 (ERG). In various database searches we observed no new...... associations between the lead AAA SNPs and coronary artery disease, blood pressure, lipids or diabetes. Network analyses identified ERG, IL6R and LDLR as modifiers of MMP9, with a direct interaction between ERG and MMP9. The 4 new risk loci for AAA appear to be specific for AAA compared with other...

Using c-Jun to identify fear extinction learning-specific patterns of neural activity that are affected by single prolonged stress.

Science.gov (United States)

Knox, Dayan; Stanfield, Briana R; Staib, Jennifer M; David, Nina P; DePietro, Thomas; Chamness, Marisa; Schneider, Elizabeth K; Keller, Samantha M; Lawless, Caroline

2018-04-02

Neural circuits via which stress leads to disruptions in fear extinction is often explored in animal stress models. Using the single prolonged stress (SPS) model of post traumatic stress disorder and the immediate early gene (IEG) c-Fos as a measure of neural activity, we previously identified patterns of neural activity through which SPS disrupts extinction retention. However, none of these stress effects were specific to fear or extinction learning and memory. C-Jun is another IEG that is sometimes regulated in a different manner to c-Fos and could be used to identify emotional learning/memory specific patterns of neural activity that are sensitive to SPS. Animals were either fear conditioned (CS-fear) or presented with CSs only (CS-only) then subjected to extinction training and testing. C-Jun was then assayed within neural substrates critical for extinction memory. Inhibited c-Jun levels in the hippocampus (Hipp) and enhanced functional connectivity between the ventromedial prefrontal cortex (vmPFC) and basolateral amygdala (BLA) during extinction training was disrupted by SPS in the CS-fear group only. As a result, these effects were specific to emotional learning/memory. SPS also disrupted inhibited Hipp c-Jun levels, enhanced BLA c-Jun levels, and altered functional connectivity among the vmPFC, BLA, and Hipp during extinction testing in SPS rats in the CS-fear and CS-only groups. As a result, these effects were not specific to emotional learning/memory. Our findings suggest that SPS disrupts neural activity specific to extinction memory, but may also disrupt the retention of fear extinction by mechanisms that do not involve emotional learning/memory. Copyright © 2017 Elsevier B.V. All rights reserved.

Use of rank sum method in identifying high occupational dose jobs for ALARA implementation

International Nuclear Information System (INIS)

Cho, Yeong Ho; Kang, Chang Sun

1998-01-01

The cost-effective reduction of occupational radiation exposure (ORE) dose at a nuclear power plant could not be achieved without going through an extensive analysis of accumulated ORE dose data of existing plants. It is necessary to identify what are high ORE jobs for ALARA implementation. In this study, the Rank Sum Method (RSM) is used in identifying high ORE jobs. As a case study, the database of ORE-related maintenance and repair jobs for Kori Units 3 and 4 is used for assessment, and top twenty high ORE jobs are identified. The results are also verified and validated using the Friedman test, and RSM is found to be a very efficient way of analyzing the data. (author)

Chapter 1: Introduction. The Uniform Methods Project: Methods for Determining Energy-Efficiency Savings for Specific Measures

Energy Technology Data Exchange (ETDEWEB)

Li, Michael [Dept. of Energy (DOE), Washington DC (United States). Office of Energy Efficiency and Renewable Energy; Haeri, Hossein [The Cadmus Group, Portland, OR (United States); Reynolds, Arlis [The Cadmus Group, Portland, OR (United States)

2017-09-28

This chapter provides a set of model protocols for determining energy and demand savings that result from specific energy efficiency measures implemented through state and utility efficiency programs. The methods described here are approaches that are or are among the most commonly used and accepted in the energy efficiency industry for certain measures or programs. As such, they draw from the existing body of research and best practices for energy efficiency program evaluation, measurement, and verification (EM&V). These protocols were developed as part of the Uniform Methods Project (UMP), funded by the U.S. Department of Energy (DOE). The principal objective for the project was to establish easy-to-follow protocols based on commonly accepted methods for a core set of widely deployed energy efficiency measures.

Bridging the Gap: Identifying Perceptions of Effective Teaching Methods for Age 50+ Baby Boomer Learners

Science.gov (United States)

Newberry, Sheila

2013-01-01

The purpose of this study was to identify effective teaching methods for age 50+ baby boomer learners. The study used a mixed methods research design. The qualitative paradigm used focus group sessions and the quantitative paradigm was completed through surveys. Fifteen age 50+ baby boomer learners and 11 faculty who teach them comprised the two…

[Molecular authentication of Jinyinhua formula granule by using allele-specific PCR].

Science.gov (United States)

Jiang, Chao; Tu, Li-Chan; Yuan, Yuan; Huang, Lu-Qi; Gao, Wei; Jin, Yan

2017-07-01

Traditional authentication method is hard to identify herb's authenticity of traditional Chinese medicine(TCM) formula granules because they have lost all their morphological characteristics. In this study, a new allele-specific PCR method was established for identifying the authentication of Jinyinhua formula granule (made from Lonicerae Japonicae Flos) based on an SNP site in trnL-trnF fragment. Genomic DNA was successfully extracted from Lonicerae Japonicae Flos and its formula granules by using an improved spin column method and then PCR was performed with the designed primer. Approximately 110 bp specific bands was obtained only in the authentic Lonicerae Japonicae Flos and its formula granules, while no bands were found in fake mixed products. In addition, the PCR product sequence was proved from Lonicerae Japonicae Flos trnL-trnF sequence by using BLAST method. Therefore, DNA molecular authentication method could make up the limitations of character identification method and microscopic identification, and quickly identify herb's authenticity of TCM formula granules, with enormous potential for market supervision and quality control. Copyright© by the Chinese Pharmaceutical Association.

Assessing Method to Identifying Water Resilience Against Natural and Climate Change Hazards.

Science.gov (United States)

Amril, Rofi; Maryono

2018-02-01

A geographic region may become vulnerable toward water resources in a variety of ways. Common issues arise when man-made infrastructure such as housing, industrial, agriculture and other spatial land use policy implementation exceeds more than desired level. Vulnerability of a region due to water resources could be interpreted as the inability of the region to sustaining economic and social activity associated to socio-economic water availability. This study assess four aspects of water resilience: water quantity, water distribution, water quality, and water requirements. Literature review then followed by interview with academic expert used as method of study. This study found that four aspect of water vulnerability mostly have been applied to asses water resource vulnerability. Each aspect have a specific characteristic and could be define more specific and detail indicator according to the local content.

Identifying Emotions on the Basis of Neural Activation.

Science.gov (United States)

Kassam, Karim S; Markey, Amanda R; Cherkassky, Vladimir L; Loewenstein, George; Just, Marcel Adam

2013-01-01

We attempt to determine the discriminability and organization of neural activation corresponding to the experience of specific emotions. Method actors were asked to self-induce nine emotional states (anger, disgust, envy, fear, happiness, lust, pride, sadness, and shame) while in an fMRI scanner. Using a Gaussian Naïve Bayes pooled variance classifier, we demonstrate the ability to identify specific emotions experienced by an individual at well over chance accuracy on the basis of: 1) neural activation of the same individual in other trials, 2) neural activation of other individuals who experienced similar trials, and 3) neural activation of the same individual to a qualitatively different type of emotion induction. Factor analysis identified valence, arousal, sociality, and lust as dimensions underlying the activation patterns. These results suggest a structure for neural representations of emotion and inform theories of emotional processing.

Geriatric-specific triage criteria are more sensitive than standard adult criteria in identifying need for trauma center care in injured older adults.

Science.gov (United States)

Ichwan, Brian; Darbha, Subrahmanyam; Shah, Manish N; Thompson, Laura; Evans, David C; Boulger, Creagh T; Caterino, Jeffrey M

2015-01-01

We evaluate the sensitivity of Ohio's 2009 emergency medical services (EMS) geriatric trauma triage criteria compared with the previous adult triage criteria in identifying need for trauma center care among older adults. We studied a retrospective cohort of injured patients aged 16 years or older in the 2006 to 2011 Ohio Trauma Registry. Patients aged 70 years or older were considered geriatric. We identified whether each patient met the geriatric and the adult triage criteria. The outcome measure was need for trauma center care, defined by surrogate markers: Injury Severity Score greater than 15, operating room in fewer than 48 hours, any ICU stay, and inhospital mortality. We calculated sensitivity and specificity of both triage criteria for both age groups. We included 101,577 patients; 33,379 (33%) were geriatric. Overall, 57% of patients met adult criteria and 68% met geriatric criteria. Using Injury Severity Score, for older adults geriatric criteria were more sensitive for need for trauma center care (93%; 95% confidence interval [CI] 92% to 93%) than adult criteria (61%; 95% CI 60% to 62%). Geriatric criteria decreased specificity in older adults from 61% (95% CI 61% to 62%) to 49% (95% CI 48% to 49%). Geriatric criteria in older adults (93% sensitivity, 49% specificity) performed similarly to the adult criteria in younger adults (sensitivity 87% and specificity 44%). Similar patterns were observed for other outcomes. Standard adult EMS triage guidelines provide poor sensitivity in older adults. Ohio's geriatric trauma triage guidelines significantly improve sensitivity in identifying Injury Severity Score and other surrogate markers of the need for trauma center care, with modest decreases in specificity for older adults. Copyright © 2014 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

Research of coincidence method for calculation model of the specific detector

Energy Technology Data Exchange (ETDEWEB)

Guangchun, Hu; Suping, Liu; Jian, Gong [China Academy of Engineering Physics, Mianyang (China). Inst. of Nuclear Physics and Chemistry

2003-07-01

The physical size of specific detector is known normally, but production business is classified for some sizes that is concerned with the property of detector, such as the well diameter, well depth of detector and dead region. The surface source of even distribution and the sampling method of source particle isotropy sport have been established with the method of Monte Carlo, and gamma ray respond spectral with the {sup 152}Eu surface source been calculated. The experiment have been performed under the same conditions. Calculation and experiment results are compared with relative efficiency coincidence method and spectral similar degree coincidence method. According to comparison as a result, detector model is revised repeatedly to determine the calculation model of detector and to calculate efficiency of detector and spectra. (authors)

SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity.

Directory of Open Access Journals (Sweden)

Tzong-Yi Lee

Full Text Available S-nitrosylation, the covalent attachment of a nitric oxide to (NO the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-nitrosylation remains unknown. Based on a total of 586 experimentally identified S-nitrosylation sites from SNAP/L-cysteine-stimulated mouse endothelial cells, this work presents an informatics investigation on S-nitrosylation sites including structural factors such as the flanking amino acids composition, the accessible surface area (ASA and physicochemical properties, i.e. positive charge and side chain interaction parameter. Due to the difficulty to obtain the conserved motifs by conventional motif analysis, maximal dependence decomposition (MDD has been applied to obtain statistically significant conserved motifs. Support vector machine (SVM is applied to generate predictive model for each MDD-clustered motif. According to five-fold cross-validation, the MDD-clustered SVMs could achieve an accuracy of 0.902, and provides a promising performance in an independent test set. The effectiveness of the model was demonstrated on the correct identification of previously reported S-nitrosylation sites of Bos taurus dimethylarginine dimethylaminohydrolase 1 (DDAH1 and human hemoglobin subunit beta (HBB. Finally, the MDD-clustered model was adopted to construct an effective web-based tool, named SNOSite (http://csb.cse.yzu.edu.tw/SNOSite/, for identifying S-nitrosylation sites on the uncharacterized protein sequences.

Least-squares methods for identifying biochemical regulatory networks from noisy measurements

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Heslop-Harrison Pat

2007-01-01

Full Text Available Abstract Background We consider the problem of identifying the dynamic interactions in biochemical networks from noisy experimental data. Typically, approaches for solving this problem make use of an estimation algorithm such as the well-known linear Least-Squares (LS estimation technique. We demonstrate that when time-series measurements are corrupted by white noise and/or drift noise, more accurate and reliable identification of network interactions can be achieved by employing an estimation algorithm known as Constrained Total Least Squares (CTLS. The Total Least Squares (TLS technique is a generalised least squares method to solve an overdetermined set of equations whose coefficients are noisy. The CTLS is a natural extension of TLS to the case where the noise components of the coefficients are correlated, as is usually the case with time-series measurements of concentrations and expression profiles in gene networks. Results The superior performance of the CTLS method in identifying network interactions is demonstrated on three examples: a genetic network containing four genes, a network describing p53 activity and mdm2 messenger RNA interactions, and a recently proposed kinetic model for interleukin (IL-6 and (IL-12b messenger RNA expression as a function of ATF3 and NF-κB promoter binding. For the first example, the CTLS significantly reduces the errors in the estimation of the Jacobian for the gene network. For the second, the CTLS reduces the errors from the measurements that are corrupted by white noise and the effect of neglected kinetics. For the third, it allows the correct identification, from noisy data, of the negative regulation of (IL-6 and (IL-12b by ATF3. Conclusion The significant improvements in performance demonstrated by the CTLS method under the wide range of conditions tested here, including different levels and types of measurement noise and different numbers of data points, suggests that its application will enable

Use of next generation sequencing data to develop a qPCR method for specific detection of EU-unauthorized genetically modified Bacillus subtilis overproducing riboflavin.

Science.gov (United States)

Barbau-Piednoir, Elodie; De Keersmaecker, Sigrid C J; Delvoye, Maud; Gau, Céline; Philipp, Patrick; Roosens, Nancy H

2015-11-11

Recently, the presence of an unauthorized genetically modified (GM) Bacillus subtilis bacterium overproducing vitamin B2 in a feed additive was notified by the Rapid Alert System for Food and Feed (RASFF). This has demonstrated that a contamination by a GM micro-organism (GMM) may occur in feed additives and has confronted for the first time,the enforcement laboratories with this type of RASFF. As no sequence information of this GMM nor any specific detection or identification method was available, Next GenerationSequencing (NGS) was used to generate sequence information. However, NGS data analysis often requires appropriate tools, involving bioinformatics expertise which is not alwayspresent in the average enforcement laboratory. This hampers the use of this technology to rapidly obtain critical sequence information in order to be able to develop a specific qPCRdetection method. Data generated by NGS were exploited using a simple BLAST approach. A TaqMan® qPCR method was developed and tested on isolated bacterial strains and on the feed additive directly. In this study, a very simple strategy based on the common BLAST tools that can be used by any enforcement lab without profound bioinformatics expertise, was successfully used toanalyse the B. subtilis data generated by NGS. The results were used to design and assess a new TaqMan® qPCR method, specifically detecting this GM vitamin B2 overproducing bacterium. The method complies with EU critical performance parameters for specificity, sensitivity, PCR efficiency and repeatability. The VitB2-UGM method also could detect the B. subtilis strain in genomic DNA extracted from the feed additive, without prior culturing step. The proposed method, provides a crucial tool for specifically and rapidly identifying this unauthorized GM bacterium in food and feed additives by enforcement laboratories. Moreover, this work can be seen as a case study to substantiate how the use of NGS data can offer an added value to easily

A Pattern-Oriented Approach to a Methodical Evaluation of Modeling Methods

Directory of Open Access Journals (Sweden)

Michael Amberg

1996-11-01

Full Text Available The paper describes a pattern-oriented approach to evaluate modeling methods and to compare various methods with each other from a methodical viewpoint. A specific set of principles (the patterns is defined by investigating the notations and the documentation of comparable modeling methods. Each principle helps to examine some parts of the methods from a specific point of view. All principles together lead to an overall picture of the method under examination. First the core ("method neutral" meaning of each principle is described. Then the methods are examined regarding the principle. Afterwards the method specific interpretations are compared with each other and with the core meaning of the principle. By this procedure, the strengths and weaknesses of modeling methods regarding methodical aspects are identified. The principles are described uniformly using a principle description template according to descriptions of object oriented design patterns. The approach is demonstrated by evaluating a business process modeling method.

Theoretical and Numerical Modeling of Transport of Land Use-Specific Fecal Source Identifiers

Science.gov (United States)

Bombardelli, F. A.; Sirikanchana, K. J.; Bae, S.; Wuertz, S.

2008-12-01

Microbial contamination in coastal and estuarine waters is of particular concern to public health officials. In this work, we advocate that well-formulated and developed mathematical and numerical transport models can be combined with modern molecular techniques in order to predict continuous concentrations of microbial indicators under diverse scenarios of interest, and that they can help in source identification of fecal pollution. As a proof of concept, we present initially the theory, numerical implementation and validation of one- and two-dimensional numerical models aimed at computing the distribution of fecal source identifiers in water bodies (based on Bacteroidales marker DNA sequences) coming from different land uses such as wildlife, livestock, humans, dogs or cats. These models have been developed to allow for source identification of fecal contamination in large bodies of water. We test the model predictions using diverse velocity fields and boundary conditions. Then, we present some preliminary results of an application of a three-dimensional water quality model to address the source of fecal contamination in the San Pablo Bay (SPB), United States, which constitutes an important sub-embayment of the San Francisco Bay. The transport equations for Bacteroidales include the processes of advection, diffusion, and decay of Bacteroidales. We discuss the validation of the developed models through comparisons of numerical results with field campaigns developed in the SPB. We determine the extent and importance of the contamination in the bay for two decay rates obtained from field observations, corresponding to total host-specific Bacteroidales DNA and host-specific viable Bacteroidales cells, respectively. Finally, we infer transport conditions in the SPB based on the numerical results, characterizing the fate of outflows coming from the Napa, Petaluma and Sonoma rivers.

Reducing uncertainty at minimal cost: a method to identify important input parameters and prioritize data collection

NARCIS (Netherlands)

Uwizeye, U.A.; Groen, E.A.; Gerber, P.J.; Schulte, Rogier P.O.; Boer, de I.J.M.

2016-01-01

The study aims to illustrate a method to identify important input parameters that explain most of the output variance ofenvironmental assessment models. The method is tested for the computation of life-cycle nitrogen (N) use efficiencyindicators among mixed dairy production systems in Rwanda. We

Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs

Directory of Open Access Journals (Sweden)

Ye Zhi-Qiang

2011-08-01

Full Text Available Abstract Background Differential coexpression analysis (DCEA is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. Results We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links. Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. Conclusions This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum.

An extensible and successful method of identifying collaborators for National Library of Medicine informationist projects.

Science.gov (United States)

Williams, Jeff D; Rambo, Neil H

2015-07-01

The New York University (NYU) Health Sciences Library used a new method to arrange in-depth discussions with basic science researchers. The objective was to identify collaborators for a new National Library of Medicine administrative supplement. The research took place at the NYU Health Sciences Library. Using the National Institutes of Health (NIH) RePORTER, forty-four researchers were identified and later contacted through individualized emails. Nine researchers responded to the email followed by six in-person or phone discussions. At the conclusion of this process, two researchers submitted applications for supplemental funding, and both of these applications were successful. This method confirmed these users could benefit from the skills and knowledge of health sciences librarians, but they are largely unaware of this.

Specific olfactory receptor populations projecting to identified glomeruli in the rat olfactory bulb.

Science.gov (United States)

Jastreboff, P J; Pedersen, P E; Greer, C A; Stewart, W B; Kauer, J S; Benson, T E; Shepherd, G M

1984-08-01

A critical gap exists in our knowledge of the topographical relationship between the olfactory epithelium and olfactory bulb. The present report describes the application to this problem of a method involving horseradish peroxidase conjugated to wheat germ agglutinin. This material was iontophoretically delivered to circumscribed glomeruli in the olfactory bulb and the characteristics and distribution of retrogradely labeled receptor cells were assessed. After discrete injections into small glomerular groups in the caudomedial bulb, topographically defined populations of receptor cells were labeled. Labeled receptor cell somata appeared at several levels within the epithelium. The receptor cell apical dendrites followed a tight helical course towards the surface of the epithelium. The data thus far demonstrate that functional units within the olfactory system may include not only glomeruli as previously suggested but, in addition, a corresponding matrix of receptor cells possessing functional and topographical specificity.

The global equilibrium method and its hybrid implementation for identifying heterogeneous elastic material parameters

KAUST Repository

Lubineau, Gilles

2011-04-01

New identification strategies have to be developed in order to perform the identification quickly and at very-low cost. A popular class of approaches relies on full-field measurement obtained through digital image correlation. We propose here a global equilibrium approach. It is based on the virtual field method in case specific virtual fields are used. It can also be seen as a generalization of the equilibrium gap method. This approach is easy to implement and we prove that it provides better or comparable results to the constitutive equation gap method that is known to be a very accurate reference. © 2010 Elsevier B.V.

Performance of the lot quality assurance sampling method compared to surveillance for identifying inadequately-performing areas in Matlab, Bangladesh.

Science.gov (United States)

Bhuiya, Abbas; Hanifi, S M A; Roy, Nikhil; Streatfield, P Kim

2007-03-01

This paper compared the performance of the lot quality assurance sampling (LQAS) method in identifying inadequately-performing health work-areas with that of using health and demographic surveillance system (HDSS) data and examined the feasibility of applying the method by field-level programme supervisors. The study was carried out in Matlab, the field site of ICDDR,B, where a HDSS has been in place for over 30 years. The LQAS method was applied in 57 work-areas of community health workers in ICDDR,B-served areas in Matlab during July-September 2002. The performance of the LQAS method in identifying work-areas with adequate and inadequate coverage of various health services was compared with those of the HDSS. The health service-coverage indicators included coverage of DPT, measles, BCG vaccination, and contraceptive use. It was observed that the difference in the proportion of work-areas identified to be inadequately performing using the LQAS method with less than 30 respondents, and the HDSS was not statistically significant. The consistency between the LQAS method and the HDSS in identifying work-areas was greater for adequately-performing areas than inadequately-performing areas. It was also observed that the field managers could be trained to apply the LQAS method in monitoring their performance in reaching the target population.

Utilising identifier error variation in linkage of large administrative data sources

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Katie Harron

2017-02-01

Full Text Available Abstract Background Linkage of administrative data sources often relies on probabilistic methods using a set of common identifiers (e.g. sex, date of birth, postcode. Variation in data quality on an individual or organisational level (e.g. by hospital can result in clustering of identifier errors, violating the assumption of independence between identifiers required for traditional probabilistic match weight estimation. This potentially introduces selection bias to the resulting linked dataset. We aimed to measure variation in identifier error rates in a large English administrative data source (Hospital Episode Statistics; HES and to incorporate this information into match weight calculation. Methods We used 30,000 randomly selected HES hospital admissions records of patients aged 0–1, 5–6 and 18–19 years, for 2011/2012, linked via NHS number with data from the Personal Demographic Service (PDS; our gold-standard. We calculated identifier error rates for sex, date of birth and postcode and used multi-level logistic regression to investigate associations with individual-level attributes (age, ethnicity, and gender and organisational variation. We then derived: i weights incorporating dependence between identifiers; ii attribute-specific weights (varying by age, ethnicity and gender; and iii organisation-specific weights (by hospital. Results were compared with traditional match weights using a simulation study. Results Identifier errors (where values disagreed in linked HES-PDS records or missing values were found in 0.11% of records for sex and date of birth and in 53% of records for postcode. Identifier error rates differed significantly by age, ethnicity and sex (p < 0.0005. Errors were less frequent in males, in 5–6 year olds and 18–19 year olds compared with infants, and were lowest for the Asian ethic group. A simulation study demonstrated that substantial bias was introduced into estimated readmission rates in the presence

A novel method to identify hub pathways of rheumatoid arthritis based on differential pathway networks.

Science.gov (United States)

Wei, Shi-Tong; Sun, Yong-Hua; Zong, Shi-Hua

2017-09-01

The aim of the current study was to identify hub pathways of rheumatoid arthritis (RA) using a novel method based on differential pathway network (DPN) analysis. The present study proposed a DPN where protein‑protein interaction (PPI) network was integrated with pathway‑pathway interactions. Pathway data was obtained from background PPI network and the Reactome pathway database. Subsequently, pathway interactions were extracted from the pathway data by building randomized gene‑gene interactions and a weight value was assigned to each pathway interaction using Spearman correlation coefficient (SCC) to identify differential pathway interactions. Differential pathway interactions were visualized using Cytoscape to construct a DPN. Topological analysis was conducted to identify hub pathways that possessed the top 5% degree distribution of DPN. Modules of DPN were mined according to ClusterONE. A total of 855 pathways were selected to build pathway interactions. By filtrating pathway interactions of weight values >0.7, a DPN with 312 nodes and 791 edges was obtained. Topological degree analysis revealed 15 hub pathways, such as heparan sulfate/heparin‑glycosaminoglycan (HS‑GAG) degradation, HS‑GAG metabolism and keratan sulfate degradation for RA based on DPN. Furthermore, hub pathways were also important in modules, which validated the significance of hub pathways. In conclusion, the proposed method is a computationally efficient way to identify hub pathways of RA, which identified 15 hub pathways that may be potential biomarkers and provide insight to future investigation and treatment of RA.

A rapid and robust method of identifying transformed Arabidopsis thaliana seedlings following floral dip transformation

Directory of Open Access Journals (Sweden)

Gray John C

2006-11-01

Full Text Available Abstract Background The floral dip method of transformation by immersion of inflorescences in a suspension of Agrobacterium is the method of choice for Arabidopsis transformation. The presence of a marker, usually antibiotic- or herbicide-resistance, allows identification of transformed seedlings from untransformed seedlings. Seedling selection is a lengthy process which does not always lead to easily identifiable transformants. Selection for kanamycin-, phosphinothricin- and hygromycin B-resistance commonly takes 7–10 d and high seedling density and fungal contamination may result in failure to recover transformants. Results A method for identifying transformed seedlings in as little as 3.25 d has been developed. Arabidopsis T1 seeds obtained after floral dip transformation are plated on 1% agar containing MS medium and kanamycin, phosphinothricin or hygromycin B, as appropriate. After a 2-d stratification period, seeds are subjected to a regime of 4–6 h light, 48 h dark and 24 h light (3.25 d. Kanamycin-resistant and phosphinothricin-resistant seedlings are easily distinguished from non-resistant seedlings by green expanded cotyledons whereas non-resistant seedlings have pale unexpanded cotyledons. Seedlings grown on hygromycin B differ from those grown on kanamycin and phosphinothricin as both resistant and non-resistant seedlings are green. However, hygromycin B-resistant seedlings are easily identified as they have long hypocotyls (0.8–1.0 cm whereas non-resistant seedlings have short hypocotyls (0.2–0.4 cm. Conclusion The method presented here is an improvement on current selection methods as it allows quicker identification of transformed seedlings: transformed seedlings are easily discernable from non-transformants in as little as 3.25 d in comparison to the 7–10 d required for selection using current protocols.

H-classic: a new method to identify classic articles in Implant Dentistry, Periodontics, and Oral Surgery.

Science.gov (United States)

De la Flor-Martínez, Maria; Galindo-Moreno, Pablo; Sánchez-Fernández, Elena; Piattelli, Adriano; Cobo, Manuel Jesus; Herrera-Viedma, Enrique

2016-10-01

The study of classic papers permits analysis of the past, present, and future of a specific area of knowledge. This type of analysis is becoming more frequent and more sophisticated. Our objective was to use the H-classics method, based on the h-index, to analyze classic papers in Implant Dentistry, Periodontics, and Oral Surgery (ID, P, and OS). First, an electronic search of documents related to ID, P, and OS was conducted in journals indexed in Journal Citation Reports (JCR) 2014 within the category 'Dentistry, Oral Surgery & Medicine'. Second, Web of Knowledge databases were searched using Mesh terms related to ID, P, and OS. Finally, the H-classics method was applied to select the classic articles in these disciplines, collecting data on associated research areas, document type, country, institutions, and authors. Of 267,611 documents related to ID, P, and OS retrieved from JCR journals (2014), 248 were selected as H-classics. They were published in 35 journals between 1953 and 2009, most frequently in the Journal of Clinical Periodontology (18.95%), the Journal of Periodontology (18.54%), International Journal of Oral and Maxillofacial Implants (9.27%), and Clinical Oral Implant Research (6.04%). These classic articles derived from the USA in 49.59% of cases and from Europe in 47.58%, while the most frequent host institution was the University of Gothenburg (17.74%) and the most frequent authors were J. Lindhe (10.48%) and S. Socransky (8.06%). The H-classics approach offers an objective method to identify core knowledge in clinical disciplines such as ID, P, and OS. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Genome-wide association studies identify four ER negative-specific breast cancer risk loci.

Science.gov (United States)

Garcia-Closas, Montserrat; Couch, Fergus J; Lindstrom, Sara; Michailidou, Kyriaki; Schmidt, Marjanka K; Brook, Mark N; Orr, Nick; Rhie, Suhn Kyong; Riboli, Elio; Feigelson, Heather S; Le Marchand, Loic; Buring, Julie E; Eccles, Diana; Miron, Penelope; Fasching, Peter A; Brauch, Hiltrud; Chang-Claude, Jenny; Carpenter, Jane; Godwin, Andrew K; Nevanlinna, Heli; Giles, Graham G; Cox, Angela; Hopper, John L; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Dicks, Ed; Howat, Will J; Schoof, Nils; Bojesen, Stig E; Lambrechts, Diether; Broeks, Annegien; Andrulis, Irene L; Guénel, Pascal; Burwinkel, Barbara; Sawyer, Elinor J; Hollestelle, Antoinette; Fletcher, Olivia; Winqvist, Robert; Brenner, Hermann; Mannermaa, Arto; Hamann, Ute; Meindl, Alfons; Lindblom, Annika; Zheng, Wei; Devillee, Peter; Goldberg, Mark S; Lubinski, Jan; Kristensen, Vessela; Swerdlow, Anthony; Anton-Culver, Hoda; Dörk, Thilo; Muir, Kenneth; Matsuo, Keitaro; Wu, Anna H; Radice, Paolo; Teo, Soo Hwang; Shu, Xiao-Ou; Blot, William; Kang, Daehee; Hartman, Mikael; Sangrajrang, Suleeporn; Shen, Chen-Yang; Southey, Melissa C; Park, Daniel J; Hammet, Fleur; Stone, Jennifer; Veer, Laura J Van't; Rutgers, Emiel J; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Peto, Julian; Schrauder, Michael G; Ekici, Arif B; Beckmann, Matthias W; Dos Santos Silva, Isabel; Johnson, Nichola; Warren, Helen; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Marme, Federick; Schneeweiss, Andreas; Sohn, Christof; Truong, Therese; Laurent-Puig, Pierre; Kerbrat, Pierre; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Milne, Roger L; Perez, Jose Ignacio Arias; Menéndez, Primitiva; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Lichtner, Peter; Lochmann, Magdalena; Justenhoven, Christina; Ko, Yon-Dschun; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Greco, Dario; Heikkinen, Tuomas; Ito, Hidemi; Iwata, Hiroji; Yatabe, Yasushi; Antonenkova, Natalia N; Margolin, Sara; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Balleine, Rosemary; Tseng, Chiu-Chen; Berg, David Van Den; Stram, Daniel O; Neven, Patrick; Dieudonné, Anne-Sophie; Leunen, Karin; Rudolph, Anja; Nickels, Stefan; Flesch-Janys, Dieter; Peterlongo, Paolo; Peissel, Bernard; Bernard, Loris; Olson, Janet E; Wang, Xianshu; Stevens, Kristen; Severi, Gianluca; Baglietto, Laura; McLean, Catriona; Coetzee, Gerhard A; Feng, Ye; Henderson, Brian E; Schumacher, Fredrick; Bogdanova, Natalia V; Labrèche, France; Dumont, Martine; Yip, Cheng Har; Taib, Nur Aishah Mohd; Cheng, Ching-Yu; Shrubsole, Martha; Long, Jirong; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Knight, Julia A; Glendon, Gord; Mulligan, Anna Marie; Tollenaar, Robertus A E M; Seynaeve, Caroline M; Kriege, Mieke; Hooning, Maartje J; van den Ouweland, Ans M W; van Deurzen, Carolien H M; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Balasubramanian, Sabapathy P; Cross, Simon S; Reed, Malcolm W R; Signorello, Lisa; Cai, Qiuyin; Shah, Mitul; Miao, Hui; Chan, Ching Wan; Chia, Kee Seng; Jakubowska, Anna; Jaworska, Katarzyna; Durda, Katarzyna; Hsiung, Chia-Ni; Wu, Pei-Ei; Yu, Jyh-Cherng; Ashworth, Alan; Jones, Michael; Tessier, Daniel C; González-Neira, Anna; Pita, Guillermo; Alonso, M Rosario; Vincent, Daniel; Bacot, Francois; Ambrosone, Christine B; Bandera, Elisa V; John, Esther M; Chen, Gary K; Hu, Jennifer J; Rodriguez-Gil, Jorge L; Bernstein, Leslie; Press, Michael F; Ziegler, Regina G; Millikan, Robert M; Deming-Halverson, Sandra L; Nyante, Sarah; Ingles, Sue A; Waisfisz, Quinten; Tsimiklis, Helen; Makalic, Enes; Schmidt, Daniel; Bui, Minh; Gibson, Lorna; Müller-Myhsok, Bertram; Schmutzler, Rita K; Hein, Rebecca; Dahmen, Norbert; Beckmann, Lars; Aaltonen, Kirsimari; Czene, Kamila; Irwanto, Astrid; Liu, Jianjun; Turnbull, Clare; Rahman, Nazneen; Meijers-Heijboer, Hanne; Uitterlinden, Andre G; Rivadeneira, Fernando; Olswold, Curtis; Slager, Susan; Pilarski, Robert; Ademuyiwa, Foluso; Konstantopoulou, Irene; Martin, Nicholas G; Montgomery, Grant W; Slamon, Dennis J; Rauh, Claudia; Lux, Michael P; Jud, Sebastian M; Bruning, Thomas; Weaver, Joellen; Sharma, Priyanka; Pathak, Harsh; Tapper, Will; Gerty, Sue; Durcan, Lorraine; Trichopoulos, Dimitrios; Tumino, Rosario; Peeters, Petra H; Kaaks, Rudolf; Campa, Daniele; Canzian, Federico; Weiderpass, Elisabete; Johansson, Mattias; Khaw, Kay-Tee; Travis, Ruth; Clavel-Chapelon, Françoise; Kolonel, Laurence N; Chen, Constance; Beck, Andy; Hankinson, Susan E; Berg, Christine D; Hoover, Robert N; Lissowska, Jolanta; Figueroa, Jonine D; Chasman, Daniel I; Gaudet, Mia M; Diver, W Ryan; Willett, Walter C; Hunter, David J; Simard, Jacques; Benitez, Javier; Dunning, Alison M; Sherman, Mark E; Chenevix-Trench, Georgia; Chanock, Stephen J; Hall, Per; Pharoah, Paul D P; Vachon, Celine; Easton, Douglas F; Haiman, Christopher A; Kraft, Peter

2013-04-01

Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10(-12) and LGR6, P = 1.4 × 10(-8)), 2p24.1 (P = 4.6 × 10(-8)) and 16q12.2 (FTO, P = 4.0 × 10(-8)), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers.

Systems and methods for automatically identifying and linking names in digital resources

Science.gov (United States)

Parker, Charles T.; Lyons, Catherine M.; Roston, Gerald P.; Garrity, George M.

2017-06-06

The present invention provides systems and methods for automatically identifying name-like-strings in digital resources, matching these name-like-string against a set of names held in an expertly curated database, and for those name-like-strings found in said database, enhancing the content by associating additional matter with the name, wherein said matter includes information about the names that is held within said database and pointers to other digital resources which include the same name and it synonyms.

Applying Machine Learning to Workers' Compensation Data to Identify Industry-Specific Ergonomic and Safety Prevention Priorities: Ohio, 2001 to 2011.

Science.gov (United States)

Meyers, Alysha R; Al-Tarawneh, Ibraheem S; Wurzelbacher, Steven J; Bushnell, P Timothy; Lampl, Michael P; Bell, Jennifer L; Bertke, Stephen J; Robins, David C; Tseng, Chih-Yu; Wei, Chia; Raudabaugh, Jill A; Schnorr, Teresa M

2018-01-01

This study leveraged a state workers' compensation claims database and machine learning techniques to target prevention efforts by injury causation and industry. Injury causation auto-coding methods were developed to code more than 1.2 million Ohio Bureau of Workers' Compensation claims for this study. Industry groups were ranked for soft-tissue musculoskeletal claims that may have been preventable with biomechanical ergonomic (ERGO) or slip/trip/fall (STF) interventions. On the basis of the average of claim count and rate ranks for more than 200 industry groups, Skilled Nursing Facilities (ERGO) and General Freight Trucking (STF) were the highest risk for lost-time claims (>7 days). This study created a third, major causation-specific U.S. occupational injury surveillance system. These findings are being used to focus prevention resources on specific occupational injury types in specific industry groups, especially in Ohio. Other state bureaus or insurers may use similar methods.

Identifying deterministic signals in simulated gravitational wave data: algorithmic complexity and the surrogate data method

International Nuclear Information System (INIS)

Zhao Yi; Small, Michael; Coward, David; Howell, Eric; Zhao Chunnong; Ju Li; Blair, David

2006-01-01

We describe the application of complexity estimation and the surrogate data method to identify deterministic dynamics in simulated gravitational wave (GW) data contaminated with white and coloured noises. The surrogate method uses algorithmic complexity as a discriminating statistic to decide if noisy data contain a statistically significant level of deterministic dynamics (the GW signal). The results illustrate that the complexity method is sensitive to a small amplitude simulated GW background (SNR down to 0.08 for white noise and 0.05 for coloured noise) and is also more robust than commonly used linear methods (autocorrelation or Fourier analysis)

Identifying Emotions on the Basis of Neural Activation.

Directory of Open Access Journals (Sweden)

Karim S Kassam

Full Text Available We attempt to determine the discriminability and organization of neural activation corresponding to the experience of specific emotions. Method actors were asked to self-induce nine emotional states (anger, disgust, envy, fear, happiness, lust, pride, sadness, and shame while in an fMRI scanner. Using a Gaussian Naïve Bayes pooled variance classifier, we demonstrate the ability to identify specific emotions experienced by an individual at well over chance accuracy on the basis of: 1 neural activation of the same individual in other trials, 2 neural activation of other individuals who experienced similar trials, and 3 neural activation of the same individual to a qualitatively different type of emotion induction. Factor analysis identified valence, arousal, sociality, and lust as dimensions underlying the activation patterns. These results suggest a structure for neural representations of emotion and inform theories of emotional processing.

To Demonstrate the Specificity of an Enzymatic Method for Plasma Paracetamol Estimation.

Science.gov (United States)

O'Mullane, John A.

1987-01-01

Describes an experiment designed to introduce biochemistry students to the specificity of an analytical method which uses an enzyme to quantitate its substrate. Includes the use of toxicity charts together with the concept of the biological half-life of a drug. (TW)

Specific RNP capture with antisense LNA/DNA mixmers.

Science.gov (United States)

Rogell, Birgit; Fischer, Bernd; Rettel, Mandy; Krijgsveld, Jeroen; Castello, Alfredo; Hentze, Matthias W

2017-08-01

RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins. © 2017 Rogell et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Method of preparing tritium-labelled thymidine-5'-monophosphates of high specific activity

International Nuclear Information System (INIS)

Filip, J.; Vesely, J.; Cihak, A.

1976-01-01

A method is described of preparing thymidine-5'-monophosphates labelled with tritium of high specific activity based on enzyme synthesis in vitro. Phosphorylation was carried out using the catalytic effect of an enzyme contained in the supernatant fraction prepared from Yoshida ascites carcinoma in rats. The course of the enzyme reaction can be controlled by the concentration of the individual reaction mixture components. The method described allows obtaining thymidine-5'-monophosphate of radiochemical purity better than 95%. (J.B.)

Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

Science.gov (United States)

San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

2014-12-01

Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

Integration of experimental and computational methods for identifying geometric, thermal and diffusive properties of biomaterials

Science.gov (United States)

Weres, Jerzy; Kujawa, Sebastian; Olek, Wiesław; Czajkowski, Łukasz

2016-04-01

Knowledge of physical properties of biomaterials is important in understanding and designing agri-food and wood processing industries. In the study presented in this paper computational methods were developed and combined with experiments to enhance identification of agri-food and forest product properties, and to predict heat and water transport in such products. They were based on the finite element model of heat and water transport and supplemented with experimental data. Algorithms were proposed for image processing, geometry meshing, and inverse/direct finite element modelling. The resulting software system was composed of integrated subsystems for 3D geometry data acquisition and mesh generation, for 3D geometry modelling and visualization, and for inverse/direct problem computations for the heat and water transport processes. Auxiliary packages were developed to assess performance, accuracy and unification of data access. The software was validated by identifying selected properties and using the estimated values to predict the examined processes, and then comparing predictions to experimental data. The geometry, thermal conductivity, specific heat, coefficient of water diffusion, equilibrium water content and convective heat and water transfer coefficients in the boundary layer were analysed. The estimated values, used as an input for simulation of the examined processes, enabled reduction in the uncertainty associated with predictions.

A novel method of fuzzy fault tree analysis combined with VB program to identify and assess the risk of coal dust explosions.

Directory of Open Access Journals (Sweden)

Hetang Wang

Full Text Available Coal dust explosions (CDE are one of the main threats to the occupational safety of coal miners. Aiming to identify and assess the risk of CDE, this paper proposes a novel method of fuzzy fault tree analysis combined with the Visual Basic (VB program. In this methodology, various potential causes of the CDE are identified and a CDE fault tree is constructed. To overcome drawbacks from the lack of exact probability data for the basic events, fuzzy set theory is employed and the probability data of each basic event is treated as intuitionistic trapezoidal fuzzy numbers. In addition, a new approach for calculating the weighting of each expert is also introduced in this paper to reduce the error during the expert elicitation process. Specifically, an in-depth quantitative analysis of the fuzzy fault tree, such as the importance measure of the basic events and the cut sets, and the CDE occurrence probability is given to assess the explosion risk and acquire more details of the CDE. The VB program is applied to simplify the analysis process. A case study and analysis is provided to illustrate the effectiveness of this proposed method, and some suggestions are given to take preventive measures in advance and avoid CDE accidents.

Statistical methods for site-specific analysis of cancer among the A-bomb survivors

International Nuclear Information System (INIS)

Pierce, D.A.; Preston, D.L.

1992-01-01

Statistical methods are presented for joint, or simultaneous, analysis of the risks of several types of cancer for the A-bomb survivors. Previous analyses have been made either for all cancers except leukemia together, or have been done separately by cancer type. Either of these approaches has serious limitations, and the aim of joint analysis is to overcome these, while taking advantage of the strengths of each. The primary advantage of joint analysis is that models for risks of various cancer types can have some parameters in common, and others which are type-specific. This serves to overcome difficulties due to the limited data on specific cancer types. It also provides for significant tests comparing both type-specific risks and type-specific effects of modifying factors such as sex and age. These methods are exemplified here by joint analysis of three classes of cancer considered by the BEIR-V committee: (i) respiratory, (ii) digestive, and (iii) other cancers, excluding leukemia and breast cancer. The primary aim is to illustrate the general advantages of joint analyses, but in addition some comparison is made between the results of such joint analyses and the conclusions drawn by BEIR-V committee from separate analyses. (author)

LGscore: A method to identify disease-related genes using biological literature and Google data.

Science.gov (United States)

Kim, Jeongwoo; Kim, Hyunjin; Yoon, Youngmi; Park, Sanghyun

2015-04-01

Since the genome project in 1990s, a number of studies associated with genes have been conducted and researchers have confirmed that genes are involved in disease. For this reason, the identification of the relationships between diseases and genes is important in biology. We propose a method called LGscore, which identifies disease-related genes using Google data and literature data. To implement this method, first, we construct a disease-related gene network using text-mining results. We then extract gene-gene interactions based on co-occurrences in abstract data obtained from PubMed, and calculate the weights of edges in the gene network by means of Z-scoring. The weights contain two values: the frequency and the Google search results. The frequency value is extracted from literature data, and the Google search result is obtained using Google. We assign a score to each gene through a network analysis. We assume that genes with a large number of links and numerous Google search results and frequency values are more likely to be involved in disease. For validation, we investigated the top 20 inferred genes for five different diseases using answer sets. The answer sets comprised six databases that contain information on disease-gene relationships. We identified a significant number of disease-related genes as well as candidate genes for Alzheimer's disease, diabetes, colon cancer, lung cancer, and prostate cancer. Our method was up to 40% more accurate than existing methods. Copyright © 2015 Elsevier Inc. All rights reserved.

A new method of identifying target groups for pronatalist policy applied to Australia.

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Mengni Chen

Full Text Available A country's total fertility rate (TFR depends on many factors. Attributing changes in TFR to changes of policy is difficult, as they could easily be correlated with changes in the unmeasured drivers of TFR. A case in point is Australia where both pronatalist effort and TFR increased in lock step from 2001 to 2008 and then decreased. The global financial crisis or other unobserved confounders might explain both the reducing TFR and pronatalist incentives after 2008. Therefore, it is difficult to estimate causal effects of policy using econometric techniques. The aim of this study is to instead look at the structure of the population to identify which subgroups most influence TFR. Specifically, we build a stochastic model relating TFR to the fertility rates of various subgroups and calculate elasticity of TFR with respect to each rate. For each subgroup, the ratio of its elasticity to its group size is used to evaluate the subgroup's potential cost effectiveness as a pronatalist target. In addition, we measure the historical stability of group fertility rates, which measures propensity to change. Groups with a high effectiveness ratio and also high propensity to change are natural policy targets. We applied this new method to Australian data on fertility rates broken down by parity, age and marital status. The results show that targeting parity 3+ is more cost-effective than lower parities. This study contributes to the literature on pronatalist policies by investigating the targeting of policies, and generates important implications for formulating cost-effective policies.

A new method of identifying target groups for pronatalist policy applied to Australia

Science.gov (United States)

Chen, Mengni; Lloyd, Chris J.

2018-01-01

A country’s total fertility rate (TFR) depends on many factors. Attributing changes in TFR to changes of policy is difficult, as they could easily be correlated with changes in the unmeasured drivers of TFR. A case in point is Australia where both pronatalist effort and TFR increased in lock step from 2001 to 2008 and then decreased. The global financial crisis or other unobserved confounders might explain both the reducing TFR and pronatalist incentives after 2008. Therefore, it is difficult to estimate causal effects of policy using econometric techniques. The aim of this study is to instead look at the structure of the population to identify which subgroups most influence TFR. Specifically, we build a stochastic model relating TFR to the fertility rates of various subgroups and calculate elasticity of TFR with respect to each rate. For each subgroup, the ratio of its elasticity to its group size is used to evaluate the subgroup’s potential cost effectiveness as a pronatalist target. In addition, we measure the historical stability of group fertility rates, which measures propensity to change. Groups with a high effectiveness ratio and also high propensity to change are natural policy targets. We applied this new method to Australian data on fertility rates broken down by parity, age and marital status. The results show that targeting parity 3+ is more cost-effective than lower parities. This study contributes to the literature on pronatalist policies by investigating the targeting of policies, and generates important implications for formulating cost-effective policies. PMID:29425220

Using Cluster Ensemble and Validation to Identify Subtypes of Pervasive Developmental Disorders

OpenAIRE

Shen, Jess J.; Lee, Phil Hyoun; Holden, Jeanette J.A.; Shatkay, Hagit

2007-01-01

Pervasive Developmental Disorders (PDD) are neurodevelopmental disorders characterized by impairments in social interaction, communication and behavior.1 Given the diversity and varying severity of PDD, diagnostic tools attempt to identify homogeneous subtypes within PDD. Identifying subtypes can lead to targeted etiology studies and to effective type-specific intervention. Cluster analysis can suggest coherent subsets in data; however, different methods and assumptions lead to different resu...

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

Science.gov (United States)

Raviram, Ramya; Rocha, Pedro P; Müller, Christian L; Miraldi, Emily R; Badri, Sana; Fu, Yi; Swanzey, Emily; Proudhon, Charlotte; Snetkova, Valentina; Bonneau, Richard; Skok, Jane A

2016-03-01

4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait") that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

Directory of Open Access Journals (Sweden)

Ramya Raviram

2016-03-01

Full Text Available 4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or "bait" that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cis and trans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cis and trans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition, we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cis and trans chromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.

A qualitative study examining methods of accessing and identifying research relevant to clinical practice among rehabilitation clinicians

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Patel D

2017-12-01

Full Text Available Drasti Patel,1 Christine Koehmstedt,1 Rebecca Jones,1 Nathan T Coffey,1 Xinsheng Cai,2 Steven Garfinkel,2 Dahlia M Shaewitz,2 Ali A Weinstein1 1Center for Study of Chronic Illness and Disability, College of Health and Human Services, George Mason University, Fairfax, VA, 2American Institutes for Research, Washington, DC, USA Purpose: Research examining the utilization of evidence-based practice (EBP specifically among rehabilitation clinicians is limited. The objective of this study was to examine how various rehabilitative clinicians including physical therapists, occupational therapists, rehabilitation counselors, and physiatrists are gaining access to literature and whether they are able to implement the available research into practice.Methods: A total of 21 total clinicians were interviewed via telephone. Using NVivo, a qualitative analysis of the responses was performed.Results: There were similarities found with respect to the information-seeking behaviors and translation of research across the different clinician types. Lack of time was reported to be a barrier for both access to literature and implementation of research across all clinician types. The majority of clinicians who reported having difficulty with utilizing the published literature indicated that the literature was not applicable to their practice, the research was not specific enough to be put into practice, or the research found was too outdated to be relevant. In addition, having a supportive work environment aided in the search and utilization of research through providing resources central to assisting clinicians in gaining access to health information.Conclusion: Our study identified several barriers that affect EBP for rehabilitation clinicians. The findings suggest the need for researchers to ensure that their work is applicable and specific to clinical practice for implementation to occur. Keywords: health information, information behavior, knowledge utilization

Formal specification level concepts, methods, and algorithms

CERN Document Server

Soeken, Mathias

2015-01-01

This book introduces a new level of abstraction that closes the gap between the textual specification of embedded systems and the executable model at the Electronic System Level (ESL). Readers will be enabled to operate at this new, Formal Specification Level (FSL), using models which not only allow significant verification tasks in this early stage of the design flow, but also can be extracted semi-automatically from the textual specification in an interactive manner.  The authors explain how to use these verification tasks to check conceptual properties, e.g. whether requirements are in conflict, as well as dynamic behavior, in terms of execution traces. • Serves as a single-source reference to a new level of abstraction for embedded systems, known as the Formal Specification Level (FSL); • Provides a variety of use cases which can be adapted to readers’ specific design flows; • Includes a comprehensive illustration of Natural Language Processing (NLP) techniques, along with examples of how to i...

Comparing Three Patterns of Strengths and Weaknesses Models for the Identification of Specific Learning Disabilities

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Miller, Daniel C.; Maricle, Denise E.; Jones, Alicia M.

2016-01-01

Processing Strengths and Weaknesses (PSW) models have been proposed as a method for identifying specific learning disabilities. Three PSW models were examined for their ability to predict expert identified specific learning disabilities cases. The Dual Discrepancy/Consistency Model (DD/C; Flanagan, Ortiz, & Alfonso, 2013) as operationalized by…

Radioimmunoassay (RIA), a highly specific, extremely sensitive quantitative method of analysis

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Strecker, H; Hachmann, H; Seidel, L [Farbwerke Hoechst A.G., Frankfurt am Main (Germany, F.R.). Radiochemisches Lab.

1979-02-01

Radioimmunoassay is an analytical method combining the sensitivity of radioactivity measurements and the specificity of the antigen-antibody-reaction. Thus, substances can be measured in concentrations as low as picograms per milliliter serum besides a millionfold excess of otherwise disturbing material (for example in serum). The method is simple to perform and is at present mainly used in the field of endocrinology. Further areas of possible application are in the diagnosis of infectious disease, drug research, environmental protection, forensic medicine as well as general analytics. Quantities of radioactivity, exclusively used in vitro, are in the nano-Curie range. Therefore the radiation dose is negligible.

The sensitivity and specificity of four questions (HARK to identify intimate partner violence: a diagnostic accuracy study in general practice

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Feder Gene

2007-08-01

Full Text Available Abstract Background Intimate partner violence (IPV including physical, sexual and emotional violence, causes short and long term ill-health. Brief questions that reliably identify women experiencing IPV who present in clinical settings are a pre-requisite for an appropriate response from health services to this substantial public health problem. We estimated the sensitivity and specificity of four questions (HARK developed from the Abuse Assessment screen, compared to a 30-item abuse questionnaire, the Composite Abuse Scale (CAS. Methods We administered the four HARK questions and the CAS to women approached by two researchers in general practice waiting rooms in Newham, east London. Inclusions: women aged more than 17 years waiting to see a doctor or nurse, who had been in an intimate relationship in the last year. Exclusions: women who were accompanied by children over four years of age or another adult, too unwell to complete the questionnaires, unable to understand English or unable to give informed consent. Results Two hundred and thirty two women were recruited. The response rate was 54%. The prevalence of current intimate partner violence, within the last 12 months, using the CAS cut off score of ≥3, was 23% (95% C.I. 17% to 28% with pre-test odds of 0.3 (95% C.I. 0.2 to 0.4. The receiver operator characteristic curve demonstrated that a HARK cut off score of ≥1 maximises the true positives whilst minimising the false positives. The sensitivity of the optimal HARK cut-off score of ≥1 was 81% (95% C.I. 69% to 90%, specificity 95% (95% C.I. 91% to 98%, positive predictive value 83% (95% C.I. 70% to 91%, negative predictive value 94% (95% C.I. 90% to 97%, likelihood ratio 16 (95% C.I. 8 to 31 and post-test odds 5. Conclusion The four HARK questions accurately identify women experiencing IPV in the past year and may help women disclose abuse in general practice. The HARK questions could be incorporated into the electronic medical record

METHOD FOR SECURITY SPECIFICATION SOFTWARE REQUIREMENTS AS A MEANS FOR IMPLEMENTING A SOFTWARE DEVELOPMENT PROCESS SECURE - MERSEC

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Castro Mecías, L.T.

2015-06-01

Full Text Available Often security incidents that have the object or use the software as a means of causing serious damage and legal, economic consequences, etc. Results of a survey by Kaspersky Lab reflectvulnerabilities in software are the main cause of security incidents in enterprises, the report shows that 85% of them have reported security incidents and vulnerabilities in software are the main reason is further estimated that incidents can cause significant losses estimated from 50,000 to $ 649.000. (1 In this regard academic and industry research focuses on proposals based on reducing vulnerabilities and failures of technology, with a positive influence on how the software is developed. A development process for improved safety practices and should include activities from the initial phases of the software; so that security needs are identified, manage risk and appropriate measures are implemented. This article discusses a method of analysis, acquisition and requirements specification of the software safety analysis on the basis of various proposals and deficiencies identified from participant observation in software development teams. Experiments performed using the proposed yields positive results regarding the reduction of security vulnerabilities and compliance with the safety objectives of the software.

Testing a Novel Method to Approximate Wood Specific Gravity of Trees

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Michael C. Wiemann; G. Bruce. Williamson

2012-01-01

Wood specific gravity (SG) has long been used by foresters as an index for wood properties. More recently, SG has been widely used by ecologists as a plant functional trait and as a key variable in estimates of biomass. However, sampling wood to determine SG can be problematic; at present, the most common method is sampling with an increment borer to extract a bark-to-...

A method for the specific detection of resident bacteria in brine shrimp larvae.

Science.gov (United States)

Niu, Yufeng; Defoirdt, Tom; Rekecki, Anamaria; De Schryver, Peter; Van den Broeck, Wim; Dong, Shuanglin; Sorgeloos, Patrick; Boon, Nico; Bossier, Peter

2012-04-01

In this study, we describe an easy but efficient method to specifically target the intestinal resident microbiota in brine shrimp larvae during DGGE analysis, hereby excluding the interference of both transient (luminal) bacteria and body surface bacteria. This effective technique has several advantages over alternative methods, with respect of ease of use and rapidity. Copyright © 2012 Elsevier B.V. All rights reserved.

Chapter 16: Retrocommissioning Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

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Kurnik, Charles W. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Tiessen, Alex [Posterity Group, Derwood, MD (United States)

2017-10-09

Retrocommissioning (RCx) is a systematic process for optimizing energy performance in existing buildings. It specifically focuses on improving the control of energy-using equipment (e.g., heating, ventilation, and air conditioning [HVAC] equipment and lighting) and typically does not involve equipment replacement. Field results have shown proper RCx can achieve energy savings ranging from 5 percent to 20 percent, with a typical payback of two years or less (Thorne 2003). The method presented in this protocol provides direction regarding: (1) how to account for each measure's specific characteristics and (2) how to choose the most appropriate savings verification approach.

Development and evaluation of event-specific quantitative PCR method for genetically modified soybean A2704-12.

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Takabatake, Reona; Akiyama, Hiroshi; Sakata, Kozue; Onishi, Mari; Koiwa, Tomohiro; Futo, Satoshi; Minegishi, Yasutaka; Teshima, Reiko; Mano, Junichi; Furui, Satoshi; Kitta, Kazumi

2011-01-01

A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) soybean event; A2704-12. During the plant transformation, DNA fragments derived from pUC19 plasmid were integrated in A2704-12, and the region was found to be A2704-12 specific. The pUC19-derived DNA sequences were used as primers for the specific detection of A2704-12. We first tried to construct a standard plasmid for A2704-12 quantification using pUC19. However, non-specific signals appeared with both qualitative and quantitative PCR analyses using the specific primers with pUC19 as a template, and we then constructed a plasmid using pBR322. The conversion factor (C(f)), which is required to calculate the amount of the genetically modified organism (GMO), was experimentally determined with two real-time PCR instruments, the Applied Biosystems 7900HT and the Applied Biosystems 7500. The determined C(f) values were both 0.98. The quantitative method was evaluated by means of blind tests in multi-laboratory trials using the two real-time PCR instruments. The limit of quantitation for the method was estimated to be 0.1%. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSD(R)), and the determined bias and RSD(R) values for the method were each less than 20%. These results suggest that the developed method would be suitable for practical analyses for the detection and quantification of A2704-12.

Identifying microRNA/mRNA dysregulations in ovarian cancer.

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Miles, Gregory D; Seiler, Michael; Rodriguez, Lorna; Rajagopal, Gunaretnam; Bhanot, Gyan

2012-03-27

MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory mechanisms. Our findings identify

Genome-Wide Association Study Identifies Two Novel Loci with Sex-Specific Effects for Type 2 Diabetes Mellitus and Glycemic Traits in a Korean Population

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Min Jin Go

2014-10-01

Full Text Available BackgroundUntil recently, genome-wide association study (GWAS-based findings have provided a substantial genetic contribution to type 2 diabetes mellitus (T2DM or related glycemic traits. However, identification of allelic heterogeneity and population-specific genetic variants under consideration of potential confounding factors will be very valuable for clinical applicability. To identify novel susceptibility loci for T2DM and glycemic traits, we performed a two-stage genetic association study in a Korean population.MethodsWe performed a logistic analysis for T2DM, and the first discovery GWAS was analyzed for 1,042 cases and 2,943 controls recruited from a population-based cohort (KARE, n=8,842. The second stage, de novo replication analysis, was performed in 1,216 cases and 1,352 controls selected from an independent population-based cohort (Health 2, n=8,500. A multiple linear regression analysis for glycemic traits was further performed in a total of 14,232 nondiabetic individuals consisting of 7,696 GWAS and 6,536 replication study participants. A meta-analysis was performed on the combined results using effect size and standard errors estimated for stage 1 and 2, respectively.ResultsA combined meta-analysis for T2DM identified two new (rs11065756 and rs2074356 loci reaching genome-wide significance in CCDC63 and C12orf51 on the 12q24 region. In addition, these variants were significantly associated with fasting plasma glucose and homeostasis model assessment of β-cell function. Interestingly, two independent single nucleotide polymorphisms were associated with sex-specific stratification in this study.ConclusionOur study showed a strong association between T2DM and glycemic traits. We further observed that two novel loci with multiple diverse effects were highly specific to males. Taken together, these findings may provide additional insights into the clinical assessment or subclassification of disease risk in a Korean population.

Genome-wide association studies identify four ER negative–specific breast cancer risk loci

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Garcia-Closas, Montserrat; Couch, Fergus J; Lindstrom, Sara; Michailidou, Kyriaki; Schmidt, Marjanka K; Brook, Mark N; orr, Nick; Rhie, Suhn Kyong; Riboli, Elio; Feigelson, Heather s; Le Marchand, Loic; Buring, Julie E; Eccles, Diana; Miron, Penelope; Fasching, Peter A; Brauch, Hiltrud; Chang-Claude, Jenny; Carpenter, Jane; Godwin, Andrew K; Nevanlinna, Heli; Giles, Graham G; Cox, Angela; Hopper, John L; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Dicks, Ed; Howat, Will J; Schoof, Nils; Bojesen, Stig E; Lambrechts, Diether; Broeks, Annegien; Andrulis, Irene L; Guénel, Pascal; Burwinkel, Barbara; Sawyer, Elinor J; Hollestelle, Antoinette; Fletcher, Olivia; Winqvist, Robert; Brenner, Hermann; Mannermaa, Arto; Hamann, Ute; Meindl, Alfons; Lindblom, Annika; Zheng, Wei; Devillee, Peter; Goldberg, Mark S; Lubinski, Jan; Kristensen, Vessela; Swerdlow, Anthony; Anton-Culver, Hoda; Dörk, Thilo; Muir, Kenneth; Matsuo, Keitaro; Wu, Anna H; Radice, Paolo; Teo, Soo Hwang; Shu, Xiao-Ou; Blot, William; Kang, Daehee; Hartman, Mikael; Sangrajrang, Suleeporn; Shen, Chen-Yang; Southey, Melissa C; Park, Daniel J; Hammet, Fleur; Stone, Jennifer; Veer, Laura J Van’t; Rutgers, Emiel J; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Peto, Julian; Schrauder, Michael G; Ekici, Arif B; Beckmann, Matthias W; Silva, Isabel dos Santos; Johnson, Nichola; Warren, Helen; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Marme, Federick; Schneeweiss, Andreas; Sohn, Christof; Truong, Therese; Laurent-Puig, Pierre; Kerbrat, Pierre; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Milne, Roger L; Perez, Jose Ignacio Arias; Menéndez, Primitiva; Müller, Heiko; Arndt, Volker; Stegmaier, Christa; Lichtner, Peter; Lochmann, Magdalena; Justenhoven, Christina; Ko, Yon-Dschun; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Greco, Dario; Heikkinen, Tuomas; Ito, Hidemi; Iwata, Hiroji; Yatabe, Yasushi; Antonenkova, Natalia N; Margolin, Sara; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Balleine, Rosemary; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Neven, Patrick; Dieudonné, Anne-Sophie; Leunen, Karin; Rudolph, Anja; Nickels, Stefan; Flesch-Janys, Dieter; Peterlongo, Paolo; Peissel, Bernard; Bernard, Loris; Olson, Janet E; Wang, Xianshu; Stevens, Kristen; Severi, Gianluca; Baglietto, Laura; Mclean, Catriona; Coetzee, Gerhard A; Feng, Ye; Henderson, Brian E; Schumacher, Fredrick; Bogdanova, Natalia V; Labrèche, France; Dumont, Martine; Yip, Cheng Har; Taib, Nur Aishah Mohd; Cheng, Ching-Yu; Shrubsole, Martha; Long, Jirong; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; knight, Julia A; Glendon, Gord; Mulligan, Anna Marie; Tollenaar, Robertus A E M; Seynaeve, Caroline M; Kriege, Mieke; Hooning, Maartje J; Van den Ouweland, Ans M W; Van Deurzen, Carolien H M; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Balasubramanian, Sabapathy P; Cross, Simon S; Reed, Malcolm W R; Signorello, Lisa; Cai, Qiuyin; Shah, Mitul; Miao, Hui; Chan, Ching Wan; Chia, Kee Seng; Jakubowska, Anna; Jaworska, Katarzyna; Durda, Katarzyna; Hsiung, Chia-Ni; Wu, Pei-Ei; Yu, Jyh-Cherng; Ashworth, Alan; Jones, Michael; Tessier, Daniel C; González-Neira, Anna; Pita, Guillermo; Alonso, M Rosario; Vincent, Daniel; Bacot, Francois; Ambrosone, Christine B; Bandera, Elisa V; John, Esther M; Chen, Gary K; Hu, Jennifer J; Rodriguez-gil, Jorge L; Bernstein, Leslie; Press, Michael F; Ziegler, Regina G; Millikan, Robert M; Deming-Halverson, Sandra L; Nyante, Sarah; Ingles, Sue A; Waisfisz, Quinten; Tsimiklis, Helen; Makalic, Enes; Schmidt, Daniel; Bui, Minh; Gibson, Lorna; Müller-Myhsok, Bertram; Schmutzler, Rita K; Hein, Rebecca; Dahmen, Norbert; Beckmann, Lars; Aaltonen, Kirsimari; Czene, Kamila; Irwanto, Astrid; Liu, Jianjun; Turnbull, Clare; Rahman, Nazneen; Meijers-Heijboer, Hanne; Uitterlinden, Andre G; Rivadeneira, Fernando; Olswold, Curtis; Slager, Susan; Pilarski, Robert; Ademuyiwa, Foluso; Konstantopoulou, Irene; Martin, Nicholas G; Montgomery, Grant W; Slamon, Dennis J; Rauh, Claudia; Lux, Michael P; Jud, Sebastian M; Bruning, Thomas; Weaver, Joellen; Sharma, Priyanka; Pathak, Harsh; Tapper, Will; Gerty, Sue; Durcan, Lorraine; Trichopoulos, Dimitrios; Tumino, Rosario; Peeters, Petra H; Kaaks, Rudolf; Campa, Daniele; Canzian, Federico; Weiderpass, Elisabete; Johansson, Mattias; Khaw, Kay-Tee; Travis, Ruth; Clavel-Chapelon, Françoise; Kolonel, Laurence N; Chen, Constance; Beck, Andy; Hankinson, Susan E; Berg, Christine D; Hoover, Robert N; Lissowska, Jolanta; Figueroa, Jonine D; Chasman, Daniel I; Gaudet, Mia M; Diver, W Ryan; Willett, Walter C; Hunter, David J; Simard, Jacques; Benitez, Javier; Dunning, Alison M; Sherman, Mark E; Chenevix-Trench, Georgia; Chanock, Stephen J; Hall, Per; Pharoah, Paul D P; Vachon, Celine; Easton, Douglas F; Haiman, Christopher A; Kraft, Peter

2013-01-01

Estrogen receptor (ER)-negative tumors represent 20–30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry1. The etiology2 and clinical behavior3 of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition4. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS). SNPs at four loci, 1q32.1 (MDM4, P = 2.1 × 10−12 and LGR6, P = 1.4 × 10−8), 2p24.1 (P = 4.6 × 10−8) and 16q12.2 (FTO, P = 4.0 × 10−8), were associated with ER-negative but not ER-positive breast cancer (P > 0.05). These findings provide further evidence for distinct etiological pathways associated with invasive ER-positive and ER-negative breast cancers. PMID:23535733

Comparison of two biochemical methods for identifying Corynebacterium pseudotuberculosis isolated from sheep and goats.

Science.gov (United States)

Huerta, Belén; Gómez-Gascón, Lidia; Vela, Ana I; Fernández-Garayzábal, José F; Casamayor, Almudena; Tarradas, Carmen; Maldonado, Alfonso

2013-06-01

The biochemical pattern of Cowan and Steel (BPCS) was compared with a commercial biochemical strip for the identification of Corynebacterium pseudotuberculosis isolated from small ruminants. On 16S rRNA gene sequencing, 40/78 coryneform isolates from the lymph nodes of sheep and goats with lesions resembling caseous lymphadenitis were identified as C. pseudotuberculosis. The sensitivities of the BPCS and the commercial biochemical strip relative to 16S rRNA sequencing were 80% and 85%, and their specificities were 92.1% and 94.7%, respectively; the level of agreement between the BPCS and the commercial biochemical strip was high (κ=0.82). Likelihood ratios for positive and negative results were 10.0 and 0.22 for the BPCS, and 16.0 and 0.16 for the commercial biochemical strip, respectively. These results indicate that the BPCS and the commercial biochemical strip are both useful for identifying C. pseudotuberculosis in veterinary microbiology laboratories. Copyright © 2012 Elsevier Ltd. All rights reserved.

A nonmusical paradigm for identifying absolute pitch possessors

Science.gov (United States)

Ross, David A.; Olson, Ingrid R.; Marks, Lawrence E.; Gore, John C.

2004-09-01

The ability to identify and reproduce sounds of specific frequencies is remarkable and uncommon. The etiology and defining characteristics of this skill, absolute pitch (AP), have been very controversial. One theory suggests that AP requires a specific type of early musical training and that the ability to encode and remember tones depends on these learned musical associations. An alternate theory argues that AP may be strongly dependent on hereditary factors and relatively independent of musical experience. To date, it has been difficult to test these hypotheses because all previous paradigms for identifying AP have required subjects to employ knowledge of musical nomenclature. As such, these tests are insensitive to the possibility of discovering AP in either nonmusicians or musicians of non-Western training. Based on previous literature in pitch memory, a paradigm is presented that is intended to distinguish between AP possessors and nonpossessors independent of the subjects' musical experience. The efficacy of this method is then tested with 20 classically defined AP possessors and 22 nonpossessors. Data from these groups strongly support the validity of the paradigm. The use of a nonmusical paradigm to identify AP may facilitate research into many aspects of this phenomenon.

Prediction of disease-related genes based on weighted tissue-specific networks by using DNA methylation.

Science.gov (United States)

Li, Min; Zhang, Jiayi; Liu, Qing; Wang, Jianxin; Wu, Fang-Xiang

2014-01-01

Predicting disease-related genes is one of the most important tasks in bioinformatics and systems biology. With the advances in high-throughput techniques, a large number of protein-protein interactions are available, which make it possible to identify disease-related genes at the network level. However, network-based identification of disease-related genes is still a challenge as the considerable false-positives are still existed in the current available protein interaction networks (PIN). Considering the fact that the majority of genetic disorders tend to manifest only in a single or a few tissues, we constructed tissue-specific networks (TSN) by integrating PIN and tissue-specific data. We further weighed the constructed tissue-specific network (WTSN) by using DNA methylation as it plays an irreplaceable role in the development of complex diseases. A PageRank-based method was developed to identify disease-related genes from the constructed networks. To validate the effectiveness of the proposed method, we constructed PIN, weighted PIN (WPIN), TSN, WTSN for colon cancer and leukemia, respectively. The experimental results on colon cancer and leukemia show that the combination of tissue-specific data and DNA methylation can help to identify disease-related genes more accurately. Moreover, the PageRank-based method was effective to predict disease-related genes on the case studies of colon cancer and leukemia. Tissue-specific data and DNA methylation are two important factors to the study of human diseases. The same method implemented on the WTSN can achieve better results compared to those being implemented on original PIN, WPIN, or TSN. The PageRank-based method outperforms degree centrality-based method for identifying disease-related genes from WTSN.

Determination of the thermal conductivity and specific heat capacity of neem seeds by inverse problem method

Directory of Open Access Journals (Sweden)

S.N. Nnamchi

2010-01-01

Full Text Available Determination of the thermal conductivity and the specific heat capacity of neem seeds (Azadirachta indica A. Juss usingthe inverse method is the main subject of this work. One-dimensional formulation of heat conduction problem in a spherewas used. Finite difference method was adopted for the solution of the heat conduction problem. The thermal conductivityand the specific heat capacity were determined by least square method in conjunction with Levenberg-Marquardt algorithm.The results obtained compare favourably with those obtained experimentally. These results are useful in the analysis ofneem seeds drying and leaching processes.

A novel method for monitoring functional lesion-specific recruitment of repair proteins in live cells

Energy Technology Data Exchange (ETDEWEB)

Woodrick, Jordan; Gupta, Suhani; Khatkar, Pooja; Dave, Kalpana; Levashova, Darya; Choudhury, Sujata; Elias, Hadi; Saha, Tapas; Mueller, Susette; Roy, Rabindra, E-mail: rr228@georgetown.edu

2015-05-15

Highlights: • A method of monitoring lesion-specific recruitment of proteins in vivo is described. • Recruitment of repair enzymes to abasic sites is monitored by co-localization. • Repair protein recruitment is consistent with known protein–protein relationships. • Cells demonstrated complete repair of abasic sites by 90 min. - Abstract: DNA–protein relationships have been studied by numerous methods, but a particular gap in methodology lies in the study of DNA adduct-specific interactions with proteins in vivo, which particularly affects the field of DNA repair. Using the repair of a well-characterized and ubiquitous adduct, the abasic (AP) site, as a model, we have developed a comprehensive method of monitoring DNA lesion-specific recruitment of proteins in vivo over time. We utilized a surrogate system in which a Cy3-labeled plasmid containing a single AP-site was transfected into cells, and the interaction of the labeled DNA with BER enzymes, including APE1, Polβ, LIG1, and FEN1, was monitored by immunofluorescent staining of the enzymes by Alexafluor-488-conjugated secondary antibody. The recruitment of enzymes was characterized by quantification of Cy3-Alexafluor-488 co-localization. To validate the microscopy-based method, repair of the transfected AP-site DNA was also quantified at various time points post-transfection using a real time PCR-based method. Notably, the recruitment time kinetics for each enzyme were consistent with AP-site repair time kinetics. This microscopy-based methodology is reliable in detecting the recruitment of proteins to specific DNA substrates and can be extended to study other in vivo DNA–protein relationships in any DNA sequence and in the context of any DNA structure in transfectable proliferating or quiescent cells. The method may be applied to a variety of disciplines of nucleic acid transaction pathways, including repair, replication, transcription, and recombination.

A novel method for monitoring functional lesion-specific recruitment of repair proteins in live cells

International Nuclear Information System (INIS)

Woodrick, Jordan; Gupta, Suhani; Khatkar, Pooja; Dave, Kalpana; Levashova, Darya; Choudhury, Sujata; Elias, Hadi; Saha, Tapas; Mueller, Susette; Roy, Rabindra

2015-01-01

Highlights: • A method of monitoring lesion-specific recruitment of proteins in vivo is described. • Recruitment of repair enzymes to abasic sites is monitored by co-localization. • Repair protein recruitment is consistent with known protein–protein relationships. • Cells demonstrated complete repair of abasic sites by 90 min. - Abstract: DNA–protein relationships have been studied by numerous methods, but a particular gap in methodology lies in the study of DNA adduct-specific interactions with proteins in vivo, which particularly affects the field of DNA repair. Using the repair of a well-characterized and ubiquitous adduct, the abasic (AP) site, as a model, we have developed a comprehensive method of monitoring DNA lesion-specific recruitment of proteins in vivo over time. We utilized a surrogate system in which a Cy3-labeled plasmid containing a single AP-site was transfected into cells, and the interaction of the labeled DNA with BER enzymes, including APE1, Polβ, LIG1, and FEN1, was monitored by immunofluorescent staining of the enzymes by Alexafluor-488-conjugated secondary antibody. The recruitment of enzymes was characterized by quantification of Cy3-Alexafluor-488 co-localization. To validate the microscopy-based method, repair of the transfected AP-site DNA was also quantified at various time points post-transfection using a real time PCR-based method. Notably, the recruitment time kinetics for each enzyme were consistent with AP-site repair time kinetics. This microscopy-based methodology is reliable in detecting the recruitment of proteins to specific DNA substrates and can be extended to study other in vivo DNA–protein relationships in any DNA sequence and in the context of any DNA structure in transfectable proliferating or quiescent cells. The method may be applied to a variety of disciplines of nucleic acid transaction pathways, including repair, replication, transcription, and recombination

A strategy for evaluating pathway analysis methods.

Science.gov (United States)

Yu, Chenggang; Woo, Hyung Jun; Yu, Xueping; Oyama, Tatsuya; Wallqvist, Anders; Reifman, Jaques

2017-10-13

Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biological interpretation of high-throughput data. Before practically applying such pathway analysis (PA) methods, we must first evaluate their performance and reliability, using datasets where the pathways perturbed by the conditions of interest have been well characterized in advance. However, such 'ground truths' (or gold standards) are often unavailable. Furthermore, previous evaluation strategies that have focused on defining 'true answers' are unable to systematically and objectively assess PA methods under a wide range of conditions. In this work, we propose a novel strategy for evaluating PA methods independently of any gold standard, either established or assumed. The strategy involves the use of two mutually complementary metrics, recall and discrimination. Recall measures the consistency of the perturbed pathways identified by applying a particular analysis method to an original large dataset and those identified by the same method to a sub-dataset of the original dataset. In contrast, discrimination measures specificity-the degree to which the perturbed pathways identified by a particular method to a dataset from one experiment differ from those identifying by the same method to a dataset from a different experiment. We used these metrics and 24 datasets to evaluate six widely used PA methods. The results highlighted the common challenge in reliably identifying significant pathways from small datasets. Importantly, we confirmed the effectiveness of our proposed dual-metric strategy by showing that previous comparative studies corroborate the performance evaluations of the six methods obtained by our strategy. Unlike any previously proposed strategy for evaluating the performance of PA methods, our dual-metric strategy does not rely on any ground truth

A systematic design method for robust synthetic biology to satisfy design specifications.

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Chen, Bor-Sen; Wu, Chih-Hung

2009-06-30

Synthetic biology is foreseen to have important applications in biotechnology and medicine, and is expected to contribute significantly to a better understanding of the functioning of complex biological systems. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to intrinsic parameter uncertainties, external disturbances and functional variations of intra- and extra-cellular environments. The design method for a robust synthetic gene network that works properly in a host cell under these intrinsic parameter uncertainties and external disturbances is the most important topic in synthetic biology. In this study, we propose a stochastic model that includes parameter fluctuations and external disturbances to mimic the dynamic behaviors of a synthetic gene network in the host cell. Then, based on this stochastic model, four design specifications are introduced to guarantee that a synthetic gene network can achieve its desired steady state behavior in spite of parameter fluctuations, external disturbances and functional variations in the host cell. We propose a systematic method to select a set of appropriate design parameters for a synthetic gene network that will satisfy these design specifications so that the intrinsic parameter fluctuations can be tolerated, the external disturbances can be efficiently filtered, and most importantly, the desired steady states can be achieved. Thus the synthetic gene network can work properly in a host cell under intrinsic parameter uncertainties, external disturbances and functional variations. Finally, a design procedure for the robust synthetic gene network is developed and a design example is given in silico to confirm the performance of the proposed method. Based on four design specifications, a systematic design procedure is developed for designers to engineer a robust synthetic biology network that can achieve its desired steady state behavior

Trans-ethnic fine-mapping of lipid loci identifies population-specific signals and allelic heterogeneity that increases the trait variance explained.

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Ying Wu

2013-03-01

Full Text Available Genome-wide association studies (GWAS have identified ~100 loci associated with blood lipid levels, but much of the trait heritability remains unexplained, and at most loci the identities of the trait-influencing variants remain unknown. We conducted a trans-ethnic fine-mapping study at 18, 22, and 18 GWAS loci on the Metabochip for their association with triglycerides (TG, high-density lipoprotein cholesterol (HDL-C, and low-density lipoprotein cholesterol (LDL-C, respectively, in individuals of African American (n = 6,832, East Asian (n = 9,449, and European (n = 10,829 ancestry. We aimed to identify the variants with strongest association at each locus, identify additional and population-specific signals, refine association signals, and assess the relative significance of previously described functional variants. Among the 58 loci, 33 exhibited evidence of association at P<1 × 10(-4 in at least one ancestry group. Sequential conditional analyses revealed that ten, nine, and four loci in African Americans, Europeans, and East Asians, respectively, exhibited two or more signals. At these loci, accounting for all signals led to a 1.3- to 1.8-fold increase in the explained phenotypic variance compared to the strongest signals. Distinct signals across ancestry groups were identified at PCSK9 and APOA5. Trans-ethnic analyses narrowed the signals to smaller sets of variants at GCKR, PPP1R3B, ABO, LCAT, and ABCA1. Of 27 variants reported previously to have functional effects, 74% exhibited the strongest association at the respective signal. In conclusion, trans-ethnic high-density genotyping and analysis confirm the presence of allelic heterogeneity, allow the identification of population-specific variants, and limit the number of candidate SNPs for functional studies.

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

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Martin Darren P

2009-04-01

Full Text Available Abstract Background Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences. Results Analysis of phylogenetic simulations reveal that identifying the descendents of relatively old recombination events is a challenging task for all methods available, and that quartet scanning performs relatively well compared to the triplet based methods. The use of quartet scanning is further demonstrated by analyzing both well-established and putative HIV-1 recombinant strains. In agreement with recent findings, we provide evidence that the presumed circulating recombinant CRF02_AG is a 'pure' lineage, whereas the presumed parental lineage subtype G has a recombinant origin. We also demonstrate HIV-1 intrasubtype recombination, confirm the hybrid origin of SIV in chimpanzees and further disentangle the recombinant history of SIV lineages in a primate immunodeficiency virus data set. Conclusion Quartet scanning makes a valuable addition to triplet-based methods for identifying recombinant sequences without prior specifications of either query and reference sequences. The new method is available in the VisRD v.3.0 package http://www.cmp.uea.ac.uk/~vlm/visrd.

Brief report: Comparison of methods to identify Iraq and Afghanistan war veterans using Department of Veterans Affairs administrative data.

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Bangerter, Ann; Gravely, Amy; Cutting, Andrea; Clothier, Barb; Spoont, Michele; Sayer, Nina

2010-01-01

The Department of Veterans Affairs (VA) has made treatment and care of Operation Iraqi Freedom/Operation Enduring Freedom (OIF/OEF) veterans a priority. Researchers face challenges identifying the OIF/OEF population because until fiscal year 2008, no indicator of OIF/OEF service was present in the Veterans Health Administration (VHA) administrative databases typically used for research. In this article, we compare an algorithm we developed to identify OIF/OEF veterans using the Austin Information Technology Center administrative data with the VHA Support Service Center OIF/OEF Roster and veterans' self-report of military service. We drew data from two different institutional review board-approved funded studies. The positive predictive value of our algorithm compared with the VHA Support Service Center OIF/OEF Roster and self-report was 92% and 98%, respectively. However, this method of identifying OIF/OEF veterans failed to identify a large proportion of OIF/OEF veterans listed in the VHA Support Service Center OIF/OEF Roster. Demographic, diagnostic, and VA service use differences were found between veterans identified using our method and those we failed to identify but who were in the VHA Support Service Center OIF/OEF Roster. Therefore, depending on the research objective, this method may not be a viable alternative to the VHA Support Service Center OIF/OEF Roster for identifying OIF/OEF veterans.

New Method to Identify Field Joint Coating Failures Based on MFL In-Line Inspection Signals

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Lianshuang Dai

2018-02-01

Full Text Available Above ground indirect detections and random excavations that have applied the past years for buried long distance oil and gas pipelines can only identify some damaged coating locations. Hence, large number of field joint coating (FJC failures happen unconsciously until they lead to failures of the pipelines. Based on the analysis of magnetic flux leakage (MFL in-line inspection (ILI signals, combined with the statistical results of 414 excavations from two different pipeline sections, a new method to identify the failed FJC is established. Though it can only identify FJC failures when there are signs of corrosion on pipe body, it is much more efficient and cost-saving. The concluded identification rule still needs more validations and improvements to be more applicable and accuracy.

Methods for identifying 30 chronic conditions: application to administrative data.

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Tonelli, Marcello; Wiebe, Natasha; Fortin, Martin; Guthrie, Bruce; Hemmelgarn, Brenda R; James, Matthew T; Klarenbach, Scott W; Lewanczuk, Richard; Manns, Braden J; Ronksley, Paul; Sargious, Peter; Straus, Sharon; Quan, Hude

2015-04-17

Multimorbidity is common and associated with poor clinical outcomes and high health care costs. Administrative data are a promising tool for studying the epidemiology of multimorbidity. Our goal was to derive and apply a new scheme for using administrative data to identify the presence of chronic conditions and multimorbidity. We identified validated algorithms that use ICD-9 CM/ICD-10 data to ascertain the presence or absence of 40 morbidities. Algorithms with both positive predictive value and sensitivity ≥70% were graded as "high validity"; those with positive predictive value ≥70% and sensitivity <70% were graded as "moderate validity". To show proof of concept, we applied identified algorithms with high to moderate validity to inpatient and outpatient claims and utilization data from 574,409 people residing in Edmonton, Canada during the 2008/2009 fiscal year. Of the 40 morbidities, we identified 30 that could be identified with high to moderate validity. Approximately one quarter of participants had identified multimorbidity (2 or more conditions), one quarter had a single identified morbidity and the remaining participants were not identified as having any of the 30 morbidities. We identified a panel of 30 chronic conditions that can be identified from administrative data using validated algorithms, facilitating the study and surveillance of multimorbidity. We encourage other groups to use this scheme, to facilitate comparisons between settings and jurisdictions.

A method to identify dependencies between organizational factors using statistical independence test

International Nuclear Information System (INIS)

Kim, Y.; Chung, C.H.; Kim, C.; Jae, M.; Jung, J.H.

2004-01-01

A considerable number of studies on organizational factors in nuclear power plants have been made especially in recent years, most of which have assumed organizational factors to be independent. However, since organizational factors characterize the organization in terms of safety and efficiency etc. and there would be some factors that have close relations between them. Therefore, from whatever point of view, if we want to identify the characteristics of an organization, the dependence relationships should be considered to get an accurate result. In this study the organization of a reference nuclear power plant in Korea was analyzed for the trip cases of that plant using 20 organizational factors that Jacobs and Haber had suggested: 1) coordination of work, 2) formalization, 3) organizational knowledge, 4) roles and responsibilities, 5) external communication, 6) inter-department communications, 7) intra-departmental communications, 8) organizational culture, 9) ownership, 10) safety culture, 11) time urgency, 12) centralization, 13) goal prioritization, 14) organizational learning, 15) problem identification, 16) resource allocation, 17) performance evaluation, 18) personnel selection, 19) technical knowledge, and 20) training. By utilizing the results of the analysis, a method to identify the dependence relationships between organizational factors is presented. The statistical independence test for the analysis result of the trip cases is adopted to reveal dependencies. This method is geared to the needs to utilize many kinds of data that has been obtained as the operating years of nuclear power plants increase, and more reliable dependence relations may be obtained by using these abundant data

A simple method for the determination of the specific activity of 125I-tracer used in radioimmunoassay

International Nuclear Information System (INIS)

Bhupal, V.; Mani, R.S.

1986-01-01

The specific activity of the 125 I-thyroxin used in thyroxin radioimmunoassay (RIA) was determined by a simple method involving combination of RIA and displacement analysis. It was compared with the value obtained by the conventional method based on radioiodination data. It is indicated that even for a non-protein hormone like thyroxin the specific activity of 125 I-thyroxin derived from iodination data is not reliable. The specific activites obtained by displacement analysis were consistent with the experimental findings. (author)

A gender-specific analysis of suicide methods in deliberate self-harm

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Kiran K Kumar

2017-01-01

Full Text Available Background: Deliberate self-harm (DSH is a major public health concern. Gender differences in suicide methods are a controversial realm with various regional and cultural variations. This study compared and assessed the methods used in DSH attempters as undertaken by men and women, and investigated the possible role of gender and other clinical variables in the selection of suicide method. Materials and Methods: Two hundred subjects fulfilling the inclusion and exclusion criteria were recruited in the study. The sociodemographic details were recorded in the semi-structured pro forma. Detailed assessment of psychiatric morbidity and DSH was done by clinical interview and validated by Mini International Neuropsychiatric Interview-Plus 5.0 and Beck Suicide Intent Scale. Data were analyzed using SAS version 9.2 and SPSS version 17.0. The sample was disaggregated by gender to compare the known correlates of suicide risk on the two most common methods of suicide – poison consumption and drug overdose using multivariate analyses. Results: The analysis revealed that majority of the attempters were in the age group of 11–40 years (91%. Females (63% outnumbered males (37%; poisoning was the most common type of method (50.5%, followed by drug overdose (35%. There were no statistical differences between the two genders with respect to other sociodemographic variables. Males from urban/semi-urban background (odds ratio [OR] = 4.059 and females living alone (OR = 5.723 had high odds ratio of attempting suicide by poison consumption. Females from urban/semi-urban background (P = 0.0514 and male subjects from nuclear families had an increased odds ratio (OR = 4.482 to attempt suicide by drug overdose. There were no statistical differences when the two genders were compared for other variables such as intentionality, lethality, impulsivity, and number of attempts. Conclusions: It appears that gender differences among DSH attempters appear less pronounced in

Linearized method: A new approach for kinetic analysis of central dopamine D2 receptor specific binding

International Nuclear Information System (INIS)

Watabe, Hiroshi; Hatazawa, Jun; Ishiwata, Kiichi; Ido, Tatsuo; Itoh, Masatoshi; Iwata, Ren; Nakamura, Takashi; Takahashi, Toshihiro; Hatano, Kentaro

1995-01-01

The authors proposed a new method (Linearized method) to analyze neuroleptic ligand-receptor specific binding in a human brain using positron emission tomography (PET). They derived the linear equation to solve four rate constants, k 3 , k 4 , k 5 , k 6 from PET data. This method does not demand radioactivity curve in plasma as an input function to brain, and can do fast calculations in order to determine rate constants. They also tested Nonlinearized method including nonlinear equations which is conventional analysis using plasma radioactivity corrected for ligand metabolites as an input function. The authors applied these methods to evaluate dopamine D 2 receptor specific binding of [ 11 C] YM-09151-2. The value of B max /K d = k 3 k 4 obtained by Linearized method was 5.72 ± 3.1 which was consistent with the value of 5.78 ± 3.4 obtained by Nonlinearized method

Standardized methods for the production of high specific-activity zirconium-89

Science.gov (United States)

Holland, Jason P.; Sheh, Yiauchung; Lewis, Jason S.

2009-01-01

Zirconium-89 is an attractive metallo-radionuclide for use in immunoPET due to the favorable decay characteristics. Standardized methods for the routine production and isolation of high purity and high specific-activity 89Zr using a small cyclotron are reported. Optimized cyclotron conditions reveal high average yields of 1.52 ± 0.11 mCi/μA·h at a proton beam energy of 15 MeV and current of 15 μA using a solid, commercially available 89Y-foil target (0.1 mm, 100% natural abundance). 89Zr was isolated in high radionuclidic and radiochemical purity (>99.99%) as [89Zr]Zr-oxalate by using a solid-phase hydroxamate resin with >99.5% recovery of the radioactivity. The effective specific-activity of 89Zr was found to be in the range 5.28 – 13.43 mCi/μg (470 – 1195 Ci/mmol) of zirconium. New methods for the facile production of [89Zr]Zr-chloride are reported. Radiolabeling studies using the trihydroxamate ligand desferrioxamine B (DFO) gave 100% radiochemical yields in 7 days. Small-animal PET imaging studies have demonstrated that free 89Zr(IV) ions administered as [89Zr]Zr-chloride accumulate in the liver whilst [89Zr]Zr-DFO is excreted rapidly via the kidneys within <20 min. These results have important implication for the analysis of immunoPET imaging of 89Zr-labeled monoclonal antibodies. The detailed methods described can be easily translated to other radiochemistry facilities and will facilitate the use of 89Zr in both basic science and clinical investigations. PMID:19720285

Surveillance of extreme hyperbilirubinaemia in Denmark. A method to identify the newborn infants

DEFF Research Database (Denmark)

Bjerre, J.V.; Petersen, Jes Reinholdt; Ebbesen, F.

2008-01-01

birth and the others after having been discharged. The maximum TSB was 485 (450-734) micromol/L (median [range]) and appeared latest amongst those infants admitted from home, but was not different from the maximum TSB of the nondischarged infants. Forty-three infants had symptoms of early-phase acute....... The observed incidence of extreme hyperbilirubinaemia is higher than previously reported in Denmark. This is mainly due to a very sensitive method of identifying the study group Udgivelsesdato: 2008/8...

A study on method to identify actual causes and conditions of safety rule deviations through analyzing events due to unsafe acts of workers

International Nuclear Information System (INIS)

Hirotsu, Yuko; Takeda, Daisuke

2010-01-01

The purpose of this study is to establish a method to understand actual causes and condition of intentional deviation from safety rules (including norm and written rules that has developed to anticipate, prevent, detect and recover human errors) in an organization by analyzing events due to unsafe acts of workers (human factor events) and to propose effective measures. Firstly, by reviewing literature regarding safety violations, the following two advantages of investigating actual condition of safety rule deviation through human factor event analysis were extracted, such as (a) being able to clarify relationships between deviations, human errors, and events, and (b) being able to identify specific causal factors that influenced the decision to deviate, including acts of people concerned, problems with rules, task demands, environment and management. Next, through the analysis of human factor event data in accordance with existing human error analysis method on the basis of advantages above, the following three requirements for analyzing event data were extracted, such as (a) gathering information such as rules concerning to the work activities related to the human factor events, and whether there are intentional deviations of the rules, (b) gathering information and identify interrelations among causal factors of the intentional deviations, and (c) gathering information on general condition of deviations and the causal factors. (author)

Wheelchair Propulsion Biomechanics in Junior Basketball Players: A Method for the Evaluation of the Efficacy of a Specific Training Program

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Bergamini, Elena; Morelli, Francesca; Marchetti, Flavia; Vannozzi, Giuseppe; Polidori, Lorenzo; Paradisi, Francesco; Traballesi, Marco; Cappozzo, Aurelio

2015-01-01

As participation in wheelchair sports increases, the need of quantitative assessment of biomechanical performance indicators and of sports- and population-specific training protocols has become central. The present study focuses on junior wheelchair basketball and aims at (i) proposing a method to identify biomechanical performance indicators of wheelchair propulsion using an instrumented in-field test and (ii) developing a training program specific for the considered population and assessing its efficacy using the proposed method. Twelve athletes (10 M, 2 F, age = 17.1 ± 2.7 years, years of practice = 4.5 ± 1.8) equipped with wheelchair- and wrist-mounted inertial sensors performed a 20-metre sprint test. Biomechanical parameters related to propulsion timing, progression force, and coordination were estimated from the measured accelerations and used in a regression model where the time to complete the test was set as dependent variable. Force- and coordination-related parameters accounted for 80% of the dependent variable variance. Based on these results, a training program was designed and administered for three months to six of the athletes (the others acting as control group). The biomechanical indicators proved to be effective in providing additional information about the wheelchair propulsion technique with respect to the final test outcome and demonstrated the efficacy of the developed program. PMID:26543852

Wheelchair Propulsion Biomechanics in Junior Basketball Players: A Method for the Evaluation of the Efficacy of a Specific Training Program.

Science.gov (United States)

Bergamini, Elena; Morelli, Francesca; Marchetti, Flavia; Vannozzi, Giuseppe; Polidori, Lorenzo; Paradisi, Francesco; Traballesi, Marco; Cappozzo, Aurelio; Delussu, Anna Sofia

2015-01-01

As participation in wheelchair sports increases, the need of quantitative assessment of biomechanical performance indicators and of sports- and population-specific training protocols has become central. The present study focuses on junior wheelchair basketball and aims at (i) proposing a method to identify biomechanical performance indicators of wheelchair propulsion using an instrumented in-field test and (ii) developing a training program specific for the considered population and assessing its efficacy using the proposed method. Twelve athletes (10 M, 2 F, age = 17.1 ± 2.7 years, years of practice = 4.5 ± 1.8) equipped with wheelchair- and wrist-mounted inertial sensors performed a 20-metre sprint test. Biomechanical parameters related to propulsion timing, progression force, and coordination were estimated from the measured accelerations and used in a regression model where the time to complete the test was set as dependent variable. Force- and coordination-related parameters accounted for 80% of the dependent variable variance. Based on these results, a training program was designed and administered for three months to six of the athletes (the others acting as control group). The biomechanical indicators proved to be effective in providing additional information about the wheelchair propulsion technique with respect to the final test outcome and demonstrated the efficacy of the developed program.

Wheelchair Propulsion Biomechanics in Junior Basketball Players: A Method for the Evaluation of the Efficacy of a Specific Training Program

Directory of Open Access Journals (Sweden)

Elena Bergamini

2015-01-01

Full Text Available As participation in wheelchair sports increases, the need of quantitative assessment of biomechanical performance indicators and of sports- and population-specific training protocols has become central. The present study focuses on junior wheelchair basketball and aims at (i proposing a method to identify biomechanical performance indicators of wheelchair propulsion using an instrumented in-field test and (ii developing a training program specific for the considered population and assessing its efficacy using the proposed method. Twelve athletes (10 M, 2 F, age = 17.1 ± 2.7 years, years of practice = 4.5 ± 1.8 equipped with wheelchair- and wrist-mounted inertial sensors performed a 20-metre sprint test. Biomechanical parameters related to propulsion timing, progression force, and coordination were estimated from the measured accelerations and used in a regression model where the time to complete the test was set as dependent variable. Force- and coordination-related parameters accounted for 80% of the dependent variable variance. Based on these results, a training program was designed and administered for three months to six of the athletes (the others acting as control group. The biomechanical indicators proved to be effective in providing additional information about the wheelchair propulsion technique with respect to the final test outcome and demonstrated the efficacy of the developed program.

Risk factors of non-specific spinal pain in childhood.

Science.gov (United States)

Szita, Julia; Boja, Sara; Szilagyi, Agnes; Somhegyi, Annamaria; Varga, Peter Pal; Lazary, Aron

2018-05-01

Non-specific spinal pain can occur at all ages and current evidence suggests that pediatric non-specific spinal pain is predictive for adult spinal conditions. A 5-year long, prospective cohort study was conducted to identify the lifestyle and environmental factors leading to non-specific spinal pain in childhood. Data were collected from school children aged 7-16 years, who were randomly selected from three different geographic regions in Hungary. The risk factors were measured with a newly developed patient-reported questionnaire (PRQ). The quality of the instrument was assessed by the reliability with the test-retest method. Test (N = 952) and validity (N = 897) datasets were randomly formed. Risk factors were identified with uni- and multivariate logistic regression models and the predictive performance of the final model was evaluated using the receiver operating characteristic (ROC) method. The final model was built up by seven risk factors for spinal pain for days; age > 12 years, learning or watching TV for more than 2 h/day, uncomfortable school-desk, sleeping problems, general discomfort and positive familiar medical history (χ 2  = 101.07; df = 8; p < 0.001). The probabilistic performance was confirmed with ROC analysis on the test and validation cohorts (AUC = 0.76; 0.71). A simplified risk scoring system showed increasing possibility for non-specific spinal pain depending on the number of the identified risk factors (χ 2  = 65.0; df = 4; p < 0.001). Seven significant risk factors of non-specific spinal pain in childhood were identified using the new, easy to use and reliable PRQ which makes it possible to stratify the children according to their individual risk. These slides can be retrieved under Electronic Supplementary Material.

Identifying Gender-Specific Developmental Trajectories of Nonviolent and Violent Delinquency from Adolescence to Young Adulthood

Science.gov (United States)

Zheng, Yao; Cleveland, H. Harrington

2013-01-01

Most research examining gender differences in developmental trajectories of antisocial behavior does not consider subtypes of antisocial behavior and is difficult to generalize due to small nonrepresentative samples. The current study investigated gender difference in developmental trajectories from adolescence to young adulthood while addressing those limitations. Analyses were limited to respondents ages 15 and 16 in wave 1 (16–17 in wave 2, and 21–22 in wave 3) of the National Longitudinal Study of Adolescent Health (n = 6244, 49.5% males). Self-report nonviolent and violent delinquencies were simultaneously entered into latent class analysis. Four latent classes were identified: low, desister, decliner, and chronic (male-only). In addition to finding a male-specific chronic class, gender differences included differences in levels of nonviolent and violent delinquency between synonymous classes of males and females, and differences in prevalence of classes across genders. Neighborhood disadvantage and family support predicted trajectories. PMID:23375843

Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2.

Science.gov (United States)

Bheda, Poonam; Swatkoski, Stephen; Fiedler, Katherine L; Boeke, Jef D; Cotter, Robert J; Wolberger, Cynthia

2012-04-17

Although the biological roles of many members of the sirtuin family of lysine deacetylases have been well characterized, a broader understanding of their role in biology is limited by the challenges in identifying new substrates. We present here an in vitro method that combines biotinylation and mass spectrometry (MS) to identify substrates deacetylated by sirtuins. The method permits labeling of deacetylated residues with amine-reactive biotin on the ε-nitrogen of lysine. The biotin can be utilized to purify the substrate and identify the deacetylated lysine by MS. The biotinyl-lysine method was used to compare deacetylation of chemically acetylated histones by the yeast sirtuins, Sir2 and Hst2. Intriguingly, Sir2 preferentially deacetylates histone H3 lysine 79 as compared to Hst2. Although acetylation of K79 was not previously reported in Saccharomyces cerevisiae, we demonstrate that a minor population of this residue is indeed acetylated in vivo and show that Sir2, and not Hst2, regulates the acetylation state of H3 lysine 79. The in vitro biotinyl-lysine method combined with chemical acetylation made it possible to identify this previously unknown, low-abundance histone acetyl modification in vivo. This method has further potential to identify novel sirtuin deacetylation substrates in whole cell extracts, enabling large-scale screens for new deacetylase substrates.

Country-Specific Dietary Patterns and Associations with Socioeconomic Status in European Children

DEFF Research Database (Denmark)

Fernandez-Alvira, Juan M.; Bammann, Karin; Pala, Valeria

2014-01-01

Background/objectives:Children from lower socioeconomic status (SES) may be at higher risk of unhealthy eating. We described country-specific dietary patterns among children aged 2-9 years from eight European countries participating in the IDEFICS study and assessed the association of dietary...... patterns with an additive SES indicator.Subjects/Methods:Children aged 2-9 years from eight European countries were recruited in 2007-2008. Principal component analysis was applied to identify dietary country-specific patterns. Linear regression analyses were applied to assess their association with SES....... Results:Two to four dietary patterns were identified in the participating regions. The existence of a 'processed' pattern was found in the eight regions. Also, a 'healthy' pattern was identified in seven of the eight regions. In addition, region-specific patterns were identified, reflecting the existing...

New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background

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Marocchi Alessandro

2008-05-01

Full Text Available Abstract Background Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactions between environmental and genetic susceptibility factors take place. The purpose of this study was to approach genetic data with an innovative statistical method such as artificial neural networks to identify a possible genetic background predisposing to the disease. A DNA multiarray panel was applied to genotype more than 60 polymorphisms within 35 genes selected from pathways of lipid and homocysteine metabolism, regulation of blood pressure, coagulation, inflammation, cellular adhesion and matrix integrity, in 54 sporadic ALS patients and 208 controls. Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis Results Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis. An unexpected discovery of a strong genetic background in sporadic ALS using a DNA multiarray panel and analytical processing of the data with advanced artificial neural networks was found. The predictive accuracy obtained with Linear Discriminant Analysis and Standard Artificial Neural Networks ranged from 70% to 79% (average 75.31% and from 69.1 to 86.2% (average 76.6% respectively. The corresponding value obtained with Advanced Intelligent Systems reached an average of 96.0% (range 94.4 to 97.6%. This latter approach allowed the identification of seven genetic variants essential to differentiate cases from controls: apolipoprotein E arg

New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background.

Science.gov (United States)

Penco, Silvana; Buscema, Massimo; Patrosso, Maria Cristina; Marocchi, Alessandro; Grossi, Enzo

2008-05-30

Few genetic factors predisposing to the sporadic form of amyotrophic lateral sclerosis (ALS) have been identified, but the pathology itself seems to be a true multifactorial disease in which complex interactions between environmental and genetic susceptibility factors take place. The purpose of this study was to approach genetic data with an innovative statistical method such as artificial neural networks to identify a possible genetic background predisposing to the disease. A DNA multiarray panel was applied to genotype more than 60 polymorphisms within 35 genes selected from pathways of lipid and homocysteine metabolism, regulation of blood pressure, coagulation, inflammation, cellular adhesion and matrix integrity, in 54 sporadic ALS patients and 208 controls. Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis Advanced intelligent systems based on novel coupling of artificial neural networks and evolutionary algorithms have been applied. The results obtained have been compared with those derived from the use of standard neural networks and classical statistical analysis. An unexpected discovery of a strong genetic background in sporadic ALS using a DNA multiarray panel and analytical processing of the data with advanced artificial neural networks was found. The predictive accuracy obtained with Linear Discriminant Analysis and Standard Artificial Neural Networks ranged from 70% to 79% (average 75.31%) and from 69.1 to 86.2% (average 76.6%) respectively. The corresponding value obtained with Advanced Intelligent Systems reached an average of 96.0% (range 94.4 to 97.6%). This latter approach allowed the identification of seven genetic variants essential to differentiate cases from controls: apolipoprotein E arg158cys; hepatic lipase -480 C/T; endothelial

Airing method-specific advertisements.

Science.gov (United States)

Yaser, Y

1992-06-01

The Turkish Family Health and Planning Foundation initiated the commercial marketing of contraceptives in 1989 as part of a Contraceptive Social Marketing (CSM) program to make available low-cost contraceptives. In 1988 modern methods were used by 31% and traditional methods by 32.3%, while 36.6% used no contraceptives. Only 6.2% were current pill users mainly because of health reasons since high-dose pills dominated the market. A 1990 survey among urban consumers indicated a 94% awareness of contraceptive methods, 76.1% of current use, and preference for the IUD. The side effects of the pill were cited for disliking it, and the condom was rated higher. The CSM project aims at popularizing low-dose pills by explaining the differences and benefits regarding high-dose pills. It collaborated with manufacturers: Schering, Wyeth, Organon, and Eczacibasi Ilac. In 1991 a TV and radio advertisement campaign started that involves the low-dose products Microgynon, Triquilar, Desolet, Lo-Ovral, and Tri-Nordial. The introduction of the Okey condom by Eczacibasi Ilac. In June 1991 also entailed extensive promotion with newspaper ads and TV spots after getting official permission. 1.3 million condoms were sold in the 1st 2 months in 13,000 retail outlets, and 4 million more were projected to be sold. A shift of the attitude of supermarket owners allowing stocking of condoms and the support of the Turkish Ministry of Health, USAID, and the Turkish Radio and Television Bureau has facilitated the CSM project implementation that will profoundly affect family planning in Turkey.

Development of an Analytic Method for Sulfur Compounds in Aged Garlic Extract with the Use of a Postcolumn High Performance Liquid Chromatography Method with Sulfur-Specific Detection.

Science.gov (United States)

Matsutomo, Toshiaki; Kodera, Yukihiro

2016-02-01

Garlic and its processed preparations contain numerous sulfur compounds that are difficult to analyze in a single run using HPLC. The aim of this study was to develop a rapid and convenient sulfur-specific HPLC method to analyze sulfur compounds in aged garlic extract (AGE). We modified a conventional postcolumn HPLC method by employing a hexaiodoplatinate reagent. Identification and structural analysis of sulfur compounds were conducted by LC-mass spectrometry (LC-MS) and nuclear magnetic resonance. The production mechanisms of cis-S-1-propenylcysteine (cis-S1PC) and S-allylmercaptocysteine (SAMC) were examined by model reactions. Our method has the following advantages: less interference from nonsulfur compounds, high sensitivity, good correlation coefficients (r > 0.98), and high resolution that can separate >20 sulfur compounds, including several isomers, in garlic preparations in a single run. This method was adapted for LC-MS analysis. We identified cis-S1PC and γ-glutamyl-S-allyl-mercaptocysteine in AGE. The results of model reactions suggest that cis-S1PC is produced from trans-S1PC through an isomerization reaction and that SAMC is produced by a reaction involving S-allylcysteine/S1PC and diallyldisulfide during the aging period. We developed a rapid postcolumn HPLC method for both qualitative and quantitative analyses of sulfur compounds, and this method helped elucidate a potential mechanism of cis-S1PC and SAMC action in AGE. © 2016 American Society for Nutrition.

Comparative analyses identified species-specific functional roles in oral microbial genomes

Science.gov (United States)

Chen, Tsute; Gajare, Prasad; Olsen, Ingar; Dewhirst, Floyd E.

2017-01-01

ABSTRACT The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to

A method for projecting age-specific mortality rates for certain causes of death

International Nuclear Information System (INIS)

Leggett, R.W.; Crawford, D.J.

1981-01-01

A method is presented for projecting mortality rates for certain causes on the basis of observed rates during past years. This method arose from a study of trends in age-specific mortality rates for respiratory cancers, and for heuristic purposes it is shown how the method can be developed from certain theories of cancer induction. However, the method is applicable in the more common situation in which the underlying physical processes cannot be modeled with any confidence but the mortality rates are approximable over short time intervals by functions of the form a exp(bt), where b may vary in a continuous, predictable fashion as the time interval is varied. It appears from applications to historical data that this projection method is in some cases a substantial improvement over conventional curve-fitting methods and often uncovers trends which are not from observed data

Methodological proposal for environmental impact evaluation since different specific methods

International Nuclear Information System (INIS)

Leon Pelaez, Juan Diego; Lopera Arango Gabriel Jaime

1999-01-01

Some conceptual and practical elements related to environmental impact evaluation are described and related to the preparation of technical reports (environmental impact studies and environmental management plans) to be presented to environmental authorities for obtaining the environmental permits for development projects. In the first part of the document a summary of the main aspects of normative type is made that support the studies of environmental impact in Colombia. We propose a diagram for boarding and elaboration of the evaluation of environmental impact, which begins with the description of the project and of the environmental conditions in the area of the same. Passing then to identify the impacts through a method matricial and continuing with the quantitative evaluation of the same. For which we propose the use of the method developed by Arboleda (1994). Also we propose to qualify the activities of the project and the components of the environment in their relative importance, by means of a method here denominated agglomerate evaluation. Which allows finding those activities more impacting and the mostly impacted components. Lastly it is presented some models for the elaboration and presentation of the environmental management plans. The pursuit programs and those of environmental supervision

Survey of operating experience from LERs to identify aging trends

International Nuclear Information System (INIS)

Murphy, G.A.

1985-01-01

The results of a study using the Oak Ridge National Laboratory's Nuclear Operations Analysis Center computer files of operating experience reports [licensee event reports (LERs), abnormal occurrences, etc.] are summarized in this study, specific time-related degradation mechanisms are identified as possible causes of a reportable occurrence. Data collected on domestic commercial nuclear power plants covering 1969 to 1982 yielded over 5800 events attributable to possible age related failures. Of these events, 2795 were attributable to instrument drift and are addressed separately in the report. The remaining events (3098) were reviewed, and data were collected for each event, which identified the specific system, component, and subpart: the information included the age-related mechanism, severity of the failure, and method of detection of the failure. About two-thirds of the failures were judged to be degraded, with one-third listed as catastrophic

LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins.

Science.gov (United States)

Marchis, Daniela; Altomare, Alessandra; Gili, Marilena; Ostorero, Federica; Khadjavi, Amina; Corona, Cristiano; Ru, Giuseppe; Cappelletti, Benedetta; Gianelli, Silvia; Amadeo, Francesca; Rumio, Cristiano; Carini, Marina; Aldini, Giancarlo; Casalone, Cristina

2017-12-06

An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.

Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

Directory of Open Access Journals (Sweden)

Lee Yun-Shien

2008-03-01

Full Text Available Abstract Background The hierarchical clustering tree (HCT with a dendrogram 1 and the singular value decomposition (SVD with a dimension-reduced representative map 2 are popular methods for two-way sorting the gene-by-array matrix map employed in gene expression profiling. While HCT dendrograms tend to optimize local coherent clustering patterns, SVD leading eigenvectors usually identify better global grouping and transitional structures. Results This study proposes a flipping mechanism for a conventional agglomerative HCT using a rank-two ellipse (R2E, an improved SVD algorithm for sorting purpose seriation by Chen 3 as an external reference. While HCTs always produce permutations with good local behaviour, the rank-two ellipse seriation gives the best global grouping patterns and smooth transitional trends. The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene expression profiles that preserves coherent local clusters and identifies global grouping trends. Conclusion We demonstrate, through four examples, that the proposed method not only possesses better numerical and statistical properties, it also provides more meaningful biomedical insights than other sorting algorithms. We suggest that sorted proximity matrices for genes and arrays, in addition to the gene-by-array expression matrix, can greatly aid in the search for comprehensive understanding of gene expression structures. Software for the proposed methods can be obtained at http://gap.stat.sinica.edu.tw/Software/GAP.

Identifying Patient-Specific Epstein-Barr Nuclear Antigen-1 Genetic Variation and Potential Autoreactive Targets Relevant to Multiple Sclerosis Pathogenesis.

Directory of Open Access Journals (Sweden)

Monika Tschochner

Full Text Available Epstein-Barr virus (EBV infection represents a major environmental risk factor for multiple sclerosis (MS, with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome.Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan and candidates were evaluated for cross recognition with human brain proteins.EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3% nucleotide positions at a 1% cut-off. In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes ('AEG': aa 481-496 and 'MVF': aa 562-577, and two putative epitopes between positions 502-543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogenesis.This study demonstrates the feasibility of obtaining autologous EBNA-1 sequences directly from buffy coat samples, and confirms divergence of these sequences from standard laboratory strains. This approach has identified a number of

HMM-Based Gene Annotation Methods

Energy Technology Data Exchange (ETDEWEB)

Haussler, David; Hughey, Richard; Karplus, Keven

1999-09-20

Development of new statistical methods and computational tools to identify genes in human genomic DNA, and to provide clues to their functions by identifying features such as transcription factor binding sites, tissue, specific expression and splicing patterns, and remove homologies at the protein level with genes of known function.

A Simplified Method for Laboratory Preparation of Organ Specific Indium 113m Compounds

Energy Technology Data Exchange (ETDEWEB)

Adatepe, M H; Potchen, E James [Washington University School of Medicine, St. Louis (United States)

1969-03-15

Generator systems producing short lived nuclides from longer lived parents have distinct clinical advantages. They are more economical, result in a lower radiation dose, and can make short lived scanning readily available even in areas remote from rapid radiopharmaceutical delivery services. The {sup 113}Sn-{sup 113m}In generator has the additional advantage that, as a transition metal, Indium can be readily complexed into organ specific preparations. 113Sn, a reactor produced nuclide with a 118 day half life, is absorbed on a zirconium or silica gel column. the generator is eluded with 5 to 8 ml of 0.05 N HCL solution at pH 1.3-1.4. The daughter nuclide, {sup 113m}In, has a half life of 1.7 hours and emits a 393 Kev monoenergetic gamma ray. Previous methods for labeling organ specific complexes with {sup 113m}In required terminal autoclaving before injection. With the recent introduction of sterile, apyrogenic {sup 113}Sn-{sup 113m}In generators, we have developed a simplified technique for the laboratory preparation of Indium labeled compounds. This method eliminates autoclaving and titration enabling us to pre-prepare organ specific complexes for blood pool, liver, spleen, brain, kidney and lung scanning.

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

Directory of Open Access Journals (Sweden)

Cooper James B

2010-03-01

Full Text Available Abstract Background Clustering the information content of large high-dimensional gene expression datasets has widespread application in "omics" biology. Unfortunately, the underlying structure of these natural datasets is often fuzzy, and the computational identification of data clusters generally requires knowledge about cluster number and geometry. Results We integrated strategies from machine learning, cartography, and graph theory into a new informatics method for automatically clustering self-organizing map ensembles of high-dimensional data. Our new method, called AutoSOME, readily identifies discrete and fuzzy data clusters without prior knowledge of cluster number or structure in diverse datasets including whole genome microarray data. Visualization of AutoSOME output using network diagrams and differential heat maps reveals unexpected variation among well-characterized cancer cell lines. Co-expression analysis of data from human embryonic and induced pluripotent stem cells using AutoSOME identifies >3400 up-regulated genes associated with pluripotency, and indicates that a recently identified protein-protein interaction network characterizing pluripotency was underestimated by a factor of four. Conclusions By effectively extracting important information from high-dimensional microarray data without prior knowledge or the need for data filtration, AutoSOME can yield systems-level insights from whole genome microarray expression studies. Due to its generality, this new method should also have practical utility for a variety of data-intensive applications, including the results of deep sequencing experiments. AutoSOME is available for download at http://jimcooperlab.mcdb.ucsb.edu/autosome.

Use of percentile rank sum method in identifying repetitive high occupational radiation dose jobs in a nuclear power plant

International Nuclear Information System (INIS)

Cho, Y.H.; Ko, H.S.; Kim, S.H.; Kang, C.S.; Moon, J.H.; Kim, K.D.

2004-01-01

The cost-effective reduction of occupational radiation dose (ORD) at a nuclear power plant could not be achieved without going through an extensive analysis of accumulated ORD data of existing plants. Through the data analysis, it is required to identify what are the jobs of repetitive high ORD at the nuclear power plant. In general the point value method commonly used, over-estimates the role of mean and median values to identify the high ORD jobs which can lead to misjudgment. In this study, Percentile Rank Sum Method (PRSM) is proposed to identify repetitive high ORD jobs, which is based on non-parametric statistical theory. As a case study, the method is applied to ORD data of maintenance and repair jobs at Kori units 3 and 4 that are pressurized water reactors with 950 MWe capacity and have been operated since 1986 and 1987, respectively in Korea. The results were verified and validated, and PRSM has been demonstrated to be an efficient method of analyzing the data. (authors)

Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method

Directory of Open Access Journals (Sweden)

Jun Ren

2014-01-01

Full Text Available Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding.” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.

A screen for kinase inhibitors identifies antimicrobial imidazopyridine aminofurazans as specific inhibitors of the Listeria monocytogenes PASTA kinase PrkA.

Science.gov (United States)

Schaenzer, Adam J; Wlodarchak, Nathan; Drewry, David H; Zuercher, William J; Rose, Warren E; Striker, Rob; Sauer, John-Demian

2017-10-13

Bacterial signaling systems such as protein kinases and quorum sensing have become increasingly attractive targets for the development of novel antimicrobial agents in a time of rising antibiotic resistance. The family of bacterial P enicillin-binding-protein A nd S erine/ T hreonine kinase- A ssociated (PASTA) kinases is of particular interest due to the role of these kinases in regulating resistance to β-lactam antibiotics. As such, small-molecule kinase inhibitors that target PASTA kinases may prove beneficial as treatments adjunctive to β-lactam therapy. Despite this interest, only limited progress has been made in identifying functional inhibitors of the PASTA kinases that have both activity against the intact microbe and high kinase specificity. Here, we report the results of a small-molecule screen that identified GSK690693, an imidazopyridine aminofurazan-type kinase inhibitor that increases the sensitivity of the intracellular pathogen Listeria monocytogenes to various β-lactams by inhibiting the PASTA kinase PrkA. GSK690693 potently inhibited PrkA kinase activity biochemically and exhibited significant selectivity for PrkA relative to the Staphylococcus aureus PASTA kinase Stk1. Furthermore, other imidazopyridine aminofurazans could effectively inhibit PrkA and potentiate β-lactam antibiotic activity to varying degrees. The presence of the 2-methyl-3-butyn-2-ol (alkynol) moiety was important for both biochemical and antimicrobial activity. Finally, mutagenesis studies demonstrated residues in the back pocket of the active site are important for GSK690693 selectivity. These data suggest that targeted screens can successfully identify PASTA kinase inhibitors with both biochemical and antimicrobial specificity. Moreover, the imidazopyridine aminofurazans represent a family of PASTA kinase inhibitors that have the potential to be optimized for selective PASTA kinase inhibition.

Disregarding population specificity: its influence on the sex assessment methods from the tibia

Czech Academy of Sciences Publication Activity Database

Kotěrová, A.; Velemínská, J.; Dupej, J.; Brzobohatá, Hana; Pilný, A.; Brůžek, J.

2017-01-01

Roč. 131, č. 1 (2017), s. 251-261 ISSN 0937-9827 Institutional support: RVO:67985912 Keywords : forensic anthropology population data * sex determination * tibia * population specificity * discriminant function analysis * GAME method Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology Impact factor: 2.382, year: 2016

Unsupervised Scalable Statistical Method for Identifying Influential Users in Online Social Networks.

Science.gov (United States)

Azcorra, A; Chiroque, L F; Cuevas, R; Fernández Anta, A; Laniado, H; Lillo, R E; Romo, J; Sguera, C

2018-05-03

Billions of users interact intensively every day via Online Social Networks (OSNs) such as Facebook, Twitter, or Google+. This makes OSNs an invaluable source of information, and channel of actuation, for sectors like advertising, marketing, or politics. To get the most of OSNs, analysts need to identify influential users that can be leveraged for promoting products, distributing messages, or improving the image of companies. In this report we propose a new unsupervised method, Massive Unsupervised Outlier Detection (MUOD), based on outliers detection, for providing support in the identification of influential users. MUOD is scalable, and can hence be used in large OSNs. Moreover, it labels the outliers as of shape, magnitude, or amplitude, depending of their features. This allows classifying the outlier users in multiple different classes, which are likely to include different types of influential users. Applying MUOD to a subset of roughly 400 million Google+ users, it has allowed identifying and discriminating automatically sets of outlier users, which present features associated to different definitions of influential users, like capacity to attract engagement, capacity to attract a large number of followers, or high infection capacity.

A Time-Space Domain Information Fusion Method for Specific Emitter Identification Based on Dempster-Shafer Evidence Theory.

Science.gov (United States)

Jiang, Wen; Cao, Ying; Yang, Lin; He, Zichang

2017-08-28

Specific emitter identification plays an important role in contemporary military affairs. However, most of the existing specific emitter identification methods haven't taken into account the processing of uncertain information. Therefore, this paper proposes a time-space domain information fusion method based on Dempster-Shafer evidence theory, which has the ability to deal with uncertain information in the process of specific emitter identification. In this paper, radars will generate a group of evidence respectively based on the information they obtained, and our main task is to fuse the multiple groups of evidence to get a reasonable result. Within the framework of recursive centralized fusion model, the proposed method incorporates a correlation coefficient, which measures the relevance between evidence and a quantum mechanical approach, which is based on the parameters of radar itself. The simulation results of an illustrative example demonstrate that the proposed method can effectively deal with uncertain information and get a reasonable recognition result.

A Novel Method for Assessing Sex-Specific and Genotype-Specific Response to Injury in Astrocyte Culture

Science.gov (United States)

Liu, Mingyue; Oyarzabal, Esteban; Yang, Rui; Murphy, Stephanie J; Hurn, Patricia D.

2008-01-01

Female astrocytes sustain less cell death from oxygen-glucose deprivation (OGD) than male astrocytes. Arimidex, an aromatase inhibitor, abolishes these sex differences. To verify sex-dependent differences in P450 aromatase function in astrocyte cell death following OGD, we developed a novel method that uses sex-specific and genotype-specific single pup primary astrocyte cultures from wild-type (WT) and aromatase-knockout (ArKO) mice. After determining sex by external and internal examination as well as PCR and genotype by PCR amplification of tail cDNA, we established cultures from 1−3 day-old male and female, WT and ArKO mice pups and grew them to confluence in estrogen-free media. Cell death was measured by lactate dehydrogenase (LDH) assay. Our study shows that, while WT female astrocytes are more resistant to OGD than WT male cells, sex differences disappear in ArKO cells. Cell death is significantly increased in ArKO compared to WT in female astrocytes but not male cells. Therefore, P450 aromatase appears to be essential in endogenous neuroprotection in females, and this finding may have clinical implications. This innovative technique may also be applied to other in vitro studies of sex-related functional differences. PMID:18436308

Specification and Preliminary Validation of IAT (Integrated Analysis Techniques) Methods: Executive Summary.

Science.gov (United States)

1985-03-01

conceptual framwork , and preliminary validation of IAT concepts. Planned work for FY85, including more extensive validation, is also described. 20...Developments: Required Capabilities .... ......... 10 2-1 IAT Conceptual Framework - FY85 (FEO) ..... ........... 11 2-2 Recursive Nature of Decomposition...approach: 1) Identify needs & requirements for IAT. 2) Develop IAT conceptual framework. 3) Validate IAT methods. 4) Develop applications materials. To

Identifiability of PBPK Models with Applications to ...

Science.gov (United States)

Any statistical model should be identifiable in order for estimates and tests using it to be meaningful. We consider statistical analysis of physiologically-based pharmacokinetic (PBPK) models in which parameters cannot be estimated precisely from available data, and discuss different types of identifiability that occur in PBPK models and give reasons why they occur. We particularly focus on how the mathematical structure of a PBPK model and lack of appropriate data can lead to statistical models in which it is impossible to estimate at least some parameters precisely. Methods are reviewed which can determine whether a purely linear PBPK model is globally identifiable. We propose a theorem which determines when identifiability at a set of finite and specific values of the mathematical PBPK model (global discrete identifiability) implies identifiability of the statistical model. However, we are unable to establish conditions that imply global discrete identifiability, and conclude that the only safe approach to analysis of PBPK models involves Bayesian analysis with truncated priors. Finally, computational issues regarding posterior simulations of PBPK models are discussed. The methodology is very general and can be applied to numerous PBPK models which can be expressed as linear time-invariant systems. A real data set of a PBPK model for exposure to dimethyl arsinic acid (DMA(V)) is presented to illustrate the proposed methodology. We consider statistical analy

Merging K-means with hierarchical clustering for identifying general-shaped groups.

Science.gov (United States)

Peterson, Anna D; Ghosh, Arka P; Maitra, Ranjan

2018-01-01

Clustering partitions a dataset such that observations placed together in a group are similar but different from those in other groups. Hierarchical and K -means clustering are two approaches but have different strengths and weaknesses. For instance, hierarchical clustering identifies groups in a tree-like structure but suffers from computational complexity in large datasets while K -means clustering is efficient but designed to identify homogeneous spherically-shaped clusters. We present a hybrid non-parametric clustering approach that amalgamates the two methods to identify general-shaped clusters and that can be applied to larger datasets. Specifically, we first partition the dataset into spherical groups using K -means. We next merge these groups using hierarchical methods with a data-driven distance measure as a stopping criterion. Our proposal has the potential to reveal groups with general shapes and structure in a dataset. We demonstrate good performance on several simulated and real datasets.

Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

Science.gov (United States)

Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

2015-03-03

A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

Energy Technology Data Exchange (ETDEWEB)

Apel, William A.; Thompson, Vicki S; Lacey, Jeffrey A.; Gentillon, Cynthia A.

2016-08-09

A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

Using consensus methods to develop a country-specific Master of Public Health curriculum for the Republic of Maldives

Directory of Open Access Journals (Sweden)

Robotin MC

2016-02-01

Full Text Available Monica C Robotin,1,2 Muthau Shaheem,3 Aishath S Ismail3 1Faculty of Medicine, School of Public Health, University of Sydney, 2Cancer Programs Division, Cancer Council New South Wales, Sydney, Australia; 3Faculty of Health Sciences, Maldives National University, Male, Maldives Background: Over the last four decades, the health status of Maldivian people improved considerably, as reflected in child and maternal mortality indicators and the eradication or control of many communicable diseases. However, changing disease patterns are now undermining these successes, so the local public health practitioners need new skills to perform effectively in this changing environment. To address these needs, in 2013 the Faculty of Health Sciences of the Maldives National University developed the country's first Master of Public Health (MPH program.Methods: The process commenced with a wide scoping exercise and an analysis of the curricular structure of MPH programs of high-ranking universities. Thereafter, a stakeholder consultation using consensus methods reached agreement on overall course structure and the competencies required for local MPH graduates. Subsequently, a working group developed course descriptors and identified local public health research priorities, which could be addressed by MPH students.Results: Ten semistructured interviews explored specific training needs of prospective MPH students, key public health competencies required by local employers and preferred MPH training models. The recommendations informed a nominal group meeting, where participants agreed on MPH core competencies, overall curricular structure and core subjects. The 17 public health electives put forward by the group were prioritized using an online Delphi process. Participants ranked them by their propensity to address local public health needs and the locally available teaching expertise. The first student cohort commenced their MPH studies in January 2014.Conclusion

CXCR6, a newly defined biomarker of tissue-specific stem cell asymmetric self-renewal, identifies more aggressive human melanoma cancer stem cells.

Directory of Open Access Journals (Sweden)

Rouzbeh Taghizadeh

2010-12-01

Full Text Available A fundamental problem in cancer research is identifying the cell type that is capable of sustaining neoplastic growth and its origin from normal tissue cells. Recent investigations of a variety of tumor types have shown that phenotypically identifiable and isolable subfractions of cells possess the tumor-forming ability. In the present paper, using two lineage-related human melanoma cell lines, primary melanoma line IGR39 and its metastatic derivative line IGR37, two main observations are reported. The first one is the first phenotypic evidence to support the origin of melanoma cancer stem cells (CSCs from mutated tissue-specific stem cells; and the second one is the identification of a more aggressive subpopulation of CSCs in melanoma that are CXCR6+.We defined CXCR6 as a new biomarker for tissue-specific stem cell asymmetric self-renewal. Thus, the relationship between melanoma formation and ABCG2 and CXCR6 expression was investigated. Consistent with their non-metastatic character, unsorted IGR39 cells formed significantly smaller tumors than unsorted IGR37 cells. In addition, ABCG2+ cells produced tumors that had a 2-fold greater mass than tumors produced by unsorted cells or ABCG2- cells. CXCR6+ cells produced more aggressive tumors. CXCR6 identifies a more discrete subpopulation of cultured human melanoma cells with a more aggressive MCSC phenotype than cells selected on the basis of the ABCG2+ phenotype alone.The association of a more aggressive tumor phenotype with asymmetric self-renewal phenotype reveals a previously unrecognized aspect of tumor cell physiology. Namely, the retention of some tissue-specific stem cell attributes, like the ability to asymmetrically self-renew, impacts the natural history of human tumor development. Knowledge of this new aspect of tumor development and progression may provide new targets for cancer prevention and treatment.

BAC CGH-array identified specific small-scale genomic imbalances in diploid DMBA-induced rat mammary tumors

International Nuclear Information System (INIS)

Samuelson, Emma; Karlsson, Sara; Partheen, Karolina; Nilsson, Staffan; Szpirer, Claude; Behboudi, Afrouz

2012-01-01

Development of breast cancer is a multistage process influenced by hormonal and environmental factors as well as by genetic background. The search for genes underlying this malignancy has recently been highly productive, but the etiology behind this complex disease is still not understood. In studies using animal cancer models, heterogeneity of the genetic background and environmental factors is reduced and thus analysis and identification of genetic aberrations in tumors may become easier. To identify chromosomal regions potentially involved in the initiation and progression of mammary cancer, in the present work we subjected a subset of experimental mammary tumors to cytogenetic and molecular genetic analysis. Mammary tumors were induced with DMBA (7,12-dimethylbenz[a]anthrazene) in female rats from the susceptible SPRD-Cu3 strain and from crosses and backcrosses between this strain and the resistant WKY strain. We first produced a general overview of chromosomal aberrations in the tumors using conventional kartyotyping (G-banding) and Comparative Genome Hybridization (CGH) analyses. Particular chromosomal changes were then analyzed in more details using an in-house developed BAC (bacterial artificial chromosome) CGH-array platform. Tumors appeared to be diploid by conventional karyotyping, however several sub-microscopic chromosome gains or losses in the tumor material were identified by BAC CGH-array analysis. An oncogenetic tree analysis based on the BAC CGH-array data suggested gain of rat chromosome (RNO) band 12q11, loss of RNO5q32 or RNO6q21 as the earliest events in the development of these mammary tumors. Some of the identified changes appear to be more specific for DMBA-induced mammary tumors and some are similar to those previously reported in ACI rat model for estradiol-induced mammary tumors. The later group of changes is more interesting, since they may represent anomalies that involve genes with a critical role in mammary tumor development. Genetic

Competitive Enzyme-Linked Immunosorbent Assay Based on a Rhoptry-Associated Protein 1 Epitope Specifically Identifies Babesia bovis-Infected Cattle

Science.gov (United States)

Goff, Will L.; McElwain, Terry F.; Suarez, Carlos E.; Johnson, Wendell C.; Brown, Wendy C.; Norimine, Junzo; Knowles, Donald P.

2003-01-01

The competitive enzyme-linked immunosorbent assay (cELISA) format has proven to be an accurate, reliable, easily standardized, and high-throughput method for detecting hemoparasite infections. In the present study, a species-specific, broadly conserved, and tandemly repeated B-cell epitope within the C terminus of the rhoptry-associated protein 1 of the hemoparasite Babesia bovis was cloned and expressed as a histidine-tagged thioredoxin fusion peptide and used as antigen in a cELISA. The assay was optimized with defined negative and positive bovine sera, where positive sera inhibited the binding of the epitope-specific monoclonal antibody BABB75A4. The cELISA accurately differentiated animals with B. bovis-specific antibodies from uninfected animals and from animals with antibodies against other tick-borne hemoparasites (98.7% specificity). In addition, B. bovis-specific sera from Australia, Argentina, Bolivia, Puerto Rico, and Morocco inhibited the binding of BABB75A4, confirming conservation of the epitope. The assay first detected experimentally infected animals between 13 and 17 days postinfection, and with sera from naturally infected carrier cattle, was comparable to indirect immunofluorescence (98.3% concordance). The assay appears to have the characteristics necessary for an epidemiologic and disease surveillance tool. PMID:12522037

Haematoxylin and eosin staining identifies medium to large bacterial aggregates with a reliable specificity: A comparative analysis of follicular bacterial aggregates in axillary biopsies using peptide nucleic acid-fluorescence in situ hybridization and haematoxylin and eosin staining

DEFF Research Database (Denmark)

Ring, Hans Christian; Riis, Peter Theut; Bay, Lene

2017-01-01

between bacterial aggregates identified by haematoxylin and eosin (HE) staining vs bacterial aggregates in corresponding PNA-FISH samples. Axillary biopsies were obtained in 24 healthy controls. HE-stained and PNA-FISH samples were investigated using traditional light microscopy and CLSM, respectively....... The data demonstrate that HE staining identifies large bacterial aggregates (>10 μm) with a sensitivity of 0.43 and specificity of 1. The methods, however, are not equivalent as demonstrated by a McNemar's test (P=.04). Where bacterial aggregates >10 μm in diameter, HE staining may offer a rapid...... and practical low-cost tool to evaluate bacterial aggregates....

SPECIFIC MANAGEMENT AND LEADING METHODS APPLIED TO BUTTERFLY TOURISM FOR 2012

Directory of Open Access Journals (Sweden)

Eugenia ALECU

2013-12-01

Full Text Available In this paper are explained the most important management elements for managers and employees of a tour operator agency. The study showed in a concrete and realistic manner how a manager of a tour operator agency can lead, control, predict and determine the prospects utilizing a specific management method called dashboard. Given the competition in the field of tourism, Butterfly Tourism is trying to manage its business in a professional manner and offer attractive packages and favorable prices to its customers.

Parasite-specific IL-4 responses in Ascaris suum and Trichuris suis-infected pigs evaluated by ELISPOT

DEFF Research Database (Denmark)

Steenhard, N. R.; Kringel, H.; Roepstorff, A.

2007-01-01

method is a valuable tool for future experimental settings as it enables repeated and parasite-specific measurement of IL-4 at protein level when investigating, for example, immunomodulatory properties of helminths. Furthermore, the method could be used to identify specific parasite antigens inducing IL......The objective of the present study was to develop an ELISPOT method to measure parasite-specific IL-4 producing cells during experimental Ascaris suum and Trichuris suis infections in pigs. In many experimental settings it is useful to be able to measure changes in specifically induced cytokines...

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations.

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Benfeard Williams

2015-10-01

Full Text Available The increased risk of developing Alzheimer's disease (AD is associated with the APOE gene, which encodes for three variants of Apolipoprotein E, namely E2, E3, E4, differing only by two amino acids at positions 112 and 158. ApoE4 is known to be the strongest risk factor for AD onset, while ApoE3 and ApoE2 are considered to be the AD-neutral and AD-protective isoforms, respectively. It has been hypothesized that the ApoE isoforms may contribute to the development of AD by modifying the homeostasis of ApoE physiological partners and AD-related proteins in an isoform-specific fashion. Here we find that, despite the high sequence similarity among the three ApoE variants, only ApoE4 exhibits a misfolded intermediate state characterized by isoform-specific domain-domain interactions in molecular dynamics simulations. The existence of an ApoE4-specific intermediate state can contribute to the onset of AD by altering multiple cellular pathways involved in ApoE-dependent lipid transport efficiency or in AD-related protein aggregation and clearance. We present what we believe to be the first structural model of an ApoE4 misfolded intermediate state, which may serve to elucidate the molecular mechanism underlying the role of ApoE4 in AD pathogenesis. The knowledge of the structure for the ApoE4 folding intermediate provides a new platform for the rational design of alternative therapeutic strategies to fight AD.

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

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Sette Alessandro

2005-05-01

Full Text Available Abstract Background Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as a sequence motif, a scoring matrix or an artificial neural network. The purpose of these models is two-fold. First, they can provide a summary of experimental results, allowing for a deeper understanding of the mechanisms involved in sequence recognition. Second, such models can be used to predict the experimental outcome for yet untested sequences. In the past we reported the development of a method to generate such models called the Stabilized Matrix Method (SMM. This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP and proteasomal cleavage of protein sequences. Results Herein we report the implementation of the SMM algorithm as a publicly available software package. Specific features determining the type of problems the method is most appropriate for are discussed. Advantageous features of the package are: (1 the output generated is easy to interpret, (2 input and output are both quantitative, (3 specific computational strategies to handle experimental noise are built in, (4 the algorithm is designed to effectively handle bounded experimental data, (5 experimental data from randomized peptide libraries and conventional peptides can easily be combined, and (6 it is possible to incorporate pair interactions between positions of a sequence. Conclusion Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.

Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

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Jiang Wei

2008-08-01

Full Text Available Abstract Background With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. Results The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8 (p ≈ 0, desmin (DES (p = 2.71 × 10-6 and enolase 1 (ENO1 (p = 4.19 × 10-5], while two novel hub genes [RNA binding motif protein 9 (RBM9 (p = 1.50 × 10-4 and ribosomal protein L30 (RPL30 (p = 1.50 × 10-4] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO based analysis of the colon cancer-specific gene network and

Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements.

Science.gov (United States)

Jiang, Wei; Li, Xia; Rao, Shaoqi; Wang, Lihong; Du, Lei; Li, Chuanxing; Wu, Chao; Wang, Hongzhi; Wang, Yadong; Yang, Baofeng

2008-08-10

With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8) (p approximately 0), desmin (DES) (p = 2.71 x 10(-6)) and enolase 1 (ENO1) (p = 4.19 x 10(-5))], while two novel hub genes [RNA binding motif protein 9 (RBM9) (p = 1.50 x 10(-4)) and ribosomal protein L30 (RPL30) (p = 1.50 x 10(-4))] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO) based analysis of the colon cancer-specific gene network and the sub-network that

A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression

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Mao Yu

2009-07-01

Full Text Available Abstract Background The identification of gene differential co-expression patterns between cancer stages is a newly developing method to reveal the underlying molecular mechanisms of carcinogenesis. Most researches of this subject lack an algorithm useful for performing a statistical significance assessment involving cancer progression. Lacking this specific algorithm is apparently absent in identifying precise gene pairs correlating to cancer progression. Results In this investigation we studied gene pair co-expression change by using a stochastic process model for approximating the underlying dynamic procedure of the co-expression change during cancer progression. Also, we presented a novel analytical method named 'Stochastic process model for Identifying differentially co-expressed Gene pair' (SIG method. This method has been applied to two well known prostate cancer data sets: hormone sensitive versus hormone resistant, and healthy versus cancerous. From these data sets, 428,582 gene pairs and 303,992 gene pairs were identified respectively. Afterwards, we used two different current statistical methods to the same data sets, which were developed to identify gene pair differential co-expression and did not consider cancer progression in algorithm. We then compared these results from three different perspectives: progression analysis, gene pair identification effectiveness analysis, and pathway enrichment analysis. Statistical methods were used to quantify the quality and performance of these different perspectives. They included: Re-identification Scale (RS and Progression Score (PS in progression analysis, True Positive Rate (TPR in gene pair analysis, and Pathway Enrichment Score (PES in pathway analysis. Our results show small values of RS and large values of PS, TPR, and PES; thus, suggesting that gene pairs identified by the SIG method are highly correlated with cancer progression, and highly enriched in disease-specific pathways. From

Women-specific HIV/AIDS services: identifying and defining the components of holistic service delivery for women living with HIV/AIDS.

Science.gov (United States)

Carter, Allison J; Bourgeois, Sonya; O'Brien, Nadia; Abelsohn, Kira; Tharao, Wangari; Greene, Saara; Margolese, Shari; Kaida, Angela; Sanchez, Margarite; Palmer, Alexis K; Cescon, Angela; de Pokomandy, Alexandra; Loutfy, Mona R

2013-01-11

The increasing proportion of women living with HIV has evoked calls for tailored services that respond to women's specific needs. The objective of this investigation was to explore the concept of women-specific HIV/AIDS services to identify and define what key elements underlie this approach to care. A comprehensive review was conducted using online databases (CSA Social Service Abstracts, OvidSP, Proquest, Psycinfo, PubMed, CINAHL), augmented with a search for grey literature. In total, 84 articles were retrieved and 30 were included for a full review. Of these 30, 15 were specific to HIV/AIDS, 11 for mental health and addictions and four stemmed from other disciplines. The review demonstrated the absence of a consensual definition of women-specific HIV/AIDS services in the literature. We distilled this concept into its defining features and 12 additional dimensions (1) creating an atmosphere of safety, respect and acceptance; (2) facilitating communication and interaction among peers; (3) involving women in the planning, delivery and evaluation of services; (4) providing self-determination opportunities; (5) providing tailored programming for women; (6) facilitating meaningful access to care through the provision of social and supportive services; (7) facilitating access to women-specific and culturally sensitive information; (8) considering family as the unit of intervention; (9) providing multidisciplinary integration and coordination of a comprehensive array of services; (10) meeting women "where they are"; (11) providing gender-, culture- and HIV-sensitive training to health and social care providers; and (12) conducting gendered HIV/AIDS research. This review highlights that the concept of women-specific HIV/AIDS services is a complex and multidimensional one that has been shaped by diverse theoretical perspectives. Further research is needed to better understand this emerging concept and ultimately assess the effectiveness of women-specific services on HIV

Nuclear electronic equipment for control and monitoring panel. Specifications and methods for testing radiation detectors

International Nuclear Information System (INIS)

Roguin, Andre.

1976-02-01

This document will be of interest to users and makers of neutron and gamma radiations detectors in the field of nuclear reactor control and protection. Information is given which will enable users to optimize their choice and methods of using equipment, and makers to optimize their methods of fabrication. It should also serve as a model from which official specifications, technical instructions and test methods for these detectors, could be established. A detailed description is given of the appropriate parameters, terminology and notations. General specifications, operating conditions and test methods are indicated. The following detectors are studied: in-core detectors: fission ionization chambers, self powered neutron detectors (S.P.N.D.); out-core detectors: boron ionization chambers (for monitoring), boron trifluoride proportional counter tubes, boron lined proportional counter tubes, helium-3 proportional counter tubes. The devices described in the document are intended for industrial radiation monitoring applications and not for calibration standards (dosimetry) or for health physics measurement purposes. They are characterized by their fidelity, fast response, reliability and long lifetimes [fr

A Study of Scientometric Methods to Identify Emerging Technologies

Energy Technology Data Exchange (ETDEWEB)

Abercrombie, Robert K [ORNL; Udoeyop, Akaninyene W [ORNL

2011-01-01

This work examines a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain we investigated.

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

Science.gov (United States)

Boldt, Karsten; van Reeuwijk, Jeroen; Lu, Qianhao; Koutroumpas, Konstantinos; Nguyen, Thanh-Minh T; Texier, Yves; van Beersum, Sylvia E C; Horn, Nicola; Willer, Jason R; Mans, Dorus A; Dougherty, Gerard; Lamers, Ideke J C; Coene, Karlien L M; Arts, Heleen H; Betts, Matthew J; Beyer, Tina; Bolat, Emine; Gloeckner, Christian Johannes; Haidari, Khatera; Hetterschijt, Lisette; Iaconis, Daniela; Jenkins, Dagan; Klose, Franziska; Knapp, Barbara; Latour, Brooke; Letteboer, Stef J F; Marcelis, Carlo L; Mitic, Dragana; Morleo, Manuela; Oud, Machteld M; Riemersma, Moniek; Rix, Susan; Terhal, Paulien A; Toedt, Grischa; van Dam, Teunis J P; de Vrieze, Erik; Wissinger, Yasmin; Wu, Ka Man; Apic, Gordana; Beales, Philip L; Blacque, Oliver E; Gibson, Toby J; Huynen, Martijn A; Katsanis, Nicholas; Kremer, Hannie; Omran, Heymut; van Wijk, Erwin; Wolfrum, Uwe; Kepes, François; Davis, Erica E; Franco, Brunella; Giles, Rachel H; Ueffing, Marius; Russell, Robert B; Roepman, Ronald

2016-05-13

Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine.

Impedance measurement of irradiated potatoes: a method to identify radiation processing

International Nuclear Information System (INIS)

Mastro, N.L. del; Villavicencio, A.L.C.H.

1992-01-01

The potato is firmly established in many parts of the world as a major staple food. Then, radiation processing of potato is approved in many countries for sprouting inhibition and extension of shelf life in a dose range from about 0.01 to 0.15 kGy of 60 Co. The use of electrical conductance methods for the detection of Salmonella, some virus or the action of herbicides on plant has been reported and differences have been observed between instruments in respect of the magnitude of conductance change or rates of change in conductance response. A reliable technique to identify potatoes or other food products has not been established so far, though several methods have been reported. Electrical impedance might thus serve for characterization of unirradiated and irradiated tissues and cells. In this work, potato tubers from an European variety, named Bintje, grown in Sao Paulo State were employed. Potatoes were punctured with steel electrodes and impedance measured at different frequencies (1 k Hz-100 k Hz) by passing 3-5 m A alternating current through it. The impedance ratio of 50 k Hz/5 k Hz calculated from ten replicate samples decreases with the increment of the dose when doses of O 0.75 and 0.15 kGy from a Gamma Cell 220 were utilized. The impedance measurement were slightly affected by the place of puncture. (author)

The use of arithmetic average method in identifying critical success criteria for Homestay Programmes

Science.gov (United States)

Daud, Shahidah Md; Ramli, Razamin; Kasim, Maznah Mat; Kayat, Kalsom; Razak, Rafidah Abd

2015-12-01

Malaysian Homestay is very unique. It is classified as Community Based Tourism (CBT). Homestay Programme which is a community events where a tourist stays together with a host family for a period of time and enjoying cultural exchange besides having new experiences. Homestay programme has booming the tourism industry since there is over 100 Homestay Programme currently being registered with the Ministry of Culture and Tourism Malaysia. However, only few Homestay Programme enjoying the benefits of success Homestay Programme. Hence, this article seeks to identify the critical success factors for a Homestay Programme in Malaysia. An Arithmetic Average method is utilized to further evaluate the identified success factors in a more meaningful way. The findings will help Homestay Programme function as a community development tool that manages tourism resources. Thus, help the community in improving local economy and creating job opportunities.

Genetic screens to identify new Notch pathway mutants in Drosophila.

Science.gov (United States)

Giagtzoglou, Nikolaos

2014-01-01

Notch signaling controls a wide range of developmental processes, including proliferation, apoptosis, and cell fate specification during both development and adult tissue homeostasis. The functional versatility of the Notch signaling pathway is tightly linked with the complexity of its regulation in different cellular contexts. To unravel the complexity of Notch signaling, it is important to identify the different components of the Notch signaling pathway. A powerful strategy to accomplish this task is based on genetic screens. Given that the developmental context of signaling is important, these screens should be customized to specific cell populations or tissues. Here, I describe how to perform F1 clonal forward genetic screens in Drosophila to identify novel components of the Notch signaling pathway. These screens combine a classical EMS (ethyl methanesulfonate) chemical mutagenesis protocol along with clonal analysis via FRT-mediated mitotic recombination. These F1 clonal screens allow rapid phenotypic screening within clones of mutant cells induced at specific developmental stages and in tissues of interest, bypassing the pleiotropic effects of isolated mutations. More importantly, since EMS mutations have been notoriously difficult to map to specific genes in the past, I briefly discuss mapping methods that allow rapid identification of the causative mutations.

Methods of Developing User-Friendly Keys to Identify Green Sea Turtles (Chelonia mydas L. from Photographs

Directory of Open Access Journals (Sweden)

Jane R. Lloyd

2012-01-01

Full Text Available Identifying individual animals is important in understanding their ecology and behaviour, as well as providing estimates of population sizes for conservation efforts. We produce identification keys from photographs of green sea turtles to identify them while foraging in Akumal Bay, Mexico. We create three keys, which (a minimise the length of the key, (b present the most obvious differential characteristics first, and (c remove the strict dichotomy from key b. Keys were capable of identifying >99% of turtles in >2500 photographs during the six-month study period. The keys differed significantly in success rate for students to identify individual turtles, with key (c being the best with >70% success and correctly being followed further than other keys before making a mistake. User-friendly keys are, therefore, a suitable method for the photographic identification of turtles and could be used for other large marine vertebrates in conservation or behavioural studies.

Iterative Outlier Removal: A Method for Identifying Outliers in Laboratory Recalibration Studies.

Science.gov (United States)

Parrinello, Christina M; Grams, Morgan E; Sang, Yingying; Couper, David; Wruck, Lisa M; Li, Danni; Eckfeldt, John H; Selvin, Elizabeth; Coresh, Josef

2016-07-01

Extreme values that arise for any reason, including those through nonlaboratory measurement procedure-related processes (inadequate mixing, evaporation, mislabeling), lead to outliers and inflate errors in recalibration studies. We present an approach termed iterative outlier removal (IOR) for identifying such outliers. We previously identified substantial laboratory drift in uric acid measurements in the Atherosclerosis Risk in Communities (ARIC) Study over time. Serum uric acid was originally measured in 1990-1992 on a Coulter DACOS instrument using an uricase-based measurement procedure. To recalibrate previous measured concentrations to a newer enzymatic colorimetric measurement procedure, uric acid was remeasured in 200 participants from stored plasma in 2011-2013 on a Beckman Olympus 480 autoanalyzer. To conduct IOR, we excluded data points >3 SDs from the mean difference. We continued this process using the resulting data until no outliers remained. IOR detected more outliers and yielded greater precision in simulation. The original mean difference (SD) in uric acid was 1.25 (0.62) mg/dL. After 4 iterations, 9 outliers were excluded, and the mean difference (SD) was 1.23 (0.45) mg/dL. Conducting only one round of outlier removal (standard approach) would have excluded 4 outliers [mean difference (SD) = 1.22 (0.51) mg/dL]. Applying the recalibration (derived from Deming regression) from each approach to the original measurements, the prevalence of hyperuricemia (>7 mg/dL) was 28.5% before IOR and 8.5% after IOR. IOR is a useful method for removal of extreme outliers irrelevant to recalibrating laboratory measurements, and identifies more extraneous outliers than the standard approach. © 2016 American Association for Clinical Chemistry.

Using the Domain Specific Innovativeness Scale To Identify Innovative Internet Consumers.

Science.gov (United States)

Goldsmith, Ronald E.

2001-01-01

The Domain Specific Innovativeness Scale was included in a survey of student consumers to measure how innovative participants were with regard to buying online. Data analyses confirmed hypotheses that an innovative predisposition toward online buying would be associated positively with more hours of Internet use, greater Internet purchasing,…

Specification Search for Identifying the Correct Mean Trajectory in Polynomial Latent Growth Models

Science.gov (United States)

Kim, Minjung; Kwok, Oi-Man; Yoon, Myeongsun; Willson, Victor; Lai, Mark H. C.

2016-01-01

This study investigated the optimal strategy for model specification search under the latent growth modeling (LGM) framework, specifically on searching for the correct polynomial mean or average growth model when there is no a priori hypothesized model in the absence of theory. In this simulation study, the effectiveness of different starting…

Spectroscopy methods for identifying the country of origin

Science.gov (United States)

Hondrogiannis, Ellen; Ehrlinger, Erin; Miziolek, Andrzej W.

2013-05-01

There is a need in many industries and government functions to identify the source of origin for various materials. For example, the food industry needs to ensure that the claimed source of some of the food products (e.g. coffee, spices) are in fact legitimate due to the variation of quality from different source locations world-wide. Another example is to identify the source country for imported commodities going through Customs so as to assess the correct tariff which varies depending on the source country. Laser Induced Breakdown Spectroscopy (LIBS) holds promise for being a field-portable tool for rapid identification of the country of origin of various materials. Recent research at Towson University has identified the elemental markers needed for discrimination of select spices back to their country of origin using wavelength dispersive X-ray fluorescence (WDXRF). The WDXRF device, however, is not particularly suitable for convenient and fast field analysis. We are extending this study to evaluate the potential of a benchtop commercial LIBS device that could be located at ports of entry and to compare its performance with WDXRF. Our initial study on the spice cumin has demonstrated that discriminant function models can not only be created with 100% separation between the 4 countries of origin (China, India, Syria, and Turkey), but also when tested they show 100% correct matching to the country of origin. This study adds to the growing number of publications that indicate the power of LIBS elemental fingerprinting for provenance determinations.

Methodical Specifics of Thermal Experiments with Thin Carbon Reinforced Plates

Directory of Open Access Journals (Sweden)

O. V. Denisov

2015-01-01

Full Text Available Polymer composite materials (CM are widely used in creation of large space constructions, especially reflectors of space antennas. Composite materials should provide high level of specific stiffness and strength for space structures. Thermal conductivity in reinforcement plane is a significant factor in case of irregular heating space antennas. Nowadays, data on CM reinforcement plane thermal conductivity are limited and existing methods of its defining are imperfect. Basically, traditional methods allow us to define thermal conductivity in perpendicular direction towards the reinforcement plane on the samples of round or rectangular plate. In addition, the thickness of standard samples is larger than space antenna thickness. Consequently, new methods are required. Method of contact heating, which was developed by BMSTU specialists with long hollow carbon beam, could be a perspective way. This article is devoted to the experimental method of contact heating on the thin carbon plates.Thermal tests were supposed to provide a non-stationary temperature field with a gradient being co-directional with the plane reinforcement in the material sample. Experiments were conducted in vacuum chamber to prevent unstructured convection. Experimental thermo-grams processing were calculated by 1-d thermal model for a thin plate. Influence of uncertainty of experimental parameters, such as (radiation emission coefficients of sample surface, glue, temperature sensors and uncertainty of sensors placement on the result of defined thermal conductivity has been estimated. New data on the thermal conductivity in reinforcement plane were obtained within 295 - 375 K temperature range, which can be used to design and develop reflectors of precision space antennas. In the future it is expedient to conduct tests of thin-wall plates from carbon fiber-reinforced plastic in wide temperature range, especially in the low-range temperatures.