Science.gov

Sample records for general screening method

  1. General method for cloning amplified DNA by differential screening with genomic probes.

    PubMed Central

    Brison, O; Ardeshir, F; Stark, G R

    1982-01-01

    Mutant Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate, a potent and specific inhibitor of aspartate transcarbamylase, have amplified the gene coding for the multifunctional protein (CAD) that includes this activity. The average amount of DNA amplified is approximately 500 kilobases per gene copy, about 20 times the length of the CAD gene itself. A differential screening method which uses genomic DNAs as probes was developed to isolate recombinant phage containing fragments of amplified DNA. One probe was prepared by reassociating fragments of total genomic DNA from 165-28, a mutant cell line with 190 times the wild-type complement of CAD genes, until all of the sequences repeated about 200 times were annealed and then isolating the double-stranded DNA with hydroxyapatite.This DNA was highly enriched in sequences from the entire amplified region, whereas the same sequences were very rare in DNA prepared similarly from wild-type cells. After both DNAs were labeled by nick translation, highly repeated sequences were removed by hybridization to immobilized total genomic DNA from wild-type cells. A library of cloned DNA fragments from mutant 165-28 was screened with both probes, and nine independent fragments containing about 165 kilobases of amplified DNA, including the CAD gene, have been isolated so far. These cloned DNAs can be used to study the structure of the amplified region, to evaluate the nature of the amplification event, and to investigate gene expression from the amplified DNA. For example, one amplified fragment included a gene coding for a 3.8-kilobase, cytoplasmic, polyadenylated RNA which was overproduced greatly in cells resistant to N-(phosphonacetyl)-L-aspartate. The method for cloning amplified DNA is general and can be used to evaluate the possible involvement of gene amplification in phenomena such as drug resistance, transformation, or differentiation. DNA fragments corresponding to any region amplified about 10-fold or

  2. Comparison of two methods of screening for genital chlamydial infection in women attending in general practice: cross sectional survey.

    PubMed Central

    Grun, L.; Tassano-Smith, J.; Carder, C.; Johnson, A. M.; Robinson, A.; Murray, E.; Stephenson, J.; Haines, A.; Copas, A.; Ridgway, G.

    1997-01-01

    OBJECTIVES: To estimate the prevalence of Chlamydia trachomatis in asymptomatic women attending general practice: to assess the potential of the ligase chain reaction as a screening tool; and to evaluate selective screening criteria. DESIGN: Cross sectional survey. SETTING: Four general practices in northeast London. SUBJECTS: 890 women aged 18-35 years attending general practice for a cervical smear or a "young well woman" check between October 1994 and January 1996. The women were tested for C trachomatis with confirmed enzyme immunoassay (endocervical specimens) and ligase chain reaction assay on urine specimens. MAIN OUTCOME MEASURES: Prevalence of C trachomatis infection in women aged 18-35 on the basis of each test; sensitivity and specificity of both tests in this population. RESULTS: Prevalence of confirmed infection was 2.6% (95% confidence interval 1.6% to 3.6%) in all women. Prevalence on the basis of enzyme immunoassay was 1.6% (0.8% to 2.7%), with a sensitivity of 60% and a specificity of 100%. Prevalence on the basis of ligase chain reaction was 2.5% (1.5% to 3.9%), with 90% sensitivity and 99.8% specificity. Screening all women aged < or = 25 and all women who had had two or more partners in the past year would have detected 87% (20/23) of infections. CONCLUSION: Ligase chain reaction on urine samples performs at least as well as enzyme immunoassay on cervical specimens in this low prevalence population. It offers potential as a non-invasive screening tool. A simple selective screening strategy might be appropriate and would be able to detect most cases of infection. However, a rigorous economic evaluation of possible screening strategies is needed first. PMID:9253271

  3. Allergic sensitization: screening methods

    PubMed Central

    2014-01-01

    Experimental in silico, in vitro, and rodent models for screening and predicting protein sensitizing potential are discussed, including whether there is evidence of new sensitizations and allergies since the introduction of genetically modified crops in 1996, the importance of linear versus conformational epitopes, and protein families that become allergens. Some common challenges for predicting protein sensitization are addressed: (a) exposure routes; (b) frequency and dose of exposure; (c) dose-response relationships; (d) role of digestion, food processing, and the food matrix; (e) role of infection; (f) role of the gut microbiota; (g) influence of the structure and physicochemical properties of the protein; and (h) the genetic background and physiology of consumers. The consensus view is that sensitization screening models are not yet validated to definitively predict the de novo sensitizing potential of a novel protein. However, they would be extremely useful in the discovery and research phases of understanding the mechanisms of food allergy development, and may prove fruitful to provide information regarding potential allergenicity risk assessment of future products on a case by case basis. These data and findings were presented at a 2012 international symposium in Prague organized by the Protein Allergenicity Technical Committee of the International Life Sciences Institute’s Health and Environmental Sciences Institute. PMID:24739743

  4. Screening methods for thyroid hormone disruptors.

    PubMed Central

    DeVito, M; Biegel, L; Brouwer, A; Brown, S; Brucker-Davis, F; Cheek, A O; Christensen, R; Colborn, T; Cooke, P; Crissman, J; Crofton, K; Doerge, D; Gray, E; Hauser, P; Hurley, P; Kohn, M; Lazar, J; McMaster, S; McClain, M; McConnell, E; Meier, C; Miller, R; Tietge, J; Tyl, R

    1999-01-01

    The U.S. Congress has passed legislation requiring the EPA to implement screening tests for identifying endocrine-disrupting chemicals. A series of workshops was sponsored by the EPA, the Chemical Manufacturers Association, and the World Wildlife Fund; one workshop focused on screens for chemicals that alter thyroid hormone function and homeostasis. Participants at this meeting identified and examined methods to detect alterations in thyroid hormone synthesis, transport, and catabolism. In addition, some methods to detect chemicals that bind to the thyroid hormone receptors acting as either agonists or antagonists were also identified. Screening methods used in mammals as well as other vertebrate classes were examined. There was a general consensus that all known chemicals which interfere with thyroid hormone function and homeostasis act by either inhibiting synthesis, altering serum transport proteins, or by increasing catabolism of thyroid hormones. There are no direct data to support the assertion that certain environmental chemicals bind and activate the thyroid hormone receptors; further research is indicated. In light of this, screening methods should reflect known mechanisms of action. Most methods examined, albeit useful for mechanistic studies, were thought to be too specific and therefore would not be applicable for broad-based screening. Determination of serum thyroid hormone concentrations following chemical exposure in rodents was thought to be a reasonable initial screen. Concurrent histologic evaluation of the thyroid would strengthen this screen. Similar methods in teleosts may be useful as screens, but would require indicators of tissue production of thyroid hormones. The use of tadpole metamorphosis as a screen may also be useful; however, this method requires validation and standardization prior to use as a broad-based screen. PMID:10210697

  5. Preclinical screening methods in cancer

    PubMed Central

    Kumar, Sachin; Bajaj, Sakshi; Bodla, Ramesh Babu

    2016-01-01

    Cancer, a group of diseases of unregulated cell proliferation, is a leading cause of death worldwide. More than 80% of compounds which have shown promising effects in preclinical studies could not get through Phase II of clinical trials. Such high attrition rate is due to improper or selective use of preclinical modalities in anticancer drug screening. The various preclinical screening methods available such as in vitro human cancer cell lines, in vivo tumor xenograft model, or genetically engineered mouse model have their respective pros and cons. Scrupulous use of these preclinical screening methods vis-à-vis efficacy of potential anticancer compound with diverse mechanism of action can help in bringing down the rate of failure of anticancer compound at clinical phase. This article provides an insight into the various preclinical methods used in anticancer studies along with their advantages and disadvantages. PMID:27721530

  6. Display screen and method of manufacture therefor

    NASA Technical Reports Server (NTRS)

    Dubin, Matthew B. (Inventor); Larson, Brent D. (Inventor)

    2002-01-01

    A screen assembly that combines an angle re-distributing prescreen with a conventional diffusion screen. The prescreen minimizes or eliminates the sensitivity of the screen assembly to projector location. The diffusion screen provides other desirable screen characteristics. Compatible screen structures, along with methods for fabricating high resolution prescreens and methods and devices for maintaining the desired relationship between the prescreen and the diffusion screen are contemplated.

  7. Fast 3-D seismic modeling and prestack depth migration using generalized screen methods. Final report for period January 1, 1998 - December 31, 2000

    SciTech Connect

    Toksoz, M. Nafi

    2001-03-31

    Completed a theoretical analysis of phase screen propagators to answer several critical questions: the existence of a singularity in the Green's function for the case of a zero vertical wavenumber, the stability and accuracy of such propagators, and the effects of backscattering for large contrast heterogeneous media. The theory is based on separating the wavefield into forescattering and backscattering parts. The approach is robust and appropriate for earth structures with high velocity contrast. This theory also resolves the apparent singularity problem that has persisted in generalized screen propagator formulations. With this formulation we studied the effects of the commonly used approximations as a function of the degree of velocity contrast in the media.

  8. General relativistic screening in cosmological simulations

    NASA Astrophysics Data System (ADS)

    Hahn, Oliver; Paranjape, Aseem

    2016-10-01

    We revisit the issue of interpreting the results of large volume cosmological simulations in the context of large-scale general relativistic effects. We look for simple modifications to the nonlinear evolution of the gravitational potential ψ that lead on large scales to the correct, fully relativistic description of density perturbations in the Newtonian gauge. We note that the relativistic constraint equation for ψ can be cast as a diffusion equation, with a diffusion length scale determined by the expansion of the Universe. Exploiting the weak time evolution of ψ in all regimes of interest, this equation can be further accurately approximated as a Helmholtz equation, with an effective relativistic "screening" scale ℓ related to the Hubble radius. We demonstrate that it is thus possible to carry out N-body simulations in the Newtonian gauge by replacing Poisson's equation with this Helmholtz equation, involving a trivial change in the Green's function kernel. Our results also motivate a simple, approximate (but very accurate) gauge transformation—δN(k )≈δsim(k )×(k2+ℓ-2)/k2 —to convert the density field δsim of standard collisionless N -body simulations (initialized in the comoving synchronous gauge) into the Newtonian gauge density δN at arbitrary times. A similar conversion can also be written in terms of particle positions. Our results can be interpreted in terms of a Jeans stability criterion induced by the expansion of the Universe. The appearance of the screening scale ℓ in the evolution of ψ , in particular, leads to a natural resolution of the "Jeans swindle" in the presence of superhorizon modes.

  9. Screening fifth forces in generalized Proca theories

    NASA Astrophysics Data System (ADS)

    De Felice, Antonio; Heisenberg, Lavinia; Kase, Ryotaro; Tsujikawa, Shinji; Zhang, Ying-li; Zhao, Gong-Bo

    2016-05-01

    For a massive vector field with derivative self-interactions, the breaking of the gauge invariance allows the propagation of a longitudinal mode in addition to the two transverse modes. We consider generalized Proca theories with second-order equations of motion in a curved space-time and study how the longitudinal scalar mode of the vector field gravitates on a spherically symmetric background. We show explicitly that cubic-order self-interactions lead to the suppression of the longitudinal mode through the Vainshtein mechanism. Provided that the dimensionless coupling of the interaction is not negligible, this screening mechanism is sufficiently efficient to give rise to tiny corrections to gravitational potentials consistent with solar-system tests of gravity. We also study the quartic interactions with the presence of nonminimal derivative coupling with the Ricci scalar and find the existence of solutions where the longitudinal mode completely vanishes. Finally, we discuss the case in which the effect of the quartic interactions dominates over the cubic one and show that local gravity constraints can be satisfied under a mild bound on the parameters of the theory.

  10. Early estimates of 2014/15 seasonal influenza vaccine effectiveness in preventing influenza-like illness in general practice using the screening method in France

    PubMed Central

    Souty, Cécile; Blanchon, Thierry; Bonmarin, Isabelle; Lévy-Bruhl, Daniel; Behillil, Sylvie; Enouf, Vincent; Valette, Martine; Bouscambert, Maude; Turbelin, Clément; Capai, Lisandru; Roussel, Victoire; Hanslik, Thomas; Falchi, Alessandra

    2015-01-01

    The ongoing influenza epidemic is characterized by intense activity with most influenza infections due to the A (H3N2) viruses. Using the screening method, mid-season vaccine effectiveness (VE) in preventing influenza-like illness in primary care was estimated to 32% (95% CI; 23 to 40) among risk groups and was 11% (95% CI; −4 to 23) among the elderly (≥ 65 y). The VE in ≥ 65 y was the lowest estimate regarding the 4 previous seasonal influenza epidemics. PMID:26061896

  11. Cancer distress screening. Needs, models, and methods.

    PubMed

    Carlson, Linda E; Bultz, Barry D

    2003-11-01

    The idea of screening for distress in oncology populations is not new. Many recommendations have been made regarding the need for routine screening, and methods have been suggested for accomplishing this. However, a synthesis of this body of research is not readily available. This paper summarizes the literature documenting the levels of distress commonly found in cancer patients, followed by discussion of recommended standards for routine distress screening, and a summary of various programs that have attempted to establish clinical screening programs. The computerized quality of life (QL) screening literature is also briefly reviewed as potentially instructive. This review is followed by a theoretical and psychometric assessment of the various screening instruments and screening models that have been suggested in the literature or used clinically and a brief assessment of possible economic costs of psychosocial screening, ending with concrete suggestions for methods and models that could be widely adopted by psychosocial oncology programs.

  12. Generalized subspace correction methods

    SciTech Connect

    Kolm, P.; Arbenz, P.; Gander, W.

    1996-12-31

    A fundamental problem in scientific computing is the solution of large sparse systems of linear equations. Often these systems arise from the discretization of differential equations by finite difference, finite volume or finite element methods. Iterative methods exploiting these sparse structures have proven to be very effective on conventional computers for a wide area of applications. Due to the rapid development and increasing demand for the large computing powers of parallel computers, it has become important to design iterative methods specialized for these new architectures.

  13. LANL seismic screening method for existing buildings

    SciTech Connect

    Dickson, S.L.; Feller, K.C.; Fritz de la Orta, G.O.

    1997-01-01

    The purpose of the Los Alamos National Laboratory (LANL) Seismic Screening Method is to provide a comprehensive, rational, and inexpensive method for evaluating the relative seismic integrity of a large building inventory using substantial life-safety as the minimum goal. The substantial life-safety goal is deemed to be satisfied if the extent of structural damage or nonstructural component damage does not pose a significant risk to human life. The screening is limited to Performance Category (PC) -0, -1, and -2 buildings and structures. Because of their higher performance objectives, PC-3 and PC-4 buildings automatically fail the LANL Seismic Screening Method and will be subject to a more detailed seismic analysis. The Laboratory has also designated that PC-0, PC-1, and PC-2 unreinforced masonry bearing wall and masonry infill shear wall buildings fail the LANL Seismic Screening Method because of their historically poor seismic performance or complex behavior. These building types are also recommended for a more detailed seismic analysis. The results of the LANL Seismic Screening Method are expressed in terms of separate scores for potential configuration or physical hazards (Phase One) and calculated capacity/demand ratios (Phase Two). This two-phase method allows the user to quickly identify buildings that have adequate seismic characteristics and structural capacity and screen them out from further evaluation. The resulting scores also provide a ranking of those buildings found to be inadequate. Thus, buildings not passing the screening can be rationally prioritized for further evaluation. For the purpose of complying with Executive Order 12941, the buildings failing the LANL Seismic Screening Method are deemed to have seismic deficiencies, and cost estimates for mitigation must be prepared. Mitigation techniques and cost-estimate guidelines are not included in the LANL Seismic Screening Method.

  14. Screening for Chlamydia is acceptable and feasible during Cervical Screening in General Practice.

    PubMed

    Hassan, S J; Dunphy, E; Navin, E; Marron, L; Fitzsimmons, C; Loy, A; O'Shea, B

    2016-01-01

    The incidence of Chlamydia trachomatis (CT) & Neisseria gonorrhoeae (NG) are rising in Ireland. Both are often undiagnosed and may cause infertility amongst other complications. CT/NG screening is not routinely offered during cervical cancer screening. This study aimed to ascertain the feasibility and acceptability of screening for CT/NG at time of smear and to measure the diagnostic yield. Screening was offered to women aged 25-40 years attending four participating general practices as part of Cervical Check. A retrospective review of the three months preceding the study period, indicated that out of 138 smears, CT/NG testing was performed in 10 (7%) of cases. 236 (93%) patients consented to screening for CT/NG. The detection rate for Chlamydia was 6 (2.4%), with no positive results for NG. Feedback from patients was positive. Interestingly, 42 (18%) of participants who completed the questionnaire believed STI screening was already part of the routine smear. PMID:26904785

  15. Generalized charge-screening in relativistic Thomas-Fermi model

    NASA Astrophysics Data System (ADS)

    Akbari-Moghanjoughi, M.

    2014-10-01

    In this paper, we study the charge shielding within the relativistic Thomas-Fermi model for a wide range of electron number-densities and the atomic-number of screened ions. A generalized energy-density relation is obtained using the force-balance equation and taking into account the Chandrasekhar's relativistic electron degeneracy pressure. By numerically solving a second-order nonlinear differential equation, the Thomas-Fermi screening length is investigated, and the results are compared for three distinct regimes of the solid-density, warm-dense-matter, and white-dwarfs (WDs). It is revealed that our nonlinear screening theory is compatible with the exponentially decaying Thomas-Fermi-type shielding predicted by the linear response theory. Moreover, the variation of relative Thomas-Fermi screening length shows that extremely dense quantum electron fluids are relatively poor charge shielders. Calculation of the total number of screening electrons around a nucleus shows that there is a position of maximum number of screening localized electrons around the screened nucleus, which moves closer to the point-like nucleus by increase in the plasma number density but is unaffected due to increase in the atomic-number value. It is discovered that the total number of screening electrons, ( N s ∝ r T F 3 / r d 3 where rTF and rd are the Thomas-Fermi and interparticle distance, respectively) has a distinct limit for extremely dense plasmas such as WD-cores and neutron star crusts, which is unique for all given values of the atomic-number. This is equal to saying that in an ultrarelativistic degeneracy limit of electron-ion plasma, the screening length couples with the system dimensionality and the plasma becomes spherically self-similar. Current analysis can provide useful information on the effects of relativistic correction to the charge screening for a wide range of plasma density, such as the inertial-confined plasmas and compact stellar objects.

  16. Randomised trial of two approaches to screening for atrial fibrillation in UK general practice.

    PubMed Central

    Morgan, Stephen; Mant, David

    2002-01-01

    BACKGROUND: Atrial fibrillation is a common and treatable cause of stroke that often remains unrecognised. Screening has been suggested but there is very little evidence concerning the uptake of screening in the elderly population at risk, nor of the optimal method of screening in a general practice setting AIM: To compare the uptake and effectiveness of two methods of screening for atrial fibrillation in general practice--systematic nurse-led screening and prompted opportunistic case finding. DESIGN OF STUDY: Randomised controlled trial. SETTING: Patients aged 65 to 100 years (n = 3,001) from four general practices within the MRC general practice framework. METHOD: Each of the four study practices were selected from one quartile, after ranking all framework practices according to the small area standardised mortality ratio of the geographical area served. Patients were randomised either to nurse-led screening or to prompted opportunistic casefinding. The proportion of patients assessed and the proportion found to have atrial fibrillation were compared. The sensitivity and specificity of clinical assessment of pulse are also reported. RESULTS: Substantially more patients had their pulse assessed through systematic screening by invitation (1,099/1,499 [73%]) than through opportunistic case finding (439/1,502 [29%], difference = 44%, 95% confidence interval [CI] = 41% to 47%). Atrial fibrillation was detected in 67 (4.5%) and 19 (1.3%) patients respectively (difference = 3.2%, 95% CI= 2.0 to 4.4). Invitation to nurse-led screening achieved significantly higher assessment rates than case finding in all practices; however, the proportion of patients assessed in the case-finding arm varied markedly between practices (range = 8% to 52%). The number needed to screen to identify one additional patient with atrial fibrillation was 31 (95% CI = 23 to 50). The proportion of screened patients with atrial fibrillation receiving anticoagulation treatment was 25%, although in the

  17. Methods for Similarity-based Virtual Screening.

    PubMed

    Kristensen, Thomas G; Nielsen, Jesper; Pedersen, Christian N S

    2013-01-01

    Developing new medical drugs is expensive. Among the first steps is a screening process, in which molecules in existing chemical libraries are tested for activity against a given target. This requires a lot of resources and manpower. Therefore it has become common to perform a virtual screening, where computers are used for predicting the activity of very large libraries of molecules, to identify the most promising leads for further laboratory experiments. Since computer simulations generally require fewer resources than physical experimentation this can lower the cost of medical and biological research significantly. In this paper we review practically fast algorithms for screening databases of molecules in order to find molecules that are sufficiently similar to a query molecule. PMID:24688702

  18. Generalized high order compact methods.

    SciTech Connect

    Spotz, William F.; Kominiarczuk, Jakub

    2010-09-01

    The fundamental ideas of the high order compact method are combined with the generalized finite difference method. The result is a finite difference method that works on unstructured, nonuniform grids, and is more accurate than one would classically expect from the number of grid points employed.

  19. Diagnostic Methods for Platelet Bacteria Screening: Current Status and Developments

    PubMed Central

    Störmer, Melanie; Vollmer, Tanja

    2014-01-01

    Summary Bacterial contamination of blood components and the prevention of transfusion-associated bacterial infection still remains a major challenge in transfusion medicine. Over the past few decades, a significant reduction in the transmission of viral infections has been achieved due to the introduction of mandatory virus screening. Platelet concentrates (PCs) represent one of the highest risks for bacterial infection. This is due to the required storage conditions for PCs in gas-permeable containers at room temperature with constant agitation, which support bacterial proliferation from low contamination levels to high titers. In contrast to virus screening, since 1997 in Germany bacterial testing of PCs is only performed as a routine quality control or, since 2008, to prolong the shelf life to 5 days. In general, bacterial screening of PCs by cultivation methods is implemented by the various blood services. Although these culturing systems will remain the gold standard, the significance of rapid methods for screening for bacterial contamination has increased over the last few years. These new methods provide powerful tools for increasing the bacterial safety of blood components. This article summarizes the course of policies and provisions introduced to increase bacterial safety of blood components in Germany. Furthermore, we give an overview of the different diagnostic methods for bacterial screening of PCs and their current applicability in routine screening processes. PMID:24659944

  20. Generalized charge-screening in relativistic Thomas–Fermi model

    SciTech Connect

    Akbari-Moghanjoughi, M.

    2014-10-15

    In this paper, we study the charge shielding within the relativistic Thomas-Fermi model for a wide range of electron number-densities and the atomic-number of screened ions. A generalized energy-density relation is obtained using the force-balance equation and taking into account the Chandrasekhar's relativistic electron degeneracy pressure. By numerically solving a second-order nonlinear differential equation, the Thomas-Fermi screening length is investigated, and the results are compared for three distinct regimes of the solid-density, warm-dense-matter, and white-dwarfs (WDs). It is revealed that our nonlinear screening theory is compatible with the exponentially decaying Thomas-Fermi-type shielding predicted by the linear response theory. Moreover, the variation of relative Thomas-Fermi screening length shows that extremely dense quantum electron fluids are relatively poor charge shielders. Calculation of the total number of screening electrons around a nucleus shows that there is a position of maximum number of screening localized electrons around the screened nucleus, which moves closer to the point-like nucleus by increase in the plasma number density but is unaffected due to increase in the atomic-number value. It is discovered that the total number of screening electrons, (N{sub s}∝r{sub TF}{sup 3}/r{sub d}{sup 3} where r{sub TF} and r{sub d} are the Thomas-Fermi and interparticle distance, respectively) has a distinct limit for extremely dense plasmas such as WD-cores and neutron star crusts, which is unique for all given values of the atomic-number. This is equal to saying that in an ultrarelativistic degeneracy limit of electron-ion plasma, the screening length couples with the system dimensionality and the plasma becomes spherically self-similar. Current analysis can provide useful information on the effects of relativistic correction to the charge screening for a wide range of plasma density, such as the inertial-confined plasmas and compact stellar

  1. Generalized multidimensional dynamic allocation method.

    PubMed

    Lebowitsch, Jonathan; Ge, Yan; Young, Benjamin; Hu, Feifang

    2012-12-10

    Dynamic allocation has received considerable attention since it was first proposed in the 1970s as an alternative means of allocating treatments in clinical trials which helps to secure the balance of prognostic factors across treatment groups. The purpose of this paper is to present a generalized multidimensional dynamic allocation method that simultaneously balances treatment assignments at three key levels: within the overall study, within each level of each prognostic factor, and within each stratum, that is, combination of levels of different factors Further it offers capabilities for unbalanced and adaptive designs for trials. The treatment balancing performance of the proposed method is investigated through simulations which compare multidimensional dynamic allocation with traditional stratified block randomization and the Pocock-Simon method. On the basis of these results, we conclude that this generalized multidimensional dynamic allocation method is an improvement over conventional dynamic allocation methods and is flexible enough to be applied for most trial settings including Phases I, II and III trials.

  2. A Screening Method for Assessing Cumulative Impacts

    PubMed Central

    Alexeeff, George V.; Faust, John B.; August, Laura Meehan; Milanes, Carmen; Randles, Karen; Zeise, Lauren; Denton, Joan

    2012-01-01

    The California Environmental Protection Agency (Cal/EPA) Environmental Justice Action Plan calls for guidelines for evaluating “cumulative impacts.” As a first step toward such guidelines, a screening methodology for assessing cumulative impacts in communities was developed. The method, presented here, is based on the working definition of cumulative impacts adopted by Cal/EPA [1]: “Cumulative impacts means exposures, public health or environmental effects from the combined emissions and discharges in a geographic area, including environmental pollution from all sources, whether single or multi-media, routinely, accidentally, or otherwise released. Impacts will take into account sensitive populations and socio-economic factors, where applicable and to the extent data are available.” The screening methodology is built on this definition as well as current scientific understanding of environmental pollution and its adverse impacts on health, including the influence of both intrinsic, biological factors and non-intrinsic socioeconomic factors in mediating the effects of pollutant exposures. It addresses disparities in the distribution of pollution and health outcomes. The methodology provides a science-based tool to screen places for relative cumulative impacts, incorporating both the pollution burden on a community- including exposures to pollutants, their public health and environmental effects- and community characteristics, specifically sensitivity and socioeconomic factors. The screening methodology provides relative rankings to distinguish more highly impacted communities from less impacted ones. It may also help identify which factors are the greatest contributors to a community’s cumulative impact. It is not designed to provide quantitative estimates of community-level health impacts. A pilot screening analysis is presented here to illustrate the application of this methodology. Once guidelines are adopted, the methodology can serve as a screening

  3. General health screening as part of a periodontal examination.

    PubMed

    Raphael, Sarah L

    2010-12-21

    Cardiovascular disease (CVD) and type 2 diabetes are common systemic illnesses with reliable, predictive risk factors. CVD is the number one killer worldwide accounting for nearly 30% of deaths and type 2 diabetes has reached epidemic proportions in many western industrialized countries. Both of these illnesses can go undiagnosed in an alarming number of people for significant periods of time. The relationship between oral health and systemic health has become the focus of much discussion and research in recent times. It is now widely accepted that periodontal disease is associated with systemic illnesses such as CVD and type 2 diabetes. Cigarette smoking and obesity are major risk factors accounting for a large portion of the global disease burden. Many periodontal patients may be at risk of systemic conditions but be asymptomatic and undiagnosed. With an aging population who are mostly retaining their natural dentition, the need for periodontal management will continue to rise in the future. Dental professionals are well placed to perform general health screening for their patients. Therefore, risk assessment during the periodontal examination may facilitate the early identification of the large proportion of people who are unaware of their risk status. As identification and intervention of patients with increased risk factors is key to lowering the systemic disease burden, general health screening during periodontal examinations may present an important opportunity for many patients.

  4. 42 CFR 455.452 - Other State screening methods.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Other State screening methods. 455.452 Section 455....452 Other State screening methods. Nothing in this subpart must restrict the State Medicaid agency from establishing provider screening methods in addition to or more stringent than those required...

  5. Apparatus and method for radioactive waste screening

    DOEpatents

    Akers, Douglas W.; Roybal, Lyle G.; Salomon, Hopi; Williams, Charles Leroy

    2012-09-04

    An apparatus and method relating to screening radioactive waste are disclosed for ensuring that at least one calculated parameter for the measurement data of a sample falls within a range between an upper limit and a lower limit prior to the sample being packaged for disposal. The apparatus includes a radiation detector configured for detecting radioactivity and radionuclide content of the of the sample of radioactive waste and generating measurement data in response thereto, and a collimator including at least one aperture to direct a field of view of the radiation detector. The method includes measuring a radioactive content of a sample, and calculating one or more parameters from the radioactive content of the sample.

  6. Screening system and method of using same

    DOEpatents

    Jones, David A; Gresham, Christopher A; Basiliere, Marc L; Spates, James J; Rodacy, Philip J

    2014-04-15

    An integrated apparatus and method for screening an object for a target material is provided. The integrated apparatus comprises a housing and an integrated screener. The housing is positionable adjacent the object, and has a channel therethrough. The integrated screener is positionable in the housing, and comprises a fan, at least one filter, a heater and an analyzer. The fan is for drawing air carrying particles and vapor through the channel of the housing. The filter(s) is/are positionable in the channel of the housing for passage of the air therethrough. The filter(s) comprise(s) at least one metal foam having a plurality of pores therein for collecting and adsorbing a sample from the particles and vapor passing therethrough. The heater is for applying heat to the at least one metal foam whereby the collected sample is desorbed from the metal foam. The analyzer detects the target material from the desorbed sample.

  7. Display screen and method of manufacture therefor

    NASA Technical Reports Server (NTRS)

    Dubin, Matthew B. (Inventor); Larson, Brent D. (Inventor)

    2001-01-01

    A screen assembly that combines an angle re-distributing prescreen with a conventional diffusion screen is disclosed. The prescreen minimizes or eliminates the sensitivity of the screen assembly to projector location. The diffusion screen provides other desirable screen characteristics. The prescreen is preferably formed by a collection of light transmitting and refracting elements, preferably spheres 80, partially embedded in a light blocking layer. Toward the back of the spheres 80 are effective apertures 82 where the light blocking layer 81 is absent or at least thinner than in other regions toward the side of the spheres. The projected image enters spheres 80 through the effective apertures 82, and exits the spheres 80 centered orientationally about the normal to the lens axis. The re-oriented light rays then enter the diffusion screen for viewing.

  8. Generalizing Screen Inferiority--Does the Medium, Screen versus Paper, Affect Performance Even with Brief Tasks?

    ERIC Educational Resources Information Center

    Sidi, Yael; Ophir, Yael; Ackerman, Rakefet

    2016-01-01

    Screen inferiority in performance and metacognitive processes has been repeatedly found with text learning. Common explanations for screen inferiority relate to technological and physiological disadvantages associated with extensive reading on screen. However, recent studies point to lesser recruitment of mental effort on screen than on paper.…

  9. CHEMICAL SENSOR AND FIELD SCREENING TECHNOLOGY DEVELOPMENT: FUELS IN SOILS FIELD SCREENING METHOD VALIDATION

    SciTech Connect

    Susan S. Sorini; John F. Schabron

    1997-04-01

    A new screening method for fuel contamination in soils was recently developed as American Society for Testing and Materials (ASTM) Method D-583 1-95, Standard Test Method for Screening Fuels in Soils. This method uses low-toxicity chemicals and can be used to screen organic-rich soils. In addition, it is fast, easy, and inexpensive to perform. The screening method calls for extracting a sample of soil with isopropyl alcohol following treatment with calcium oxide. The resulting extract is filtered, and the ultraviolet absorbance of the extract is measured at 254 nm. Depending on the available information concerning the contaminant fuel type and availability of the contaminant fuel for calibration, the method can be used to determine the approximate concentration of fuel contamination, an estimated value of fuel contamination, or an indication of the presence or absence of fuel contamination. Fuels containing aromatic compounds, such as diesel fuel and gasoline, as well as other aromatic-containing hydrocarbon materials, such as motor oil, crude oil, and coal oil, can be determined. The screening method for fuels in soils was evaluated by conducting a collaborative study on the method and by using the method to screen soil samples at an actual field site. In the collaborative study, a sand and an organic soil spiked with various concentrations of diesel fuel were tested. Data from the collaborative study were used to determine the reproducibility (between participants) and repeatability (within participant) precision of the method for screening the test materials. The collaborative study data also provide information on the performance of portable field equipment versus laboratory equipment for performing the screening method and a comparison of diesel concentration values determined using the screening method versus a laboratory method. Data generated using the method to screen soil samples in the field provide information on the performance of the method in

  10. High-throughput screening method for lipases/esterases.

    PubMed

    Mateos-Díaz, Eduardo; Rodríguez, Jorge Alberto; de Los Ángeles Camacho-Ruiz, María; Mateos-Díaz, Juan Carlos

    2012-01-01

    High-throughput screening (HTS) methods for lipases and esterases are generally performed by using synthetic chromogenic substrates (e.g., p-nitrophenyl, resorufin, and umbelliferyl esters) which may be misleading since they are not their natural substrates (e.g., partially or insoluble triglycerides). In previous works, we have shown that soluble nonchromogenic substrates and p-nitrophenol (as a pH indicator) can be used to quantify the hydrolysis and estimate the substrate selectivity of lipases and esterases from several sources. However, in order to implement a spectrophotometric HTS method using partially or insoluble triglycerides, it is necessary to find particular conditions which allow a quantitative detection of the enzymatic activity. In this work, we used Triton X-100, CHAPS, and N-lauroyl sarcosine as emulsifiers, β-cyclodextrin as a fatty acid captor, and two substrate concentrations, 1 mM of tributyrin (TC4) and 5 mM of trioctanoin (TC8), to improve the test conditions. To demonstrate the utility of this method, we screened 12 enzymes (commercial preparations and culture broth extracts) for the hydrolysis of TC4 and TC8, which are both classical substrates for lipases and esterases (for esterases, only TC4 may be hydrolyzed). Subsequent pH-stat experiments were performed to confirm the preference of substrate hydrolysis with the hydrolases tested. We have shown that this method is very useful for screening a high number of lipases (hydrolysis of TC4 and TC8) or esterases (only hydrolysis of TC4) from wild isolates or variants generated by directed evolution using nonchromogenic triglycerides directly in the test.

  11. High-throughput screening method for lipases/esterases.

    PubMed

    Mateos-Díaz, Eduardo; Rodríguez, Jorge Alberto; de Los Ángeles Camacho-Ruiz, María; Mateos-Díaz, Juan Carlos

    2012-01-01

    High-throughput screening (HTS) methods for lipases and esterases are generally performed by using synthetic chromogenic substrates (e.g., p-nitrophenyl, resorufin, and umbelliferyl esters) which may be misleading since they are not their natural substrates (e.g., partially or insoluble triglycerides). In previous works, we have shown that soluble nonchromogenic substrates and p-nitrophenol (as a pH indicator) can be used to quantify the hydrolysis and estimate the substrate selectivity of lipases and esterases from several sources. However, in order to implement a spectrophotometric HTS method using partially or insoluble triglycerides, it is necessary to find particular conditions which allow a quantitative detection of the enzymatic activity. In this work, we used Triton X-100, CHAPS, and N-lauroyl sarcosine as emulsifiers, β-cyclodextrin as a fatty acid captor, and two substrate concentrations, 1 mM of tributyrin (TC4) and 5 mM of trioctanoin (TC8), to improve the test conditions. To demonstrate the utility of this method, we screened 12 enzymes (commercial preparations and culture broth extracts) for the hydrolysis of TC4 and TC8, which are both classical substrates for lipases and esterases (for esterases, only TC4 may be hydrolyzed). Subsequent pH-stat experiments were performed to confirm the preference of substrate hydrolysis with the hydrolases tested. We have shown that this method is very useful for screening a high number of lipases (hydrolysis of TC4 and TC8) or esterases (only hydrolysis of TC4) from wild isolates or variants generated by directed evolution using nonchromogenic triglycerides directly in the test. PMID:22426713

  12. Wafer screening device and methods for wafer screening

    DOEpatents

    Sopori, Bhushan; Rupnowski, Przemyslaw

    2014-07-15

    Wafer breakage is a serious problem in the photovoltaic industry because a large fraction of wafers (between 5 and 10%) break during solar cell/module fabrication. The major cause of this excessive wafer breakage is that these wafers have residual microcracks--microcracks that were not completely etched. Additional propensity for breakage is caused by texture etching and incomplete edge grinding. To eliminate the cost of processing the wafers that break, it is best to remove them prior to cell fabrication. Some attempts have been made to develop optical techniques to detect microcracks. Unfortunately, it is very difficult to detect microcracks that are embedded within the roughness/texture of the wafers. Furthermore, even if such detection is successful, it is not straightforward to relate them to wafer breakage. We believe that the best way to isolate the wafers with fatal microcracks is to apply a stress to wafers--a stress that mimics the highest stress during cell/module processing. If a wafer survives this stress, it has a high probability of surviving without breakage during cell/module fabrication. Based on this, we have developed a high throughput, noncontact method for applying a predetermined stress to a wafer. The wafers are carried on a belt through a chamber that illuminates the wafer with an intense light of a predetermined intensity distribution that can be varied by changing the power to the light source. As the wafers move under the light source, each wafer undergoes a dynamic temperature profile that produces a preset elastic stress. If this stress exceeds the wafer strength, the wafer will break. The broken wafers are separated early, eliminating cost of processing into cell/module. We will describe details of the system and show comparison of breakage statistics with the breakage on a production line.

  13. TranScreen-N: Method for rapid screening of trans-ungual drug delivery enhancers.

    PubMed

    Murthy, S Narasimha; Vaka, Siva Ram Kiran; Sammeta, Srinivasa Murthy; Nair, Anroop B

    2009-11-01

    Topical monotherapy of nail diseases such as onychomycosis and nail psoriasis has been less successful due to poor permeability of the human nail plate to topically administered drugs. Chemical enhancers are utilized to improve the drug delivery across the nail plate. Choosing the most effective chemical enhancers for the given drug and formulation is highly critical in determining the efficacy of topical therapy of nail diseases. Screening the large pool of enhancers using currently followed diffusion cell experiments would be tedious and expensive. The main objective of this study is to develop TranScreen-N, a high throughput method of screening trans-ungual drug permeation enhancers. It is a rapid microwell plate based method which involves two different treatment procedures; the simultaneous exposure treatment and the sequential exposure treatment. In the present study, several chemicals were evaluated by TranScreen-N and by diffusion studies in the Franz diffusion cell (FDC). Good agreement of in vitro drug delivery data with TranScreen-N data provided validity to the screening technique. In TranScreen-N technique, the enhancers can be grouped according to whether they need to be applied before or simultaneously with drugs (or by either procedures) to enhance the drug delivery across the nail plate. TranScreen-N technique can significantly reduce the cost and duration required to screen trans-ungual drug delivery enhancers. PMID:19363796

  14. TranScreen-N: Method for rapid screening of trans-ungual drug delivery enhancers.

    PubMed

    Murthy, S Narasimha; Vaka, Siva Ram Kiran; Sammeta, Srinivasa Murthy; Nair, Anroop B

    2009-11-01

    Topical monotherapy of nail diseases such as onychomycosis and nail psoriasis has been less successful due to poor permeability of the human nail plate to topically administered drugs. Chemical enhancers are utilized to improve the drug delivery across the nail plate. Choosing the most effective chemical enhancers for the given drug and formulation is highly critical in determining the efficacy of topical therapy of nail diseases. Screening the large pool of enhancers using currently followed diffusion cell experiments would be tedious and expensive. The main objective of this study is to develop TranScreen-N, a high throughput method of screening trans-ungual drug permeation enhancers. It is a rapid microwell plate based method which involves two different treatment procedures; the simultaneous exposure treatment and the sequential exposure treatment. In the present study, several chemicals were evaluated by TranScreen-N and by diffusion studies in the Franz diffusion cell (FDC). Good agreement of in vitro drug delivery data with TranScreen-N data provided validity to the screening technique. In TranScreen-N technique, the enhancers can be grouped according to whether they need to be applied before or simultaneously with drugs (or by either procedures) to enhance the drug delivery across the nail plate. TranScreen-N technique can significantly reduce the cost and duration required to screen trans-ungual drug delivery enhancers.

  15. Improvement of screening methods for silicon planar semiconductor devices

    NASA Technical Reports Server (NTRS)

    Berger, W. M.

    1972-01-01

    The results of the program for the development of a more sensitive method for selecting silicon planar semiconductor devices for long life applications are reported. The manufacturing technologies (MOS and Bipolar) are discussed along with the screening procedures developed as a result of the tests and evaluations, and the effectiveness of the MOS and Bilayer screening procedures are evaluated.

  16. High Throughput Screening and Selection Methods for Directed Enzyme Evolution

    PubMed Central

    2015-01-01

    Successful evolutionary enzyme engineering requires a high throughput screening or selection method, which considerably increases the chance of obtaining desired properties and reduces the time and cost. In this review, a series of high throughput screening and selection methods are illustrated with significant and recent examples. These high throughput strategies are also discussed with an emphasis on compatibility with phenotypic analysis during directed enzyme evolution. Lastly, certain limitations of current methods, as well as future developments, are briefly summarized. PMID:26074668

  17. FIELD ANALYTICAL SCREENING PROGRAM: PCB METHOD - INNOVATIVE TECHNOLOGY REPORT

    EPA Science Inventory

    This innovative technology evaluation report (ITER) presents information on the demonstration of the U.S. Environmental Protection Agency (EPA) Region 7 Superfund Field Analytical Screening Program (FASP) method for determining polychlorinated biphenyl (PCB) contamination in soil...

  18. Outcomes of hepatitis C screening programs targeted at risk groups hidden in the general population: a systematic review

    PubMed Central

    2014-01-01

    Background Effective screening programs are urgently needed to provide undiagnosed hepatitis C virus (HCV)-infected individuals with therapy. This systematic review of characteristics and outcomes of screening programs for HCV focuses on strategies to identify HCV risk groups hidden in the general population. Methods We conducted a comprehensive search of MEDLINE and EMBASE databases for articles published between 1991–2010, including studies that screened the general population using either a newly developed (nonintegrated) screening program or one integrated in existing health care facilities. Look-back studies, prevalence studies, and programs targeting high-risk groups in care (e.g., current drug users) were excluded. Results After reviewing 7052 studies, we identified 67 screening programs: 24 nonintegrated; 41 programs integrated in a variety of health care facilities (e.g., general practitioner); and 2 programs with both integrated and nonintegrated strategies. Together, these programs identified approximately 25,700 HCV-infected individuals. In general, higher HCV prevalence was found in programs in countries with intermediate to high HCV prevalence, in psychiatric clinics, and in programs that used a prescreening selection based on HCV risk factors. Only 6 programs used a comparison group for evaluation purposes, and 1 program used theory about effective promotion for screening. Comparison of the programs and their effectiveness was hampered by lack of reported data on program characteristics, clinical follow-up, and type of diagnostic test. Conclusions A prescreening selection based on risk factors can increase the efficiency of screening in low-prevalence populations, and we need programs with comparison groups to evaluate effectiveness. Also, program characteristics such as type of diagnostic test, screening uptake, and clinical outcomes should be reported systematically. PMID:24450797

  19. A New Screening Programme for Autism in a General Population of Swedish Toddlers

    ERIC Educational Resources Information Center

    Nygren, Gudrun; Sandberg, Eva; Gillstedt, Fredrik; Ekeroth, Gunnar; Arvidsson, Thomas; Gillberg, Christopher

    2012-01-01

    The evidence from early intervention studies of autism has emphasised the need for early diagnosis. Insight into the early presentation of autism is crucial for early recognition, and routine screening can optimise the possibility for early diagnosis. General population screening was conducted for 2.5-year-old children at child health centres in…

  20. Increasing opportunistic oral cancer screening examinations: findings from focus groups with general dentists in Puerto Rico

    PubMed Central

    Psoter, Walter J.; Morse, Douglas E.; Sánchez-Ayendez, Melba; Vega, Carmen M Vélez; Aguilar, Maria L.; Buxó-Martinez, Carmen J; Psoter, Jodi A.; Kerr, Alexander R.; Lane, Christina M.; Scaringi, Vincent J; Elias, Augusto

    2014-01-01

    Purpose To identify educational and training modalities that dentists in Puerto Rico (PR) believe will increase the quality and quantity of opportunistic oral cancer screening examinations (OCS) in dental offices on the island. Methods The study was conducted in three phases: a systematic search of relevant literature, an expert review and consensus panel, and focus groups (FG) involving PR general dentists. Results To increase OCS by dentists in PR, the FG participants proposed small group, hands-on OCS training, an integrated oral cancer course, and readily-available videos, photographs, and computer simulations to further demonstrate OCS performance and facilitate differential diagnosis. OCS training requirements for licensure and relicensure, improving OCS dentist-patient communication skills, and establishment of an oral lesion referral center were also viewed favorably. Conclusions General dentists in our FGs believed the quality and quantity of OCS in Puerto Rico can be increased through the application of specific continuing education and training modalities. PMID:24894606

  1. A comparison between Pap and HPV screening tests and screening methods

    PubMed Central

    Altobelli, Emma; Scarselli, Giorgio; Lattanzi, Amedeo; Fortunato, Carmine; Profeta, Valerio F.

    2016-01-01

    The present study assesses the results of cervical cancer (CC) screening over two 3-year periods (2008–2010 and 2011–2013) by comparing two screening tests [Papanicolaou (Pap) and human papillomavirus (HPV) tests] and two screening methods (organized and spontaneous). The study population includes women aged 25–64 years who underwent CC screening between 2008 and 2010 and/or 2011 and 2013, divided into those who responded to an invitation letter (organized screening) and those who spontaneously underwent testing at a public or private facility (non-programmed screening). Between 2008 and 2010, the response rates increased from 27.7% in 2008 to 44.5% in 2009 and 67.6% in 2010 (P<0.001). Women aged 25–34 years had the lowest response rate, whereas respondents were more frequent among women aged 35–44 and 45–54 years. Significant differences (P<0.001) were identified between organized and spontaneous screening test results with regard to diagnostic categories high-grade squamous intraepithelial lesion (50.5 vs. 49.5%), low-grade squamous intraepithelial lesion (42.8 vs. 57.2%) and undetermined lesion atypical glandular cells (AGC; 57.5 vs. 42.5%) or atypical squamous cells of undetermined significance (ASC-US; 54.2 vs. 45.8%). Compared with spontaneous screening, the organized programme resulted in a larger number of women screened for CC; it reduced the frequency of undetermined diagnoses (AGC, ASC-US), and identified a larger number of high-grade lesions. PMID:27446578

  2. Item Selection Methods for the Adolescent Domain Screening Inventory

    ERIC Educational Resources Information Center

    Corrigan, Matthew J.

    2009-01-01

    Objective: The purpose of this article is to describe the method of item selection tested in the development of the Adolescent Domain Screening Inventory. Method: The convenience sampling frame used for these analyses consisted of 26,781 Communities That Care Youth Surveys. The three item selection methods were used to assess known instrument,…

  3. Method For Screening Microcrystallizations For Crystal Formation

    DOEpatents

    Santarsiero, Bernard D. , Stevens, Raymond C. , Schultz, Peter G. , Jaklevic, Joseph M. , Yegian, Derek T. , Cornell, Earl W. , Nordmeyer, Robert A.

    2003-10-07

    A method is provided for performing array microcrystallizations to determine suitable crystallization conditions for a molecule, the method comprising: forming an array of microcrystallizations, each microcrystallization comprising a drop comprising a mother liquor solution whose composition varies within the array and a molecule to be crystallized, the drop having a volume of less than 1 microliter; storing the array of microcrystallizations under conditions suitable for molecule crystals to form in the drops in the array; and detecting molecule crystal formation in the drops by taking images of the drops.

  4. NEW METHODS TO SCREEN FOR DEVELOPMENTAL NEUROTOXICITY.

    EPA Science Inventory

    The development of alternative methods for toxicity testing is driven by the need for scientifically valid data (i.e. predictive of a toxic effect) that can be obtained in a rapid and cost-efficient manner. These predictions will enable decisions to be made as to whether further ...

  5. The Implementation of an Integrated Information System for Substance Use Screening in General Medical Settings

    PubMed Central

    Sorensen-Alawad, A.; Carney, B.L.; Persand, I.; Cruz, A.; Botticelli, M.; Pressman, K.; Adams, W.G.; Brolin, M.; Alford, D.P.

    2014-01-01

    Summary The Massachusetts Screening, Brief Intervention and Referral to Treatment (MASBIRT) Program, a substance use screening program in general medical settings, created a web-based, point-of-care (POC), application – the MASBIRT Portal (the “Portal”) to meet program goals. Objectives We report on development and implementation of the Portal. Methods Five year program process outcomes recorded by an independent evaluator and an anonymous survey of Health Educator’s (HEs) adoption, perceptions and Portal use with a modified version of the Technology Readiness Index are described. [8] Specific management team members, selected based on their roles in program leadership, development and implementation of the Portal and supervision of HEs, participated in semi-structured, qualitative interviews. Results At the conclusion of the program 73% (24/33) of the HEs completed a survey on their experience using the Portal. HEs reported that the Portal made recording screening information easy (96%); improved planning their workday (83%); facilitated POC data collection (84%); decreased time dedicated to data entry (100%); and improved job satisfaction (59%). The top two barriers to use were “no or limited wireless connectivity” (46%) and “the tablet was too heavy/bulky to carry” (29%). Qualitative management team interviews identified strategies for successful HIT implementation: importance of engaging HEs in outlining specifications and workflow needs, collaborative testing prior to implementation and clear agreement on data collection purpose, quality requirements and staff roles. Discussion Overall, HEs perceived the Portal favorably with regard to time saving ability and improved workflow. Lessons learned included identifying core requirements early during system development and need for managers to institute and enforce consistent behavioral work norms. Conclusion Barriers and HEs’ views of technology impacted the utilization of the MASBIRT Portal

  6. Bayesian methods in virtual screening and chemical biology.

    PubMed

    Bender, Andreas

    2011-01-01

    The Naïve Bayesian Classifier, as well as related classification and regression approaches based on Bayes' theorem, has experienced increased attention in the cheminformatics world in recent years. In this contribution, we first review the mathematical framework on which Bayes' methods are built, and then continue to discuss implications of this framework as well as practical experience under which conditions Bayes' methods give the best performance in virtual screening settings. Finally, we present an overview of applications of Bayes' methods to both virtual screening and the chemical biology arena, where applications range from bridging phenotypic and mechanistic space of drug action to the prediction of ligand-target interactions.

  7. Domain-specific versus generalized cognitive screening in acute stroke.

    PubMed

    Demeyere, Nele; Riddoch, M J; Slavkova, E D; Jones, K; Reckless, I; Mathieson, P; Humphreys, G W

    2016-02-01

    Cognitive assessments after stroke are typically short form tests developed for dementia that generates pass/fail classifications (e.g. the MoCA). The Oxford Cognitive Screen (OCS) provides a domain-specific cognitive profile designed for stroke survivors. This study compared the use of the MoCA and the OCS in acute stroke with respect to symptom specificity and aspects of clinical utility. A cross-sectional study with a consecutive sample of 200 stroke patients within 3 weeks of stroke completing MoCA and OCS. Demographic data, lesion side and Barthel scores were recorded. Inclusivity was assessed in terms of completion rates and reasons for non-completion were evaluated. The incidence of cognitive impairments on both the MoCA and OCS sub-domains was calculated and differences in stroke specificity, cognitive profiles and independence of the measures were addressed. The incidence of acute cognitive impairment was high: 76% of patients were impaired on MoCA, and 86% demonstrated at least one impairment on the cognitive domains assessed in the OCS. OCS was more sensitive than MoCA overall (87 vs 78% sensitivity) and OCS alone provided domain-specific information on prevalent post-stroke cognitive impairments (neglect, apraxia and reading/writing ability). Unlike the MOCA, the OCS was not dominated by left hemisphere impairments but gave differentiated profiles across the contrasting domains. The OCS detects important cognitive deficits after stroke not assessed in the MoCA, it is inclusive for patients with aphasia and neglect and it is less confounded by co-occurring difficulties in these domains. PMID:26588918

  8. A General Symbolic Method with Physical Applications

    NASA Astrophysics Data System (ADS)

    Smith, Gregory M.

    2000-06-01

    A solution to the problem of unifying the General Relativistic and Quantum Theoretical formalisms is given which introduces a new non-axiomatic symbolic method and an algebraic generalization of the Calculus to non-finite symbolisms without reference to the concept of a limit. An essential feature of the non-axiomatic method is the inadequacy of any (finite) statements: Identifying this aspect of the theory with the "existence of an external physical reality" both allows for the consistency of the method with the results of experiments and avoids the so-called "measurement problem" of quantum theory.

  9. FIELD ANALYTICAL SCREENING PROGRAM: PCP METHOD - INNOVATIVE TECHNOLOGY EVALUATION REPORT

    EPA Science Inventory

    The Field Analytical Screening Program (FASP) pentachlorophenol (PCP) method uses a gas chromatograph (GC) equipped with a megabore capillary column and flame ionization detector (FID) and electron capture detector (ECD) to identify and quantify PCP. The FASP PCP method is design...

  10. A straightforward ninhydrin-based method for collagenase activity and inhibitor screening of collagenase using spectrophotometry.

    PubMed

    Zhang, Yanfang; Fu, Yun; Zhou, Sufeng; Kang, Lixia; Li, Changzheng

    2013-06-01

    Currently protease assay kits, requiring substrate that is either radiolabeled or fluorescence labeled and specialized instruments, are all expensive. A simple, reliable assay of protease activity and its inhibitor screening for general laboratory is rare. Here we demonstrated a straightforward ninhydrin-based method for assay of collagenase activity and its inhibitor screening using spectrophotometry. In the method, without multistep sample treatments and substrate labeling, the hydrolytic products were directly traced by ninhydrin. The method is expected to be suitable for not only the assay of collagenase activity but also the others matrix metalloproteinases activities, and can be used for kinetic study.

  11. Down syndrome screening methods in Iranian pregnant women

    PubMed Central

    Farshbaf Khalili, Azizeh; Shahnazi, Mahnaz; Hajizadeh, Khadijeh; Shekari Khaniani, Mahmoud

    2012-01-01

    Introduction: Down syndrome is one of the most prevalent genetic diseases. Screening methods for this syndrome are easy and safe and are recommended to all pregnant women particularly mothers over 35 years of age. This study aimed to review the status of Down syndrome screening and related factors in Iranian pregnant women. Methods: This descriptive analytical study was carried out in 2011. It included 400 women who were randomly selected from those referring to Alzahra Hospital (Tabriz, Iran) during their third trimester of pregnancy. Data was collected through a question-naire whose reliability and validity have been approved. The data was analyzed by chi-square test in SPSS13. Results: The results showed that while 28 and 26 women imple-mented screening tests during the first and second trimesters, respectively, only 5 sub-jects benefited from both (integrated test). Chi-square test showed significant correla-tions between the implementation of screening methods and age, education level, in-come, and the location of prenatal care (p < 0.05). Conclusion: The findings of the present study showed women to poorly implement Down syndrome screening methods. Therefore, the necessity of providing appropriate educational programs for health staff and mothers seems undeniable. Moreover, paying attention to the related factors such as income, educational level, and adequate training of mothers during pregnancy is essential. PMID:25276689

  12. Spectral Methods in General Relativistic MHD Simulations

    NASA Astrophysics Data System (ADS)

    Garrison, David

    2012-03-01

    In this talk I discuss the use of spectral methods in improving the accuracy of a General Relativistic Magnetohydrodynamic (GRMHD) computer code. I introduce SpecCosmo, a GRMHD code developed as a Cactus arrangement at UHCL, and show simulation results using both Fourier spectral methods and finite differencing. This work demonstrates the use of spectral methods with the FFTW 3.3 Fast Fourier Transform package integrated with the Cactus Framework to perform spectral differencing using MPI.

  13. Estimating rotavirus vaccine effectiveness in Japan using a screening method

    PubMed Central

    Araki, Kaoru; Hara, Megumi; Sakanishi, Yuta; Shimanoe, Chisato; Nishida, Yuichiro; Matsuo, Muneaki; Tanaka, Keitaro

    2016-01-01

    abstract Rotavirus gastroenteritis is a highly contagious, acute viral disease that imposes a significant health burden worldwide. In Japan, rotavirus vaccines have been commercially available since 2011 for voluntary vaccination, but vaccine coverage and effectiveness have not been evaluated. In the absence of a vaccination registry in Japan, vaccination coverage in the general population was estimated according to the number of vaccines supplied by the manufacturer, the number of children who received financial support for vaccination, and the size of the target population. Patients with rotavirus gastroenteritis were identified by reviewing the medical records of all children who consulted 6 major hospitals in Saga Prefecture with gastroenteritis symptoms. Vaccination status among these patients was investigated by reviewing their medical records or interviewing their guardians by telephone. Vaccine effectiveness was determined using a screening method. Vaccination coverage increased with time, and it was 2-times higher in municipalities where the vaccination fee was supported. In the 2012/13 season, vaccination coverage in Saga Prefecture was 14.9% whereas the proportion of patients vaccinated was 5.1% among those with clinically diagnosed rotavirus gastroenteritis and 1.9% among those hospitalized for rotavirus gastroenteritis. Thus, vaccine effectiveness was estimated as 69.5% and 88.8%, respectively. This is the first study to evaluate rotavirus vaccination coverage and effectiveness in Japan since vaccination began. PMID:26680277

  14. General practitioners' perceptions of private health screening: too much paper, anxiety, and reassurance.

    PubMed Central

    Paynton, D; Dunleavey, J; Smith, H

    1998-01-01

    There is no evidence to support the practice of screening consultations that include general physical examinations and batteries of tests; however, many patients may choose, or be sent by their employers, to have private full health screening (FHS). General practitioners (GPs) are routinely sent the results of these screening examinations and are expected to deal with any subsequent care required. GPs recognize some positive aspects of FHS, but in our survey there was a groundswell of dislike for these examinations because of uncertainty about patient benefit (raised anxiety or false assurance) and a potential to irritate the GP. The implications for workload were minimal but resented. GPs would welcome a precise summary of significant findings and for the screening doctor to take greater responsibility for follow-up. PMID:9747551

  15. Nonlocal exchange correlation in screened-exchange densityfunctional methods

    SciTech Connect

    Lee, Byounghak; Wang, Lin-Wang; Spataru, Catalin D.; Louie,Steven G.

    2007-04-22

    We present a systematic study on the exchange-correlationeffects in screened-exchange local density functional method. Toinvestigate the effects of the screened-exchange potential in the bandgap correction, we have compared the exchange-correlation potential termin the sX-LDA formalism with the self-energy term in the GWapproximation. It is found that the band gap correction of the sX-LDAmethod primarily comes from the downshift of valence band states,resulting from the enhancement of bonding and the increase of ionizationenergy. The band gap correction in the GW method, on the contrary, comesin large part from the increase of theconduction band energies. We alsostudied the effects of the screened-exchange potential in the totalenergy by investigating the exchange-correlation hole in comparison withquantum Monte Carlo calculations. When the Thomas-Fermi screening isused, the sX-LDA method overestimates (underestimates) theexchange-correlation hole in short (long) range. From theexchange-correlation energy analysis we found that the LDA method yieldsbetter absolute total energy than sX-LDA method.

  16. Using the Screened Coulomb Potential to Illustrate the Variational Method

    ERIC Educational Resources Information Center

    Zuniga, Jose; Bastida, Adolfo; Requena, Alberto

    2012-01-01

    The screened Coulomb potential, or Yukawa potential, is used to illustrate the application of the single and linear variational methods. The trial variational functions are expressed in terms of Slater-type functions, for which the integrals needed to carry out the variational calculations are easily evaluated in closed form. The variational…

  17. Screening Methods for Metal-Containing Nanoparticles in Water

    EPA Science Inventory

    Screening-level analysis of water for metal-containing nanoparticles is achieved with single particle-inductively coupled plasma mass spectrometry (SP-ICPMS). This method measures both the concentration of nanoparticles containing an analyte metal and the mass of the metal in eac...

  18. Method for manufacturing a well production and sand screen assembly

    SciTech Connect

    Widmyer, R.H.

    1982-10-12

    A method for forming and assembling a well production and sand screen assembly in a well having a screen therein forming an outer annulus and a wash pipe internally of the screen forming an inner annulus comprising further (A) mounting a high pressure fluid pump means and a valve means on each wash pipe, inner annulus, and outer annulus, and (B) connecting the valve means in fluid communication with the high pressure fluid pump means for controlling the ingress and egress of the high pressure fluids and removed formation material for forming a sand pack in the well and simultaneously for applying and maintaining a positive fluid pressure against the overburden during work in the well for preventing cave-ins and sloughing of the unconsolidated formation well walls until the sand pack is formed.

  19. Emerging methods for ensemble-based virtual screening.

    PubMed

    Amaro, Rommie E; Li, Wilfred W

    2010-01-01

    Ensemble based virtual screening refers to the use of conformational ensembles from crystal structures, NMR studies or molecular dynamics simulations. It has gained greater acceptance as advances in the theoretical framework, computational algorithms, and software packages enable simulations at longer time scales. Here we focus on the use of computationally generated conformational ensembles and emerging methods that use these ensembles for discovery, such as the Relaxed Complex Scheme or Dynamic Pharmacophore Model. We also discuss the more rigorous physics-based computational techniques such as accelerated molecular dynamics and thermodynamic integration and their applications in improving conformational sampling or the ranking of virtual screening hits. Finally, technological advances that will help make virtual screening tools more accessible to a wider audience in computer aided drug design are discussed.

  20. Indicators of depression in elderly and different screening methods

    PubMed Central

    Matias, Amanda Gilvani Cordeiro; Fonsêca, Marília de Andrade; Gomes, Maria de Lourdes de Freitas; Matos, Marcos Antonio Almeida

    2016-01-01

    ABSTRACT Objective To determine the prevalence of depressive symptoms among elderly and correlate the agreement between the screening methods used. Methods A cross-section study of 137 elderly attending the Programa Vivendo a Terceira Idade [Living for the Elderly Program]. Depressive symptoms were screened by the Patient Health Questionnaire-9 and the 15-item Geriatric Depression Scale, by Yesavage. Cohen´s kappa analyzed the degree of agreement of these scales. Results The prevalence of depressive symptoms screened by the Patient Health Questionnaire-9 was 62.8% and, by the Geriatric Depression Scale, 52.6%. The Spearman correlation between the results of scales obtained rho=0.387, p<0.000. The Kappa reliability coefficient was 0.41 and significance level of p<0.001. The screening methods showed sensitivity of 80% and specificity of 44%. Conclusion Both scales showed moderate agreement and were useful for detecting a relevant prevalence of the target outcome of depression among the elderly. PMID:27074227

  1. Hilbert's axiomatic method and Carnap's general axiomatics.

    PubMed

    Stöltzner, Michael

    2015-10-01

    This paper compares the axiomatic method of David Hilbert and his school with Rudolf Carnap's general axiomatics that was developed in the late 1920s, and that influenced his understanding of logic of science throughout the 1930s, when his logical pluralism developed. The distinct perspectives become visible most clearly in how Richard Baldus, along the lines of Hilbert, and Carnap and Friedrich Bachmann analyzed the axiom system of Hilbert's Foundations of Geometry—the paradigmatic example for the axiomatization of science. Whereas Hilbert's axiomatic method started from a local analysis of individual axiom systems in which the foundations of mathematics as a whole entered only when establishing the system's consistency, Carnap and his Vienna Circle colleague Hans Hahn instead advocated a global analysis of axiom systems in general. A primary goal was to evade, or formalize ex post, mathematicians' 'material' talk about axiom systems for such talk was held to be error-prone and susceptible to metaphysics.

  2. Multiscale generalized Born modeling of ligand binding energies for virtual database screening

    PubMed Central

    Liu, Hao-Yang; Grinter, Sam Z.; Zou, Xiaoqin

    2009-01-01

    Generalized Born (GB) models are widely used to study the electrostatic energetics of solute molecules including proteins. Previous work demonstrates that GB models may produce satisfactory solvation energies if accurate effective Born radii are computed for all atoms. Our previous study showed that a GB model which reproduces the solvation energy may not necessarily be suitable for ligand binding calculations. In this work, we studied binding energetics using the exact GB model, in which Born radii are computed from the Poisson-Boltzmann (PB) equation. Our results showed that accurate Born radii lead to very good agreement between GB and PB in electrostatic calculations for ligand binding. However, recently developed GB models with high Born radii accuracy, when used in large database screening, may suffer from time constraints which make accurate, large-scale Born radii calculations impractical. We therefore present a multiscale GB approach in which atoms are divided into two groups. For atoms in the first group, those few atoms which are most likely to be critical to binding electrostatics, the Born radii are computed accurately at the sacrifice of speed. We propose two alternative approaches for atoms in the second group. The Born radii of these atoms may simply be computed by a fast GB method. Alternatively, the Born radii of these atoms may be computed accurately in the free state, then a variational form of a fast GB method may be used to compute the change in Born radii experienced by these atoms during binding. This strategy provides an accuracy advantage while still being fast enough for use in the virtual screening of large databases. PMID:19678651

  3. The Promise and Peril of Genomic Screening in the General Population

    PubMed Central

    Adams, Michael C.; Evans, James P.; Henderson, Gail E.; Berg, Jonathan S.

    2015-01-01

    Purpose Utilization of sequencing to screen the general population for preventable monogenic conditions is receiving substantial attention due to its potential to decrease morbidity and mortality. However, the selection of which variants to return is a serious implementation challenge. Procedures must be investigated to ensure optimal test characteristics and avoidance of harm from false positive test results. Methods We scanned exome sequences from 478 well-phenotyped individuals for potentially pathogenic variants in 17 genes representing 11 conditions that are among the most medically actionable Mendelian disorders in adults. We developed 5 variant selection algorithms with increasing sensitivity and measured their specificity in these 17 genes. Results Variant selection algorithms with increasing sensitivity exhibited decreased specificity, and performance was highly dependent on the genes analyzed. The most sensitive algorithm ranged from 88.8% to 99.6% specificity among the 17 genes. Conclusion For very low prevalence conditions, small reductions in specificity greatly increase false positives. This inescapable test characteristic governs the predictive value of genomic sequencing in the general population. To address this issue, test performance must be evaluated systematically for each condition so that the false negatives and false positives can be tailored for optimal outcomes, depending on the downstream clinical consequences. PMID:26540154

  4. High Throughput Screening Method to Explore Protein Interactions with Nanoparticles

    PubMed Central

    Nasir, Irem; Fatih, Warda; Svensson, Anja; Radu, Dennis; Linse, Sara; Cabaleiro Lago, Celia; Lundqvist, Martin

    2015-01-01

    The interactions of biological macromolecules with nanoparticles underlie a wide variety of current and future applications in the fields of biotechnology, medicine and bioremediation. The same interactions are also responsible for mediating potential biohazards of nanomaterials. Some applications require that proteins adsorb to the nanomaterial and that the protein resists or undergoes structural rearrangements. This article presents a screening method for detecting nanoparticle-protein partners and conformational changes on time scales ranging from milliseconds to days. Mobile fluorophores are used as reporters to study the interaction between proteins and nanoparticles in a high-throughput manner in multi-well format. Furthermore, the screening method may reveal changes in colloidal stability of nanomaterials depending on the physicochemical conditions. PMID:26313757

  5. High Throughput Screening Method to Explore Protein Interactions with Nanoparticles.

    PubMed

    Nasir, Irem; Fatih, Warda; Svensson, Anja; Radu, Dennis; Linse, Sara; Cabaleiro Lago, Celia; Lundqvist, Martin

    2015-01-01

    The interactions of biological macromolecules with nanoparticles underlie a wide variety of current and future applications in the fields of biotechnology, medicine and bioremediation. The same interactions are also responsible for mediating potential biohazards of nanomaterials. Some applications require that proteins adsorb to the nanomaterial and that the protein resists or undergoes structural rearrangements. This article presents a screening method for detecting nanoparticle-protein partners and conformational changes on time scales ranging from milliseconds to days. Mobile fluorophores are used as reporters to study the interaction between proteins and nanoparticles in a high-throughput manner in multi-well format. Furthermore, the screening method may reveal changes in colloidal stability of nanomaterials depending on the physicochemical conditions. PMID:26313757

  6. 7 CFR 361.2 - Preemption of State and local laws; general restrictions on the importation of seed and screenings.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... restrictions on the importation of seed and screenings. 361.2 Section 361.2 Agriculture Regulations of the... IMPORTATION OF SEED AND SCREENINGS UNDER THE FEDERAL SEED ACT § 361.2 Preemption of State and local laws; general restrictions on the importation of seed and screenings. (a) The regulations in this part...

  7. 7 CFR 361.2 - Preemption of State and local laws; general restrictions on the importation of seed and screenings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... restrictions on the importation of seed and screenings. 361.2 Section 361.2 Agriculture Regulations of the... IMPORTATION OF SEED AND SCREENINGS UNDER THE FEDERAL SEED ACT § 361.2 Preemption of State and local laws; general restrictions on the importation of seed and screenings. (a) The regulations in this part...

  8. 7 CFR 361.2 - Preemption of State and local laws; general restrictions on the importation of seed and screenings.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... restrictions on the importation of seed and screenings. 361.2 Section 361.2 Agriculture Regulations of the... IMPORTATION OF SEED AND SCREENINGS UNDER THE FEDERAL SEED ACT § 361.2 Preemption of State and local laws; general restrictions on the importation of seed and screenings. (a) The regulations in this part...

  9. 7 CFR 361.2 - Preemption of State and local laws; general restrictions on the importation of seed and screenings.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... restrictions on the importation of seed and screenings. 361.2 Section 361.2 Agriculture Regulations of the... IMPORTATION OF SEED AND SCREENINGS UNDER THE FEDERAL SEED ACT § 361.2 Preemption of State and local laws; general restrictions on the importation of seed and screenings. (a) The regulations in this part...

  10. 7 CFR 361.2 - Preemption of State and local laws; general restrictions on the importation of seed and screenings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... restrictions on the importation of seed and screenings. 361.2 Section 361.2 Agriculture Regulations of the... IMPORTATION OF SEED AND SCREENINGS UNDER THE FEDERAL SEED ACT § 361.2 Preemption of State and local laws; general restrictions on the importation of seed and screenings. (a) The regulations in this part...

  11. Method for making generally cylindrical underground openings

    DOEpatents

    Routh, J.W.

    1983-05-26

    A rapid, economical and safe method for making a generally cylindrical underground opening such as a shaft or a tunnel is described. A borehole is formed along the approximate center line of where it is desired to make the underground opening. The borehole is loaded with an explodable material and the explodable material is detonated. An enlarged cavity is formed by the explosive action of the detonated explodable material forcing outward and compacting the original walls of the borehole. The enlarged cavity may be increased in size by loading it with a second explodable material, and detonating the second explodable material. The process may be repeated as required until the desired underground opening is made. The explodable material used in the method may be free-flowing, and it may be contained in a pipe.

  12. A simple parallel analytical method of prenatal screening.

    PubMed

    Li, Ding; Yang, Hao; Zhang, Wen-Hong; Pan, Hao; Wen, Dong-Qing; Han, Feng-Chan; Guo, Hui-Fang; Wang, Xiao-Ming; Yan, Xiao-Jun

    2006-01-01

    Protein microarray has progressed rapidly in the past few years, but it is still hard to popularize it in many developing countries or small hospitals owing to the technical expertise required in practice. We developed a cheap and easy-to-use protein microarray based on dot immunogold filtration assay for parallel analysis of ToRCH-related antibodies including Toxoplasma gondii, rubella virus, cytomegalovirus and herpes simplex virus type 1 and 2 in sera of pregnant women. It does not require any expensive instruments and the assay results can be clearly recognized by the naked eye. We analyzed 186 random sera of outpatients at the gynecological department with our microarray and commercial ELISA kit, and the results showed there was no significant difference between the two detection methods. Validated by clinical application, the microarray is easy to use and has a unique advantage in cost and time. It is more suitable for mass prenatal screening or epidemiological screening than the ELISA format.

  13. Cytological screening for cervical cancer and human papillomavirus in general practice.

    PubMed Central

    Hiscock, E.; Reece, G.

    1988-01-01

    In a retrospective study of cervical screening in a general practice in Birmingham 156 out of 1913 smears taken over three years showed some abnormality. Smears from 65 women showed severe non-specific inflammation, and 91 women had various grades of cervical intraepithelial neoplasia, of whom 53 were aged under 30 and 13 over 40. Of 35 women with clinical evidence of human papillomavirus, 21 had normal results on cervical testing and 14 abnormal results. The incidence of genital warts among sexually active young people is growing, but the association of human papillomavirus with abnormal cervical smears is not clear. The efficacy of screening in the United Kingdom must be improved by actively encouraging younger patients to attend for regular screening. PMID:2852515

  14. Prenatal screening for fetal aneuploidies with cell-free DNA in the general pregnancy population: a cost-effectiveness analysis

    PubMed Central

    Fairbrother, Genevieve; Burigo, John; Sharon, Thomas; Song, Ken

    2016-01-01

    Abstract Objective: To estimate the cost-effectiveness of fetal aneuploidy screening in the general pregnancy population using non-invasive prenatal testing (NIPT) as compared to first trimester combined screening (FTS) with serum markers and NT ultrasound. Methods: Using a decision-analytic model, we estimated the number of fetal T21, T18, and T13 cases identified prenatally, the number of invasive procedures performed, corresponding normal fetus losses, and costs of screening using FTS or NIPT with cell-free DNA (cfDNA). Modeling was based on a 4 million pregnant women cohort, which represents annual births in the U.S. Results: For the general pregnancy population, NIPT identified 15% more trisomy cases, reduced invasive procedures by 88%, and reduced iatrogenic fetal loss by 94% as compared to FTS. The cost per trisomy case identified with FTS was $497 909. At a NIPT unit, cost of $453 and below, there were cost savings as compared to FTS. Accounting for additional trisomy cases identified by NIPT, a NIPT unit cost of $665 provided the same per trisomy cost as that of FTS. Conclusions: NIPT in the general pregnancy population leads to more prenatal identification of fetal trisomy cases as compared to FTS and is more economical at a NIPT unit cost of $453. PMID:26000626

  15. Screening for celiac disease in the general population and in high-risk groups

    PubMed Central

    Card, Timothy R; Kaukinen, Katri; Bai, Julio; Zingone, Fabiana; Sanders, David S; Murray, Joseph A

    2015-01-01

    Background Celiac disease (CD) occurs in approximately 1% of the Western population. It is a lifelong disorder that is associated with impaired quality of life (QOL) and an excessive risk of comorbidity and death. Objectives To review the literature on screening for CD in relation to the current World Health Organization (WHO) criteria for mass screening. Methods We performed a PubMed search to identify indexed papers on CD screening with a publication date from 1900 until 1 June 2014. When we deemed an abstract relevant, we read the corresponding paper in detail. Results CD fulfills several WHO criteria for mass screening (high prevalence, available treatment and difficult clinical detection), but it has not yet been established that treatment of asymptomatic CD may reduce the excessive risk of severe complications, leading to higher QOL nor that it is cost-effective. Conclusions Current evidence is not sufficient to support mass screening for CD, but active case-finding may be appropriate, as we recognize that most patients with CD will still be missed by this strategy. Although proof of benefit is still lacking, screening for CD may be appropriate in high-risk groups. PMID:25922671

  16. A rapid, inexpensive high throughput screen method for neurite outgrowth.

    PubMed

    Yeyeodu, Susan T; Witherspoon, Sam M; Gilyazova, Nailya; Ibeanu, Gordon C

    2010-01-01

    Neurite outgrowth assays are the most common phenotypic screen to assess chemical effects on neuronal cells. Current automated assays involve expensive equipment, lengthy sample preparation and handling, costly reagents and slow rates of data acquisition and analysis. We have developed a high throughput screen (HTS) for neurite outgrowth using a robust neuronal cell model coupled to fast and inexpensive visualization methods, reduced data volume and rapid data analysis. Neuroscreen-1 (NS-1) cell, a subclone of PC12, possessing rapid growth and enhanced sensitivity to NGF was used as a model neuron. This method reduces preparation time by using cells expressing GFP or native cells stained with HCS CellMask(™) Red in a multiplexed 30 min fixation and staining step. A 2x2 camera binning process reduced both image data files and analysis times by 75% and 60% respectively, compared to current protocols. In addition, eliminating autofocus steps during montage generation reduced data collection time. Pharmacological profiles for stimulation and inhibition of neurite outgrowth by NGF and SU6656 were comparable to current standard method utilizing immunofluorescence detection of tubulin. Potentiation of NGF-induced neurite outgrowth by members of a 1,120-member Prestwick compound library as assayed using this method identified six molecules, including etoposide, isoflupredone acetate, fludrocortisone acetate, thioguanosine, oxyphenbutazone and gibberellic acid, that more than doubled the neurite mass primed by 2 ng/ml NGF. This simple procedure represents an important routine approach in high throughput screening of large chemical libraries using the neurite outgrowth phenotype as a measure of the effects of chemical molecules on neuronal cells. PMID:21347208

  17. Generalized HPC method for the Poisson equation

    NASA Astrophysics Data System (ADS)

    Bardazzi, A.; Lugni, C.; Antuono, M.; Graziani, G.; Faltinsen, O. M.

    2015-10-01

    An efficient and innovative numerical algorithm based on the use of Harmonic Polynomials on each Cell of the computational domain (HPC method) has been recently proposed by Shao and Faltinsen (2014) [1], to solve Boundary Value Problem governed by the Laplace equation. Here, we extend the HPC method for the solution of non-homogeneous elliptic boundary value problems. The homogeneous solution, i.e. the Laplace equation, is represented through a polynomial function with harmonic polynomials while the particular solution of the Poisson equation is provided by a bi-quadratic function. This scheme has been called generalized HPC method. The present algorithm, accurate up to the 4th order, proved to be efficient, i.e. easy to be implemented and with a low computational effort, for the solution of two-dimensional elliptic boundary value problems. Furthermore, it provides an analytical representation of the solution within each computational stencil, which allows its coupling with existing numerical algorithms within an efficient domain-decomposition strategy or within an adaptive mesh refinement algorithm.

  18. A Quantum-Based Similarity Method in Virtual Screening.

    PubMed

    Al-Dabbagh, Mohammed Mumtaz; Salim, Naomie; Himmat, Mubarak; Ahmed, Ali; Saeed, Faisal

    2015-10-02

    One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.

  19. Wide-angle elastic wave one-way propagation in heterogeneous media and an elastic wave complex-screen method

    NASA Astrophysics Data System (ADS)

    Wu, Ru-Shan

    1994-01-01

    In this paper a system of equations for wide-angle one-way elastic wave propagation in arbitrarily heterogeneous media is formulated in both the space and wavenumber domains using elastic Rayleigh integrals and local elastic Born scattering theory. The wavenumber domain formulation leads to compact solutions to one-way propagation and scattering problems. It is shown that wide-angle scattering in heterogeneous elastic media cannot be formulated as passage through regular phase-screens, since the interaction between the incident wavefield and the heterogeneities is not local in both the space domain and the wavenumber domain. Our more generally valid formulation is called the 'thin-slap; formulation. After applying the small-angle approximation, the thin slab effect degenerates to that of an elastic complex-screen (or generalized phase-screen). For the complex-screen method the cross-coupling term is neglected because it is higher order small quantity for small-angle scattering. Relative to prior derivations of vector phase-screen method, our method can correctly treat the conversion between P and S waves and the cross-coupling between differently polarized S waves. A comparison with solutions from three-dimensional finite difference and exact solutions using eigenfunctions expansion is made for two special cases. One is for a solid sphere with only P velocity pertubation; the other is with only S velocity perturbation. The Elastic complex-screen method generally agrees well with the three-dimensional finite difference method and the exact solutions. In the limiting case of scalar waves, the derivation in this paper leads to a move generally valid new method, namely, a scaler thin-slab method. When making the small-angle approximation to the interaction term while keeping the propagation term unchanged, the thin-slab method approaches the currently available scalar wide-angle phase screen method.

  20. Method for rapid screening of pesticide mineralization in soil.

    PubMed

    Rasmussen, Jim; Jensen, Pia Haugaard; Holm, Peter E; Jacobsen, Ole Stig

    2004-05-01

    A method has been developed for the analysis of (14)CO(2) evolution from the mineralization of (14)C-labelled organic compounds in soil samples. The new method is less space demanding and substantially cuts down laborious manual work compared to the traditional incubation bottle method used. Furthermore, the use of scintillation cocktail is largely reduced with the new method. In the new method, (14)CO(2) is trapped in filter paper held in the lid of a 20 ml glass vial by surface tension. The trapping solution used is Ca(OH)(2), which fixates CO(2) in the filter paper and the analysis of trapped (14)CO(2) is done using the Cyclone trade mark Storage Phosphor system. The lids are placed in a 32 well holder and exposed to a phosphor screen prior to scanning in a Cyclone trade mark scanner. The new filter method has been tested and compared to results obtained using the traditional method. The results show good agreement but due to a smaller capacity for CO(2) with the filter method compared to the traditional method, the interval between sampling has to be shorter using the filter method when the CO(2) development is high. The detection limits for the filter method is higher compared to the traditional method. With the filter method, the level of radioactivity has to exceed 300 dpm before detection is possible, while the same limit for the traditional method is around 30 dpm. On the other hand, the gas trapping faster and the efficiency is higher with the filter method. PMID:15063054

  1. DESI MS based screening method for phthalates in consumer goods.

    PubMed

    Schulz, Sabine; Wagner, Sebastian; Gerbig, Stefanie; Wächter, Herbert; Sielaff, Detlef; Bohn, Dieter; Spengler, Bernhard

    2015-05-21

    Phthalates are used as plasticizes in many everyday items, but some of them are known as hormone disruptors, being especially harmful during childhood. The European Union therefore restricted their application in children's toys and certain food packaging to 0.1%w. Due to the ever increasing number of plastic-containing consumer goods, rapid screening methods are needed to ensure and improve consumer safety in the future. In this study we evaluated the performance of desorption electrospray ionization (DESI) mass spectrometry (MS) for rapid quantitative screening of phthalates in toys. DESI allowed for direct surface sampling of the toys under atmospheric conditions with minimal sample preparation, while the high performance mass spectrometer used provided a high sensitivity and reliable identification via accurate mass measurements, high mass resolving power and MS/MS capabilities. External calibration curves for six banned phthalates (DBP, BBP, DEHP, DNOP, DINP and DIDP) were obtained from matrix-matched reference materials. Coefficients of determination were greater than 0.985, LOQs ranged from 0.02%w (DIDP) to 2.26%w (DINP) and the relative standard deviation of the calibration curve slope was less than 7.8% for intraday and 11.4% for interday comparison. The phthalate contents of eleven authentic samples were determined in a proof-of-concept approach using DESI MS and results were compared to those from confirmatory methods. The phthalate content was correctly assigned with relative deviations ranging from -20% to +10% for the majority of samples. Given further optimization and automation, DESI MS is likely to become a useful tool for rapid and accurate phthalate screening in the future. PMID:25827613

  2. DESI MS based screening method for phthalates in consumer goods.

    PubMed

    Schulz, Sabine; Wagner, Sebastian; Gerbig, Stefanie; Wächter, Herbert; Sielaff, Detlef; Bohn, Dieter; Spengler, Bernhard

    2015-05-21

    Phthalates are used as plasticizes in many everyday items, but some of them are known as hormone disruptors, being especially harmful during childhood. The European Union therefore restricted their application in children's toys and certain food packaging to 0.1%w. Due to the ever increasing number of plastic-containing consumer goods, rapid screening methods are needed to ensure and improve consumer safety in the future. In this study we evaluated the performance of desorption electrospray ionization (DESI) mass spectrometry (MS) for rapid quantitative screening of phthalates in toys. DESI allowed for direct surface sampling of the toys under atmospheric conditions with minimal sample preparation, while the high performance mass spectrometer used provided a high sensitivity and reliable identification via accurate mass measurements, high mass resolving power and MS/MS capabilities. External calibration curves for six banned phthalates (DBP, BBP, DEHP, DNOP, DINP and DIDP) were obtained from matrix-matched reference materials. Coefficients of determination were greater than 0.985, LOQs ranged from 0.02%w (DIDP) to 2.26%w (DINP) and the relative standard deviation of the calibration curve slope was less than 7.8% for intraday and 11.4% for interday comparison. The phthalate contents of eleven authentic samples were determined in a proof-of-concept approach using DESI MS and results were compared to those from confirmatory methods. The phthalate content was correctly assigned with relative deviations ranging from -20% to +10% for the majority of samples. Given further optimization and automation, DESI MS is likely to become a useful tool for rapid and accurate phthalate screening in the future.

  3. Method for in vitro screening of aquatic fungicides

    USGS Publications Warehouse

    Bailey, T.A.

    1983-01-01

    Methods were developed for in vitro screening of candidate aquatic fungicides for efficacy against Achlya fiagellata, A. racemosa, Saprolegnia hypogyna and S. megasperma. Agar plugs containing fungal hyphae, removed from the edge of actively growing colonies, were placed in the depressions of spot plates containing 1a??0, 10a??0 and 100 mg/I of the candidate compounds for 15 or 60 min. After exposure, the plugs were transferred on to filter papers (0a??45-A?m pore) in a holder, rinsed, and then placed on cornmeal agar medium in tri-petri dishes. The plates were checked for mycelial growth after 48, 96 and 168 h of incubation in a lighted (400-800 A?m) environmental control chamber at 20A?2A?C. Criteria for the acceptance or rejection of candidate aquatic fungicides for further study were based on the antifungal spectrum index (ASI) comparisons between respective compounds and malachite green after 48 h and the concentration level producing complete growth inhibition. Candidate compounds whose ASI was less than 50% that of malachite green after 48 h or did not inhibit growth at levels less than 100 mg/l were rejected. This method provides a base from which in vivo and definitive test regimens can be developed. Preliminary in vitro screening of candidate fungicides reduces the need for costly in vivo tests on compounds that have low antifungal activity.

  4. Screening and confirmation methods for GHB determination in biological fluids.

    PubMed

    Ingels, Ann-Sofie M E; Wille, Sarah M R; Samyn, Nele; Lambert, Willy E; Stove, Christophe P

    2014-06-01

    The purpose of this review is to provide a comprehensive overview of reported methods for screening and confirmation of the low-molecular-weight compound and drug of abuse gamma-hydroxybutyric acid (GHB) in biological fluids. The polarity of the compound, its endogenous presence, its rapid metabolism after ingestion, and its instability during storage (de novo formation and interconversion between GHB and its lactone form gamma-butyrolactone) are challenges for the analyst and for interpretation of a positive result. First, possible screening procedures for GHB are discussed, including colorimetric, enzymatic, and chromatography-based procedures. Confirmation methods for clinical and forensic cases mostly involve gas chromatography (coupled to mass spectrometry), although liquid chromatography and capillary zone electrophoresis have also been used. Before injection, sample-preparation techniques include (a combination of) liquid-liquid, solid-phase, or headspace extraction, and chemical modification of the polar compound. Also simple "dilute-and-shoot" may be sufficient for urine or serum. Advantages, limitations, and trends are discussed.

  5. The views of general practitioners and practice nurses towards the barriers and facilitators of proactive, internet-based chlamydia screening for reaching young heterosexual men

    PubMed Central

    2014-01-01

    Background Chlamydia trachomatis is a common bacterial sexually transmitted infection (STI), which disproportionately affects young people under 25 years. Commonly, more women are offered screening than men. This study obtained the views of general practitioners and practice nurses towards Internet-based screening and assessed levels of support for the development of proactive screening targeting young heterosexual men via the Internet. Methods Semi-structured telephone interviews with 10 general practitioners and 8 practice nurses, across Central Scotland. Topics covered: experience of screening heterosexual men for chlamydia, views on the use of the Internet as a way to reach young men for chlamydia screening, beliefs about the potential barriers and facilitators to Internet-based screening. Transcripts from audio recordings were analysed with Framework Analysis, using QSR NVivo10. Results Experiences of chlamydia screening were almost exclusively with women, driven by the nature of consultations and ease of raising sexual health issues with female patients; few practice nurses reported seeing men during consultations. All participants spoke in favour of Internet-based screening for young men. Participants reported ease of access and convenience as potential facilitators of an Internet-based approach but anonymity and confidentiality could be potential barriers and facilitators to the success of an Internet approach to screening. Concerns over practical issues as well as those pertaining to gender and socio-cultural issues were raised. Conclusions Awareness of key barriers and facilitators, such as confidentiality, practicality and socio-cultural influences, will inform the development of an Internet-based approach to screening. However, this approach may have its limits in terms of being able to tackle wider social and cultural barriers, along with shifts in young people’s and health professionals’ attitudes towards screening. Nevertheless, employing

  6. Methods for external event screening quantification: Risk Methods Integration and Evaluation Program (RMIEP) methods development

    SciTech Connect

    Ravindra, M.K.; Banon, H. )

    1992-07-01

    In this report, the scoping quantification procedures for external events in probabilistic risk assessments of nuclear power plants are described. External event analysis in a PRA has three important goals; (1) the analysis should be complete in that all events are considered; (2) by following some selected screening criteria, the more significant events are identified for detailed analysis; (3) the selected events are analyzed in depth by taking into account the unique features of the events: hazard, fragility of structures and equipment, external-event initiated accident sequences, etc. Based on the above goals, external event analysis may be considered as a three-stage process: Stage I: Identification and Initial Screening of External Events; Stage II: Bounding Analysis; Stage III: Detailed Risk Analysis. In the present report, first, a review of published PRAs is given to focus on the significance and treatment of external events in full-scope PRAs. Except for seismic, flooding, fire, and extreme wind events, the contributions of other external events to plant risk have been found to be negligible. Second, scoping methods for external events not covered in detail in the NRC's PRA Procedures Guide are provided. For this purpose, bounding analyses for transportation accidents, extreme winds and tornadoes, aircraft impacts, turbine missiles, and chemical release are described.

  7. Methods for external event screening quantification: Risk Methods Integration and Evaluation Program (RMIEP) methods development

    SciTech Connect

    Ravindra, M.K.; Banon, H.

    1992-07-01

    In this report, the scoping quantification procedures for external events in probabilistic risk assessments of nuclear power plants are described. External event analysis in a PRA has three important goals; (1) the analysis should be complete in that all events are considered; (2) by following some selected screening criteria, the more significant events are identified for detailed analysis; (3) the selected events are analyzed in depth by taking into account the unique features of the events: hazard, fragility of structures and equipment, external-event initiated accident sequences, etc. Based on the above goals, external event analysis may be considered as a three-stage process: Stage I: Identification and Initial Screening of External Events; Stage II: Bounding Analysis; Stage III: Detailed Risk Analysis. In the present report, first, a review of published PRAs is given to focus on the significance and treatment of external events in full-scope PRAs. Except for seismic, flooding, fire, and extreme wind events, the contributions of other external events to plant risk have been found to be negligible. Second, scoping methods for external events not covered in detail in the NRC`s PRA Procedures Guide are provided. For this purpose, bounding analyses for transportation accidents, extreme winds and tornadoes, aircraft impacts, turbine missiles, and chemical release are described.

  8. A walk-in screening of dementia in the general population in Taiwan.

    PubMed

    Chen, Chun-Hung; Wang, Ling-Chun; Ma, Tzu-Chiao; Yang, Yuan-Han

    2014-01-01

    Alzheimer's disease (AD) has increased in its prevalence due to the increasing aged population. Currently there is no updated data on the prevalence of dementia including its very mild stage in Taiwan. Under the extensive coverage of Mentality Protection Center (MPC), Fo Guang Shan, Taiwan, the volunteers of MPC have conducted the medicine-related services and the screening of dementia by AD8 (ascertainment of dementia 8) that can screen the dementia even at its very mild stage in general population in all Taiwan. From 2011 to 2013, in total, 2,171 participants, 368 in the northern, 549 in the central, 877 in the southern, and 377 in the eastern part, were recruited with the mean age being 66.9 ± 10.2 years old. The ratio of suspected dementia patients, AD8 score greater than or equal to 2, was 13.6% of all recruited participants with their mean AD8 score being 2.9 ± 1.3, mean age being 69.4 ± 10.8 years old, and female predominance being 73.0%. Although this is a screening study, it has extensive coverage of all Taiwan and the use of AD8 is capable of screening very mild dementia. A further study with a randomized sampling to examine the prevalence and incidence of dementia including its very mild stage is encouraged. PMID:24883363

  9. Hyperlipidaemia in general practice: three year follow up of an opportunistic screening project.

    PubMed Central

    Mann, J I; Morgan, B; Ball, M; Mant, D; Jones, L; Robertson, I

    1990-01-01

    As part of the national lipid screening project 927 people with a plasma cholesterol level greater than 6.5 mM were detected by screening 4006 men and women aged 25-59 years. Three years later 801 of the 878 patients eligible for a follow-up study (91%) had been followed up at least once. The median number of follow-up visits was two. The bulk of the workload fell on the nursing staff. The mean decrease in cholesterol level was 8-14% in those receiving dietary advice only, 15-25% in those receiving additional drug treatment and 12% for all patients. A proportion of this decrease must be attributable to regression to the mean, loss to follow up when patients were doing well, and the patients' knowledge of their follow-up date. Data on a group of patients not attending for regular follow up suggest that regression to the mean could account for up to 7% of the cholesterol reduction observed. Screening for hyperlipidaemia in general practice is feasible when the necessary infrastructure is provided, but even with a fairly conservative protocol 3% of those screened received drug treatment. PMID:2271263

  10. The appropriateness of employing imaging screening technologies: report of the methods committee of the ACR task force on screening technologies.

    PubMed

    Hillman, Bruce J; Black, William C; D'orsi, Carl; Hauser, J Bruce; Smith, Robert

    2004-11-01

    Screening for disease using imaging technologies is a growing phenomenon. For some applications (e.g., mammography and breast cancer), there is solid evidence that imaging screening reduces disease-specific mortality. However, for other applications, the public interest in imaging screening is progressing despite a lack of valid scientific evidence that such screening improves the public's health. Clinical trials promise to eventually shed light on the value of imaging screening, but the results of these trials will not be known for several years. In the meantime, physicians and the public need guidance on whether specific imaging screening examinations are appropriate. The ACR charged the Methods Committee of its Task Force on Screening Technologies to advise the organization on how it could best use available evidence to make public recommendations on imaging screening technologies. This article is the outcome of the committee's deliberations, including recommendations for the method of arriving at a recommendation, the approach to dissemination, and to whom the recommendations should be targeted.

  11. Knowledge and practice of prostate cancer screening among general practitioners in Malaysia: a cross-sectional study

    PubMed Central

    Tun Firzara, Abdul Malik; Ng, Chirk Jenn

    2016-01-01

    Objective Screening for prostate cancer remains controversial. General practitioners (GPs) play an important role in assisting men to make an informed decision on prostate cancer screening. The aim of this study was to determine the knowledge and practice of prostate cancer screening among private GPs in Malaysia. Design A cross-sectional study. Setting Private general practices in Selangor, Malaysia. Participants 311 randomly selected full-time private GPs were recruited between September 2013 and January 2014. Outcome measures Questionnaires were distributed to the GPs via postal mail and clinic visits. The main outcomes were: knowledge of prostate cancer risk factors and screening tests; GPs' prostate cancer screening practices; and factors influencing GPs' decision to screen for prostate cancer. Associations between covariates and propensity to screen for prostate cancer were determined using logistic regression. Results The response rate was 65%. The proportion of GPs who overestimated the positive predictive values of prostrate-specific antigen (PSA), digital rectal examination (DRE) and a combination of PSA and DRE was 63%, 57% and 64%, respectively. About 49.5% of the respondents would routinely screen asymptomatic men for prostate cancer; of them, 94.9% would use PSA to screen. Male GPs who would consider having a PSA test performed on themselves were six times more likely to screen asymptomatic men than GPs who would not have the test (OR=6.88, 95% CI 1.40 to 33.73), after adjusting for age and duration of practice. Conclusions GPs overestimated the accuracy of PSA in prostate cancer screening. Their intention to screen for prostate cancer themselves predicted their propensity to screen their patients for prostate cancer. This finding highlights the potential of using a new approach to change GPs' screening practices via addressing GPs' own screening behaviour. PMID:27687897

  12. Otoacoustic emissions: a new method for newborn hearing screening.

    PubMed

    Saurini, P; Nola, G; Lendvai, D

    2004-01-01

    Pediatric deafness is a handicap affecting approximately 2/1000 newborns. Currently, its diagnosis is markedly delayed, since it occurs approximately at 24 to 36 months of age; at this age rehabilitation procedures (i.e., acoustic prosthesis, speech therapy, psychological interventions on the family, or cochlear implants in the most serious situations) are unable to ensure a complete development of both the voice and the speech, thus preventing the full participation of the deaf child in social living. The turning point has taken place when methods and techniques were developed; they are aimed at the very early diagnosis of infantile deafness and are based on the recordings of otoacoustic emissions, that is, acoustic signals of extremely weak intensity originating in the inner ear, which not only is a passive transducer, but is able to generate sounds also. Any lack of or any change in otoacoustic emissions is a accurate index of disabling deafness. The test under study allows to perform selectively a mass screening on newborns (it is carried out 2 or 3 days after birth) since it is definetely non-invasive, it is done very rapidly (a few seconds only), it is cost-effective and higly reliable. The newborn hearing screening is being accepted, at a faster growing pace, by an increasing number of health systems in the whole world.

  13. SLCA/IP power alternative screening method (SPASM)

    SciTech Connect

    Palmer, S.C. |; Ancrile, J.D.

    1995-03-01

    This report describes the SLCA/IP Power Alternative Screening Method (SPASM), which was used to screen 784 possible combinations of electric power marketing alternatives and dam operational scenarios to provide a representative range for analysis in the Western Area Power Administration Salt Lake City Area Integrated Projects (SLCA/IP) Electric Power Marketing Environmental Impact Statement (EIS). Each combination consists of one energy and capacity commitment level and one operational scenario for each of the hydroelectric facilities at Glen Canyon Dam, Flaming Gorge Dam, and the Aspinall Unit. The total annual cost to the SLCA/IP firm power customers of each of the 784 combinations is estimated and included in a relative frequency distribution. A relative frequency distribution is also generated for each marketing alternative. The number of combinations is reduced to 12 by taking the mean value and endpoint value for each of four marketing alternatives. Some minor deviations from this procedure, which are made for political purposes, are explained. 9 figs., 14 tabs.

  14. Antibody screening & identification in the general patient population at a tertiary care hospital in New Delhi, India

    PubMed Central

    Makroo, Raj Nath; Bhatia, Aakanksha; Hegde, Vikas; Chowdhry, Mohit; Thakur, Uday Kumar; Rosamma, N.L.

    2014-01-01

    Background & objectives: The development of alloantibodies can significantly complicate transfusion therapy and results in difficulties in cross-matching of blood. Most literature on alloimmunization is limited to multitransfused individuals, with very few studies on the general hospital patients. This study was aimed at assessing the frequency and type of unexpected red cell antibodies in the general patient population at a multispecialty tertiary care centre in New Delhi, India. Methods: The results of 49,077 antibody screening tests carried out on patients, from January 2009 to December 2012 were analyzed. The clinical and transfusion records were reviewed. The data were compiled and statistically analysed. Results: A total of 49,077 (29,917; 60.96% males and 19,160; 39.04% females) patient samples were screened for the presence of unexpected antibodies. Antibody screening was positive in 403 patients (0.82%). In the serum samples of 164 patients only autoantibodies were identified, 27 revealed autoantibodies with one or more underlying alloantibodies, while 212 patients had only alloantibody/ies in their serum. The overall alloimmunization rate was 0.49 per cent. Antibodies against the Rh system were the most frequent (64.1%), the most common alloantibody identified being anti E (37.2%), followed by anti D (19.2%). Interpretation & conclusions: Since clinically significant antibodies are frequently detected in our patient population, antibody screening and if required, identification is the need of the hour. Since antibodies against the common Rh and Kell blood group antigens are the most frequent, provision of Rh and Kell matched red cells may be of protective value. PMID:25366208

  15. Chemical screening methods for flagellar phenotypes in Chlamydomonas.

    PubMed

    Avasthi, Prachee; Marshall, Wallace F

    2013-01-01

    Cilia and flagella are important organelles used for sensing the external cellular environment or for motility. Abnormalities in ciliary structure or function can have devastating pathological consequences ranging from sinusitis and obesity to polycystic kidney disease, retinal degeneration, and mental retardation. Chlamydomonas flagella are excellent models to study the regulation and normal function of cilia. We utilized the 1280 compound Sigma LOPAC annotated library to screen for phenotypes in Chlamydomonas flagellar length, motility, deflagellation, and cellular toxicity. Phenotypes were assessed by quantitation from direct microscopic visualization and custom-designed motility/viability assays. Compounds were clustered based on data across all assays to facilitate the identification of novel pathways regulating flagella in Chlamydomonas. These methods can both aid our understanding of the basic biology of flagellar regulation and provide useful points of therapeutic intervention for cilia-related disorders.

  16. Screening portal, system and method of using same

    DOEpatents

    Linker, Kevin L.; Hunter, John A.; Brusseau, Charles A.

    2013-04-30

    A portal, system and method for screening an object for a target substance is provided. The portal includes an inflatable bladder expandable to form a test space for receiving the object and a plurality of nozzles positioned about the inflatable bladder. The nozzles are in fluid communication with a fluid source for directing air over the object whereby samples are removed from the object for examination. A collector is operatively connected to the inflatable bladder for collecting the samples removed from the object. A detector is operatively connected to the collector for examining the removed samples for the presence of the target substance. At least one preconcentrator may be operatively connected to the collector for concentrating the samples collected thereby.

  17. SCREENING METHODS FOR SELECTION OF SURFACTANT FORMULATIONS FOR IOR FROM FRACTURED CARBONATE RESERVOIRS

    SciTech Connect

    William A. Goddard III; Yongchun Tang; Patrick Shuler; Mario Blanco; Yongfu Wu; Seung Soon Jang

    2005-07-01

    This topical report presents details of the laboratory work performed to complete Task 1 of this project; developing rapid screening methods to assess surfactant performance for IOR (Improved Oil Recovery) from fractured carbonate reservoirs. The desired outcome is to identify surfactant formulations that increase the rate and amount of aqueous phase imbibition into oil-rich, oil-wet carbonate reservoir rock. Changing the wettability from oil-wet to water-wet is one key to enhancing this water-phase imbibition process that in turn recovers additional oil from the matrix portion of a carbonate reservoir. The common laboratory test to evaluate candidate surfactant formulations is to measure directly the aqueous imbibition rate and oil recovery from small outcrop or reservoir cores, but this procedure typically requires several weeks. Two methods are presented here for the rapid screening of candidate surfactant formulations for their potential IOR performance in carbonate reservoirs. One promising surfactant screening protocol is based on the ability of a surfactant solution to remove aged crude oil that coats a clear calcite crystal (Iceland Spar). Good surfactant candidate solutions remove the most oil the quickest from the chips, plus change the apparent contact angle of the remaining oil droplets on the surface that thereby indicate increased water-wetting. The other fast surfactant screening method is based on the flotation behavior of powdered calcite in water. In this test protocol, first the calcite power is pre-treated to make the surface oil-wet. The next step is to add the pre-treated powder to a test tube and add a candidate aqueous surfactant formulation; the greater the percentage of the calcite that now sinks to the bottom rather than floats, the more effective the surfactant is in changing the solids to become now preferentially water-wet. Results from the screening test generally are consistent with surfactant performance reported in the literature.

  18. Validation of a two-plate microbiological method for screening antibiotic residues in shrimp tissue.

    PubMed

    Dang, Pham Kim; Degand, Guy; Danyi, Sophie; Pierret, Gilles; Delahaut, Philippe; Ton, Vu Dinh; Maghuin-Rogister, Guy; Scippo, Marie-Louise

    2010-07-01

    Microbiological inhibition screening tests could play an important role to detect residues of antibiotics in the different animal food products, but very few are available for the aquaculture products in general, and for shrimps in particular. A two-plate microbiological method to screen shrimp for residues of the most commonly used antibiotics has been developed and validated according to criteria derived from the European Commission Decision 2002/657/CE. Bacillus subtilis was used as a sensitive strain to target antibiotics. Culture conditions on Petri plates (pH of medium) were selected to enhance the capacity of antibiotic detection. Antibiotic residues were extracted from shrimps using acetonitrile/acetone (70/30, v/v) before application on Petri plates seeded with B. subtilis. The method was validated using spiked blank tissues as well as antibiotic treated shrimps with enrofloxacin and tetracycline, two antibiotics often found to be used in shrimp production. For tetracyclines and (fluoro)quinolones, the detection capability was below the maximum residue limit (MRL), while it was around the MRL for sulfonamides. The specificity of the microbiological screening was 100% in all cases while the sensitivity and accuracy was 100% in almost all cases. The capacity of the method to detect contaminated samples was confirmed on antibiotic treated shrimps, analyzed in parallel with a confirmatory method (Liquid Chromatography coupled to mass spectrometry (LC-MS)).

  19. A Method for Universal Screening of Elementary School Students: Development of the Social Challenges Screening Questionnaire

    ERIC Educational Resources Information Center

    Smith, Christopher J.; Pollard, Elena; Stein, Alexander J.; Ober-Reynolds, Sharman; Kirwan, Janet; Malligo, Amanda; Matthews, Nicole L.; Openden, Daniel; Melmed, Raun D.

    2015-01-01

    Schools regularly screen students for hearing and vision impairments because they present impediments to academic progress. For the same reason, schools should consider adding a universal screening for social challenges, which may also impede the learning process. This study reports on the development of the Social Challenges Screening…

  20. Can we evaluate population screening strategies in UK general practice? A pilot randomised controlled trial comparing postal and opportunistic screening for genital chlamydial infection

    PubMed Central

    Senok, A.; Wilson, P.; Reid, M.; Scoular, A.; Craig, N.; McConnachie, A.; Fitzpatrick, B.; MacDonald, A.

    2005-01-01

    Study objective: To assess whether opportunistic and postal screening strategies for Chlamydia trachomatis can be compared with usual care in a randomised trial in general practice. Design: Feasibility study for a randomised controlled trial. Setting: Three West of Scotland general medical practices: one rural, one urban/deprived, and one urban/affluent. Participants: 600 women aged 16–30 years, 200 from each of three participating practices selected at random from a sample of West of Scotland practices that had expressed interest in the study. The women could opt out of the study. Those who did not were randomly assigned to one of three groups: postal screening, opportunistic screening, or usual care. Results: 38% (85 of 221) of the approached practices expressed interest in the study. Data were collected successfully from the three participating practices. There were considerable workload implications for staff. Altogether 124 of the 600 women opted out of the study. During the four month study period, 55% (81 of 146) of the control group attended their practice but none was offered screening. Some 59% (80 of 136) women in the opportunistic group attended their practice of whom 55% (44 of 80) were offered screening. Of those, 64% (28 of 44) accepted, representing 21% of the opportunistic group. Forty eight per cent (59 of 124) of the postal group returned samples. Conclusion: A randomised controlled trial comparing postal and opportunistic screening for chlamydial infection in general practice is feasible, although resource intensive. There may be problems with generalising from screening trials in which patients may opt out from the offer of screening. PMID:15709078

  1. Screening methods to identify TALEN-mediated knockout mice.

    PubMed

    Nakagawa, Yoshiko; Yamamoto, Takashi; Suzuki, Ken-Ichi; Araki, Kimi; Takeda, Naoki; Ohmuraya, Masaki; Sakuma, Tetsushi

    2014-01-01

    Genome editing with site-specific nucleases, such as zinc-finger nucleases or transcription activator-like effector nucleases (TALENs), and RNA-guided nucleases, such as the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system, is becoming the new standard for targeted genome modification in various organisms. Application of these techniques to the manufacture of knockout mice would be greatly aided by simple and easy methods for genotyping of mutant and wild-type pups among litters. However, there are no detailed or comparative reports concerning the identification of mutant mice generated using genome editing technologies. Here, we genotyped TALEN-derived enhanced green fluorescent protein (eGFP) knockout mice using a combination of approaches, including fluorescence observation, heteroduplex mobility assay, restriction fragment length polymorphism analysis and DNA sequencing. The detection sensitivities for TALEN-induced mutations differed among these methods, and we therefore concluded that combinatorial testing is necessary for the screening and determination of mutant genotypes. Since the analytical methods tested can be carried out without specialized equipment, costly reagents and/or sophisticated protocols, our report should be of interest to a broad range of researchers who are considering the application of genome editing technologies in various organisms.

  2. A Method of Screening for Genes of Major Effect

    PubMed Central

    Kinghorn, B. P.; Kennedy, B. W.; Smith, C.

    1993-01-01

    This paper describes a method for screening animal populations on an index of calculated probabilities of genotype status at an unknown single locus. Animals selected by such a method might then be candidates in test matings and genetic marker analyses for major gene detection. The method relies on phenotypic measures for a continuous trait plus identification of sire and dam. Some missing phenotypes and missing pedigree information are permitted. The method is an iterative two-step procedure, the first step estimates genotype probabilities and the second step estimates genotypic effects by regressing phenotypes on genotype probabilities, modeled as true genotype status plus error. Prior knowledge or choice of major locus-free heritability for the trait of interest is required, plus initial starting estimates of the effect on phenotype of carrying one and two copies of the unknown gene. Gene frequency can be estimated by this method, but it is demonstrated that the consequences of using an incorrect fixed prior for gene frequency are not particularly adverse where true frequency of the allele with major effect is low. Simulations involving deterministic sampling from the normal distribution lead to convergence for estimates of genotype effects at the true values, for a reasonable range of starting values, illustrating that estimation of major gene effects has a rational basis. In the absence of polygenic effects, stochastic simulations of 600 animals in five generations resulted in estimates of genotypic effects close to the true values. However, stochastic simulations involving generation and fitting of both major genotype and animal polygenic effects showed upward bias in estimates of major genotype effects. This can be partially overcome by not using information from relatives when calculating genotype probabilities-a result which suggests a route to a modified method which is unbiased and yet does use this information. PMID:8514142

  3. General method for sequence-independent site-directed chimeragenesis.

    PubMed

    Hiraga, Kaori; Arnold, Frances H

    2003-07-01

    We have developed a simple and general method that allows for the facile recombination of distantly related (or unrelated) proteins at multiple discrete sites. To evaluate the sequence-independent site-directed chimeragenesis (SISDC) method, we have recombined beta-lactamases TEM-1 and PSE-4 at seven sites, examined the quality of the chimeric genes created, and screened the library of 2(8) (256) chimeras for functional enzymes. Probe hybridization and sequencing analyses revealed that SISDC generated a random library with little sequence bias and in which all targeted fragments were recombined in the desired order. Sequencing the genes from clones having functional lactamases identified 14 unique chimeras. These chimeras are characterized by a lower level of disruption, as calculated by the SCHEMA algorithm, than the library as a whole. These results illustrate the use of SISDC in creating designed chimeric protein libraries and further illustrate the ability of SCHEMA to identify chimeras whose folded structures are likely not to be disrupted by recombination. PMID:12823968

  4. Which screening method is appropriate for older cancer patients at risk for malnutrition?

    PubMed

    Isenring, Elizabeth; Elia, Marinos

    2015-04-01

    The risk for malnutrition increases with age and presence of cancer, and it is particularly common in older cancer patients. A range of simple and validated nutrition screening tools can be used to identify malnutrition risk in cancer patients (e.g., Malnutrition Screening Tool, Mini Nutritional Assessment Short Form Revised, Nutrition Risk Screening, and the Malnutrition Universal Screening Tool). Unintentional weight loss and current body mass index are common components of screening tools. Patients with cancer should be screened at diagnosis, on admission to hospitals or care homes, and during follow-up at outpatient or general practitioner clinics, at regular intervals depending on clinical status. Nutritional assessment is a comprehensive assessment of dietary intake, anthropometrics, and physical examination often conducted by dietitians or geriatricians after simple screening has identified at-risk patients. The result of nutritional screening, assessment and the associated care plans should be documented, and communicated, within and between care settings for best patient outcomes.

  5. A molecular beacon-based method for screening cervical cancer.

    PubMed

    Han, Suxia; Li, Ling; Jia, Xi; Ou, Wei; Ma, Jinlu; Wang, Hao; Zhao, Jing; Zhu, Qing

    2012-11-01

    The aim of this study is to develop a new screening method, molecular beacon (MB) imaging, for detection of cervical cancer and to determine its potential clinical applications by examining the sensitivity and specificity of target-specific MBs. Two target-specific molecular beacons were designed and synthesized for survivin and HPV16E6 mRNA. The two designed MBs and a random control MB were used to detect cervical cancer cell lines and a normal cell line. RT-PCR and western blot targeting survivin and HPV16E6 was done for verification. Furthermore the sensitivity and the specificity of the survivin and HPV16E6 mRNA MBs were examined in smears from 125 clinical cervical patients. The survivin and HPV16E6 mRNA MBs generated a strong fluorescence signal in cervical cancer cell lines, but not in the normal cell line, while the random control MB did not generated any signal in both cell lines. The fluorescence intensity correlated well with the gene expression levels in the cells determined by reverse transcription-PCR and Western blot analysis. The clinical sensitivity and the specificity of survivin MB-FITC were 72.5 and 77% while those of HPV16E6 MB-Cy3 were 96.1% and 71.6%, respectively. A parallel test of the two target MBs showed that the sensitivity increased to 98% and the specificity was 70.2%. The survivin and HPV16E6 mRNA MBs showed good reliability and sensitivity. They have great potential for clinical use in cervical cancer screening.

  6. Predicting Child Physical Activity and Screen Time: Parental Support for Physical Activity and General Parenting Styles

    PubMed Central

    Crain, A. Lauren; Senso, Meghan M.; Levy, Rona L.; Sherwood, Nancy E.

    2014-01-01

    Objective: To examine relationships between parenting styles and practices and child moderate-to-vigorous physical activity (MVPA) and screen time. Methods: Participants were children (6.9 ± 1.8 years) with a body mass index in the 70–95th percentile and their parents (421 dyads). Parent-completed questionnaires assessed parental support for child physical activity (PA), parenting styles and child screen time. Children wore accelerometers to assess MVPA. Results: Parenting style did not predict MVPA, but support for PA did (positive association). The association between support and MVPA, moreover, varied as a function of permissive parenting. For parents high in permissiveness, the association was positive (greater support was related to greater MVPA and therefore protective). For parents low in permissiveness, the association was neutral; support did not matter. Authoritarian and permissive parenting styles were both associated with greater screen time. Conclusions: Parenting practices and styles should be considered jointly, offering implications for tailored interventions. PMID:24812256

  7. Use of unbalanced laminates as a screening method for microcracking

    NASA Technical Reports Server (NTRS)

    Papadopoulos, Demetrios S.; Bowles, Kenneth J.

    1990-01-01

    State-of-the-art, high temperature polyimide matrix composites, reinforced with continuous graphite fibers are known to be susceptible to intraply cracking when thermally cycled over their useful service temperature range. It is believed that the transply cracking, in part, results from residual stresses caused by differences in coefficients of thermal expansion (CTE) between the polymer matrix and the reinforcement. Thermal cycling tests to investigate this phenomenon involve expensive time and energy consuming programs which are not economically feasible for use as a part of a materials screening process. As an alternative to thermal cycling studies, a study of unbalanced crossply graphite fiber reinforcement composites was conducted to assess the effect of the composite ply layup and surface condition on the residual stresses that remain after the processing of these materials. The residual stresses were assessed by measuring the radii of curvature of the types of laminates that were studied. The temperature at which stress-free conditions existed were determined and a dye penetrant method was used to observe surface damage resulting from excessive residual stress buildup. These results are compared with some published results of thermal cycling tests that were previously conducted on balanced polyimide composites.

  8. Genomic DNA microextraction: a method to screen numerous samples.

    PubMed

    Ramírez-Solis, R; Rivera-Pérez, J; Wallace, J D; Wims, M; Zheng, H; Bradley, A

    1992-03-01

    Many experimental designs require the analysis of genomic DNA from a large number of samples. Although the polymerase chain reaction (PCR) can be used, the Southern blot is preferred for many assays because of its inherent reliability. The rapid acceptance of PCR, despite a significant rate of false positive/negative results, is partly due to the disadvantages of the sample preparation process for Southern blot analysis. We have devised a rapid protocol to extract high-molecular-weight genomic DNA from a large number of samples. It involves the use of a single 96-well tissue culture dish to carry out all the steps of the sample preparation. This, coupled with the use of a multichannel pipette, facilitates the simultaneous analysis of multiple samples. The procedure may be automated since no centrifugation, mixing, or transferring of the samples is necessary. The method has been used to screen embryonic stem cell clones for the presence of targeted mutations at the Hox-2.6 locus and to obtain data from human blood.

  9. A simple method for evaluating image quality of screen-film system using a high-performance digital camera

    NASA Astrophysics Data System (ADS)

    Fujita, Naotoshi; Yamazaki, Asumi; Ichikawa, Katsuhiro; Kodera, Yoshie

    2009-02-01

    Screen-film systems are used in mammography even now. Therefore, it is important to measure their physical properties such as modulation transfer function (MTF) or noise power spectrum (NPS). The MTF and NPS of screen-film systems are mostly measured by using a microdensitometer. However, since microdensitometers are not commonly used in general hospitals, it is difficult to carry out these measurements regularly. In the past, Ichikawa et al. have measured and evaluated the physical properties of medical liquid crystal displays by using a high-performance digital camera. By this method, the physical properties of screen-film systems can be measured easily without using a microdensitometer. Therefore, we have proposed a simple method for measuring the MTF and NPS of screen-film systems by using a high-performance digital camera. The proposed method is based on the edge method (for evaluating MTF) and the one-dimensional fast Fourier transform (FFT) method (for evaluating NPS), respectively. As a result, the MTF and NPS evaluated by using the high-performance digital camera approximately corresponded with those evaluated by using a microdensitometer. It is possible to substitute the calculation of MTF and NPS by using a high-performance digital camera for that by using a microdensitometer. Further, this method also simplifies the evaluation of the physical properties of screen-film systems.

  10. Screening the fifth force in the Horndeski's most general scalar-tensor theories

    SciTech Connect

    Kase, Ryotaro; Tsujikawa, Shinji E-mail: shinji@rs.kagu.tus.ac.jp

    2013-08-01

    We study how the Vainshtein mechanism operates in the most general scalar-tensor theories with second-order equations of motion. The field equations of motion, which can be also applicable to most of other screening scenarios proposed in literature, are generally derived in a spherically symmetric space-time with a matter source. In the presence of a field coupling to the Ricci scalar, we clarify conditions under which the Vainshtein mechanism is at work in a weak gravitational background. We also obtain the solutions of the field equation inside a spherically symmetric body and show how they can be connected to exterior solutions that accommodate the Vainshtein mechanism. We apply our general results to a number of concrete models such as the covariant/extended Galileons and the DBI Galileons with Gauss-Bonnet and other terms. In these models the fifth force can be suppressed to be compatible with solar-system constraints, provided that non-linear field kinetic terms coupled to the Einstein tensor do not dominate over other non-linear field self-interactions.

  11. Optimization of solid-phase extraction for a liquid chromatographic-tandem mass spectrometric general unknown screening procedure by means of computational techniques.

    PubMed

    Decaestecker, Tineke N; Lambert, Willy E; Van Peteghem, Carlos H; Deforce, Dieter; Van Bocxlaer, Jan F

    2004-11-12

    A solid-phase extraction (SPE) method was optimized to suit the particular demands of an information-dependent acquisition LC-MS-MS procedure for general unknown screening in a forensic toxicology setting. In a first phase, a Plackett-Burman screening design with fold-over was carried out to distinguish the significant factors affecting the extraction procedure. This part eventuated in the determination of only three statistically relevant parameters, requiring consecutive optimization. To that end, in phase II of this study, a rotatable central composite design was applied to define the response surface as a function of the significant parameters and to choose the optimal conditions for the SPE.

  12. Screening of cider yeasts for sparkling cider production (Champenoise method).

    PubMed

    Suárez Valles, Belén; Pando Bedriñana, Rosa; Lastra Queipo, Ana; Mangas Alonso, Juan José

    2008-08-01

    A total of 350 colonies isolated from a cider cellar in Asturias (Spain) were identified by rDNA ITS-RFLP restriction analysis. Saccharomyces spp. strains were characterized by mitochondrial DNA (mtDNA) restriction analysis. Fifty-four different Saccharomyces spp. strains were identified and tested to ascertain their capacity to carry out secondary fermentation of sparkling ciders. The screening of yeasts to determine their principal enological characteristics (tolerance to ethanol, production of volatile acidity and hydrogen sulphide) was accomplished by means of rapid, non-expensive assays (plate agar). As a result, 13 (24%) of the 54 initial Saccharomyces spp. yeast strains were eliminated. The technological properties assessed were flocculation capacity, ethanol and sulphite tolerance, and production of major volatiles. Ten Saccharomyces cerevisiae strains were characterized as true flocculants; all of these strains were able to grow in ethanolic medium and in the presence of 200mg/l of sulphite. Applying cluster analysis to the production of amyl alcohols, isobutanol, propanol and 2-phenylethanol, the strains were classified in two natural groups. Two flocculent yeast strains referred to as 3' and 50', representative of the each statistical group, were selected together with two reference strains (Saccharomyces bayanus C6 and S. cerevisiae Levuline CHP) to elaborate four sparkling ciders by the Champenoise method. The analysis of variance (p<0.01) among ciders revealed that glycerol, acetaldehyde, ethyl acetate, methanol, propanol, i-butanol and 2-phenylethanol were significantly influenced by the secondary yeast strain. The results of sensory analysis indicated that all the sparkling ciders were scored as good. No significant differences among sparkling ciders were found for odour attributes and taste intensity. PMID:18541168

  13. Screening of Potential Remediation Methods for the 200-ZP-1 Operable Unit at the Hanford Site

    SciTech Connect

    Truex, Michael J.; Nimmons, Michael J.; Johnson, Christian D.; Dresel, P EVAN.; Murray, Christopher J.

    2006-08-07

    A screening-level evaluation of potential remediation methods for application to the contaminants of concern (COC) in the 200-ZP-1 Operable Unit at the Hanford Site was conducted based on the methods outlined in the Guidance for Conducting Remedial Investigations and Feasibility Studies under CERCLA Interim Final. The scope of this screening was to identify the most promising remediation methods for use in the more detailed analysis of remediation alternatives that will be conducted as part of the full feasibility study. The screening evaluation was conducted for the primary COC (potential major risk drivers). COC with similar properties were grouped for the screening evaluation. The screening evaluation was conducted in two primary steps. The initial screening step evaluated potential remediation methods based on whether they can be effectively applied within the environmental setting of the 200-ZP-1 Operable Unit for the specified contaminants. In the second step, potential remediation methods were screened using scoping calculations to estimate the scale of infrastructure, overall quantities of reagents, and conceptual approach for applying the method for each defined grouping of COC. Based on these estimates, each method was screened with respect to effectiveness, implementability, and relative cost categories of the CERCLA feasibility study screening process defined in EPA guidance.

  14. Adaptive multiscale model reduction with Generalized Multiscale Finite Element Methods

    NASA Astrophysics Data System (ADS)

    Chung, Eric; Efendiev, Yalchin; Hou, Thomas Y.

    2016-09-01

    In this paper, we discuss a general multiscale model reduction framework based on multiscale finite element methods. We give a brief overview of related multiscale methods. Due to page limitations, the overview focuses on a few related methods and is not intended to be comprehensive. We present a general adaptive multiscale model reduction framework, the Generalized Multiscale Finite Element Method. Besides the method's basic outline, we discuss some important ingredients needed for the method's success. We also discuss several applications. The proposed method allows performing local model reduction in the presence of high contrast and no scale separation.

  15. Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods.

    PubMed

    Duan, Jianxin; Dixon, Steven L; Lowrie, Jeffrey F; Sherman, Woody

    2010-09-01

    Virtual screening is a widely used strategy in modern drug discovery and 2D fingerprint similarity is an important tool that has been successfully applied to retrieve active compounds from large datasets. However, it is not always straightforward to select an appropriate fingerprint method and associated settings for a given problem. Here, we applied eight different fingerprint methods, as implemented in the new cheminformatics package Canvas, on a well-validated dataset covering five targets. The fingerprint methods include Linear, Dendritic, Radial, MACCS, MOLPRINT2D, Pairwise, Triplet, and Torsion. We find that most fingerprints have similar retrieval rates on average; however, each has special characteristics that distinguish its performance on different query molecules and ligand sets. For example, some fingerprints exhibit a significant ligand size dependency whereas others are more robust with respect to variations in the query or active compounds. In cases where little information is known about the active ligands, MOLPRINT2D fingerprints produce the highest average retrieval actives. When multiple queries are available, we find that a fingerprint averaged over all query molecules is generally superior to fingerprints derived from single queries. Finally, a complementarity metric is proposed to determine which fingerprint methods can be combined to improve screening results.

  16. A Polytomous Extension of the Generalized Distance Discriminating Method

    ERIC Educational Resources Information Center

    Sun, Jianan; Xin, Tao; Zhang, Shumei; de la Torre, Jimmy

    2013-01-01

    This article proposes a generalized distance discriminating method for test with polytomous response (GDD-P). The new method is the polytomous extension of an item response theory (IRT)-based cognitive diagnostic method, which can identify examinees' ideal response patterns (IRPs) based on a generalized distance index. The similarities…

  17. Use of a Hospital-Wide Screening Program for Early Detection of Sepsis in General Surgery Patients.

    PubMed

    MacQueen, Ian T; Dawes, Aaron J; Hadnott, Tracy; Strength, Kristen; Moran, Gregory J; Holschneider, Christine; Russell, Marcia M; Maggard-Gibbons, Melinda

    2015-10-01

    Sepsis remains a significant source of mortality among hospitalized patients. This study examines the usage of a vital sign-based screening protocol in identifying postoperative patients at risk for sepsis at an academic-affiliated medical center. We identified all general surgery inpatients undergoing abdominopelvic surgery from January to June 2014, and compared those with positive screening tests to a sample of screen-negative controls. Multivariate logistic regression was used to identify predictors of positive screening tests and progression to severe sepsis. In total, 478 patients underwent abdominopelvic operations, 59 had positive screening tests, 33 qualified for sepsis, and six progressed to severe sepsis. Predictors of a positive screening test were presence of cancer [odds ratio (OR) 30.7, 95% confidence interval (CI) 2.2-420], emergency operation (OR 6.5, 95% CI 1.7-24), longer operative time (OR 2.2/h, 95% CI 1.2-4.1), and presence of postoperative infection (OR 6.4, 95% CI 1.5-27). The screening protocol had sensitivity 100 per cent and specificity 88 per cent for severe sepsis. We identified no predictors of severe sepsis. In conclusion, vital sign-based screening provides value by drawing early attention to patients with potential to develop sepsis, but escalation of care for these patients should be based on clinical judgment. PMID:26463311

  18. Diabetic Retinopathy Screening and Monitoring of Early Stage Disease in Australian General Practice: Tackling Preventable Blindness within a Chronic Care Model

    PubMed Central

    Crossland, Lisa; Askew, Deborah; Ware, Robert; Cranstoun, Peter; Mitchell, Paul; Bryett, Andrew; Jackson, Claire

    2016-01-01

    Introduction. Diabetic retinopathy (DR) is the leading cause of preventable blindness in Australia. Up to 50% of people with proliferative DR who do not receive timely treatment will become legally blind within five years. Innovative and accessible screening, involving a variety of primary care providers, will become increasingly important if patients with diabetes are to receive optimal eye care. Method. An open controlled trial design was used. Five intervention practices in urban, regional, and rural Australia partnered with ophthalmologists via telehealth undertook DR screening and monitoring of type 2 diabetes patients and were compared with control practices undertaking usual care 2011–2014. Results. Recorded screening rates were 100% across intervention practices, compared with 22–53% in control practices. 31/577 (5%) of patients in the control practices were diagnosed with mild-moderate DR, of whom 9 (29%) had appropriate follow-up recorded. This was compared with 39/447 (9%) of patients in the intervention group, of whom 37 (95%) had appropriate follow-up recorded. Discussion and Conclusion. General practice-based DR screening via Annual Cycle of Care arrangements is effective across differing practice locations. It offers improved recording of screening outcomes for Australians with type 2 diabetes and better follow-up of those with screen abnormalities. PMID:26798655

  19. Cross-screening: a new method to assemble clones rapidly and unambiguously into contigs.

    PubMed

    Locke, J; Rairdan, G; McDermid, H; Nash, D; Pilgrim, D; Bell, J; Roy, K; Hodgetts, R

    1996-02-01

    We have developed a new procedure that relies on an array of cross-hybridization tests to order a set of random clones into a contig. The method, called cross-screening, uses each clone as a target and its end sequences as probes, in a matrix of reciprocal cross-hybridization tests performed on a single blot. The relationships among the clones are determined rapidly from the pairwise tests, allowing clone order to be determined directly. We have applied this technique to DNAs from a set of overlapping lambda clones from Drosophila chromosome 4. The location and orientation of each clone derived from the cross-screening data was that expected from the map assembled from overlapping restriction sites and chromosomal walking. The procedure provided additional information on a previously unknown, internally repeated DNA sequence. To demonstrate the general utility of the procedure, we have applied it to a previously described clone set within a contig in region 22q12 of human chromosome 22. The correct relative position and orientation of these clones were derived from the cross-screening data without knowledge of, or reference to, any nucleotide sequence or restriction site analysis of the DNA concerned. The cross-screening procedure is fast, economical, and robust and allows clone overlaps to be determined efficiently, with minimal interference from repeated DNA sequences. This new procedure is specifically designed for small groups of overlapping clones (tens to hundreds) and should facilitate the ordering of subclone libraries derived from small chromosomes or the large cloned inserts carried in YAC, BAC, and P1 vectors.

  20. Postal urine specimens: are they a feasible method for genital chlamydial infection screening?

    PubMed Central

    Macleod, J; Rowsell, R; Horner, P; Crowley, T; Caul, E O; Low, N; Smith, G D

    1999-01-01

    BACKGROUND: A United Kingdom (UK) screening programme for Chlamydia trachomatis has recently been announced. Pilot projects involving the opportunistic testing of women attending health facilities are due to commence in several sites. There is a danger that this approach will fail to obtain adequate population coverage. The alternative--true systematic population screening--is generally assumed to be unfeasible. Studies in Denmark using postal urine specimens have challenged this assumption. No such studies have been reported from the UK. AIM: To assess the potential of urine specimens sent by post as the basis for a UK population screening strategy for genital chlamydial infection. METHOD: Two hundred patients (100 men, 100 women) aged 18 to 45 years were randomly sampled from the list of one urban group practice. Subjects were mailed an explanatory letter, a urine sample container, a sexual lifestyle questionnaire, and a prepaid return envelope. Non-responders were contacted by telephone; persistent non-responders were visited at home. Samples were tested for Chlamydia by DNA amplification and enzyme immunoassay. RESULTS: Sixty-four (32%) subjects were no longer living at their GP registered address. Of the remaining 136, 126 (93%) responded to the survey and 113 (83%) accepted the request for a urine sample and completed a questionnaire. Acceptance rates were similar for men and women and across age groups. Four samples (3%) were Chlamydia positive. CONCLUSION: Home mailed urine specimen collection in conjunction with a self-completed postal questionnaire is feasible. This could provide a viable basis both for determining population Chlamydia prevalence and for a UK Chlamydia population screening strategy. Overall cost effectiveness of such a strategy will depend on the cost of the test used. Comparative performance characteristics of the different currently available tests in this setting have yet to be fully determined. PMID:10562745

  1. Data screening methods for baseline ecological risk assessments

    SciTech Connect

    Schmeising, L.M.

    1994-12-31

    In conducting ecological risk assessments (ERAs), it is commonplace to take a phased approach in assessing potential impacts to ecological receptors. The first phase, the baseline ecological risk assessment (BERA) often includes a component which involves the systematic screening of the analytical data for abiotic media (i.e., surface water, sediment, surface soil) versus available ecology-based criteria, standards, guidelines, and benchmark values. Examples of ecological benchmark values include applicable toxicity data, such as no observed effects levels (NOELS) , lowest observed effects levels (LOELS) , or lethal doses (LC50, LD50) for selected indicator species or surrogates. An additional step often included in the screening process, is the calculation of ecological quotients (EQs), or environmental concentration/ benchmark ratios. The intent of the data screening process in performing BERAs is to determine which contaminants at a site are potentially posing a threat to ecological receptors. These contaminants, known as the ecological contaminants of concern (COCS) , are retained for further, detailed evaluations in later phases of the risk assessment. Application of these screening methodologies is presented, along with examples of ecology-based criteria, standards, and guidelines, and benchmark values.

  2. Mounting method improves electrical and vibrational characteristics of screen electrodes

    NASA Technical Reports Server (NTRS)

    Nelson, R. E.

    1969-01-01

    Electrical characteristics of the mesh or screen electrodes used in electron tubes are improved by decreasing the shunt capacitance of the tube while retaining the close spacing needed for the required resolution. Vibrational characteristics are enhanced by raising the natural resonant frequency.

  3. Evaluation of a standard test method for screening fuels in soils

    SciTech Connect

    Sorini, S.S.; Schabron, J.F.

    1996-12-31

    A new screening method for fuel contamination in soils was recently developed as American Society for Testing and Materials (ASTM) Method D-5831-95, Standard Test Method for Screening Fuels in Soils. This method uses low-toxicity chemicals and can be sued to screen organic- rich soils, as well as being fast, easy, and inexpensive to perform. Fuels containing aromatic compounds, such as diesel fuel and gasoline, as well as other aromatic-containing hydrocarbon materials, such as motor oil, crude oil, and cola oil, can be determined. The screening method for fuels in soils was evaluated by conducting a Collaborative study on the method. In the Collaborative study, a sand and an organic soil spiked with various concentrations of diesel fuel were tested. Data from the Collaborative study were used to determine the reproducibility (between participants) and repeatability (within participants) precision of the method for screening the test materials. The Collaborative study data also provide information on the performance of portable field equipment (patent pending) versus laboratory equipment for performing the screening method and a comparison of diesel concentration values determined using the screening method versus a laboratory method.

  4. Comparison of three screening methods to select mixed-microbial inoculum for mixed-acid fermentations.

    PubMed

    Golub, Kristina W; Forrest, Andrea K; Wales, Melinda E; Hammett, Amy Jo M; Cope, Julia L; Wilkinson, Heather H; Holtzapple, Mark T

    2013-02-01

    Using a mixed culture of microorganisms, the carboxylate platform converts biomass into hydrocarbons and chemicals. To develop a method that identifies the highest performing inoculum for carboxylate fermentations, five bacterial communities were screened and ranked by three fermentation performance tests: (1) 30-day batch screen, (2) 28-day continuum particle distribution model (CPDM), and (3) 5-month continuous countercurrent fermentation trains. To screen numerous inocula sources, these tests were used sequentially in an aseptic environment. For the batch-fermentation screen, Inoculum 1 achieved the highest conversion. For the CPDM evaluation, the operating map for Inoculum 1 had the highest performance. For the continuous countercurrent fermentation, the train resulting from Inoculum 1 was among the best performers. This study suggests that the three screens are a useful and predictive method for choosing optimal inocula sources. The bacterial community with optimal performance in these three screens could be considered for use in commercial-scale fermentations. PMID:23334035

  5. A weak Galerkin generalized multiscale finite element method

    DOE PAGES

    Mu, Lin; Wang, Junping; Ye, Xiu

    2016-03-31

    In this study, we propose a general framework for weak Galerkin generalized multiscale (WG-GMS) finite element method for the elliptic problems with rapidly oscillating or high contrast coefficients. This general WG-GMS method features in high order accuracy on general meshes and can work with multiscale basis derived by different numerical schemes. A special case is studied under this WG-GMS framework in which the multiscale basis functions are obtained by solving local problem with the weak Galerkin finite element method. Convergence analysis and numerical experiments are obtained for the special case.

  6. Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles

    PubMed Central

    2016-01-01

    Ensemble docking can be a successful virtual screening technique that addresses the innate conformational heterogeneity of macromolecular drug targets. Yet, lacking a method to identify a subset of conformational states that effectively segregates active and inactive small molecules, ensemble docking may result in the recommendation of a large number of false positives. Here, three knowledge-based methods that construct structural ensembles for virtual screening are presented. Each method selects ensembles by optimizing an objective function calculated using the receiver operating characteristic (ROC) curve: either the area under the ROC curve (AUC) or a ROC enrichment factor (EF). As the number of receptor conformations, N, becomes large, the methods differ in their asymptotic scaling. Given a set of small molecules with known activities and a collection of target conformations, the most resource intense method is guaranteed to find the optimal ensemble but scales as O(2N). A recursive approximation to the optimal solution scales as O(N2), and a more severe approximation leads to a faster method that scales linearly, O(N). The techniques are generally applicable to any system, and we demonstrate their effectiveness on the androgen nuclear hormone receptor (AR), cyclin-dependent kinase 2 (CDK2), and the peroxisome proliferator-activated receptor δ (PPAR-δ) drug targets. Conformations that consisted of a crystal structure and molecular dynamics simulation cluster centroids were used to form AR and CDK2 ensembles. Multiple available crystal structures were used to form PPAR-δ ensembles. For each target, we show that the three methods perform similarly to one another on both the training and test sets. PMID:27097522

  7. DEMONSTRATION BULLETIN: FIELD ANALYTICAL SCREENING PROGRAM: PCB METHOD - U.S. ENVIRONMENTAL PROTECTION AGENCY

    EPA Science Inventory

    The field analytical screening program (FASP) polychlorinated biphenyl (PCB) method uses a temperature-programmable gas chromatograph (GC) equipped with an electron capture detector (ECD) to identify and quantify PCBs. Gas chromatography is an EPA-approved method for determi...

  8. Challenges to implementation of developmental screening in urban primary care: a mixed methods study

    PubMed Central

    2014-01-01

    Background Research is needed to identify challenges to developmental screening and strategies for screening in an urban pediatric setting. Methods Parents of young children and clinicians at four urban pediatric practices participated in focus groups prior to implementation of screening. Participants were queried regarding attitudes, social norms, and barriers to developmental screening. Using information from the focus groups, workflow strategies were developed for implementing screening. Referral rates and satisfaction with screening were gathered at the conclusion. Results Six focus groups of parents and clinicians were conducted. Major themes identified included 1) parents desired greater input on child development and increased time with physicians, 2) physicians did not fully trust parental input, 3) physicians preferred clinical acumen over screening tools, and 4) physicians lacked time and training to conduct screening. For the intervention, developmental screening was implemented at the 9-, 18-, 24-, and 30-month well visits using the Ages & Stages Questionnaire-II and the Modified Checklist for Toddlers. 1397 (98% of eligible) children under 36 months old were enrolled, and 1184 (84%) were screened at least once. 1002 parents (85%) completed a survey at the conclusion of the screening trial. Most parents reported no difficulty completing the screens (99%), felt the screens covered important areas of child development (98%), and felt they learned about their child’s strengths and limitations (88%). Conclusions Developmental screening in urban low-income practices is feasible and acceptable, but requires strategies to capture parental input, provide training, facilitate referrals, and develop workflow procedures and electronic decision support. PMID:24447411

  9. Novel screening method for potential skin-whitening compounds by a luciferase reporter assay.

    PubMed

    Shirasugi, Ichiro; Sakakibara, Yoichi; Yamasaki, Masao; Nishiyama, Kazuo; Matsui, Takashi; Liu, Ming-Cheh; Suiko, Masahito

    2010-01-01

    Measurement of the melanin content by using B16 melanoma cells is generally applied to find novel skin-whitening agents. However, this measurement method using B16 melanoma cells has such disadvantages, as the time taken, its sensitivity, and troublesomeness. We therefore attempted in the present study to establish a reporter assay system by measuring the tyrosinase promoter activity to use for convenient, high-throughput screening of new melanogenesis inhibitors. We first confirmed the validity of this reporter assay system by using such known skin-whitening agents, as arbutin, sulforaphane, and theaflavin 3,3'-digallate. We then compared the effect of 56 compounds on the tyrosinase promoter activity to test this reporter assay system. Carnosol, and rottlerin strongly inhibited the tyrosinase promoter activity. Moreover, carnosol and rottlerin decreased melanin synthesis and tyrosinase expression in a dose-dependent manner when using B16 melanoma cells. These results indicate this new luciferase reported assay system to be an effective and convenient method for screening potential skin-whitening compounds. PMID:21071833

  10. High-throughput method for optimum solubility screening for homogeneity and crystallization of proteins

    DOEpatents

    Kim, Sung-Hou; Kim, Rosalind; Jancarik, Jamila

    2012-01-31

    An optimum solubility screen in which a panel of buffers and many additives are provided in order to obtain the most homogeneous and monodisperse protein condition for protein crystallization. The present methods are useful for proteins that aggregate and cannot be concentrated prior to setting up crystallization screens. A high-throughput method using the hanging-drop method and vapor diffusion equilibrium and a panel of twenty-four buffers is further provided. Using the present methods, 14 poorly behaving proteins have been screened, resulting in 11 of the proteins having highly improved dynamic light scattering results allowing concentration of the proteins, and 9 were crystallized.

  11. An Open Source Based High Content Screening Method for Cell Biology Laboratories Investigating Cell Spreading and Adhesion

    PubMed Central

    Pietro, Maurianne A.; Schwab, Martin E.

    2013-01-01

    Background Adhesion dependent mechanisms are increasingly recognized to be important for a wide range of biological processes, diseases and therapeutics. This has led to a rising demand of pharmaceutical modulators. However, most currently available adhesion assays are time consuming and/or lack sensitivity and reproducibility or depend on specialized and expensive equipment often only available at screening facilities. Thus, rapid and economical high-content screening approaches are urgently needed. Results We established a fully open source high-content screening method for identifying modulators of adhesion. We successfully used this method to detect small molecules that are able to influence cell adhesion and cell spreading of Swiss-3T3 fibroblasts in general and/or specifically counteract Nogo-A-Δ20-induced inhibition of adhesion and cell spreading. The tricyclic anti-depressant clomipramine hydrochloride was shown to not only inhibit Nogo-A-Δ20-induced cell spreading inhibition in 3T3 fibroblasts but also to promote growth and counteract neurite outgrowth inhibition in highly purified primary neurons isolated from rat cerebellum. Conclusions We have developed and validated a high content screening approach that can be used in any ordinarily equipped cell biology laboratory employing exclusively freely available open-source software in order to find novel modulators of adhesion and cell spreading. The versatility and adjustability of the whole screening method will enable not only centers specialized in high-throughput screens but most importantly also labs not routinely employing screens in their daily work routine to investigate the effects of a wide range of different compounds or siRNAs on adhesion and adhesion-modulating molecules. PMID:24205161

  12. Educational paper: screening in cancer predisposition syndromes: guidelines for the general pediatrician.

    PubMed

    Teplick, Alexis; Kowalski, Megan; Biegel, Jaclyn A; Nichols, Kim E

    2011-03-01

    Improvements in our understanding of the genetic basis of human disease and increased utilization of genetic testing have identified a variety of heritable disorders associated with the onset of benign or malignant neoplasms during childhood. In many cases, the optimal management of affected children is dependent upon the early detection and treatment of tumors. Surveillance strategies based on the natural history of these lesions are often complex, requiring clinical examinations and radiologic and laboratory studies that evolve over a patient's lifetime. A general pediatrician may be the first to suspect one of these disorders in a patient, or may be faced with questions regarding genetic testing, cancer risk, and cancer screening. The pediatrician may also coordinate and interpret the results of specific surveillance studies. In this review, we present the genetic etiology, presentation, natural history, and surveillance recommendations for four disparate hereditary tumor predisposing syndromes, including Beckwith-Wiedemann syndrome/idiopathic hemihyperplasia, von Hippel-Lindau disease, Li-Fraumeni syndrome, and rhabdoid tumor/schwannomatosis. These examples are meant to offer the clinician practical recommendations as well as a framework upon which to base the understanding and management of other conditions associated with an increased risk to develop tumors in childhood. PMID:21210147

  13. General Practitioners’ Experiences of, and Responses to, Uncertainty in Prostate Cancer Screening: Insights from a Qualitative Study

    PubMed Central

    2016-01-01

    Background Prostate-specific antigen (PSA) testing for prostate cancer is controversial. There are unresolved tensions and disagreements amongst experts, and clinical guidelines conflict. This both reflects and generates significant uncertainty about the appropriateness of screening. Little is known about general practitioners’ (GPs’) perspectives and experiences in relation to PSA testing of asymptomatic men. In this paper we asked the following questions: (1) What are the primary sources of uncertainty as described by GPs in the context of PSA testing? (2) How do GPs experience and respond to different sources of uncertainty? Methods This was a qualitative study that explored general practitioners’ current approaches to, and reasoning about, PSA testing of asymptomatic men. We draw on accounts generated from interviews with 69 general practitioners located in Australia (n = 40) and the United Kingdom (n = 29). The interviews were conducted in 2013–2014. Data were analysed using grounded theory methods. Uncertainty in PSA testing was identified as a core issue. Findings Australian GPs reported experiencing substantially more uncertainty than UK GPs. This seemed partly explainable by notable differences in conditions of practice between the two countries. Using Han et al’s taxonomy of uncertainty as an initial framework, we first outline the different sources of uncertainty GPs (mostly Australian) described encountering in relation to prostate cancer screening and what the uncertainty was about. We then suggest an extension to Han et al’s taxonomy based on our analysis of data relating to the varied ways that GPs manage uncertainties in the context of PSA testing. We outline three broad strategies: (1) taking charge of uncertainty; (2) engaging others in managing uncertainty; and (3) transferring the responsibility for reducing or managing some uncertainties to other parties. Conclusion Our analysis suggests some GPs experienced uncertainties associated

  14. Time-resolved luminescence screening method for enrofloxacin in beef serum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enrofloxacin is one of only two fluoroquinolone antibiotics approved for use in cattle in the U.S. Microbial screening methods currently used in the U.S. for monitoring veterinary drug residues are not sensitive or selective for fluoroquinolones. In this work, a luminescence-based screening assay ...

  15. Terbium-sensitized luminescence screening method for fluoroquinolones in beef serum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enrofloxacin is one of only two fluoroquinolone antibiotics approved for use in cattle in the U.S. Microbial screening methods commonly used for monitoring veterinary drug residues are not sensitive or selective for fluoroquinolones. In this work, a luminescence-based screening assay was developed...

  16. Toward Harmonization of Performance Criteria for Mycotoxin Screening Methods: The EU Perspective.

    PubMed

    Lattanzio, Veronica M T

    2016-07-01

    Screening methods are defined as methods that are used to detect the presence of a substance or class of substances at the level of interest. These methods must have the capability of high sample throughput when being used to screen large numbers of samples for potential noncompliant results. Before using a screening method for practical applications, its fitness for the intended purpose needs to be demonstrated. This is normally achieved by conducting a validation study, comparing method performance against predefined criteria. Official guidelines recently established by the European Union for the evaluation of fitness-for-purpose performance parameters of screening methods to be used for the detection of mycotoxins in foods are presented and discussed herein. Practical applications of this evaluation scheme for single- and interlaboratory validation studies, as well as relevant information on screening method performances are reviewed, with emphasis on the impact of mycotoxin contamination in real samples on the fitness-for-purpose of the screening test. Lastly, validation follow-up is discussed in terms of extension of the scope of the method (increasing the range of application in terms of mycotoxin/matrix combinations), method implementation and verification, and evaluation of the method's applicability to modified mycotoxins. PMID:27455932

  17. New strategies for blood donor screening for hepatitis B virus: nucleic acid testing versus immunoassay methods.

    PubMed

    Kuhns, Mary C; Busch, Michael P

    2006-01-01

    Serologic testing for hepatitis B virus (HBV) surface antigen (HBsAg) and antibody to HBV core antigen (anti-HBc) has historically been the foundation of blood screening, while HBV nucleic acid testing (NAT) was recently developed to detect HBsAg-negative, anti-HBc-negative blood units donated during early acute infection. Comparison data on seroconversion panels using HBsAg assays of varying sensitivities and pooled- or single-sample NAT, along with viral load estimates corresponding to HBsAg assay detection limits, have provided information on the theoretical benefits of NAT relative to HBsAg. Model-derived estimates have generally been predictive of the yields of DNA-positive, HBsAg-negative window period blood units detected in a number of studies from Europe, Japan, and the US. Studies indicate that the added benefit of pooled-sample NAT is relatively small in areas of low endemicity, with greater yields in areas highly endemic for HBV. Single-sample NAT would offer more significant early window period closure and could prevent a moderate number of residual HBV transmissions not detected by HBsAg assays; however, no fully automated single-sample HBV NAT systems are currently available.Even single-sample HBV NAT may not substitute for anti-HBc screening, as indicated by studies of donors with isolated anti-HBc who have extremely low DNA levels undetectable by standard single-sample NAT and who have been associated with transfusion-transmitted HBV. Moreover, HBsAg testing may still be needed even in the setting of combined anti-HBc and NAT screening. HBsAg-positive units from donors in the chronic stage of infection may contain very low or intermittently detectable DNA levels that single-sample NAT would miss. Although such donors are usually anti-HBc reactive and would be interdicted by anti-HBc screening, some lack anti-HBc. Extensive parallel testing will be needed to determine whether single-sample NAT in combination with anti-HBc might be sufficient to

  18. Feasibility of an electromagnetic compatibility method for MRgFUS using a wire mesh screen.

    PubMed

    Wu, Hao; Shen, Guofeng; Chen, Yazhu

    2016-12-01

    This study evaluated an electromagnetic compatibility method for high-intensity focused ultrasound (HIFU) and magnetic resonance (MR) imaging in an MR-guided focused ultrasound surgery using a conductive wire mesh screen. This screen has a good ultrasound transmission and shielding effectiveness. A hybrid acoustic simulation method was developed to analyze the effects of mesh parameters and the HIFU working frequency on the acoustic field. Experiments were performed to measure both acoustic pressure profile and radiated electromagnetic noise. With the proposed mesh screen, the electromagnetic radiation emission was reduced by 14dB at 128MHz while the acoustic focal intensity was reduced by less than 11% using one screen. This shielding method is easy to implement and requires no additional phase correction method. This method also improves the quality of MR images. PMID:27448456

  19. An improved generalized Newton method for absolute value equations.

    PubMed

    Feng, Jingmei; Liu, Sanyang

    2016-01-01

    In this paper, we suggest and analyze an improved generalized Newton method for solving the NP-hard absolute value equations [Formula: see text] when the singular values of A exceed 1. We show that the global and local quadratic convergence of the proposed method. Numerical experiments show the efficiency of the method and the high accuracy of calculation. PMID:27462490

  20. The Othmer and DeSouza test for screening of somatisation disorder: is it useful in general practice?

    PubMed Central

    Zaballa, P; Crega, Y; Grandes, G; Peralta, C

    2001-01-01

    BACKGROUND: Somatisation disorder is an underdiagnosed and difficult problem for family physicians. Early diagnosis of somatisers is a very important factor in improving health outcomes. AIM: To assess the validity of the Othmer and DeSouza test (a seven-item questionnaire) used by general practitioners as a screening instrument for the diagnosis of somatisation disorder in primary care. DESIGN OF STUDY: A cross-sectional study of patients presenting with unexplained multiple chronic physical symptoms. SETTING: A total of 149 patients were selected for the study by 29 family physicians in the primary health care centres of the Basque Health Service in the metropolitan area of Bilbao, Bizkaia, Spain. METHODS: Participating patients completed the Othmer and DeSouza test, carried out by family physicians. Their answers were compared with the results of the Schedules for Clinical Assessment in Neuropsychiatry (SCAN). This psychiatric interview was administered blind to 144 patients by trained psychiatrists. RESULTS: A total of 19% of patients were diagnosed as having somatisation disorder by the SCAN psychiatric interview. The discriminating capacity of the Othmer and DeSouza test for all possible screening thresholds (> or = 1, > or = 2, ... > or = 6 symptoms) was very low and positive predictive values ranged between 19% and 33%. With respect to negative predictive values, even in the absence of affirmative responses to all seven questions, the pretest probability of being a non-somatiser case remained unchanged. CONCLUSION: Our data indicate that the Othmer and DeSouza test does not present clinically useful predictive values in primary care patients with suggestive symptoms of somatisation disorder. PMID:11255898

  1. Optical method for the screening of doping substances

    NASA Astrophysics Data System (ADS)

    Lademann, J.; Shevtsova, J.; Patzelt, A.; Richter, H.; Gladkowa, N. D.; Gelikonov, V. M.; Gonchukov, S. A.; Sterry, W.; Blume-Peytavi, U.

    2008-12-01

    During the last years, an increased misuse of doping substances in sport has been observed. The action of doping substances characterized by the stimulation of blood flow and metabolic processes is also reflected in the hair structure. In the present study it was demonstrated that optical coherent tomography is well suited for the analysis of hair parameters influenced by doping. Analyzing 20 patients, systemically treated with steroids which also represent doping substances, it was found that in all cases a significant increase in the cross-section of the hairs could be detected. The results obtained in the study are not only important for the screening of doping substances but also for medical diagnostics and control of compliance of patients.

  2. Method for screening inhibitors of the toxicity of Bacillus anthracis

    SciTech Connect

    Cirino, Nick M.; Jackson, Paul J.; Lehnert, Bruce E.

    2001-01-01

    The protective antigen (PA) of Bacillus anthracis is integral to the mechanism of anthrax poisoning. The cloning, expression and purification of a 32 kDa B. anthracis PA fragment (PA32) is described. This fragment has also been expressed as a fusion construct to stabilized green fluorescent protein (EGFP-PA32). Both proteins were capable of binding to specific cell surface receptors as determined by fluorescent microscopy and a flow cytometric assay. To confirm binding specificity in the flow cytometric assay, non-fluorescent PA83 or PA32 was used to competitively inhibit fluorescent EGFP-PA32 binding to cell receptors. This assay can be employed as a rapid screen for compounds which disrupts binding of PA to cells. Additionally, the high intracellular expression levels and ease of purification make this recombinant protein an attractive vaccine candidate or therapeutic treatment for anthrax poisoning.

  3. Optimal explicit strong-stability-preserving general linear methods.

    SciTech Connect

    Constantinescu, E.; Sandu, A.

    2010-07-01

    This paper constructs strong-stability-preserving general linear time-stepping methods that are well suited for hyperbolic PDEs discretized by the method of lines. These methods generalize both Runge-Kutta (RK) and linear multistep schemes. They have high stage orders and hence are less susceptible than RK methods to order reduction from source terms or nonhomogeneous boundary conditions. A global optimization strategy is used to find the most efficient schemes that have low storage requirements. Numerical results illustrate the theoretical findings.

  4. EVALUATION OF A FLUOROMETRIC SCREENING METHOD FOR PREDICTING TOTAL PAH CONCENTRATIONS IN CONTAMINATED SEDIMENTS

    EPA Science Inventory

    A flurorometric screening method was used to estimate total polycyclic aromatic hydrocarbon concentrations in sediments collected from the St. Louis River Area of Concern in northeastern Minnesota. Sediments were collected as part of a Regional Environmental Monitoring and Asses...

  5. DEMONSTRATION BULLETIN: FIELD ANALYTICAL SCREENING PROGRAM: PCP METHOD - U.S. ENVIRONMENTAL PROTECTION AGENCY

    EPA Science Inventory

    The Superfund Innovative Technology Evaluation (SITE) Program evaluates new technologies to assess their effectiveness. This bulletin summarizes results from the 1993 SITE demonstration of the Field Analytical Screening Program (FASP) Pentachlorophenol (PCP) Method to determine P...

  6. Using pre-screening methods for an effective and reliable site characterization at megasites.

    PubMed

    Algreen, Mette; Kalisz, Mariusz; Stalder, Marcel; Martac, Eugeniu; Krupanek, Janusz; Trapp, Stefan; Bartke, Stephan

    2015-10-01

    This paper illustrates the usefulness of pre-screening methods for an effective characterization of polluted sites. We applied a sequence of site characterization methods to a former Soviet military airbase with likely fuel and benzene, toluene, ethylbenzene, and xylene (BTEX) contamination in shallow groundwater and subsoil. The methods were (i) phytoscreening with tree cores; (ii) soil gas measurements for CH4, O2, and photoionization detector (PID); (iii) direct-push with membrane interface probe (MIP) and laser-induced fluorescence (LIF) sensors; (iv) direct-push sampling; and (v) sampling from soil and from groundwater monitoring wells. Phytoscreening and soil gas measurements are rapid and inexpensive pre-screening methods. Both indicated subsurface pollution and hot spots successfully. The direct-push sensors yielded 3D information about the extension and the volume of the subsurface plume. This study also expanded the applicability of tree coring to BTEX compounds and tested the use of high-resolution direct-push sensors for light hydrocarbons. Comparison of screening results to results from conventional soil and groundwater sampling yielded in most cases high rank correlation and confirmed the findings. The large-scale application of non- or low-invasive pre-screening can be of help in directing and focusing the subsequent, more expensive investigation methods. The rapid pre-screening methods also yielded useful information about potential remediation methods. Overall, we see several benefits of a stepwise screening and site characterization scheme, which we propose in conclusion.

  7. Flow method and apparatus for screening chemicals using micro x-ray fluorescence

    DOEpatents

    Warner, Benjamin P.; Havrilla, George J.; Miller, Thomasin C.; Lewis, Cris; Mahan, Cynthia A.; Wells, Cyndi A.

    2009-04-14

    Method and apparatus for screening chemicals using micro x-ray fluorescence. A method for screening a mixture of potential pharmaceutical chemicals for binding to at least one target binder involves flow-separating a solution of chemicals and target binders into separated components, exposing them to an x-ray excitation beam, detecting x-ray fluorescence signals from the components, and determining from the signals whether or not a binding event between a chemical and target binder has occurred.

  8. Flow method and apparatus for screening chemicals using micro x-ray fluorescence

    DOEpatents

    Warner, Benjamin P.; Havrilla, George J.; Miller, Thomasin C.; Lewis, Cris; Mahan, Cynthia A.; Wells, Cyndi A.

    2011-04-26

    Method and apparatus for screening chemicals using micro x-ray fluorescence. A method for screening a mixture of potential pharmaceutical chemicals for binding to at least one target binder involves flow separating a solution of chemicals and target binders into separated components, exposing them to an x-ray excitation beam, detecting x-ray fluorescence signals from the components, and determining from the signals whether or not a binding event between a chemical and target binder has occurred.

  9. Inclusion of populations at risk of advanced melanoma in an opportunistic targeted screening project involving general practitioners

    PubMed Central

    Rat, Cédric; Quereux, Gaelle; Grimault, Charlotte; Fernandez, Jérémy; Poiraud, Mickael; Gaultier, Aurélie; Chaslerie, Anicet; Pivette, Jacques; Khammari, Amir; Dreno, Brigitte; Nguyen, Jean-Michel

    2016-01-01

    Objective The study objective was to measure the rates of inclusion of populations at risk of advanced melanoma in a pilot targeted screening project involving general practitioners. Design This cross-sectional database study compared the inclusion rates of patients who signed inclusion in a targeted screening project with those of patients who did not, during a period in which both groups of patients consulted investigators. Setting Data were extracted from the national healthcare insurance records in western France from 11 April to 30 October 2011. Patients Patients, older than 18, considered for the data extraction had consulted one of the 78 participating GPs during the study period, and were affiliated with the national healthcare insurance. Main outcome measures Inclusion in the screening was the main outcome measure. Patients at risk of advanced melanoma were characterized by male gender, age over 50, low income, rural residence, farmer, and presence of chronic disease. Results A total of 57,279 patients consulted GPs during the inclusion period and 2711 (4.73%) were included in the targeted screening. Populations at risk of advanced melanoma were less included: men (OR = 0.67; 95%CI [0.61–0.73]; p < 0.001), older than 50 (OR = 0.67; 95%CI [0.60–0.74]; p < 0.001), low income (OR = 0.65; 95%CI [0.55–0.77]; p < 0.001), farmer (OR = 0.23; 95%CI [0.17–0.30]; p < 0.001) and presence of a chronic disease (OR = 0.87; 95%CI [0.77–0.98]; p < 0.028). Conclusion This study demonstrated inequalities in the inclusion of patients in a melanoma screening. Patients at risk of advanced cancer were screened less often. Further studies should focus on GPs ability to identify and screen these patients. Key Points Advanced melanoma is more frequently diagnosed in men, older patients and socioeconomically disadvantaged populations, which leads to survival inequalities.• Despite the involvement of general practitioners, the

  10. Accelerated Discovery in Photocatalysis using a Mechanism-Based Screening Method.

    PubMed

    Hopkinson, Matthew N; Gómez-Suárez, Adrián; Teders, Michael; Sahoo, Basudev; Glorius, Frank

    2016-03-18

    Herein, we report a conceptually novel mechanism-based screening approach to accelerate discovery in photocatalysis. In contrast to most screening methods, which consider reactions as discrete entities, this approach instead focuses on a single constituent mechanistic step of a catalytic reaction. Using luminescence spectroscopy to investigate the key quenching step in photocatalytic reactions, an initial screen of 100 compounds led to the discovery of two promising substrate classes. Moreover, a second, more focused screen provided mechanistic insights useful in developing proof-of-concept reactions. Overall, this fast and straightforward approach both facilitated the discovery and aided the development of new light-promoted reactions and suggests that mechanism-based screening strategies could become useful tools in the hunt for new reactivity.

  11. Accelerated Discovery in Photocatalysis using a Mechanism-Based Screening Method.

    PubMed

    Hopkinson, Matthew N; Gómez-Suárez, Adrián; Teders, Michael; Sahoo, Basudev; Glorius, Frank

    2016-03-18

    Herein, we report a conceptually novel mechanism-based screening approach to accelerate discovery in photocatalysis. In contrast to most screening methods, which consider reactions as discrete entities, this approach instead focuses on a single constituent mechanistic step of a catalytic reaction. Using luminescence spectroscopy to investigate the key quenching step in photocatalytic reactions, an initial screen of 100 compounds led to the discovery of two promising substrate classes. Moreover, a second, more focused screen provided mechanistic insights useful in developing proof-of-concept reactions. Overall, this fast and straightforward approach both facilitated the discovery and aided the development of new light-promoted reactions and suggests that mechanism-based screening strategies could become useful tools in the hunt for new reactivity. PMID:27000485

  12. A method for screening climate change-sensitive infectious diseases.

    PubMed

    Wang, Yunjing; Rao, Yuhan; Wu, Xiaoxu; Zhao, Hainan; Chen, Jin

    2015-01-01

    Climate change is a significant and emerging threat to human health, especially where infectious diseases are involved. Because of the complex interactions between climate variables and infectious disease components (i.e., pathogen, host and transmission environment), systematically and quantitatively screening for infectious diseases that are sensitive to climate change is still a challenge. To address this challenge, we propose a new statistical indicator, Relative Sensitivity, to identify the difference between the sensitivity of the infectious disease to climate variables for two different climate statuses (i.e., historical climate and present climate) in non-exposure and exposure groups. The case study in Anhui Province, China has demonstrated the effectiveness of this Relative Sensitivity indicator. The application results indicate significant sensitivity of many epidemic infectious diseases to climate change in the form of changing climatic variables, such as temperature, precipitation and absolute humidity. As novel evidence, this research shows that absolute humidity has a critical influence on many observed infectious diseases in Anhui Province, including dysentery, hand, foot and mouth disease, hepatitis A, hemorrhagic fever, typhoid fever, malaria, meningitis, influenza and schistosomiasis. Moreover, some infectious diseases are more sensitive to climate change in rural areas than in urban areas. This insight provides guidance for future health inputs that consider spatial variability in response to climate change. PMID:25594780

  13. A method for screening climate change-sensitive infectious diseases.

    PubMed

    Wang, Yunjing; Rao, Yuhan; Wu, Xiaoxu; Zhao, Hainan; Chen, Jin

    2015-01-14

    Climate change is a significant and emerging threat to human health, especially where infectious diseases are involved. Because of the complex interactions between climate variables and infectious disease components (i.e., pathogen, host and transmission environment), systematically and quantitatively screening for infectious diseases that are sensitive to climate change is still a challenge. To address this challenge, we propose a new statistical indicator, Relative Sensitivity, to identify the difference between the sensitivity of the infectious disease to climate variables for two different climate statuses (i.e., historical climate and present climate) in non-exposure and exposure groups. The case study in Anhui Province, China has demonstrated the effectiveness of this Relative Sensitivity indicator. The application results indicate significant sensitivity of many epidemic infectious diseases to climate change in the form of changing climatic variables, such as temperature, precipitation and absolute humidity. As novel evidence, this research shows that absolute humidity has a critical influence on many observed infectious diseases in Anhui Province, including dysentery, hand, foot and mouth disease, hepatitis A, hemorrhagic fever, typhoid fever, malaria, meningitis, influenza and schistosomiasis. Moreover, some infectious diseases are more sensitive to climate change in rural areas than in urban areas. This insight provides guidance for future health inputs that consider spatial variability in response to climate change.

  14. A Method for Screening Climate Change-Sensitive Infectious Diseases

    PubMed Central

    Wang, Yunjing; Rao, Yuhan; Wu, Xiaoxu; Zhao, Hainan; Chen, Jin

    2015-01-01

    Climate change is a significant and emerging threat to human health, especially where infectious diseases are involved. Because of the complex interactions between climate variables and infectious disease components (i.e., pathogen, host and transmission environment), systematically and quantitatively screening for infectious diseases that are sensitive to climate change is still a challenge. To address this challenge, we propose a new statistical indicator, Relative Sensitivity, to identify the difference between the sensitivity of the infectious disease to climate variables for two different climate statuses (i.e., historical climate and present climate) in non-exposure and exposure groups. The case study in Anhui Province, China has demonstrated the effectiveness of this Relative Sensitivity indicator. The application results indicate significant sensitivity of many epidemic infectious diseases to climate change in the form of changing climatic variables, such as temperature, precipitation and absolute humidity. As novel evidence, this research shows that absolute humidity has a critical influence on many observed infectious diseases in Anhui Province, including dysentery, hand, foot and mouth disease, hepatitis A, hemorrhagic fever, typhoid fever, malaria, meningitis, influenza and schistosomiasis. Moreover, some infectious diseases are more sensitive to climate change in rural areas than in urban areas. This insight provides guidance for future health inputs that consider spatial variability in response to climate change. PMID:25594780

  15. Development and evaluation of nursing user interface screens using multiple methods.

    PubMed

    Hyun, Sookyung; Johnson, Stephen B; Stetson, Peter D; Bakken, Suzanne

    2009-12-01

    Building upon the foundation of the Structured Narrative Electronic Health Record (EHR) model, we applied theory-based (combined Technology Acceptance Model and Task-Technology Fit Model) and user-centered methods to explore nurses' perceptions of functional requirements for an electronic nursing documentation system, design user interface screens reflective of the nurses' perspectives, and assess nurses' perceptions of the usability of the prototype user interface screens. The methods resulted in user interface screens that were perceived to be easy to use, potentially useful, and well-matched to nursing documentation tasks associated with Nursing Admission Assessment, Blood Administration, and Nursing Discharge Summary. The methods applied in this research may serve as a guide for others wishing to implement user-centered processes to develop or extend EHR systems. In addition, some of the insights obtained in this study may be informative to the development of safe and efficient user interface screens for nursing document templates in EHRs.

  16. Predicting High-Throughput Screening Results With Scalable Literature-Based Discovery Methods

    PubMed Central

    Cohen, T; Widdows, D; Stephan, C; Zinner, R; Kim, J; Rindflesch, T; Davies, P

    2014-01-01

    The identification of new therapeutic uses for existing agents has been proposed as a means to mitigate the escalating cost of drug development. A common approach to such repurposing involves screening libraries of agents for activities against cell lines. In silico methods using knowledge from the biomedical literature have been proposed to constrain the costs of screening by identifying agents that are likely to be effective a priori. However, results obtained with these methods are seldom evaluated empirically. Conversely, screening experiments have been criticized for their inability to reveal the biological basis of their results. In this paper, we evaluate the ability of a scalable literature-based approach, discovery-by-analogy, to identify a small number of active agents within a large library screened for activity against prostate cancer cells. The methods used permit retrieval of the knowledge used to infer their predictions, providing a plausible biological basis for predicted activity. PMID:25295575

  17. Predicting high-throughput screening results with scalable literature-based discovery methods.

    PubMed

    Cohen, T; Widdows, D; Stephan, C; Zinner, R; Kim, J; Rindflesch, T; Davies, P

    2014-10-08

    The identification of new therapeutic uses for existing agents has been proposed as a means to mitigate the escalating cost of drug development. A common approach to such repurposing involves screening libraries of agents for activities against cell lines. In silico methods using knowledge from the biomedical literature have been proposed to constrain the costs of screening by identifying agents that are likely to be effective a priori. However, results obtained with these methods are seldom evaluated empirically. Conversely, screening experiments have been criticized for their inability to reveal the biological basis of their results. In this paper, we evaluate the ability of a scalable literature-based approach, discovery-by-analogy, to identify a small number of active agents within a large library screened for activity against prostate cancer cells. The methods used permit retrieval of the knowledge used to infer their predictions, providing a plausible biological basis for predicted activity.

  18. General method for calculating derivatives of the lattice electrostatic energy.

    NASA Technical Reports Server (NTRS)

    Macdonald, D. E.; Eftis, J.; Arkilic, G. M.

    1972-01-01

    A method for calculating the derivatives of lattice electrostatic strain energy is proposed. It offers a computation procedure that is more general, concise, and systematic than any of the procedures previously used by Fuchs (1936), Cousins (1967), and Suzuki et al. (1968). The method can also easily be extended to fourth- and higher-order derivatives without undue difficulty.

  19. Optimal Multicomponent Analysis Using the Generalized Standard Addition Method.

    ERIC Educational Resources Information Center

    Raymond, Margaret; And Others

    1983-01-01

    Describes an experiment on the simultaneous determination of chromium and magnesium by spectophotometry modified to include the Generalized Standard Addition Method computer program, a multivariate calibration method that provides optimal multicomponent analysis in the presence of interference and matrix effects. Provides instructions for…

  20. A general numerical method to solve for dislocation configurations

    NASA Astrophysics Data System (ADS)

    Xin, X. J.; Wagoner, R. H.; Daehn, G. S.

    1999-08-01

    The shape of a mechanically equilibrated dislocation line is of considerable interest in the study of plastic deformation of metals and alloys. A general numerical method for finding such configurations in arbitrary stress fields has been developed. Analogous to the finite-element method (FEM), a general dislocation line is approximated by a series of straight segments (elements) bounded by nodes. The equilibrium configuration is found by minimizing the system energy with respect to nodal positions using a Newton-Raphson procedure. This approach, termed the finite-segment method (FSM), confers several advantages relative to segment-based, explicit formulations. The utility, generality, and robustness of the FSM is demonstrated by analyzing the Orowan bypass mechanism and a model of dislocation generation and equilibration at misfitting particles. Energy differences from previous analytical methods based on simple loop shapes are significant, up to 80 pct. Explicit expressions for the coordinate transformations, energies, and forces required for numerical implementation are presented.

  1. VARIABLE SCREENING METHODS IN META-MODEL DESIGN FOR A LARGE STRUCTURAL DYNAMICS SIMULATION

    SciTech Connect

    Cundy, A. L.; Schultze, J. F.; Hemez, F. M.; Doebling, S. W.; Bingham, D.

    2001-01-01

    This research addresses the problem of analyzing the nonlinear transient response of a large degree-of-freedom structural dynamics simulation. A threaded joint assembly's response to impulse loading has been studied. Twelve parameters relating to the input level, preloads of the joint and friction between components are thought to influence the acceleration response of the structure. Due to the high cost of physical testing and large amount of computation time to run analytical models (three hours on 504 processors of LANL's ASCI supercomputer, Blue Mountain to simulate three milliseconds of response) a fast-running metamodel is being developed. In this case, a metamodel is a statistically developed surrogate to the physics-based finite element model and can be evaluated in minutes on a single processor desktop computer. An unreasonable number of runs is required (312>500,000) to generate a three level full factorial design with 12 parameters for metamodel creation. Some manner of down-selecting or variable screening is needed in order to determine which of the parameters most affect the response and should be retained in subsequent models. A significant effects methodology has been used, involving a design of experiments technique, in which all parameters were lirst included in the model and then eliminated on the basis of statistical contributions associated with each parameter. Bayesian variable screening techniques, in which probabilities of effects are generated and updated, have also been explored. Encouraging results have been obtained, as the two methods yield similar sets of statistically significant parameters. Both methods have been compared to general sensitivity analysis (GSA). The resulting compact metarnodel can then be explored at more levels to appropriately capture the underlying physics of the threaded assembly with a much smaller set of simulations (only 64 runs required for a three level model with quadratic and some third order terms).

  2. The generalized method of moments as applied to the generalized gamma distribution

    NASA Astrophysics Data System (ADS)

    Ashkar, F.; Bobée, B.; Leroux, D.; Morisette, D.

    1988-09-01

    The generalized gamma (GG) distribution has a density function that can take on many possible forms commonly encountered in hydrologic applications. This fact has led many authors to study the properties of the distribution and to propose various estimation techniques (method of moments, mixed moments, maximum likelihood etc.). We discuss some of the most important properties of this flexible distribution and present a flexible method of parameter estimation, called the “generalized method of moments” (GMM) which combines any three moments of the GG distribution. The main advantage of this general method is that it has many of the previously proposed methods of estimation as special cases. We also give a general formula for the variance of the T-year event X T obtained by the GMM along with a general formula for the parameter estimates and also for the covariances and correlation coefficients between any pair of such estimates. By applying the GMM and carefully choosing the order of the moments that are used in the estimation one can significantly reduce the variance of T-year events for the range of return periods that are of interest.

  3. Assessment of screening methods for the identification of genetically modified potatoes in raw materials and finished products.

    PubMed

    Jaccaud, Etienne; Höhne, Michaela; Meyer, Rolf

    2003-01-29

    Qualitative polymerase chain reaction methods for the detection of genetically modified potatoes have been investigated that can be used for screening purposes and identification of insect-resistant and virus-resistant potatoes in food. The presence of the nos terminator from Agrobacterium tumefaciens and the antibiotic marker gene nptII (neomycin-phosphotransferase II) was demonstrated in three commercialized Bt-potato lines (Monsanto Co., St. Louis, MO, USA) and one noncommercial GM-potato product (high amylopectin starch, AVEBE, Veendam, The Netherlands) and allows for general screening in foods. For further identification, specific primers for the FMV promoter derived from the figwort mosaic virus, the CryIIIA gene (delta-endotoxin from Bacillus thuringiensis subsp. tenebrionis), potato leafroll virus replicase gene, and the potato virus Y coat protein gene, were designed. The methods described were successfully applied to processed potato raw materials (dehydrated potato powders and flakes), starch samples, and finished products.

  4. [Nutritional screening in heart failure patients: 5 methods review].

    PubMed

    Guerra-Sánchez, Luis; Martínez-Rincón, Carmen; Fresno-Flores, Mar

    2014-01-01

    Introduccion: La malnutrición aumenta la mortalidad y la estancia hospitalaria. Cada vez más instituciones sanitarias adoptan medidas de cribado nutricional con el fin de detectar precozmente la malnutrición o el riesgo de desarrollarla. No existe un método universalmente aceptado para la valoración nutricional. Objetivo: Determinar un método rápido y fiable, que no precise de entrenamiento previo, para el cribado nutricional de pacientes con insuficiencia cardiaca. Métodos: Estudio observacional, transversal, en el que se evaluaron mediante la valoración subjetiva global (VSG), el Mini nutritional assesment (MNA) tanto en su versión abreviada o de cribado (MNA-SF) como en su versión extendida o de valoración (MNA-LF), el nutritional Risk Screnning (NRS 2002), el Conocimiento nutricional o método Ulibarri (CONUT), el método Cardona y el Malnutrition Universal Screening Tool (MUST), el estado nutricional de 242 pacientes ingresados en un hospital terciario de alta complejidad con diagnósticos compatibles con descompensación de insuficiencia cardiaca crónica. Se analizaron la sensibilidad, especificidad, los valores predictivos, las razones de verosimilitud, la odds ratio diagnostica y el índice de correlación kappa, de los distintos métodos comparados con la valoración subjetiva global, que fue considerada como prueba cierta. Resultados: La edad media fue de 75±9. El 50,8% (n=123) fueron hombres. El índice de correlación kappa de los distintos métodos de cribado con respecto a la valoración subjetiva global fueron MNA valoración =0,637; MNA cribado =0,556; NRS =0,483; MUST =0,197; Cardona =0,188; CONUT =0,076. Discusión: El Mini Nutritional Assesment fue el método que mejor relación ofreció, tanto en su etapa de cribado como en la de valoración con la Valoración subjetiva global.

  5. Overview of Non-Volatile Testing and Screening Methods

    NASA Technical Reports Server (NTRS)

    Irom, Farokh

    2001-01-01

    Testing methods for memories and non-volatile memories have become increasingly sophisticated as they become denser and more complex. High frequency and faster rewrite times as well as smaller feature sizes have led to many testing challenges. This paper outlines several testing issues posed by novel memories and approaches to testing for radiation and reliability effects. We discuss methods for measurements of Total Ionizing Dose (TID).

  6. A Comparison of Two Educational Methods on Immigrant Latinas Breast Cancer Knowledge and Screening Behaviors

    PubMed Central

    Calderón, José Luis; Bazargan, Mohsen; Sangasubana, Nisaratana; Hays, Ron D.; Hardigan, Patrick; Baker, Richard S.

    2016-01-01

    Underutilization of screening mammography by Latinas continues unabated and may contribute to disparities in disease-free survival and mortality. Objective Comparison of two discussion group-centered educational interventions at enhancing breast cancer knowledge, breast self-exams (BSE), and screening mammography. Methods Pre-test post-test study design. Two cohorts of 200 Latinas each participated in survey screening and discussion groups at baseline. One cohort also viewed an animated video and had BSE training. Breast cancer knowledge, self-reported BSE and mammography history were measured at baseline and three months post-intervention. Results Breast cancer knowledge scores were good for both groups at baseline, and significantly increased at three month follow-up for both groups (p<.05) but no significant difference was observed between groups at baseline or post-intervention. Conclusion Community-based discussion groups are a cost-effective method for improving breast cancer knowledge and promoting screening behaviors. PMID:20675947

  7. Multiple-time-stepping generalized hybrid Monte Carlo methods

    SciTech Connect

    Escribano, Bruno; Akhmatskaya, Elena; Reich, Sebastian; Azpiroz, Jon M.

    2015-01-01

    Performance of the generalized shadow hybrid Monte Carlo (GSHMC) method [1], which proved to be superior in sampling efficiency over its predecessors [2–4], molecular dynamics and hybrid Monte Carlo, can be further improved by combining it with multi-time-stepping (MTS) and mollification of slow forces. We demonstrate that the comparatively simple modifications of the method not only lead to better performance of GSHMC itself but also allow for beating the best performed methods, which use the similar force splitting schemes. In addition we show that the same ideas can be successfully applied to the conventional generalized hybrid Monte Carlo method (GHMC). The resulting methods, MTS-GHMC and MTS-GSHMC, provide accurate reproduction of thermodynamic and dynamical properties, exact temperature control during simulation and computational robustness and efficiency. MTS-GHMC uses a generalized momentum update to achieve weak stochastic stabilization to the molecular dynamics (MD) integrator. MTS-GSHMC adds the use of a shadow (modified) Hamiltonian to filter the MD trajectories in the HMC scheme. We introduce a new shadow Hamiltonian formulation adapted to force-splitting methods. The use of such Hamiltonians improves the acceptance rate of trajectories and has a strong impact on the sampling efficiency of the method. Both methods were implemented in the open-source MD package ProtoMol and were tested on a water and a protein systems. Results were compared to those obtained using a Langevin Molly (LM) method [5] on the same systems. The test results demonstrate the superiority of the new methods over LM in terms of stability, accuracy and sampling efficiency. This suggests that putting the MTS approach in the framework of hybrid Monte Carlo and using the natural stochasticity offered by the generalized hybrid Monte Carlo lead to improving stability of MTS and allow for achieving larger step sizes in the simulation of complex systems.

  8. Interval breast cancers in screening: the effect of mammography review method on classification.

    PubMed

    Ciatto, Stefano; Catarzi, Sandra; Lamberini, Maria Perla; Risso, Gabriella; Saguatti, Gianni; Abbattista, Teresa; Martinelli, Francesca; Houssami, Nehmat

    2007-12-01

    Surveillance of interval cancers (IC) lacks standardisation of review methodologies. We investigated the extent to which 'informed' or 'blinded' review may affect IC classification. This is a retrospective study of 100 validated screening mammograms (20 IC, 80 negative screens) independently reviewed by six radiologists. Three sequenced review methods with increasing information were used: (1) blinded (no IC information, case mix), (2) partially informed, and (3) fully informed. IC 'screening error' (SE) reports averaged 24% (10-40), 33% (20-55), and 42% (35-50) for phases 1, 2, and 3, while 'minimal signs' (MS) reports averaged 6% (5-15), 10% (10-20), and 20% (15-30), respectively. Negative mammograms classification was MS in 18% (7-39) or SE in 19% (11-29), respectively. MS or SE classification was more likely for method 2 (OR=1.78, p=0.033) and method 3 (OR=3.91, p=0.000) relative to method 1, but no reader effect was evident. Inter-observer agreement in classifying at method 1 was slight (k 0.20), lowest (k 0.06) for MS, and fair (k 0.25) for negative and SE categories. More 'informed' review is more likely to yield an IC classification as MS or SE. Due to expected variability, review methods need standardisation to improve screening quality. Our data support blinded review of IC in mammography screening.

  9. [Research on the Screening Method of Soil Remediation Technology at Contaminated Sites and Its Application].

    PubMed

    Bai, Li-ping; Luo, Yun; Liu, Li; Zhou, You-ya; Yan, Zeng-guang; Li, Fa-sheng

    2015-11-01

    Soil remediation technology screening is an important procedure in the supervision of contaminated sites. The efficiency and costs of contaminated site remediation will be directly affected by the applicability of soil remediation technology. The influencing factors include characteristics of contaminants, site conditions, remediation time and costs should be considered to determine the most applicable remediation technology. The remediation technology screening was commonly evaluated by the experienced expert in China, which limited the promotion and application of the decision making method. Based on the supervision requirements of contaminated sites and the research status at home and abroad, the screening method includes preliminary screening and explicit evaluation was suggested in this paper. The screening index system was constructed, and the extension theory was used to divide the technology grade. The extension theory could solve the problem of human interference in the evaluation process and index value assignment. A chromium residue contaminated site in China was selected as the study area, and the applicable remediation technologies were suggested by the screening method. The research results could provide a scientific and technological support for the supervision and management of contaminated sites in China.

  10. Microbiological screening method for indication of irradiation of spices and herbs: a BCR collaborative study.

    PubMed

    Wirtanen, G; Sjöberg, A M; Boisen, F; Alanko, T

    1993-01-01

    A BCR1 collaborative study was conducted with a microbiological screening method based on the combined use of the direct epifluorescent filter technique (DEFT) and the conventional aerobic plate count method (APC) for detection of irradiation of spices and herbs. Collaborative samples of whole allspice, whole and powdered black peppers, whole white pepper, paprika powder, cut basil, cut marjoram, and crushed cardamom irradiated with doses of 0, 5, and 10 kGy were analyzed by 8 laboratories. The total number of the collaborative samples, with arbitrarily labeled codes, was 192. The percentage of acceptable results was 95.5%. The identification of irradiated from nonirradiated spices and herbs was analyzed statistically by using explorative techniques. The average values of the differences between DEFT and APC in samples irradiated with doses of 5 and 10 kGy were 5.1 and 6.1 logarithmic units, respectively. The differences between DEFT and APC generally increased to at least 3.5 logarithmic units, whereas the difference in the case of unirradiated spices was insignificant. However, conclusive evidence of irradiation relies on the knowledge that the sample was not fumigated or heat treated. The reproducibility relative standard deviations for the differences were 12.3, 19.9, and 20.7% with the doses of 10 and 5 kGy and for unirradiated samples, respectively, indicating acceptable variabilities among laboratories.

  11. A general method to diverse cinnolines and cinnolinium salts.

    PubMed

    Zhao, Dongbing; Wu, Qian; Huang, Xiaolei; Song, Feijie; Lv, Taiyong; You, Jingsong

    2013-05-10

    Rhodium catalysis: A highly efficient and general method has been established to prepare cinnolines, cinnolinium salts, and polycyclic cinnolinium salts through the rhodium(III)-catalyzed oxidative C-H activation/cyclization of azo compounds with alkynes (see scheme). Key features of this methodology include the unprecedented capacity to create both cinnoline and cinnolinium frameworks.

  12. GENERAL CONSIDERATIONS FOR GEOPHYSICAL METHODS APPLIED TO AGRICULTURE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Geophysics is the application of physical quantity measurement techniques to provide information on conditions or features beneath the earth’s surface. With the exception of borehole geophysical methods and soil probes like a cone penetrometer, these techniques are generally noninvasive with physica...

  13. SARS-CoV protease inhibitors design using virtual screening method from natural products libraries.

    PubMed

    Liu, Bing; Zhou, Jiaju

    2005-04-15

    Two natural products databases, the marine natural products database (MNPD) and the traditional Chinese medicines database (TCMD), were used to find novel structures of potent SARS-CoV protease inhibitors through virtual screening. Before the procedure, the databases were filtered by Lipinski's ROF and Xu's extension rules. The results were analyzed by statistic methods to eliminate the bias in target-based database screening toward higher molecular weight compounds for enhancing the hit rate. Eighteen lead compounds were recommended by the screening procedure. They were useful for experimental scientists in prioritizing drug candidates and studying the interaction mechanism. The binding mechanism was also analyzed between the best screening compound and the SARS protein. PMID:15693056

  14. A method for screening of plant species for space use

    NASA Technical Reports Server (NTRS)

    Goeschl, J. D.; Sauer, R. L.; Scheld, H. W.

    1986-01-01

    A cost-effective methodology which monitors numerous dynamic aspects of carbon assimilation and allocation kinetics in live, intact plants is discussed. Analogous methods can apply to nitrogen uptake and allocation. This methodology capitalizes on the special properties of the short-lived, positron-gamma emitting isotope C-11 especially when applied as CO2-11 in a special extended square wave (ESW) pattern. The 20.4 minute half-life allows for repeated or continuous experiments on the same plant over periods of minutes, hours, days, or weeks. The steady-state isotope equilibrium approached during the ESW experiments, and the parameters which can be analyzed by this technique are also direct results of that short half-life. Additionally, the paired .511 MeV gamma rays penetrate any amount of tissue and their 180 deg opposite orientation provides good collimation and allows coincidence counting which nearly eliminates background.

  15. Development of a rapid method to isolate polyhydroxyalkanoates from bacteria for screening studies.

    PubMed

    Vizcaino-Caston, Isaac; Kelly, Catherine A; Fitzgerald, Annabel V L; Leeke, Gary A; Jenkins, Mike; Overton, Tim W

    2016-01-01

    We describe a novel method of Polyhydroxyalkanoate (PHA) extraction using dimethyl sulphoxide (DMSO) for use in screening studies. Compared to conventional chloroform extraction, the DMSO method was shown to release comparable quantities of PHA from Cupriavidus necator cells, with comparable properties as determined using Fourier transform infrared spectroscopy and differential scanning calorimetry.

  16. Microbial screening and analytical methods for the production of polyol oils from soybean oil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study is to develop a new useful method including microbial screening and product identification for a bioprocess to produce polyol oils from soybean oil. Methods for separating of product polyol oils from soybean oil substrate and free fatty acid byproducts using HPLC and TLC...

  17. Recommendations for Developing Alternative Test Methods for Screening and Prioritization of Chemicals for Developmental Neurotoxicity

    EPA Science Inventory

    Developmental neurotoxicity testing (DNT) is perceived by many stakeholders to be an area in critical need of alternative methods to current animal testing protocols and gUidelines. An immediate goal is to develop test methods that are capable of screening large numbers of chemic...

  18. Development of a rapid method to isolate polyhydroxyalkanoates from bacteria for screening studies.

    PubMed

    Vizcaino-Caston, Isaac; Kelly, Catherine A; Fitzgerald, Annabel V L; Leeke, Gary A; Jenkins, Mike; Overton, Tim W

    2016-01-01

    We describe a novel method of Polyhydroxyalkanoate (PHA) extraction using dimethyl sulphoxide (DMSO) for use in screening studies. Compared to conventional chloroform extraction, the DMSO method was shown to release comparable quantities of PHA from Cupriavidus necator cells, with comparable properties as determined using Fourier transform infrared spectroscopy and differential scanning calorimetry. PMID:26143034

  19. Targeted Screening of Hip Dysplasia in Newborns: Experience at a District General Hospital in Scotland

    PubMed Central

    Tyagi, Rahul; Zgoda, Marcin R.; Short, Rachel

    2016-01-01

    National Health Service Quality Improvement Scotland (NHS QIS) published a health technology scoping report in 2006 acknowledging that there are serious concerns within Scotland in relation to Developmental Dysplasia of Hip (DDH) as there is no formal screening program in place and there are significant variations between NHS boards leading to confusion for staff and parents. NHS QIS identified need for audit work to improve hip screening in Scotland. The aim of this study is review of current practice of selective screening for DDH. All newborns who had their first hip scan during one year period (2014) were included in this retrospective study and followed up until June 2015 to include any surgical intervention for dysplastic hip. Out of 428 babies (856 hip scans), abnormality was seen in 119 babies/147 hips (134 Graf 2a/2b, 10 hips were 2c and 3 hips were Graf grade 3). Average age when first scan was performed was 5 weeks (range 3 weeks to 22 weeks). Analysis of risk factors in 119 babies with abnormal scan was consistent with literature (83 breech, 12 family history, 12 HBW, 10 instability and 2 twins of breech). Twelve babies (16 hips) required treatment and were successfully treated in Pavlik harness. There was one case of missed/late dislocation, which lived in outside catchment area for 3 years since birth. During this study period there was no case of avascular necrosis or femoral nerve palsy as a result of treatment. In our experience, selective hip screening by ultrasound scan is useful in avoiding overtreatment and minimizing late presentations. PMID:27761220

  20. Screening method for the detection of methamphetamine in hair using fluorescence polarization immunoassay.

    PubMed

    Cheong, Jae Chul; Suh, SungIll; Ko, Beom Jun; Lee, Jae Il; Kim, Jin Young; Suh, Yong Jun; In, Moon Kyo

    2013-05-01

    A hair screening method has been developed for the detection of methamphetamine using an immunoassay analyzer (AxSYM) with a fluorescence polarization immunoassay (FPIA) technique. The method consisted of washing, cutting and digesting a hair sample (5 mg) with an enzymatic digestion solution. The digested hair sample was centrifuged, and then an aliquot of the supernatant was used to conduct the screening. The results obtained from FPIA, in most cases, showed concentrations above 70.0 ng/mL of methamphetamine for hair samples that contained 0.5 ng/mg of methamphetamine, determined by gas chromatography-mass spectrometry (GC-MS). The percent sensitivity, defined as the true positive rate of screened and confirmed results, and the percent specificity, defined as the true negative rate of screened and confirmed results, of the FPIA screening method were 100.0 and 96.7% (false positive rate of 3.3%), respectively, when the threshold level for FPIA analysis was set at 70.0 ng/mL (n = 60).The correlation coefficient (r) for the linear relationship between FPIA and GC-MS results was 0.91 in real hair samples. The recommended amount of hair sample was found to be 5.0 mg for FPIA screening analysis when the concentration of methamphetamine in hair samples determined by GC-MS was found to be more than 0.5 ng/mg. The method developed in this study was reliable and effective for the screening of methamphetamine in routine hair analysis.

  1. Properties of the Cannabis Abuse Screening Test (CAST) in the general population.

    PubMed

    Legleye, Stéphane; Guignard, Romain; Richard, Jean-Baptiste; Ludwig, Kraus; Pabst, Alexander; Beck, François

    2015-06-01

    This paper explores the DSM-IV latent structure of cannabis users (especially its invariance towards gender and age) and assesses the psychometric properties of the Cannabis Abuse Screening Test (CAST) by confrontation with the theoretical diagnoses [dependence and cannabis use disorders (CUD)] and the latent class structure of the DSM-IV. The random sample comprised 550 French cannabis smokers aged 15-62 years interviewed by telephone. DSM-IV diagnoses were assessed with the Munich Composite International Diagnostic Interview. Internal structures of both instruments were assessed using factor analysis and latent class analysis. Optimal CAST cutoffs were determined by sensitivity, specificity and area under the receiver operating curve (AUC). CAST and DSM-IV were unidimensional (Cronbach's α = 0.742 and 0.752, respectively), although a two-factor solution showed a better fit for the CAST. CAST cutoffs for screening CUD and dependence were three (AUC = 0.851) and five (AUC = 0.868), respectively. DSM-IV latent class structure varied only marginally in age and gender. Three classes of cannabis smokers were determined, ordered along a continuum of symptoms: non-symptomatic (61.1%), moderate (32.9%) and severe (6.0%). CAST cutoff scores for screening moderate/severe and severe were, respectively, three (AUC = 0.869) and eight (AUC = 0.952). Results are compared to those obtained in previous CAST studies and discussed in line with the DSM-5.

  2. An Alternative Field Method for Screening Soybean Genotypes for Resistance to Heterodera glycines

    PubMed Central

    Arantes, N. E.; Mauro, A. O.; Tihohood, D.

    1998-01-01

    The soybean cyst nematode (Heterodera glycines) has become an increasingly severe problem in soybean production areas in Brazil. The development and use of resistant cultivars is the most efficient method of minimizing losses due to this pathogen. Our objective was to test the efficiency of an alternative method for screening soybean genotypes for resistance to H. glycines in field plots. The alternative method was compared to the standard method of sowing the test genotypes in fields found to be infested during the previous crop season. In the alternative method, the test genotypes are sown in the furrow following the uprooting of 45-day-old infected plants. The alternative method resulted in twice the cyst population and fewer escapes, and more consistent results than the standard method. The major advantage of the alternative method is that it permits screening in a more homogeneous distribution of H. glycines in the soil. PMID:19274244

  3. Generalized Jones matrix method for homogeneous biaxial samples.

    PubMed

    Ortega-Quijano, Noé; Fade, Julien; Alouini, Mehdi

    2015-08-10

    The generalized Jones matrix (GJM) is a recently introduced tool to describe linear transformations of three-dimensional light fields. Based on this framework, a specific method for obtaining the GJM of uniaxial anisotropic media was recently presented. However, the GJM of biaxial media had not been tackled so far, as the previous method made use of a simplified rotation matrix that lacks a degree of freedom in the three-dimensional rotation, thus being not suitable for calculating the GJM of biaxial media. In this work we propose a general method to derive the GJM of arbitrarily-oriented homogeneous biaxial media. It is based on the differential generalized Jones matrix (dGJM), which is the three-dimensional counterpart of the conventional differential Jones matrix. We show that the dGJM provides a simple and elegant way to describe uniaxial and biaxial media, with the capacity to model multiple simultaneous optical effects. The practical usefulness of this method is illustrated by the GJM modeling of the polarimetric properties of a negative uniaxial KDP crystal and a biaxial KTP crystal for any three-dimensional sample orientation. The results show that this method constitutes an advantageous and straightforward way to model biaxial media, which show a growing relevance for many interesting applications.

  4. Screening of Potential Remediation Methods for the 200-BP-5 Operable Unit at the Hanford Site

    SciTech Connect

    Truex, Michael J.; Dresel, P. EVAN; Nimmons, Michael J.; Johnson, Christian D.

    2006-09-21

    A screening-level evaluation of potential remediation methods for application to the contaminants of concern (COC) in the 200-BP-5 Operable Unit at the Hanford Site was conducted based on the methods outlined in the Guidance for Conducting Remedial Investigations and Feasibility Studies under CERCLA Interim Final (EPA 1988). The scope of this screening was to identify the most promising remediation methods for use in the more detailed analysis of remediation alternatives that will be conducted as part of the full feasibility study. The screening evaluation was conducted for the primary COC (potential major risk drivers) identified in the groundwater sampling and analysis plan for the operable unit (DOE/RL-2001-49, Rev. 1) with additions.

  5. Comparison Of Methods Used To Measure The Characteristic Curve Of Radiographic Screen/Film Systems

    NASA Astrophysics Data System (ADS)

    Wagner, Louis K.; Haus, Arthur G.; Barnes, Gary T.; Bencomo, Jose A.; Amtey, Sharad R.

    1980-08-01

    A systematic study was performed to investigate the accuracy and precision attained by four methods for determining the characteristic curve of radiographic screen/film systems. The four methods include: inverse square sensitometry, KVP adjusted bootstrap sensitometry step-wedge bootstrap sensitometry, and step wedge attenuation sensitometry. The inverse square method was used as the reference standard for accuracy. The extent of and the sources of the inaccurcies involved when using the alternative methods is discussed.

  6. Toward fully automated high performance computing drug discovery: a massively parallel virtual screening pipeline for docking and molecular mechanics/generalized Born surface area rescoring to improve enrichment.

    PubMed

    Zhang, Xiaohua; Wong, Sergio E; Lightstone, Felice C

    2014-01-27

    In this work we announce and evaluate a high throughput virtual screening pipeline for in-silico screening of virtual compound databases using high performance computing (HPC). Notable features of this pipeline are an automated receptor preparation scheme with unsupervised binding site identification. The pipeline includes receptor/target preparation, ligand preparation, VinaLC docking calculation, and molecular mechanics/generalized Born surface area (MM/GBSA) rescoring using the GB model by Onufriev and co-workers [J. Chem. Theory Comput. 2007, 3, 156-169]. Furthermore, we leverage HPC resources to perform an unprecedented, comprehensive evaluation of MM/GBSA rescoring when applied to the DUD-E data set (Directory of Useful Decoys: Enhanced), in which we selected 38 protein targets and a total of ∼0.7 million actives and decoys. The computer wall time for virtual screening has been reduced drastically on HPC machines, which increases the feasibility of extremely large ligand database screening with more accurate methods. HPC resources allowed us to rescore 20 poses per compound and evaluate the optimal number of poses to rescore. We find that keeping 5-10 poses is a good compromise between accuracy and computational expense. Overall the results demonstrate that MM/GBSA rescoring has higher average receiver operating characteristic (ROC) area under curve (AUC) values and consistently better early recovery of actives than Vina docking alone. Specifically, the enrichment performance is target-dependent. MM/GBSA rescoring significantly out performs Vina docking for the folate enzymes, kinases, and several other enzymes. The more accurate energy function and solvation terms of the MM/GBSA method allow MM/GBSA to achieve better enrichment, but the rescoring is still limited by the docking method to generate the poses with the correct binding modes. PMID:24358939

  7. Toward fully automated high performance computing drug discovery: a massively parallel virtual screening pipeline for docking and molecular mechanics/generalized Born surface area rescoring to improve enrichment.

    PubMed

    Zhang, Xiaohua; Wong, Sergio E; Lightstone, Felice C

    2014-01-27

    In this work we announce and evaluate a high throughput virtual screening pipeline for in-silico screening of virtual compound databases using high performance computing (HPC). Notable features of this pipeline are an automated receptor preparation scheme with unsupervised binding site identification. The pipeline includes receptor/target preparation, ligand preparation, VinaLC docking calculation, and molecular mechanics/generalized Born surface area (MM/GBSA) rescoring using the GB model by Onufriev and co-workers [J. Chem. Theory Comput. 2007, 3, 156-169]. Furthermore, we leverage HPC resources to perform an unprecedented, comprehensive evaluation of MM/GBSA rescoring when applied to the DUD-E data set (Directory of Useful Decoys: Enhanced), in which we selected 38 protein targets and a total of ∼0.7 million actives and decoys. The computer wall time for virtual screening has been reduced drastically on HPC machines, which increases the feasibility of extremely large ligand database screening with more accurate methods. HPC resources allowed us to rescore 20 poses per compound and evaluate the optimal number of poses to rescore. We find that keeping 5-10 poses is a good compromise between accuracy and computational expense. Overall the results demonstrate that MM/GBSA rescoring has higher average receiver operating characteristic (ROC) area under curve (AUC) values and consistently better early recovery of actives than Vina docking alone. Specifically, the enrichment performance is target-dependent. MM/GBSA rescoring significantly out performs Vina docking for the folate enzymes, kinases, and several other enzymes. The more accurate energy function and solvation terms of the MM/GBSA method allow MM/GBSA to achieve better enrichment, but the rescoring is still limited by the docking method to generate the poses with the correct binding modes.

  8. Design and Methods of Large-Scale RNA Interference Screens in Drosophila.

    PubMed

    Zhou, Jia; Tong, Chao

    2016-01-01

    Drosophila is an ideal model system for addressing important questions in biology. The use of RNA interference (RNAi) to knockdown gene expression in fly tissues is both very effective and relatively simple. In the past few decades, genome-wide UAS-RNAi transgenic libraries and thousands of Gal4 strains have been generated and have facilitated large-scale in vivo RNAi screening. Here, we discuss methods for the design and performance of a large-scale in vivo RNAi screen in Drosophila. Furthermore, methods for the validation of results and analysis of data will be introduced. PMID:27581292

  9. A reporter ligand NMR screening method for 2-oxoglutarate oxygenase inhibitors

    PubMed Central

    Leung, Ivanhoe K. H.; Demetriades, Marina; Hardy, Adam P.; Lejeune, Clarisse; Smart, Tristan J.; Szöllössi, Andrea; Kawamura, Akane; Schofield, Christopher J.; Claridge, Timothy D. W.

    2015-01-01

    The human 2-oxoglutarate (2OG) dependent oxygenases belong to a family of structurally related enzymes that play important roles in many biological processes. We report that competition-based NMR methods, using 2OG as a reporter ligand, can be used for quantitative and site-specific screening of ligand binding to 2OG oxygenases. The method was demonstrated using hypoxia inducible factor (HIF) hydroxylases and histone demethylases, and KD values were determined for inhibitors that compete with 2OG at the metal centre. This technique is also useful as a screening or validation tool for inhibitor discovery, as exemplified by work with protein-directed dynamic combinatorial chemistry (DCC). PMID:23234607

  10. General Characterization Methods for Photoelectrochemical Cells for Solar Water Splitting.

    PubMed

    Shi, Xinjian; Cai, Lili; Ma, Ming; Zheng, Xiaolin; Park, Jong Hyeok

    2015-10-12

    Photoelectrochemical (PEC) water splitting is a very promising technology that converts water into clean hydrogen fuel and oxygen by using solar light. However, the characterization methods for PEC cells are diverse and a systematic introduction to characterization methods for PEC cells has rarely been attempted. Unlike most other review articles that focus mainly on the material used for the working electrodes of PEC cells, this review introduces general characterization methods for PEC cells, including their basic configurations and methods for characterizing their performance under various conditions, regardless of the materials used. Detailed experimental operation procedures with theoretical information are provided for each characterization method. The PEC research area is rapidly expanding and more researchers are beginning to devote themselves to related work. Therefore, the content of this Minireview can provide entry-level knowledge to beginners in the area of PEC, which might accelerate progress in this area.

  11. General Characterization Methods for Photoelectrochemical Cells for Solar Water Splitting.

    PubMed

    Shi, Xinjian; Cai, Lili; Ma, Ming; Zheng, Xiaolin; Park, Jong Hyeok

    2015-10-12

    Photoelectrochemical (PEC) water splitting is a very promising technology that converts water into clean hydrogen fuel and oxygen by using solar light. However, the characterization methods for PEC cells are diverse and a systematic introduction to characterization methods for PEC cells has rarely been attempted. Unlike most other review articles that focus mainly on the material used for the working electrodes of PEC cells, this review introduces general characterization methods for PEC cells, including their basic configurations and methods for characterizing their performance under various conditions, regardless of the materials used. Detailed experimental operation procedures with theoretical information are provided for each characterization method. The PEC research area is rapidly expanding and more researchers are beginning to devote themselves to related work. Therefore, the content of this Minireview can provide entry-level knowledge to beginners in the area of PEC, which might accelerate progress in this area. PMID:26365789

  12. Methods and outcomes of screening for pancreatic adenocarcinoma in high-risk individuals.

    PubMed

    Capurso, Gabriele; Signoretti, Marianna; Valente, Roberto; Arnelo, Urban; Lohr, Matthias; Poley, Jan-Werner; Delle Fave, Gianfranco; Del Chiaro, Marco

    2015-07-25

    Pancreatic ductal adenocarcinoma (PDAC) is a lethal neoplasia, for which secondary prevention (i.e., screening) is advisable for high-risk individuals with "familiar pancreatic cancer" and with other specific genetic syndromes (Peutz-Jeghers, p16, BRCA2, PALB and mismatch repair gene mutation carriers). There is limited evidence regarding the accuracy of screening tests, their acceptability, costs and availability, and agreement on whom to treat. Successful target of screening are small resectable PDAC, intraductal papillary mucinous neoplasms with high-grade dysplasia and advanced pancreatic intraepithelial neoplasia. Both magnetic resonance imaging (MRI) and endoscopic ultrasound (EUS) are employed for screening, and the overall yield for pre-malignant or malignant pancreatic lesions is of about 20% with EUS and 14% with MRI/magnetic resonance colangiopancreatography. EUS performs better for solid and MRI for cystic lesions. However, only 2% of these detected lesions can be considered a successful target, and there are insufficient data demonstrating that resection of benign or low grade lesions improves survival. Many patients in the published studies therefore seemed to have received an overtreatment by undergoing surgery. It is crucial to better stratify the risk of malignancy individually, and to better define optimal screening intervals and methods either with computerized tools or molecular biomarkers, possibly in large multicentre studies. At the moment, screening should be carefully performed within research protocols at experienced centres, offering involved individuals medical and psychological advice. PMID:26240684

  13. Attempts to Improve the Method of Screening Cowpea Germplasm for Resistance to Cucumber Mosaic Virus and Blackeye Cowpea Mosaic Virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of visual symptom screening for cowpea plants in field plots improved screening for Blackeye Cowpea Mosaic Virus (BICMV)-resistance. However, the method failed to improve the speed or accuracy of screening for Cucumber Mosaic Virus (CMV)-resistance. Plants that displayed few visual virus sympt...

  14. Sensitivity analysis and approximation methods for general eigenvalue problems

    NASA Technical Reports Server (NTRS)

    Murthy, D. V.; Haftka, R. T.

    1986-01-01

    Optimization of dynamic systems involving complex non-hermitian matrices is often computationally expensive. Major contributors to the computational expense are the sensitivity analysis and reanalysis of a modified design. The present work seeks to alleviate this computational burden by identifying efficient sensitivity analysis and approximate reanalysis methods. For the algebraic eigenvalue problem involving non-hermitian matrices, algorithms for sensitivity analysis and approximate reanalysis are classified, compared and evaluated for efficiency and accuracy. Proper eigenvector normalization is discussed. An improved method for calculating derivatives of eigenvectors is proposed based on a more rational normalization condition and taking advantage of matrix sparsity. Important numerical aspects of this method are also discussed. To alleviate the problem of reanalysis, various approximation methods for eigenvalues are proposed and evaluated. Linear and quadratic approximations are based directly on the Taylor series. Several approximation methods are developed based on the generalized Rayleigh quotient for the eigenvalue problem. Approximation methods based on trace theorem give high accuracy without needing any derivatives. Operation counts for the computation of the approximations are given. General recommendations are made for the selection of appropriate approximation technique as a function of the matrix size, number of design variables, number of eigenvalues of interest and the number of design points at which approximation is sought.

  15. General guidelines for medically screening mixed population groups potentially exposed to nerve or vesicant agents

    SciTech Connect

    Watson, A.P.; Munro, N.B.; Sidell, F.R.; Leffingwell, S.S.

    1992-01-01

    A number of state and local planners have requested guidance on screening protocols and have expressed interest in sampling body fluids from exposed or potentially exposed individuals as a means of estimating agent dose. These guidelines have been developed to provide a clear statement that could be used by state and local emergency response personnel in the event of a nerve or vesicant agent incident resulting in off-post contamination; maximum protection from harm is the goal. The assumption is that any population group so exposed would be heterogeneous for age, gender, reproductive status, and state of health.

  16. Proposal of Screening Method of Sleep Disordered Breathing Using Fiber Grating Vision Sensor

    NASA Astrophysics Data System (ADS)

    Aoki, Hirooki; Nakamura, Hidetoshi; Nakajima, Masato

    Every conventional respiration monitoring technique requires at least one sensor to be attached to the body of the subject during measurement, thereby imposing a sense of restraint that results in aversion against measurements that would last over consecutive days. To solve this problem, we developed a respiration monitoring system for sleepers, and it uses a fiber-grating vision sensor, which is a type of active image sensor to achieve non-contact respiration monitoring. In this paper, we verified the effectiveness of the system, and proposed screening method of the sleep disordered breathing. It was shown that our system could equivalently measure the respiration with thermistor and accelerograph. And, the respiratory condition of sleepers can be grasped by our screening method in one look, and it seems to be useful for the support of the screening of sleep disordered breathing.

  17. A simplified method to prepare PCR template DNA for screening of transgenic and knockout mice.

    PubMed

    Ren, S; Li, M; Cai, H; Hudgins, S; Furth, P A

    2001-03-01

    Polymerase chain reaction (PCR) amplification of DNA is the most widely used technique for screening of large numbers of genetically engineered transgenic or knockout mice (Mus musculus). In this report, we present a new DNA preparation procedure for running diagnostic PCR. In this procedure, mouse ear tissue was used directly for PCR after the tissue underwent brief digestion in a solution containing only proteinase K. Using this method, we have successfully screened several lines of single, double, and triple transgenic and knockout mice. The results are reliable and reproducible. The advantage of this new method is that DNA purification by organic extraction or isolation kit was omitted. DNA purification is the limiting factor in terms of time and money when screening transgenic and knockout mice by PCR. In addition, using ear instead of tail tissue can reduce distress of animals because the samples can be obtained when the mice are labeled by ear punch.

  18. An extension of the Coconut Cream Agar method to screen Penicillium citrinum isolates for citrinin production.

    PubMed

    Mohamed, S; Flint, S; Palmer, J; Fletcher, G C; Pitt, J I

    2013-09-01

    A simple and rapid screening method was developed for the detection of citrinin in fungal cultures using Coconut Cream Agar (CCA) described previously for detecting aflatoxin and ochratoxin A. Fifteen isolates of Penicillium citrinum were inoculated onto CCA and incubated at 25 and 30°C for 10 days. All isolates produced a distinct yellow green fluorescence on CCA when the reverse side of the agar plates were viewed under long wavelength UV light. Detection was optimal at 25°C after four to 5 days of incubation. Isolates positive by the CCA method also tested positive for citrinin production by the TLC agar plug method after growth on CCA, Czapek yeast extract agar and yeast extract sucrose agar. Control cultures were negative by both methods, indicating that the CCA Petri dish method was suitable for screening cultures for citrinin production.

  19. Validation of a GC-MS screening method for anabolizing agents in aqueous nutritional supplements.

    PubMed

    Thuyne, W Van; Delbeke, F T

    2005-01-01

    A sensitive and selective method for the screening of anabolizing agents in aqueous nutritional supplements is described and validated. A total of 28 different anabolizing agents are screened for, including testosterone and prohormones, nandrolone and prohormones, stanozolol, and metandienone. The different analytes are extracted from the aqueous nutritional supplements by liquid-liquid extraction with a mixture of pentane and freshly distilled diethylether (1:1) after the supplements have been made alkaline with a NaHCO3-K2CO3 (2:1) buffer. The anabolizing agents are derivatized with a mixture of MSTFA-NH4I-ethanethiol (320:1:2) as routinely used for the screening of anabolic steroids extracted from urine. The derivatives are analyzed by gas chromatography (GC)-mass spectrometry (MS) in the selective ion monitoring mode. The limits of detection range from 1 to 10 ng/mL. One aqueous nutritional supplement (creatine serum) was analyzed with this screening method and was found to contain dehydroepiandrosterone (DHEA) at very low concentrations. The presence of DHEA could be confirmed with GC-MS-MS. Results of the application of this method and a similar method for solid nutritional supplements previously described are given. PMID:15808000

  20. Optimization and visualization of the edge weights in optimal assignment methods for virtual screening

    PubMed Central

    2013-01-01

    Background Ligand‐based virtual screening plays a fundamental part in the early drug discovery stage. In a virtual screening, a chemical library is searched for molecules with similar properties to a query molecule by means of a similarity function. The optimal assignment of chemical graphs has proven to be a valuable similarity function for many cheminformatic tasks, such as virtual screening. The optimal assignment assumes all atoms of a query molecule to be equally important, which is not realistic depending on the binding mode of a ligand. The importance of a query molecule’s atoms can be integrated in the optimal assignment by weighting the assignment edges. We optimized the edge weights with respect to the virtual screening performance by means of evolutionary algorithms. Furthermore, we propose a visualization approach for the interpretation of the edge weights. Results We evaluated two different evolutionary algorithms, differential evolution and particle swarm optimization, for their suitability for optimizing the assignment edge weights. The results showed that both optimization methods are suited to optimize the edge weights. Furthermore, we compared our approach to the optimal assignment with equal edge weights and two literature similarity functions on a subset of the Directory of Useful Decoys using sophisticated virtual screening performance metrics. Our approach achieved a considerably better overall and early enrichment performance. The visualization of the edge weights enables the identification of substructures that are important for a good retrieval of ligands and for the binding to the protein target. Conclusions The optimization of the edge weights in optimal assignment methods is a valuable approach for ligand‐based virtual screening experiments. The approach can be applied to any similarity function that employs the optimal assignment method, which includes a variety of similarity measures that have proven to be valuable in various

  1. Virtual screening of protein kinase C inhibitors from natural product library to modulate general anaesthetic effects.

    PubMed

    Zhao, Junhui; Zhou, Chuixian

    2015-01-01

    Protein kinase C (PKC) plays a key role in neurotransmission in the central nervous system, and targeting PKC domain is considered as a strategy to modulate the anaesthetic effects. In this study, we described a synthetic pipeline to perform high-throughput virtual screening against a large library of 3D structural natural products released recently in order to discover those potential PKC modulators. A total of 100 natural products with top scores were raised, from which 12 promising candidates were tested to determine their inhibitory potencies against PKC. As might be expected, the promiscuous kinase inhibitor staurosporine showed a high PKC inhibitory activity (IC50 = 64 nM), and other two tested compounds, i.e. fisetin and tetrahydropapaverine, were also highly potent with their activities at nanomolar level (IC50 = 370 and 190, respectively).

  2. Eddy Covariance Method: Overview of General Guidelines and Conventional Workflow

    NASA Astrophysics Data System (ADS)

    Burba, G. G.; Anderson, D. J.; Amen, J. L.

    2007-12-01

    Atmospheric flux measurements are widely used to estimate water, heat, carbon dioxide and trace gas exchange between the ecosystem and the atmosphere. The Eddy Covariance method is one of the most direct, defensible ways to measure and calculate turbulent fluxes within the atmospheric boundary layer. However, the method is mathematically complex, and requires significant care to set up and process data. These reasons may be why the method is currently used predominantly by micrometeorologists. Modern instruments and software can potentially expand the use of this method beyond micrometeorology and prove valuable for plant physiology, hydrology, biology, ecology, entomology, and other non-micrometeorological areas of research. The main challenge of the method for a non-expert is the complexity of system design, implementation, and processing of the large volume of data. In the past several years, efforts of the flux networks (e.g., FluxNet, Ameriflux, CarboEurope, Fluxnet-Canada, Asiaflux, etc.) have led to noticeable progress in unification of the terminology and general standardization of processing steps. The methodology itself, however, is difficult to unify, because various experimental sites and different purposes of studies dictate different treatments, and site-, measurement- and purpose-specific approaches. Here we present an overview of theory and typical workflow of the Eddy Covariance method in a format specifically designed to (i) familiarize a non-expert with general principles, requirements, applications, and processing steps of the conventional Eddy Covariance technique, (ii) to assist in further understanding the method through more advanced references such as textbooks, network guidelines and journal papers, (iii) to help technicians, students and new researchers in the field deployment of the Eddy Covariance method, and (iv) to assist in its use beyond micrometeorology. The overview is based, to a large degree, on the frequently asked questions

  3. General method for quantifying base adducts in specific mammalian genes.

    PubMed Central

    Thomas, D C; Morton, A G; Bohr, V A; Sancar, A

    1988-01-01

    A general method has been developed to measure the formation and removal of DNA adducts in defined sequences of mammalian genomes. Adducted genomic DNA is digested with an appropriate restriction enzyme, treated with Escherichia coli UvrABC excision nuclease (ABC excinuclease), subjected to alkaline gel electrophoresis, and probed for specific sequences by Southern hybridization. The ABC excinuclease incises DNA containing bulky adducts and thus reduces the intensity of the full-length fragments in Southern hybridization in proportion to the number of adducts present in the probed sequence. This method is similar to that developed by Bohr et al. [Bohr, V. A., Smith, C. A., Okumoto, D. S. & Hanawalt, P. C. (1985) Cell 40, 359-369] for quantifying pyrimidine dimers by using T4 endonuclease V. Because of the wide substrate range of ABC exinuclease, however, our method can be used to quantify a large variety of DNA adducts in specific genomic sequences. Images PMID:2836856

  4. General conformal transformation method based on Schwarz-Christoffel approach

    NASA Astrophysics Data System (ADS)

    Tang, Linlong; Yin, Jinchan; Yuan, Guishan; Du, Jinglei; Gao, Hongtao; Dong, Xiaochun; Lu, Yueguang; Du, Chunlei

    2011-08-01

    A general conformal transformation method (CTM) is proposed to construct the conformal mapping between two irregular geometries. In order to find the material parameters corresponding to the conformal transformation between two irregular geometries, two polygons are utilized to approximate the two irregular geometries, and an intermediate geometry is used to connect the mapping relations between the two polygons. Based on these manipulations, the approximate material parameters for TE and TM waves are finally obtained by calculating the Schwarz-Christoffel (SC) mappings. To demonstrate the validity of the method, a phase modulator and a plane focal surface Luneburg lens are designed and simulated by the finite element method. The results show that the conformal transformation can be expanded to the cases that the transformed objects are with irregular geometries.

  5. Generalized slave-particle method for extended Hubbard models

    NASA Astrophysics Data System (ADS)

    Georgescu, Alexandru B.; Ismail-Beigi, Sohrab

    2015-12-01

    We introduce a set of generalized slave-particle models for extended Hubbard models that treat localized electronic correlations using slave-boson decompositions. Our models automatically include two slave-particle methods of recent interest, the slave-rotor and slave-spin methods, as well as a ladder of new intermediate models where one can choose which of the electronic degrees of freedom (e.g., spin or orbital labels) are treated as correlated degrees of freedom by the slave bosons. In addition, our method removes the aberrant behavior of the slave-rotor model, where it systematically overestimates the importance of electronic correlation effects for weak interaction strength, by removing the contribution of unphysical states from the bosonic Hilbert space. The flexibility of our formalism permits one to separate and isolate the effect of correlations on the key degrees of freedom.

  6. Screening for disease resistance in barley cultivars against Bipolaris sorokiniana using callus culture method.

    PubMed

    Chand, Ramesh; Sen, Devyani; Prasad, K D; Singh, A K; Bashyal, B M; Prasad, L C; Joshi, A K

    2008-04-01

    Screening for resistant barley genotypes in response to fungal toxin of Bipolaris sorokiniana was assessed on standing barley plants as well as in selected callus lines of the same. For the standing lines tested, those manifesting chlorosis in response to toxin infiltration showed a significantly slower disease progress as compared to the necrotic lines. Also, necrosis in the callus tissues of the susceptible cultivar in MS medium supplemented with different concentrations of the crude toxin was significantly higher than in the callus tissues of the chlorotic lines studied. Similar host response to the toxin in in vitro and field situations open up the possibility of screening barley cultivars for resistance to spot blotch using callus culture as against classical methods of screening in order to increase accuracy and save time and space.

  7. Field-screening method for 2,4-dinitrotoluene in soil. Special report

    SciTech Connect

    Jenkins, T.F.; Walsh, M.E.

    1991-10-01

    2,4-Dinitrotoluene (2,4-DNT) is a major component of several munitions formulations used by the U.S. Army. It is also one of the major impurities in production grade TNT and is often found in contaminated soils at army ammunition plants, depots and explosive ordnance disposal areas. Since 2,4-DNT migrates rapidly through the soil to groundwater and is thought to be toxic in water at quite low concentrations, methods are needed to locate sources of this contaminant in the soil. Laboratory procedures to quantify the concentration of 2,4-DNT in soil samples have been developed but no rapid field method is currently available to screen for this contaminant. Field screening methods have recently been developed for TNT and RDX. The TNT method involves extraction of the soil with acetone and generation of the red-colored Janowsky complex by addition of potassium hydroxide and sodium sulfite.

  8. [Three-Iindex-Value Method for Rapid Screening Unqualified Vegetable Oil].

    PubMed

    He, Wen-xuan; Hong, Gui-shui; Fang, Run; Cai, Xian-chun; Huang, Sheng

    2015-04-01

    In the present study, by measuring the A3 005 (representing unsaturation), A985 (representing conjugated fatty acids), A960 + A985 (representing trans-fatty acid ) of southern common vegetable oils (peanut oil, corn oil, canola oil, soybean oil, sunflower oil, tea seed oil and olive oil), "waste oil" and overdue vegetable oils, the pass-setting-range of these three index values for the vegetable oils was obtained. On this basis, a method for rapid screening unqualified vegetable oil (expired, adding low-cost oil, adding "waste oil") was established. The method effectively improved the monitoring efficiency of vegetable oil. With this method of screening a number of suspected substandard oils were proved unqualified by determination of fatty acid composition and 11, 12, 13, 17 fatty acid content. Through the combination of several detection methods, the causes for disqualification of vegetable oils can be further inferred. PMID:26197591

  9. [Three-Iindex-Value Method for Rapid Screening Unqualified Vegetable Oil].

    PubMed

    He, Wen-xuan; Hong, Gui-shui; Fang, Run; Cai, Xian-chun; Huang, Sheng

    2015-04-01

    In the present study, by measuring the A3 005 (representing unsaturation), A985 (representing conjugated fatty acids), A960 + A985 (representing trans-fatty acid ) of southern common vegetable oils (peanut oil, corn oil, canola oil, soybean oil, sunflower oil, tea seed oil and olive oil), "waste oil" and overdue vegetable oils, the pass-setting-range of these three index values for the vegetable oils was obtained. On this basis, a method for rapid screening unqualified vegetable oil (expired, adding low-cost oil, adding "waste oil") was established. The method effectively improved the monitoring efficiency of vegetable oil. With this method of screening a number of suspected substandard oils were proved unqualified by determination of fatty acid composition and 11, 12, 13, 17 fatty acid content. Through the combination of several detection methods, the causes for disqualification of vegetable oils can be further inferred.

  10. A high throughout semi-quantification method for screening organic contaminants in river sediments.

    PubMed

    Bu, Qingwei; Wang, Donghong; Liu, Xin; Wang, Zijian

    2014-10-01

    A high throughout semi-quantification method for screening nearly 900 organic contaminants (OCs) in river sediments has been developed. For most OCs tested, concentrations calculated from the proposed semi-quantification method deviated from actual values by a factor of 4. The overall recovery tests indicated that most OCs can be successfully extracted from sediments with recovery rates from 84.1 to 128.6%. To demonstrate the effectiveness of our method towards OC quantification, we screened OCs from sediments collected from the Haihe River basin. Seventy unregulated OCs (including pesticides, flame retardants, PPCPs, etc.) were identified and quantified at concentrations up to 2600 ng/g from 24 sediment samples. From these results, it is confirmed that the developed method is a useful way to fulfill a comprehensive analysis of OCs in sediments and would be valuable for the identification and prioritization of priority pollutants in watershed management.

  11. A general method for unsteady heat transfer on turbine blades

    NASA Technical Reports Server (NTRS)

    Cebeci, Tuncer; Platzer, Max F.

    1989-01-01

    The development of a general method for calculating unsteady heat transfer on turbine blades is described. It is based on the numerical solution of the boundary-layer equations for laminar, transitional, and turbulent flows. A novel procedure has been developed to account for the movement of the stagnation point caused by blade-passing wakes and has been applied to the stagnation region of three model flows with results which confirm its validity for laminar flows. It has also been applied to an experimental arrangement in which the average Nusselt number has been reported for turbulent flows and the results show considerable promise.

  12. A new screening method to identify inhibitors of the Lol (localization of lipoproteins) system, a novel antibacterial target.

    PubMed

    Ito, Hideaki; Ura, Atsushi; Oyamada, Yoshihiro; Yoshida, Hiroaki; Yamagishi, Jun-Ichi; Narita, Shin-Ichiro; Matsuyama, Shin-Ichi; Tokuda, Hajime

    2007-01-01

    As the Lol system, which is involved in localization of lipoproteins, is essential for Escherichia coli growth and widely conserved among gram-negative bacteria, it is considered to be a promising target for the development of anti-gram-negative bacterial agents. However, no high-throughput screening method has so far been developed to screen for Lol system inhibitors. By combining three assay systems (anucleate cell blue assay, Lpp assay, and LolA-dependent release inhibition assay) and a drug susceptibility test, we have successfully developed a new screening method for identification of compounds that inhibit the Lol system. Using this new screening method, we screened 23,600 in-house chemical compounds and found 2 Lol system inhibitors. We therefore conclude that our new screening method can efficiently identify new antibacterial agents that target the Lol system.

  13. Development of quantitative duplex real-time PCR method for screening analysis of genetically modified maize.

    PubMed

    Oguchi, Taichi; Onishi, Mari; Minegishi, Yasutaka; Kurosawa, Yasunori; Kasahara, Masaki; Akiyama, Hiroshi; Teshima, Reiko; Futo, Satoshi; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

    2009-06-01

    A duplex real-time PCR method was developed for quantitative screening analysis of GM maize. The duplex real-time PCR simultaneously detected two GM-specific segments, namely the cauliflower mosaic virus (CaMV) 35S promoter (P35S) segment and an event-specific segment for GA21 maize which does not contain P35S. Calibration was performed with a plasmid calibrant specially designed for the duplex PCR. The result of an in-house evaluation suggested that the analytical precision of the developed method was almost equivalent to those of simplex real-time PCR methods, which have been adopted as ISO standard methods for the analysis of GMOs in foodstuffs and have also been employed for the analysis of GMOs in Japan. In addition, this method will reduce both the cost and time requirement of routine GMO analysis by half. The high analytical performance demonstrated in the current study would be useful for the quantitative screening analysis of GM maize. We believe the developed method will be useful for practical screening analysis of GM maize, although interlaboratory collaborative studies should be conducted to confirm this. PMID:19602858

  14. Development of quantitative duplex real-time PCR method for screening analysis of genetically modified maize.

    PubMed

    Oguchi, Taichi; Onishi, Mari; Minegishi, Yasutaka; Kurosawa, Yasunori; Kasahara, Masaki; Akiyama, Hiroshi; Teshima, Reiko; Futo, Satoshi; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

    2009-06-01

    A duplex real-time PCR method was developed for quantitative screening analysis of GM maize. The duplex real-time PCR simultaneously detected two GM-specific segments, namely the cauliflower mosaic virus (CaMV) 35S promoter (P35S) segment and an event-specific segment for GA21 maize which does not contain P35S. Calibration was performed with a plasmid calibrant specially designed for the duplex PCR. The result of an in-house evaluation suggested that the analytical precision of the developed method was almost equivalent to those of simplex real-time PCR methods, which have been adopted as ISO standard methods for the analysis of GMOs in foodstuffs and have also been employed for the analysis of GMOs in Japan. In addition, this method will reduce both the cost and time requirement of routine GMO analysis by half. The high analytical performance demonstrated in the current study would be useful for the quantitative screening analysis of GM maize. We believe the developed method will be useful for practical screening analysis of GM maize, although interlaboratory collaborative studies should be conducted to confirm this.

  15. Generalized method for retrieving effective parameters of anisotropic metamaterials.

    PubMed

    Castanié, A; Mercier, J-F; Félix, S; Maurel, A

    2014-12-01

    Electromagnetic or acoustic metamaterials can be described in terms of equivalent effective, in general anisotropic, media and several techniques exist to determine the effective permeability and permittivity (or effective mass density and bulk modulus in the context of acoustics). Among these techniques, retrieval methods use the measured reflection and transmission coefficients (or scattering coefficients) for waves incident on a metamaterial slab containing few unit cells. Until now, anisotropic effective slabs have been considered in the literature but they are limited to the case where one of the axes of anisotropy is aligned with the slab interface. We propose an extension to arbitrary orientations of the principal axes of anisotropy and oblique incidence. The retrieval method is illustrated in the electromagnetic case for layered media, and in the acoustic case for array of tilted elliptical particles.

  16. [A generalized chemical-kinetic method for modeling gene networks].

    PubMed

    Likhoshvaĭ, V A; Matushkin, Iu G; Ratushnyĭ, A V; Anan'ko, E A; Ignat'eva, E V; Podkolodnaia, O A

    2001-01-01

    Development of methods for mathematical simulation of biological systems and building specific simulations is an important trend of bioinformatics development. Here we describe the method of generalized chemokinetic simulation generating flexible and adequate simulations of various biological systems. Adequate simulations of complex nonlinear gene networks--control system of cholesterol by synthesis in the cell and erythrocyte differentiation and maturation--are given as the examples. The simulations were expressed in terms of unit processes--biochemical reactions. Optimal sets of parameters were determined and the systems were numerically simulated under various conditions. The simulations allow us to study possible functional conditions of these gene networks, calculate consequences of mutations, and define optimal strategies for their correction including therapeutic ones. Graphical user interface for these simulations is available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneNet/. PMID:11771132

  17. A general method for transferring graphene onto soft surfaces.

    PubMed

    Song, Jie; Kam, Fong-Yu; Png, Rui-Qi; Seah, Wei-Ling; Zhuo, Jing-Mei; Lim, Geok-Kieng; Ho, Peter K H; Chua, Lay-Lay

    2013-05-01

    Recent advances in chemical vapour deposition have led to the fabrication of large graphene sheets on metal foils for use in research and development. However, further breakthroughs are required in the way these graphenes are transferred from their growth substrates onto the final substrate. Although various methods have been developed, as yet there is no general way to reliably transfer graphene onto arbitrary surfaces, such as 'soft' ones. Here, we report a method that allows the graphene to be transferred with high fidelity at the desired location on almost all surfaces, including fragile polymer thin films and hydrophobic surfaces. The method relies on a sacrificial 'self-releasing' polymer layer placed between a conventional polydimethylsiloxane elastomer stamp and the graphene that is to be transferred. This self-releasing layer provides a low work of adhesion on the stamp, which facilitates delamination of the graphene and its placement on the new substrate. To demonstrate the generality and reliability of our method, we fabricate high field-strength polymer capacitors using graphene as the top contact over a polymer dielectric thin film. These capacitors show superior dielectric breakdown characteristics compared with those made with evaporated metal top contacts. Furthermore, we fabricate low-operation-voltage organic field-effect transistors using graphene as the gate electrode placed over a thin polymer gate dielectric layer. We finally demonstrate an artificial graphite intercalation compound by stacking alternate monolayers of graphene and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ). This compound, which comprises graphene sheets p-doped by partial hole transfer from the F4TCNQ, shows a high and remarkably stable hole conductivity, even when heated in the presence of moisture.

  18. School Locations and Traffic Emissions — Environmental (In)Justice Findings Using a New Screening Method

    PubMed Central

    Gaffron, Philine; Niemeier, Deb

    2015-01-01

    It has been shown that the location of schools near heavily trafficked roads can have detrimental effects on the health of children attending those schools. It is therefore desirable to screen both existing school locations and potential new school sites to assess either the need for remedial measures or suitability for the intended use. Current screening tools and public guidance on school siting are either too coarse in their spatial resolution for assessing individual sites or are highly resource intensive in their execution (e.g., through dispersion modeling). We propose a new method to help bridge the gap between these two approaches. Using this method, we also examine the public K-12 schools in the Sacramento Area Council of Governments Region, California (USA) from an environmental justice perspective. We find that PM2.5 emissions from road traffic affecting a school site are significantly positively correlated with the following metrics: percent share of Black, Hispanic and multi-ethnic students, percent share of students eligible for subsidized meals. The emissions metric correlates negatively with the schools’ Academic Performance Index, the share of White students and average parental education levels. Our PM2.5 metric also correlates with the traffic related, census tract level screening indicators from the California Communities Environmental Health Screening Tool and the tool’s tract level rate of asthma related emergency department visits. PMID:25679341

  19. School locations and traffic emissions—environmental (in)justice findings using a new screening method.

    PubMed

    Gaffron, Philine; Niemeier, Deb

    2015-02-01

    It has been shown that the location of schools near heavily trafficked roads can have detrimental effects on the health of children attending those schools. It is therefore desirable to screen both existing school locations and potential new school sites to assess either the need for remedial measures or suitability for the intended use. Current screening tools and public guidance on school siting are either too coarse in their spatial resolution for assessing individual sites or are highly resource intensive in their execution (e.g., through dispersion modeling). We propose a new method to help bridge the gap between these two approaches. Using this method, we also examine the public K-12 schools in the Sacramento Area Council of Governments Region, California (USA) from an environmental justice perspective. We find that PM2.5 emissions from road traffic affecting a school site are significantly positively correlated with the following metrics: percent share of Black, Hispanic and multi-ethnic students, percent share of students eligible for subsidized meals. The emissions metric correlates negatively with the schools' Academic Performance Index, the share of White students and average parental education levels. Our PM2.5 metric also correlates with the traffic related, census tract level screening indicators from the California Communities Environmental Health Screening Tool and the tool's tract level rate of asthma related emergency department visits.

  20. Local response dispersion method. II. Generalized multicenter interactions

    NASA Astrophysics Data System (ADS)

    Sato, Takeshi; Nakai, Hiromi

    2010-11-01

    Recently introduced local response dispersion method [T. Sato and H. Nakai, J. Chem. Phys. 131, 224104 (2009)], which is a first-principles alternative to empirical dispersion corrections in density functional theory, is implemented with generalized multicenter interactions involving both atomic and atomic pair polarizabilities. The generalization improves the asymptote of intermolecular interactions, reducing the mean absolute percentage error from about 30% to 6% in the molecular C6 coefficients of more than 1000 dimers, compared to experimental values. The method is also applied to calculations of potential energy curves of molecules in the S22 database [P. Jurečka et al., Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The calculated potential energy curves are in a good agreement with reliable benchmarks recently published by Molnar et al. [J. Chem. Phys. 131, 065102 (2009)]. These improvements are achieved at the price of increasing complexity in the implementation, but without losing the computational efficiency of the previous two-center (atom-atom) formulation. A set of different truncations of two-center and three- or four-center interactions is shown to be optimal in the cost-performance balance.

  1. Predict octane numbers using a generalized interaction method

    SciTech Connect

    Twu, C.H.; Coon, J.E.

    1996-02-01

    An interaction-based correlation using a new approach can be used to predict research and motor octane numbers of gasoline blends. An ultimately detailed analysis of the gasoline cut is not necessary. This correlation can describe blending behavior over the entire composition range of gasoline cuts. The component-oriented interaction approach is general and will accurately predict, without performing additional blending studies, blending behavior for new gasoline cuts. The proposed correlation fits the data quite closely for blends of many gasoline cuts. The regression gives realistic values for binary interaction parameters between components. A unique set of binary interaction parameters was found for the equation for predicting octane number of any gasoline blend. The binary interaction parameters between components contained in gasoline cuts have been converted to binary interaction parameters between gasoline cuts through a general equation to simplify the calculations. Because of the proposed method`s accuracy, optimum allocation of components among gasoline grades can be obtained and predicted values can be used for quality control of the octane number of marketed gasolines.

  2. A Novel Approach for Efficient Pharmacophore-based Virtual Screening: Method and Applications

    PubMed Central

    Dror, Oranit; Schneidman-Duhovny, Dina; Inbar, Yuval; Nussinov, Ruth; Wolfson, Haim J.

    2009-01-01

    Virtual screening is emerging as a productive and cost-effective technology in rational drug design for the identification of novel lead compounds. An important model for virtual screening is the pharmacophore. Pharmacophore is the spatial configuration of essential features that enable a ligand molecule to interact with a specific target receptor. In the absence of a known receptor structure, a pharmacophore can be identified from a set of ligands that have been observed to interact with the target receptor. Here, we present a novel computational method for pharmacophore detection and virtual screening. The pharmacophore detection module is able to: (i) align multiple flexible ligands in a deterministic manner without exhaustive enumeration of the conformational space, (ii) detect subsets of input ligands that may bind to different binding sites or have different binding modes, (iii) address cases where the input ligands have different affinities by defining weighted pharmacophores based on the number of ligands that share them, and (iv) automatically select the most appropriate pharmacophore candidates for virtual screening. The algorithm is highly efficient, allowing a fast exploration of the chemical space by virtual screening of huge compound databases. The performance of PharmaGist was successfully evaluated on a commonly used dataset of G-Protein Coupled Receptor alpha1A. Additionally, a large-scale evaluation using the DUD (directory of useful decoys) dataset was performed. DUD contains 2950 active ligands for 40 different receptors, with 36 decoy compounds for each active ligand. PharmaGist enrichment rates are comparable with other state-of-the-art tools for virtual screening. Availability The software is available for download. A user-friendly web interface for pharmacophore detection is available at http://bioinfo3d.cs.tau.ac.il/PharmaGist. PMID:19803502

  3. Reconstruction of synthetic aperture digital Fresnel hologram by use of the screen division method

    NASA Astrophysics Data System (ADS)

    Jiang, Hongzhen; Zhao, Jianlin; Di, Jianglei

    2014-12-01

    Synthetic aperture digital holography can effectively increase the recording area of digital hologram, which is propitious to extend the range and improve the resolution of the reconstruction image. However, the area of synthetic aperture digital hologram is usually very large, and thus if it is directly reconstructed, the numerical reconstruction process may can't progress in order for the limitation of the disposal capability of computer. Therefore, a screen-division reconstruction method for synthetic aperture digital Fresnel hologram is proposed in the paper. Relatively to the direct reconstruction method, the screen division reconstruction method can effectively reduce the area of the hologram participant in the numerical operation process and thus make it possible to reconstruct the synthetic aperture digital Fresnel hologram which area exceeds the disposal capability of computer. The synthetic aperture digital Fresnel hologram with large area is acquired by the precise control for the removal of CCD array and then reconstructed by the proposed screen division reconstruction method. The experimental results show that, the introduced numerical reconstruction method can well correct the position and phase distribution of the sub-reconstructed-images and obtain accurate synthetic numerical reconstruction image.

  4. Surface impedance based microwave imaging method for breast cancer screening: contrast-enhanced scenario.

    PubMed

    Güren, Onan; Çayören, Mehmet; Ergene, Lale Tükenmez; Akduman, Ibrahim

    2014-10-01

    A new microwave imaging method that uses microwave contrast agents is presented for the detection and localization of breast tumours. The method is based on the reconstruction of breast surface impedance through a measured scattered field. The surface impedance modelling allows for representing the electrical properties of the breasts in terms of impedance boundary conditions, which enable us to map the inner structure of the breasts into surface impedance functions. Later a simple quantitative method is proposed to screen breasts against malignant tumours where the detection procedure is based on weighted cross correlations among impedance functions. Numerical results demonstrate that the method is capable of detecting small malignancies and provides reasonable localization.

  5. Microarray-based method for screening of immunogenic proteins from bacteria

    PubMed Central

    2012-01-01

    Background Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures. Results Four proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168. Conclusions The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify vaccine candidates, biomarkers and potential virulence-associated factors with immunogenic behaviour furthering the knowledge of virulence and pathogenicity of studied bacteria. PMID

  6. Logically rectangular mixed methods for Darcy flow on general geometry

    SciTech Connect

    Arbogast, T.; Keenan, P.T.; Wheeler, M.F.; Yotov, I.

    1995-12-31

    The authors consider an expanded mixed finite element formulation (cell centered finite difference) for Darcy flow with a tensor absolute permeability. The reservoir can be geometrically general with internal features, but the computational domain is rectangular. The method is defined on a curvilinear grid that need not be orthogonal, obtained by mapping the rectangular, computational grid. The original flow problem becomes a similar problem with a modified permeability on the computational grid. Quadrature rules turn the mixed method into a cell-centered finite difference method with a 9 point stencil in 2-D and 19 in 3-D. As shown by theory and experiment, if the modified permeability on the computational domain is smooth, then the convergence rate is optimal and both pressure and velocity are superconvergent at certain points. If not, Lagrange multiplier pressures can be introduced on boundaries of elements so that optimal convergence is retained. This modification presents only small changes in the solution process; in fact, the same parallel domain decomposition algorithms can be applied with little or no change to the code if the modified permeability is smooth over the subdomains. This Lagrange multiplier procedure can be used to extend the difference scheme to multi-block domains, and to give a coupling with unstructured grids. In all cases, the mixed formulation is locally conservative. Computational results illustrate the advantage and convergence of this method.

  7. Amyloid oligomer structure characterization from simulations: A general method

    SciTech Connect

    Nguyen, Phuong H.; Li, Mai Suan

    2014-03-07

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ{sub 9−40}, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  8. Amyloid oligomer structure characterization from simulations: A general method

    NASA Astrophysics Data System (ADS)

    Nguyen, Phuong H.; Li, Mai Suan; Derreumaux, Philippe

    2014-03-01

    Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  9. Generalized Bootstrap Method for Assessment of Uncertainty in Semivariogram Inference

    USGS Publications Warehouse

    Olea, R.A.; Pardo-Iguzquiza, E.

    2011-01-01

    The semivariogram and its related function, the covariance, play a central role in classical geostatistics for modeling the average continuity of spatially correlated attributes. Whereas all methods are formulated in terms of the true semivariogram, in practice what can be used are estimated semivariograms and models based on samples. A generalized form of the bootstrap method to properly model spatially correlated data is used to advance knowledge about the reliability of empirical semivariograms and semivariogram models based on a single sample. Among several methods available to generate spatially correlated resamples, we selected a method based on the LU decomposition and used several examples to illustrate the approach. The first one is a synthetic, isotropic, exhaustive sample following a normal distribution, the second example is also a synthetic but following a non-Gaussian random field, and a third empirical sample consists of actual raingauge measurements. Results show wider confidence intervals than those found previously by others with inadequate application of the bootstrap. Also, even for the Gaussian example, distributions for estimated semivariogram values and model parameters are positively skewed. In this sense, bootstrap percentile confidence intervals, which are not centered around the empirical semivariogram and do not require distributional assumptions for its construction, provide an achieved coverage similar to the nominal coverage. The latter cannot be achieved by symmetrical confidence intervals based on the standard error, regardless if the standard error is estimated from a parametric equation or from bootstrap. ?? 2010 International Association for Mathematical Geosciences.

  10. Density functional theory based generalized effective fragment potential method

    SciTech Connect

    Nguyen, Kiet A. E-mail: ruth.pachter@wpafb.af.mil; Pachter, Ruth E-mail: ruth.pachter@wpafb.af.mil; Day, Paul N.

    2014-06-28

    We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.

  11. Density functional theory based generalized effective fragment potential method

    NASA Astrophysics Data System (ADS)

    Nguyen, Kiet A.; Pachter, Ruth; Day, Paul N.

    2014-06-01

    We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.

  12. Flutter and Divergence Analysis using the Generalized Aeroelastic Analysis Method

    NASA Technical Reports Server (NTRS)

    Edwards, John W.; Wieseman, Carol D.

    2003-01-01

    The Generalized Aeroelastic Analysis Method (GAAM) is applied to the analysis of three well-studied checkcases: restrained and unrestrained airfoil models, and a wing model. An eigenvalue iteration procedure is used for converging upon roots of the complex stability matrix. For the airfoil models, exact root loci are given which clearly illustrate the nature of the flutter and divergence instabilities. The singularities involved are enumerated, including an additional pole at the origin for the unrestrained airfoil case and the emergence of an additional pole on the positive real axis at the divergence speed for the restrained airfoil case. Inconsistencies and differences among published aeroelastic root loci and the new, exact results are discussed and resolved. The generalization of a Doublet Lattice Method computer code is described and the code is applied to the calculation of root loci for the wing model for incompressible and for subsonic flow conditions. The error introduced in the reduction of the singular integral equation underlying the unsteady lifting surface theory to a linear algebraic equation is discussed. Acknowledging this inherent error, the solutions of the algebraic equation by GAAM are termed 'exact.' The singularities of the problem are discussed and exponential series approximations used in the evaluation of the kernel function shown to introduce a dense collection of poles and zeroes on the negative real axis. Again, inconsistencies and differences among published aeroelastic root loci and the new 'exact' results are discussed and resolved. In all cases, aeroelastic flutter and divergence speeds and frequencies are in good agreement with published results. The GAAM solution procedure allows complete control over Mach number, velocity, density, and complex frequency. Thus all points on the computed root loci can be matched-point, consistent solutions without recourse to complex mode tracking logic or dataset interpolation, as in the k and p

  13. Population-based preconception carrier screening: how potential users from the general population view a test for 50 serious diseases.

    PubMed

    Plantinga, Mirjam; Birnie, Erwin; Abbott, Kristin M; Sinke, Richard J; Lucassen, Anneke M; Schuurmans, Juliette; Kaplan, Seyma; Verkerk, Marian A; Ranchor, Adelita V; van Langen, Irene M

    2016-10-01

    With the increased international focus on personalized health care and preventive medicine, next-generation sequencing (NGS) has substantially expanded the options for carrier screening of serious, recessively inherited diseases. NGS screening tests not only offer reproductive options not previously available to couples, but they may also ultimately reduce the number of children born with devastating disorders. To date, preconception carrier screening (PCS) has largely targeted single diseases such as cystic fibrosis, but NGS allows the testing of many genes or diseases simultaneously. We have developed an expanded NGS PCS test for couples; simultaneously it covers 50 very serious, early-onset, autosomal recessive diseases that are untreatable. This is the first, noncommercial, population-based, expanded PCS test to be offered prospectively to couples in a health-care setting in Europe. So far, little is known about how potential users view such a PCS test. We therefore performed an online survey in 2014 among 500 people from the target population in the Netherlands. We enquired about their intention to take an expanded PCS test if one was offered, and through which provider they would like to see it offered. One-third of the respondents said they would take such a test were it to be offered. The majority (44%) preferred the test to be offered via their general practitioner (GP) and 58% would be willing to pay for the test, with a median cost of [euro ]75. Our next step is to perform an implementation study in which this PCS test will be provided via selected GPs in the Northern Netherlands.

  14. FMS Scores Change With Performers' Knowledge of the Grading Criteria-Are General Whole-Body Movement Screens Capturing "Dysfunction"?

    PubMed

    Frost, David M; Beach, Tyson A C; Callaghan, Jack P; McGill, Stuart M

    2015-11-01

    Deficits in joint mobility and stability could certainly impact individuals' Functional Movement Screen (FMS) scores; however, it is also plausible that the movement patterns observed are influenced by the performers' knowledge of the grading criteria. Twenty-one firefighters volunteered to participate, and their FMS scores were graded before and immediately after receiving knowledge of the movement patterns required to achieve a perfect score on the FMS. Standardized verbal instructions were used to administer both screens, and the participants were not provided with any coaching or feedback. Time-synchronized sagittal and frontal plane videos were used to grade the FMS. The firefighters significantly (p < 0.001) improved their FMS scores from 14.1 (1.8) to 16.7 (1.9) when provided with knowledge pertaining to the specific grading criteria. Significant improvements (p < 0.05) were also noted in the deep squat (1.4 [0.7]-2.0 [0.6]), hurdle step (2.1 [0.4]-2.4 [0.5]), in-line lunge (2.1 [0.4]-2.7 [0.5]), and shoulder mobility (1.8 [0.8]-2.4 [0.7]) tests. Because a knowledge of a task's grading criteria can alter a general whole-body movement screen score, FMS or otherwise, observed changes may not solely reflect "dysfunction." The instant that individuals are provided with coaching and feedback regarding their performance on a particular task, the task may lose its utility to evaluate the transfer of training or predict musculoskeletal injury risk.

  15. Population-based preconception carrier screening: how potential users from the general population view a test for 50 serious diseases

    PubMed Central

    Plantinga, Mirjam; Birnie, Erwin; Abbott, Kristin M; Sinke, Richard J; Lucassen, Anneke M; Schuurmans, Juliette; Kaplan, Seyma; Verkerk, Marian A; Ranchor, Adelita V; van Langen, Irene M

    2016-01-01

    With the increased international focus on personalized health care and preventive medicine, next-generation sequencing (NGS) has substantially expanded the options for carrier screening of serious, recessively inherited diseases. NGS screening tests not only offer reproductive options not previously available to couples, but they may also ultimately reduce the number of children born with devastating disorders. To date, preconception carrier screening (PCS) has largely targeted single diseases such as cystic fibrosis, but NGS allows the testing of many genes or diseases simultaneously. We have developed an expanded NGS PCS test for couples; simultaneously it covers 50 very serious, early-onset, autosomal recessive diseases that are untreatable. This is the first, noncommercial, population-based, expanded PCS test to be offered prospectively to couples in a health-care setting in Europe. So far, little is known about how potential users view such a PCS test. We therefore performed an online survey in 2014 among 500 people from the target population in the Netherlands. We enquired about their intention to take an expanded PCS test if one was offered, and through which provider they would like to see it offered. One-third of the respondents said they would take such a test were it to be offered. The majority (44%) preferred the test to be offered via their general practitioner (GP) and 58% would be willing to pay for the test, with a median cost of €75. Our next step is to perform an implementation study in which this PCS test will be provided via selected GPs in the Northern Netherlands. PMID:27165008

  16. Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins

    PubMed Central

    Li, Liang; Mustafi, Debarshi; Fu, Qiang; Tereshko, Valentina; Chen, Delai L.; Tice, Joshua D.; Ismagilov, Rustem F.

    2006-01-01

    High-throughput screening and optimization experiments are critical to a number of fields, including chemistry and structural and molecular biology. The separation of these two steps may introduce false negatives and a time delay between initial screening and subsequent optimization. Although a hybrid method combining both steps may address these problems, miniaturization is required to minimize sample consumption. This article reports a “hybrid” droplet-based microfluidic approach that combines the steps of screening and optimization into one simple experiment and uses nanoliter-sized plugs to minimize sample consumption. Many distinct reagents were sequentially introduced as ≈140-nl plugs into a microfluidic device and combined with a substrate and a diluting buffer. Tests were conducted in ≈10-nl plugs containing different concentrations of a reagent. Methods were developed to form plugs of controlled concentrations, index concentrations, and incubate thousands of plugs inexpensively and without evaporation. To validate the hybrid method and demonstrate its applicability to challenging problems, crystallization of model membrane proteins and handling of solutions of detergents and viscous precipitants were demonstrated. By using 10 μl of protein solution, ≈1,300 crystallization trials were set up within 20 min by one researcher. This method was compatible with growth, manipulation, and extraction of high-quality crystals of membrane proteins, demonstrated by obtaining high-resolution diffraction images and solving a crystal structure. This robust method requires inexpensive equipment and supplies, should be especially suitable for use in individual laboratories, and could find applications in a number of areas that require chemical, biochemical, and biological screening and optimization. PMID:17159147

  17. Bacteriuria screening and antimicrobial susceptibility testing of aerobic bacteria by an electrochemical method.

    PubMed

    Strassburger, J; Tiller, F W

    1984-04-01

    A method is described for detecting significant bacteriuria and determination of minimal inhibition concentrations (MIC's) of aerobically growing bacteria by using electrochemical electrodes to measure changes of oxygen tensions in liquid nutrient media resulting from bacterial growth. Urine specimens (n = 577) were screened electrochemically, parallel investigations were performed by standard culture methods and by photometrical measurements. All the specimens showing significant bacteriuria in standard culture were selected within 3.5 h by the electrochemical technique. An oxygen index OI was introduced which quantitatively reflects changes in oxygen tension of nutrient media during growth. OI shows good agreement with extinction and light scattering indices, respectively. On the basis of OI as a parameter of inhibited and uninhibited growth a correlation between OI and MIC's of aerobically growing bacteria was found. The electrochemical method provides an useful aid for rapid, preliminary antimicrobial susceptibility testing and definite bacteriuria screening. The application of this method in bacteriological urine diagnostics significantly reduces laboratory work and costs, and can be recommended for the screening of urine specimens to exclude negative specimens from further processing.

  18. Electrochemical estrogen screen method based on the electrochemical behavior of MCF-7 cells.

    PubMed

    Li, Jinlian; Song, Jia; Bi, Sheng; Zhou, Shi; Cui, Jiwen; Liu, Jiguang; Wu, Dongmei

    2016-08-01

    It was an urgent task to develop quick, cheap and accurate estrogen screen method for evaluating the estrogen effect of the booming chemicals. In this study, the voltammetric behavior between the estrogen-free and normal fragmented MCF-7 cell suspensions were compared, and the electrochemical signal (about 0.68V attributed by xanthine and guanine) of the estrogen-free fragmented MCF-7 cell suspension was obviously lower than that of the normal one. The electrochemistry detection of ex-secretion purines showed that the ability of ex-secretion purines of cells sharp decreased due to the removing of endogenous estrogen. The results indicated that the electrochemical signal of MCF-7 cells was related to the level of intracellular estrogen. When the level of intracellular estrogen was down-regulated, the concentrations of the xanthine and hypoxanthine decreased, which led to the electrochemical signal of MCF-7 cells fall. Based on the electrochemical signal, the electrochemical estrogen screen method was established. The estrogen effect of estradiol, nonylphenol and bisphenol A was evaluated with the electrochemical method, and the result was accordant with that of MTT assay. The electrochemical estrogen screen method was simple, quickly, cheap, objective, and it exploits a new way for the evaluation of estrogenic effects of chemicals.

  19. A simple method for screening emission sources of carbonyl compounds in indoor air.

    PubMed

    Yamashita, Shohei; Kume, Kazunari; Horiike, Toshiyuki; Honma, Nobuyuki; Fusaya, Masahiro; Ohura, Takeshi; Amagai, Takashi

    2010-06-15

    Volatile organic compounds (VOCs) emitted from building and furnishing materials are frequently observed in high concentrations in indoor air. Nondestructive analytical methods that determine the main parameters influencing concentration of the chemical substances are necessary to screen for sources of VOC emissions. Toward this goal, we have developed a new flux sampler, referred to herein as an emission cell for simultaneous multi-sampling (ECSMS), that is used for screening indoor emission sources of VOCs and for determining the emission rates of these sources. Because the ECSMS is based on passive sampling, it can be easily used on-site at a low cost. Among VOCs, low-molecular-weight carbonyl compounds including formaldehyde are frequently detected at high concentrations in indoor environments. In this study, we determined the reliability of the ECSMS for the collection of formaldehyde and other carbonyl compounds emitted from wood-based composites of medium density fiberboards and particleboards. We then used emission rates determined by the ECSMS to predict airborne concentrations of formaldehyde emitted from a bookshelf in a large chamber, and these data were compared to formaldehyde concentrations that were acquired simultaneously by means of an active sampling method. The values obtained from the two methods were quite similar, suggesting that ECSMS measurement is an effective method for screening primary sources influencing indoor concentrations of formaldehyde. PMID:20149530

  20. Electrochemical estrogen screen method based on the electrochemical behavior of MCF-7 cells.

    PubMed

    Li, Jinlian; Song, Jia; Bi, Sheng; Zhou, Shi; Cui, Jiwen; Liu, Jiguang; Wu, Dongmei

    2016-08-01

    It was an urgent task to develop quick, cheap and accurate estrogen screen method for evaluating the estrogen effect of the booming chemicals. In this study, the voltammetric behavior between the estrogen-free and normal fragmented MCF-7 cell suspensions were compared, and the electrochemical signal (about 0.68V attributed by xanthine and guanine) of the estrogen-free fragmented MCF-7 cell suspension was obviously lower than that of the normal one. The electrochemistry detection of ex-secretion purines showed that the ability of ex-secretion purines of cells sharp decreased due to the removing of endogenous estrogen. The results indicated that the electrochemical signal of MCF-7 cells was related to the level of intracellular estrogen. When the level of intracellular estrogen was down-regulated, the concentrations of the xanthine and hypoxanthine decreased, which led to the electrochemical signal of MCF-7 cells fall. Based on the electrochemical signal, the electrochemical estrogen screen method was established. The estrogen effect of estradiol, nonylphenol and bisphenol A was evaluated with the electrochemical method, and the result was accordant with that of MTT assay. The electrochemical estrogen screen method was simple, quickly, cheap, objective, and it exploits a new way for the evaluation of estrogenic effects of chemicals. PMID:27108272

  1. An efficient screening method for simultaneous detection of recurrent copy number variants associated with psychiatric disorders.

    PubMed

    Rodriguez-Lopez, Julio; Carrera, Noa; Arrojo, Manuel; Amigo, Jorge; Sobrino, Beatriz; Páramo, Mario; Paz, Eduardo; Agra, Santiago; Ramos-Ríos, Ramón; Brenlla, Julio; Carracedo, Ángel; Costas, Javier

    2015-05-20

    Several recurrent copy number variants (CNVs) increasing risk to neuropsychiatric diseases have been identified in recent years. They show variable clinical expressivity, being associated with different disorders, and incomplete penetrance. However, due to its very low frequency, the full variety of clinical outcomes associated with each one of these CNVs is unknown. Current methods for detection of CNVs are labor intensive, expensive or not suitable for high throughput analysis. Quantitative interspecies competitive PCR linked to variant minisequencing and detection by mass-spectrometry may overcome these limitations. Here, we present two multiplex assays based on this method to screen for eleven psychiatric risk CNVs, such as 1q21, 16p11.2, 3q29, or 16p13.11 regions, among others. The assays were tested in our collection of 514 schizophrenia patients. Results were compared with MLPA at two CNVs. Additional positive results were confirmed by exome sequencing. A total of fourteen patients were CNV carriers. The method presents high sensitivity and specificity, showing its utility as a cheap, accurate, high throughput screening tool for recurrent CNVs. The method may be very useful for management of psychiatric patients as well as screening of different collections of samples to better identify the full spectrum of clinical variability. PMID:25797897

  2. Combined Methods for Diabetic Retinopathy Screening, Using Retina Photographs and Tear Fluid Proteomics Biomarkers.

    PubMed

    Torok, Zsolt; Peto, Tunde; Csosz, Eva; Tukacs, Edit; Molnar, Agnes M; Berta, Andras; Tozser, Jozsef; Hajdu, Andras; Nagy, Valeria; Domokos, Balint; Csutak, Adrienne

    2015-01-01

    Background. It is estimated that 347 million people suffer from diabetes mellitus (DM), and almost 5 million are blind due to diabetic retinopathy (DR). The progression of DR can be slowed down with early diagnosis and treatment. Therefore our aim was to develop a novel automated method for DR screening. Methods. 52 patients with diabetes mellitus were enrolled into the project. Of all patients, 39 had signs of DR. Digital retina images and tear fluid samples were taken from each eye. The results from the tear fluid proteomics analysis and from digital microaneurysm (MA) detection on fundus images were used as the input of a machine learning system. Results. MA detection method alone resulted in 0.84 sensitivity and 0.81 specificity. Using the proteomics data for analysis 0.87 sensitivity and 0.68 specificity values were achieved. The combined data analysis integrated the features of the proteomics data along with the number of detected MAs in the associated image and achieved sensitivity/specificity values of 0.93/0.78. Conclusions. As the two different types of data represent independent and complementary information on the outcome, the combined model resulted in a reliable screening method that is comparable to the requirements of DR screening programs applied in clinical routine.

  3. Combined Methods for Diabetic Retinopathy Screening, Using Retina Photographs and Tear Fluid Proteomics Biomarkers

    PubMed Central

    Torok, Zsolt; Peto, Tunde; Csosz, Eva; Tukacs, Edit; Molnar, Agnes M.; Berta, Andras; Tozser, Jozsef; Hajdu, Andras; Nagy, Valeria; Domokos, Balint; Csutak, Adrienne

    2015-01-01

    Background. It is estimated that 347 million people suffer from diabetes mellitus (DM), and almost 5 million are blind due to diabetic retinopathy (DR). The progression of DR can be slowed down with early diagnosis and treatment. Therefore our aim was to develop a novel automated method for DR screening. Methods. 52 patients with diabetes mellitus were enrolled into the project. Of all patients, 39 had signs of DR. Digital retina images and tear fluid samples were taken from each eye. The results from the tear fluid proteomics analysis and from digital microaneurysm (MA) detection on fundus images were used as the input of a machine learning system. Results. MA detection method alone resulted in 0.84 sensitivity and 0.81 specificity. Using the proteomics data for analysis 0.87 sensitivity and 0.68 specificity values were achieved. The combined data analysis integrated the features of the proteomics data along with the number of detected MAs in the associated image and achieved sensitivity/specificity values of 0.93/0.78. Conclusions. As the two different types of data represent independent and complementary information on the outcome, the combined model resulted in a reliable screening method that is comparable to the requirements of DR screening programs applied in clinical routine. PMID:26221613

  4. Clinical diagnostic tools for screening of perioperative stroke in general surgery: a systematic review.

    PubMed

    Sun, Z; Yue, Y; Leung, C C H; Chan, M T V; Gelb, A W

    2016-03-01

    Perioperative stroke is a devastating complication that carries high mortality and functional disability. Unfortunately, residual anaesthesia and analgesia may obscure important warning signs and may lead to a delay in the assessment and treatment of major stroke after surgery. The purpose of this review is to examine the utility of existing stroke scales, for the recognition of perioperative stroke in the general surgical population. A total of 21 stroke scales have been described in the literature. Diagnostic performance was reported in 17 scales. The majority of the stroke scales were designed to evaluate current neurological deficits after an established stroke event. Recent abbreviated stroke test, such as the Face, Arm, Speech Test (FAST), were developed to facilitate stroke identification in the emergency department. Only two stroke scales have been applied in the perioperative setting after cardiac, carotid and neurological surgeries. The modified National Institutes of Health Stroke Scale appears to be useful in detecting new subtle neurological deficits in critical care, or high dependency units after surgery. However, in the general postsurgical wards, given the concern about the workload required, abbreviated stroke tests may be more appropriate for routine regular stroke surveillance. It is hoped that these tests will provide rapid assessment of global neurological function to facilitate timely diagnosis and treatment of perioperative stroke.

  5. A Novel Two-Step Method for Screening Shade Tolerant Mutant Plants via Dwarfism

    PubMed Central

    Li, Wei; Katin-Grazzini, Lorenzo; Krishnan, Sanalkumar; Thammina, Chandra; El-Tanbouly, Rania; Yer, Huseyin; Merewitz, Emily; Guillard, Karl; Inguagiato, John; McAvoy, Richard J.; Liu, Zongrang; Li, Yi

    2016-01-01

    When subjected to shade, plants undergo rapid shoot elongation, which often makes them more prone to disease and mechanical damage. Shade-tolerant plants can be difficult to breed; however, they offer a substantial benefit over other varieties in low-light areas. Although perennial ryegrass (Lolium perenne L.) is a popular species of turf grasses because of their good appearance and fast establishment, the plant normally does not perform well under shade conditions. It has been reported that, in turfgrass, induced dwarfism can enhance shade tolerance. Here we describe a two-step procedure for isolating shade tolerant mutants of perennial ryegrass by first screening for dominant dwarf mutants, and then screening dwarf plants for shade tolerance. The two-step screening process to isolate shade tolerant mutants can be done efficiently with limited space at early seedling stages, which enables quick and efficient isolation of shade tolerant mutants, and thus facilitates development of shade tolerant new cultivars of turfgrasses. Using the method, we isolated 136 dwarf mutants from 300,000 mutagenized seeds, with 65 being shade tolerant (0.022%). When screened directly for shade tolerance, we recovered only four mutants from a population of 150,000 (0.003%) mutagenized seeds. One shade tolerant mutant, shadow-1, was characterized in detail. In addition to dwarfism, shadow-1 and its sexual progeny displayed high degrees of tolerance to both natural and artificial shade. We showed that endogenous gibberellin (GA) content in shadow-1 was higher than wild-type controls, and shadow-1 was also partially GA insensitive. Our novel, simple and effective two-step screening method should be applicable to breeding shade tolerant cultivars of turfgrasses, ground covers, and other economically important crop plants that can be used under canopies of existing vegetation to increase productivity per unit area of land. PMID:27752260

  6. Equivalence of the generalized Lie-Hori method and the method of averaging

    NASA Technical Reports Server (NTRS)

    Ahmed, A.; Tapley, B. D.

    1982-01-01

    In this investigation, a comparison is made of two methods for developing perturbation theories for non-canonical dynamical systems. The methods compared are the generalized Lie-Hori method and the method of averaging. In the comparison presented here, the equivalence of the methods up to the second order in the small parameter is shown. However, the approach used can be extended to demonstrate the equivalence for higher orders. To illustrate the equivalence both Duffing's equation and the van der Pol equation are solved using each method.

  7. Equivalence of the generalized Lie-Hori method and the method of averaging. [in celestial mechanics

    NASA Technical Reports Server (NTRS)

    Ahmed, A. H.; Tapley, B. D.

    1984-01-01

    In this investigation, a comparison is made of two methods for developing perturbation theories for non-canonical dynamical systems. The methods compared are the generalized Lie-Hori method and the method of averaging. In the comparison presented here, the equivalence of the methods up to the second order in the small parameter is shown. However, the approach used can be extended to demonstrate the equivalence for higher orders. To illustrate the equivalence Duffing's equation, the van der Pol equation and the oscillator with quadratic damping problem are solved using each method.

  8. Performance Evaluation of three Liquid Chromatography Mass Spectrometry Methods for Broad Spectrum Drug Screening

    PubMed Central

    Lynch, Kara L.; Breaud, Autumn R.; Vandenberghe, Hilde; Wu, Alan H. B.; Clarke, William

    2010-01-01

    BACKGROUND Liquid chromatography-mass spectrometry (LC-MS) and tandem LC-MS (LC-MS/MS) are increasingly used in toxicology laboratories as a complementary method to gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-ultraviolet detection (LC-UV) for comprehensive drug screening (CDS). This study was designed to characterize the sensitivity and specificity of three LC-MS(/MS) vendor-supplied methods for targeted CDS and identify the current limitations associated with the use of these technologies. METHODS Five methods for broad spectrum CDS, including LC-UV (REMEDi), full scan GC-MS, LC-MS (ZQ™-Mass Detector with MassLynx™-software), LC-QTRAP-MS/MS (3200-QTRAP® with Cliquid®-software) and LC-LIT-MS/MS (LXQ™ Linear Ion Trap with ToxID™-software) were evaluated based on their ability to detect drugs in 48 patient urine samples. RESULTS The tandem MS methods identified 15% more drugs than the single stage MS or LC-UV methods. Use of two broad spectrum screening methods identified more drugs than any single system alone. False negatives and false positives generated by the LC-MS(/MS) software programs were identified upon manual review of the raw data. CONCLUSIONS The LC-MS/MS methods detected a broader menu of drugs; however, it is essential to establish manual data review criteria for all LC-MS(/MS) drug screening methods. Use of an EI-GC-MS and ESI-LC-MS/MS combination for targeted CDS may be optimal due to the complementary nature of the chromatographic and ionization techniques. PMID:20540936

  9. A general moment expansion method for stochastic kinetic models

    NASA Astrophysics Data System (ADS)

    Ale, Angelique; Kirk, Paul; Stumpf, Michael P. H.

    2013-05-01

    Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations, our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. We show how the moment expansion method can be employed to efficiently quantify parameter sensitivity. Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.

  10. THE EXOPLANET CENSUS: A GENERAL METHOD APPLIED TO KEPLER

    SciTech Connect

    Youdin, Andrew N.

    2011-11-20

    We develop a general method to fit the underlying planetary distribution function (PLDF) to exoplanet survey data. This maximum likelihood method accommodates more than one planet per star and any number of planet or target star properties. We apply the method to announced Kepler planet candidates that transit solar-type stars. The Kepler team's estimates of the detection efficiency are used and are shown to agree with theoretical predictions for an ideal transit survey. The PLDF is fit to a joint power law in planet radius, down to 0.5 R{sub Circled-Plus }, and orbital period, up to 50 days. The estimated number of planets per star in this sample is {approx}0.7-1.4, where the range covers systematic uncertainties in the detection efficiency. To analyze trends in the PLDF we consider four planet samples, divided between shorter and longer periods at 7 days and between large and small radii at 3 R{sub Circled-Plus }. The size distribution changes appreciably between these four samples, revealing a relative deficit of {approx}3 R{sub Circled-Plus} planets at the shortest periods. This deficit is suggestive of preferential evaporation and sublimation of Neptune- and Saturn-like planets. If the trend and explanation hold, it would be spectacular observational support of the core accretion and migration hypotheses, and would allow refinement of these theories.

  11. Adaptive Elastic Net for Generalized Methods of Moments.

    PubMed

    Caner, Mehmet; Zhang, Hao Helen

    2014-01-30

    Model selection and estimation are crucial parts of econometrics. This paper introduces a new technique that can simultaneously estimate and select the model in generalized method of moments (GMM) context. The GMM is particularly powerful for analyzing complex data sets such as longitudinal and panel data, and it has wide applications in econometrics. This paper extends the least squares based adaptive elastic net estimator of Zou and Zhang (2009) to nonlinear equation systems with endogenous variables. The extension is not trivial and involves a new proof technique due to estimators lack of closed form solutions. Compared to Bridge-GMM of Caner (2009), we allow for the number of parameters to diverge to infinity as well as collinearity among a large number of variables, also the redundant parameters set to zero via a data dependent technique. This method has the oracle property, meaning that we can estimate nonzero parameters with their standard limit and the redundant parameters are dropped from the equations simultaneously. Numerical examples are used to illustrate the performance of the new method.

  12. A Multi-Layered Screening Method to Identify Plant Regulatory Genes.

    PubMed

    Kim, Chang-Kug; Kim, Jin-A; Choi, Ji-Weon; Jeong, In-Seon; Moon, Yi-Seul; Park, Dong-Suk; Seol, Young-Joo; Kim, Yong-Kab; Kim, Yong-Hwan; Kim, Yeon-Ki

    2014-01-01

    We used a seven-step process to identify genes involved in glucosinolate biosynthesis and metabolism in the Chinese cabbage (Brassica rapa). We constructed an annotated data set with 34,570 unigenes from B. rapa and predicted 11,526 glucosinolate-related candidate genes using expression profiles generated across nine stages of development on a 47k-gene microarray. Using our multi-layered screening method, we screened 392 transcription factors, 843 pathway genes, and 4,162 ortholog genes associated with glucosinolate-related biosynthesis. Finally, we identified five genes by comparison of the pathway-network genes including the transcription-factor genes and the ortholog-ontology genes. The five genes were anchored to the chromosomes of B. rapa to characterize their genetic-map positions, and phylogenetic reconstruction with homologous genes was performed. These anchored genes were verified by reverse-transcription polymerase chain reaction. While the five genes identified by our multi-layered screen require further characterization and validation, our study demonstrates the power of multi-layered screening after initial identification of genes on microarrays.

  13. Microengineering Methods for Cell Based Microarrays and High-Throughput Drug Screening Applications

    PubMed Central

    Xu, Feng; Wu, JinHui; Wang, ShuQi; Durmus, Naside Gozde; Gurkan, Umut Atakan; Demirci, Utkan

    2011-01-01

    Screening for effective therapeutic agents from millions of drug candidates is costly, time-consuming and often face ethical concerns due to extensive use of animals. To improve cost-effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems have facilitated automated and controlled component loading, significantly reducing the consumption of the candidate compounds and the target cells. Even though these methods significantly increased the throughput compared to conventional in vitro testing systems and in vivo animal models, the cost associated with these platforms remains prohibitively high. Besides, there is a need for three-dimensional (3D) cell based drug-screening models, which can mimic the in vivo microenvironment and the functionality of the native tissues. Here, we present the state-of-the-art microengineering approaches that can be used to develop 3D cell based drug screening assays. We highlight the 3D in vitro cell culture systems with live cell-based arrays, microfluidic cell culture systems, and their application to high-throughput drug screening. We conclude that among the emerging microengineering approaches, bioprinting holds a great potential to provide repeatable 3D cell based constructs with high temporal, spatial control and versatility. PMID:21725152

  14. A consolidated method for screening the endocrine activity of drinking water.

    PubMed

    Chevolleau, Sylvie; Debrauwer, Laurent; Stroheker, Thomas; Viglino, Liza; Mourahib, Issam; Meireles, Maria-Helena; Grimaldi, Marina; Balaguer, Patrick; di Gioia, Lodovico

    2016-12-15

    Endocrine activity of drinking water is a matter of growing interest for scientists as well as health authorities. A concentration technique for endocrine activity screening was developed, optimized, and transposed from 200mL to 10L water samples. To avoid any contamination during concentration, the method was developed using exclusively glass, Teflon and stainless steel materials. Any potential losses were tracked using three model radiolabeled molecules, namely BPA, DEHP and 4n-NP. The final method allowed 10L water samples to be concentrated 5000-fold, with good recovery and repeatability. After validation, by concentrating spiked and non-spiked 10L samples of EVIAN natural mineral water, 14 different drinking water samples were concentrated and screened for endocrine disrupting activity using bioluminescent assays. Samples consisting of bottled water, conditioned in various materials (glass, PET) and subjected to different storage conditions, had no hormone-like activities whereas estrogenic activity was found in the filtered tap water.

  15. Methods for efficient high-throughput screening of protein expression in recombinant Pichia pastoris strains.

    PubMed

    Camattari, Andrea; Weinhandl, Katrin; Gudiminchi, Rama K

    2014-01-01

    The methylotrophic yeast Pichia pastoris is becoming one of the favorite industrial workhorses for protein expression. Due to the widespread use of integration vectors, which generates significant clonal variability, screening methods allowing assaying hundreds of individual clones are of particular importance. Here we describe methods to detect and analyze protein expression, developed in a 96-well format for high-throughput screening of recombinant P. pastoris strains. The chapter covers essentially three common scenarios: (1) an enzymatic assay for proteins expressed in the cell cytoplasm, requiring cell lysis; (2) a whole-cell assay for a fungal cytochrome P450; and (3) a nonenzymatic assay for detection and quantification of tagged protein secreted into the supernatant. PMID:24744029

  16. [Local straight line screening method for the detection of Chinese proprietary medicines containing undeclared prescription drugs].

    PubMed

    Li, Shu; Cao, Yan; Le, Jian; Chen, Gui-Liang; Chai, Yi-Feng; Lu, Feng

    2009-02-01

    The present paper constructs a new approach named local straight-line screening (LSLS) to detect Chinese proprietary medicines (CPM) containing undeclared prescription drugs (UPD). Different from traditional methods used in analysis of multi-component spectrum, LSLS is proposed according to the characteristics of original infrared spectra of the UPD and suspected CPM, without any pattern recognition or concentration model establishment. Spectrum-subtraction leads to the variance in local straight line, which serves as a key in discrimination of whether suspected CPD is adulterated or not. Sibutramine hydrochloride, fenfluramine hydrochloride, sildenafil citrate and lovastatin were used as reference substances of UPD to analyze 16 suspected CPM samples. The results show that LSLS can obtain an accurate quantitative and qualitative analysis of suspected CPM. It is possible for the method to be potentially used in the preliminary screening of CPM containing possible UPD.

  17. Simple screening method for molds producing intracellular mycotoxins in pure cultures.

    PubMed

    Filtenborg, O; Frisvad, J C; Svendsen, J A

    1983-02-01

    A simple screening method for molds producing the intracellular mycotoxins brevianamide A, citreoviridin, cyclopiazonic acid, luteoskyrin, penitrem A, roquefortine C, sterigmatocystin, verruculogen, viomellein, and xanthomegnin was developed. After removing an agar plug from the mold culture, the mycelium on the plug is wetted with a drop of methanol-chloroform (1:2). By this treatment the intracellular mycotoxins are extracted within seconds and transferred directly to a thin-layer chromatography plate by immediately placing the plug on the plate while the mycelium is still wet. After removal of the plug, known thin-layer chromatographic procedures are carried out. The substrate (Czapek yeast autolysate agar) and growth conditions (25 degrees C for 7 days) used by Penicillium taxonomists proved suitable for the production of the mycotoxins investigated when 60 known toxigenic isolates and 865 cultures isolated from foods and feedstuffs were tested with this screening method. PMID:6338829

  18. Simple screening method for molds producing intracellular mycotoxins in pure cultures.

    PubMed Central

    Filtenborg, O; Frisvad, J C; Svendsen, J A

    1983-01-01

    A simple screening method for molds producing the intracellular mycotoxins brevianamide A, citreoviridin, cyclopiazonic acid, luteoskyrin, penitrem A, roquefortine C, sterigmatocystin, verruculogen, viomellein, and xanthomegnin was developed. After removing an agar plug from the mold culture, the mycelium on the plug is wetted with a drop of methanol-chloroform (1:2). By this treatment the intracellular mycotoxins are extracted within seconds and transferred directly to a thin-layer chromatography plate by immediately placing the plug on the plate while the mycelium is still wet. After removal of the plug, known thin-layer chromatographic procedures are carried out. The substrate (Czapek yeast autolysate agar) and growth conditions (25 degrees C for 7 days) used by Penicillium taxonomists proved suitable for the production of the mycotoxins investigated when 60 known toxigenic isolates and 865 cultures isolated from foods and feedstuffs were tested with this screening method. PMID:6338829

  19. Application of a screening method in assessing occupational safety and health of computer workstations.

    PubMed

    Niskanen, Toivo; Lehtelä, Jouni; Länsikallio, Riina

    2014-01-01

    Employers and workers need concrete guidance to plan and implement changes in the ergonomics of computer workstations. The Näppärä method is a screening tool for identifying problems requiring further assessment and corrective actions. The aim of this study was to assess the work of occupational safety and health (OSH) government inspectors who used Näppärä as part of their OSH enforcement inspections (430 assessments) related to computer work. The modifications in workstation ergonomics involved mainly adjustments to the screen, mouse, keyboard, forearm supports, and chair. One output of the assessment is an index indicating the percentage of compliance items. This method can be considered as exposure assessment and ergonomics intervention used as a benchmark for the level of ergonomics. Future research can examine whether the effectiveness of participatory ergonomics interventions should be investigated with Näppärä.

  20. A consolidated method for screening the endocrine activity of drinking water.

    PubMed

    Chevolleau, Sylvie; Debrauwer, Laurent; Stroheker, Thomas; Viglino, Liza; Mourahib, Issam; Meireles, Maria-Helena; Grimaldi, Marina; Balaguer, Patrick; di Gioia, Lodovico

    2016-12-15

    Endocrine activity of drinking water is a matter of growing interest for scientists as well as health authorities. A concentration technique for endocrine activity screening was developed, optimized, and transposed from 200mL to 10L water samples. To avoid any contamination during concentration, the method was developed using exclusively glass, Teflon and stainless steel materials. Any potential losses were tracked using three model radiolabeled molecules, namely BPA, DEHP and 4n-NP. The final method allowed 10L water samples to be concentrated 5000-fold, with good recovery and repeatability. After validation, by concentrating spiked and non-spiked 10L samples of EVIAN natural mineral water, 14 different drinking water samples were concentrated and screened for endocrine disrupting activity using bioluminescent assays. Samples consisting of bottled water, conditioned in various materials (glass, PET) and subjected to different storage conditions, had no hormone-like activities whereas estrogenic activity was found in the filtered tap water. PMID:27451182

  1. Accreditation of a screening method for non-dioxin-like polychlorinated biphenyl detection in fishery products according to European legislation.

    PubMed

    Serpe, F P; Russo, R; Ambrosio, L; Esposito, M; Severino, L

    2013-06-01

    European Commission Regulation 882/2004/EC requires that official control laboratories for foodstuffs in the member states are certified according to UNI EN ISO/IEC 17025:2005 (general requirement for the competence of calibration and testing laboratories). This mandatory requirement has resulted in a continuous adaptation and development of analytical procedures. The aim of this study was to develop a method for semiquantitative screening of polychlorinated biphenyls in fish for human consumption. According to the Commission Decision 657/2002/CE, the detection capability, the precision, the selectivity-specificity, and applicability-ruggedness-stability were determined to validate the method. Moreover, trueness was verified. This procedure resulted in rapid execution, which allowed immediate and effective intervention by the local health authorities to protect the health of consumers. Finally, the procedure has been recognized by the Italian accrediting body, ACCREDIA. PMID:23726197

  2. An efficient iterative method for the generalized Stokes problem

    SciTech Connect

    Sameh, A.; Sarin, V.

    1996-12-31

    This paper presents an efficient iterative scheme for the generalized Stokes problem, which arises frequently in the simulation of time-dependent Navier-Stokes equations for incompressible fluid flow. The general form of the linear system is where A = {alpha}M + vT is an n x n symmetric positive definite matrix, in which M is the mass matrix, T is the discrete Laplace operator, {alpha} and {nu} are positive constants proportional to the inverses of the time-step {Delta}t and the Reynolds number Re respectively, and B is the discrete gradient operator of size n x k (k < n). Even though the matrix A is symmetric and positive definite, the system is indefinite due to the incompressibility constraint (B{sup T}u = 0). This causes difficulties both for iterative methods and commonly used preconditioners. Moreover, depending on the ratio {alpha}/{nu}, A behaves like the mass matrix M at one extreme and the Laplace operator T at the other, thus complicating the issue of preconditioning.

  3. Novel Methods for Communicating Plasma Science to the General Public

    NASA Astrophysics Data System (ADS)

    Zwicker, Andrew; Merali, Aliya; Wissel, S. A.; Delooper, John

    2012-10-01

    The broader implications of Plasma Science remains an elusive topic that the general public rarely discusses, regardless of their relevance to energy, the environment, and technology. Recently, we have looked beyond print media for methods to reach large numbers of people in creative and informative ways. These have included video, art, images, and music. For example, our submission to the ``What is a Flame?'' contest was ranked in the top 15 out of 800 submissions. Images of plasmas have won 3 out of 5 of the Princeton University ``Art of Science'' competitions. We use a plasma speaker to teach students of all ages about sound generation and plasma physics. We report on the details of each of these and future videos and animations under development.

  4. Using stable isotopes to monitor forms of sulfur during desulfurization processes: A quick screening method

    USGS Publications Warehouse

    Liu, Chao-Li; Hackley, Keith C.; Coleman, D.D.; Kruse, C.W.

    1987-01-01

    A method using stable isotope ratio analysis to monitor the reactivity of sulfur forms in coal during thermal and chemical desulfurization processes has been developed at the Illinois State Geological Survey. The method is based upon the fact that a significant difference exists in some coals between the 34S/32S ratios of the pyritic and organic sulfur. A screening method for determining the suitability of coal samples for use in isotope ratio analysis is described. Making these special coals available from coal sample programs would assist research groups in sorting out the complex sulfur chemistry which accompanies thermal and chemical processing of high sulfur coals. ?? 1987.

  5. Screening for generalized anxiety disorder symptoms in the wake of terrorist attacks: a study in primary care.

    PubMed

    Ghafoori, Bita; Neria, Yuval; Gameroff, Marc J; Olfson, Mark; Lantigua, Rafael; Shea, Steven; Weissman, Myrna M

    2009-06-01

    Little is known about the mental health impact of terrorism beyond posttraumatic stress disorder (PTSD) and depression. The associations between exposure to the September 11, 2001 (9/11) attacks in New York City and generalized anxiety disorder (GAD) symptoms were examined in a sample of 929 primary care patients. After controlling for PTSD, depression, panic and substance use disorders, and pre-9/11 trauma, patients who screened positive (vs. negative) for GAD symptoms were roughly twice as likely to report having a loved one at the 9/11 disaster site, twice as likely to know someone who was killed by the attacks, and twice as likely to know someone who was involved with the rescue/recovery efforts after the disaster. Implications for treatment and future research are discussed.

  6. Screening for Generalized Anxiety Disorder Symptoms in the Wake of Terrorist Attacks: A Study in Primary Care

    PubMed Central

    Ghafoori, Bita; Neria, Yuval; Gameroff, Marc J.; Olfson, Mark; Lantigua, Rafael; Shea, Steven; Weissman, Myrna M.

    2013-01-01

    Little is known about the mental health impact of terrorism beyond posttraumatic stress disorder (PTSD) and depression. The associations between exposure to the September 11, 2001 (9/11) attacks in New York City and generalized anxiety disorder (GAD) symptoms were examined in a sample of 929 primary care patients. After controlling for PTSD, depression, panic and substance use disorders, and pre-9/11 trauma, patients who screened positive (vs. negative) for GAD symptoms were roughly twice as likely to report having a loved one at the 9/11 disaster site, twice as likely to know someone who was killed by the attacks, and twice as likely to know someone who was involved with the rescue/recovery efforts after the disaster. Implications for treatment and future research are discussed. PMID:19475656

  7. Method for screening prevention and control measures and technologies based on groundwater pollution intensity assessment.

    PubMed

    Li, Juan; Yang, Yang; Huan, Huan; Li, Mingxiao; Xi, Beidou; Lv, Ningqing; Wu, Yi; Xie, Yiwen; Li, Xiang; Yang, Jinjin

    2016-05-01

    This paper presents a system for determining the evaluation and gradation indices of groundwater pollution intensity (GPI). Considering the characteristics of the vadose zone and pollution sources, the system decides which anti-seepage measures should be implemented at the contaminated site. The pollution sources hazards (PSH) and groundwater intrinsic vulnerability (GIV) are graded by the revised Nemerow Pollution Index and an improved DRTAS model, respectively. GPI is evaluated and graded by a double-sided multi-factor coupling model, which is constructed by the matrix method. The contaminated sites are categorized as prior, ordinary, or common sites. From the GPI results, we develop guiding principles for preventing and removing pollution sources, procedural interruption and remediation, and end treatment and monitoring. Thus, we can select appropriate prevention and control technologies (PCT). To screen the technological schemes and optimize the traditional analytical hierarchy process (AHP), we adopt the technique for order preference by the similarity to ideal solution (TOPSIS) method. Our GPI approach and PCT screening are applied to three types of pollution sites: the refuse dump of a rare earth mine development project (a potential pollution source), a chromium slag dump, and a landfill (existing pollution sources). These three sites are identified as ordinary, prior, and ordinary sites, respectively. The anti-seepage materials at the refuse dump should perform as effectively as a 1.5-m-thick clay bed. The chromium slag dump should be preferentially treated by soil flushing and in situ chemical remediation. The landfill should be treated by natural attenuation technology. The proposed PCT screening approach was compared with conventional screening methods results at the three sites and proved feasible and effective. The proposed method can provide technical support for the monitoring and management of groundwater pollution in China. PMID:26878632

  8. On the Use of Accelerated Aging Methods for Screening High Temperature Polymeric Composite Materials

    NASA Technical Reports Server (NTRS)

    Gates, Thomas S.; Grayson, Michael A.

    1999-01-01

    A rational approach to the problem of accelerated testing of high temperature polymeric composites is discussed. The methods provided are considered tools useful in the screening of new materials systems for long-term application to extreme environments that include elevated temperature, moisture, oxygen, and mechanical load. The need for reproducible mechanisms, indicator properties, and real-time data are outlined as well as the methodologies for specific aging mechanisms.

  9. Statistical studies of animal response data from USF toxicity screening test method

    NASA Technical Reports Server (NTRS)

    Hilado, C. J.; Machado, A. M.

    1978-01-01

    Statistical examination of animal response data obtained using Procedure B of the USF toxicity screening test method indicates that the data deviate only slightly from a normal or Gaussian distribution. This slight departure from normality is not expected to invalidate conclusions based on theoretical statistics. Comparison of times to staggering, convulsions, collapse, and death as endpoints shows that time to death appears to be the most reliable endpoint because it offers the lowest probability of missed observations and premature judgements.

  10. Method for screening prevention and control measures and technologies based on groundwater pollution intensity assessment.

    PubMed

    Li, Juan; Yang, Yang; Huan, Huan; Li, Mingxiao; Xi, Beidou; Lv, Ningqing; Wu, Yi; Xie, Yiwen; Li, Xiang; Yang, Jinjin

    2016-05-01

    This paper presents a system for determining the evaluation and gradation indices of groundwater pollution intensity (GPI). Considering the characteristics of the vadose zone and pollution sources, the system decides which anti-seepage measures should be implemented at the contaminated site. The pollution sources hazards (PSH) and groundwater intrinsic vulnerability (GIV) are graded by the revised Nemerow Pollution Index and an improved DRTAS model, respectively. GPI is evaluated and graded by a double-sided multi-factor coupling model, which is constructed by the matrix method. The contaminated sites are categorized as prior, ordinary, or common sites. From the GPI results, we develop guiding principles for preventing and removing pollution sources, procedural interruption and remediation, and end treatment and monitoring. Thus, we can select appropriate prevention and control technologies (PCT). To screen the technological schemes and optimize the traditional analytical hierarchy process (AHP), we adopt the technique for order preference by the similarity to ideal solution (TOPSIS) method. Our GPI approach and PCT screening are applied to three types of pollution sites: the refuse dump of a rare earth mine development project (a potential pollution source), a chromium slag dump, and a landfill (existing pollution sources). These three sites are identified as ordinary, prior, and ordinary sites, respectively. The anti-seepage materials at the refuse dump should perform as effectively as a 1.5-m-thick clay bed. The chromium slag dump should be preferentially treated by soil flushing and in situ chemical remediation. The landfill should be treated by natural attenuation technology. The proposed PCT screening approach was compared with conventional screening methods results at the three sites and proved feasible and effective. The proposed method can provide technical support for the monitoring and management of groundwater pollution in China.

  11. Effect of screening and lifestyle counselling on incidence of ischaemic heart disease in general population: Inter99 randomised trial

    PubMed Central

    Jacobsen, Rikke Kart; Toft, Ulla; Aadahl, Mette; Glümer, Charlotte; Pisinger, Charlotta

    2014-01-01

    Objective To investigate the effect of systematic screening for risk factors for ischaemic heart disease followed by repeated lifestyle counselling on the 10 year development of ischaemic heart disease at a population level. Design Randomised controlled community based trial. Setting Suburbs of Copenhagen, Denmark Participants 59 616 people aged 30-60 years randomised with different age and sex randomisation ratios to an intervention group (n=11 629) and a control group (n=47 987). Intervention The intervention group was invited for screening, risk assessment, and lifestyle counselling up to four times over a five year period. All participants with an unhealthy lifestyle had individually tailored lifestyle counselling at all visits (at baseline and after one and three years); those at high risk of ischaemic heart disease, according to predefined criteria, were furthermore offered six sessions of group based lifestyle counselling on smoking cessation, diet, and physical activity. After five years all were invited for a final counselling session. Participants were referred to their general practitioner for medical treatment, if relevant. The control group was not invited for screening. Main outcome measures The primary outcome measure was incidence of ischaemic heart disease in the intervention group compared with the control group. Secondary outcome measures were stroke, combined events (ischaemic heart disease, stroke, or both), and mortality. Results 6091 (52.4%) people in the intervention group participated at baseline. Among 5978 people eligible at five year follow-up (59 died and 54 emigrated), 4028 (67.4%) attended. A total of 3163 people died in the 10 year follow-up period. Among 58 308 without a history of ischaemic heart disease at baseline, 2782 developed ischaemic heart disease. Among 58 940 without a history of stroke at baseline, 1726 developed stroke. No significant difference was seen between the intervention and control groups in the

  12. A high throughput method for rapid screening of chitosanase-producing fungal strain under acidic conditions.

    PubMed

    Ding, Su; Chen, Gui-Guang; Liang, Zhi-Qun; Zeng, Wei; Cao, Mu-Ming; Chen, Guo-Pin; Xie, Shu-Yu; Li, Wei

    2016-11-01

    A novel high-throughput method was established for rapid screening of a large numbers of Aspergillus fumigatus (A. fumigatus) mutants with high chitosanase production under acidic culture condition by exploiting the fact that iodine can be used as the indicator to stain chitosan but is ineffective for chitooligosaccharides. The mutant population was generated by irradiating A. fumigatus CICC 2434 with Co(60)-γ rays. Mutants were cultured on acidic plates containing colloidal chitosan and preliminary screened according to diameter of haloes formed around colonies. Then, chitosanase production of the isolates were verified by dinitrosalicylic acid assay. Lastly, molecular masses on enzymolysis products of isolated mutants were rapidly compared by aniline blue plate assay. Using this method, the mutant strain Co-8 was selected, which had chitosanase activity of 24.87 U/mL (increased by 369.2 % as compared to that of its parental strain).Taking together, the method is easy, efficient and particularly suited to rapid screen acidophilic fungal strains with high chitosanase-production. PMID:27628334

  13. Novel Simplified and Rapid Method for Screening and Isolation of Polyunsaturated Fatty Acids Producing Marine Bacteria

    PubMed Central

    Tilay, Ashwini; Annapure, Uday

    2012-01-01

    Bacterial production of polyunsaturated fatty acids (PUFAs) is a potential biotechnological approach for production of valuable nutraceuticals. Reliable method for screening of number of strains within short period of time is great need. Here, we report a novel simplified method for screening and isolation of PUFA-producing bacteria by direct visualization using the H2O2-plate assay. The oxidative stability of PUFAs in growing bacteria towards added H2O2 is a distinguishing characteristic between the PUFAs producers (no zone of inhibition) and non-PUFAs producers (zone of inhibition) by direct visualization. The confirmation of assay results was performed by injecting fatty acid methyl esters (FAMEs) produced by selected marine bacteria to Gas Chromatography-Mass Spectrometry (GCMS). To date, this assay is the most effective, inexpensive, and specific method for bacteria producing PUFAs and shows drastically reduction in the number of samples thus saves the time, effort, and cost of screening and isolating strains of bacterial PUFAs producers. PMID:22934188

  14. A time-scale sensitometric method for evaluating screen-film systems.

    PubMed

    Góes, E G; Pelá, C A; Ghilardi, N T

    1997-10-01

    An x-ray sensitometer is used to measure the characteristic curve of radiographic films exposed with fluorescent intensifying screens. The series of relative exposures, necessary to cover the full density range of the film, can be obtained by either time-scale or intensity-scale sensitometric methods. We have developed a convenient method of exposing film-screen systems for time-scale sensitometry. In this method, during exposure the x-ray kilovoltage, tube current and x-ray intensity remain constant and a geometric series of exposures of the film is modulated by varying the exposure time. This time variation can be obtained when a lead disc with different sector openings is rotated in front of the film system by a stepping motor. The conditions normally used are 70 kVp x-rays, 3.5 mm Al total filtration at the tube, and 2.4 m focal spot-film distance. This exposure latitude gives a complete characteristic curve of film-screen systems. PMID:9364589

  15. A time-scale sensitometric method for evaluating screen - film systems

    NASA Astrophysics Data System (ADS)

    Góes, E. G.; Pelá, C. A.; Ghilardi, Netto T.

    1997-10-01

    An x-ray sensitometer is used to measure the characteristic curve of radiographic films exposed with fluorescent intensifying screens. The series of relative exposures, necessary to cover the full density range of the film, can be obtained by either time-scale or intensity-scale sensitometric methods. We have developed a convenient method of exposing film - screen systems for time-scale sensitometry. In this method, during exposure the x-ray kilovoltage, tube current and x-ray intensity remain constant and a geometric series of exposures of the film is modulated by varying the exposure time. This time variation can be obtained when a lead disc with different sector openings is rotated in front of the film system by a stepping motor. The conditions normally used are 70 kVp x-rays, 3.5 mm Al total filtration at the tube, and 2.4 m focal spot - film distance. This exposure latitude gives a complete characteristic curve of film - screen systems.

  16. Multiparameter telemetry as a sensitive screening method to detect vaccine reactogenicity in mice.

    PubMed

    Arras, Margarete; Glauser, Daniel L; Jirkof, Paulin; Rettich, Andreas; Schade, Benjamin; Cinelli, Paolo; Pinschewer, Daniel D; Ackermann, Mathias

    2012-01-01

    Refined vaccines and adjuvants are urgently needed to advance immunization against global infectious challenges such as HIV, hepatitis C, tuberculosis and malaria. Large-scale screening efforts are ongoing to identify adjuvants with improved efficacy profiles. Reactogenicity often represents a major hurdle to the clinical use of new substances. Yet, irrespective of its importance, this parameter has remained difficult to screen for, owing to a lack of sensitive small animal models with a capacity for high throughput testing. Here we report that continuous telemetric measurements of heart rate, heart rate variability, body core temperature and locomotor activity in laboratory mice readily unmasked systemic side-effects of vaccination, which went undetected by conventional observational assessment and clinical scoring. Even minor aberrations in homeostasis were readily detected, ranging from sympathetic activation over transient pyrogenic effects to reduced physical activity and apathy. Results in real-time combined with the potential of scalability and partial automation in the industrial context suggest multiparameter telemetry in laboratory mice as a first-line screen for vaccine reactogenicity. This may accelerate vaccine discovery in general and may further the success of vaccines in combating infectious disease and cancer.

  17. Study on measurement method for projectile location based on light screen

    NASA Astrophysics Data System (ADS)

    Han, Feng; Liu, QunHua; Sun, GuoBin

    2008-09-01

    In weapon-ammunition system, firing accuracy of projectile is major characteristic parameter weighing fire effect and capability of weapon-ammunition system for target. At present, firing accuracy of projectile is obtained by measuring the two-dimensional coordinates of projectile for target. In order to measure the parameters of two-dimensional coordinates of projectile for target, a new type of measurement system is proposed. The measurement system is composed of four high sensitivity light screens (known as target) with special geometrical frame. Light source of the screens is formed by special infrared LED array. The PIN infrared photodiodes array is used as the sensors. The longest effective distance between light source and sensors is 4m. It is impossible to achieve using traditional methods. Four light screens and high-precision timers are combined in order to acquire the value of time when the projectile flies across the position of four light screens. The real-time data acquirement and processing and display of two-dimensional coordinates and the projectile velocity can be realized. The principle of measurement system and the design of high sensitivity light screen are introduced emphatically. The measurement system was verified by using five kinds of small caliber pellets. As compared with the paper target sheet, the measurement system designed can meet the demand of check-up test of gun, bullet and ammunition. The firing testing in the target field has proved that the measurement system has the advantages of simple construction, easy operation and high precision and high sensitivity.

  18. Risks of Breast Cancer Screening

    MedlinePlus

    ... of Breast & Gynecologic Cancers Breast Cancer Screening Research Breast Cancer Screening (PDQ®)–Patient Version What is screening? Go ... cancer screening: Cancer Screening Overview General Information About Breast Cancer Key Points Breast cancer is a disease in ...

  19. Increasing chlamydia screening tests in general practice: a modified Zelen prospective Cluster Randomised Controlled Trial evaluating a complex intervention based on the Theory of Planned Behaviour

    PubMed Central

    McNulty, Cliodna A M; Hogan, Angela H; Ricketts, Ellie J; Wallace, Louise; Oliver, Isabel; Campbell, Rona; Kalwij, Sebastian; O'Connell, Elaine; Charlett, Andre

    2014-01-01

    Objective To determine if a structured complex intervention increases opportunistic chlamydia screening testing of patients aged 15–24 years attending English general practitioner (GP) practices. Methods A prospective, Cluster Randomised Controlled Trial with a modified Zelen design involving 160 practices in South West England in 2010. The intervention was based on the Theory of Planned Behaviour (TPB). It comprised of practice-based education with up to two additional contacts to increase the importance of screening to GP staff and their confidence to offer tests through skill development (including videos). Practical resources (targets, posters, invitation cards, computer reminders, newsletters including feedback) aimed to actively influence social cognitions of staff, increasing their testing intention. Results Data from 76 intervention and 81 control practices were analysed. In intervention practices, chlamydia screening test rates were 2.43/100 15–24-year-olds registered preintervention, 4.34 during intervention and 3.46 postintervention; controls testing rates were 2.61/100 registered patients prior intervention, 3.0 during intervention and 2.82 postintervention. During the intervention period, testing in intervention practices was 1.76 times as great (CI 1.24 to 2.48) as controls; this persisted for 9 months postintervention (1.57 times as great, CI 1.27 to 2.30). Chlamydia infections detected increased in intervention practices from 2.1/1000 registered 15–24-year-olds prior intervention to 2.5 during the intervention compared with 2.0 and 2.3/1000 in controls (Estimated Rate Ratio intervention versus controls 1.4 (CI 1.01 to 1.93). Conclusions This complex intervention doubled chlamydia screening tests in fully engaged practices. The modified Zelen design gave realistic measures of practice full engagement (63%) and efficacy of this educational intervention in general practice; it should be used more often. Trial registration The trial was

  20. High-Solids Enzymatic Saccharification Screening Method for Lignocellulosic Biomass (Poster)

    SciTech Connect

    Roche, C. M.; Stickel, J. J.

    2009-05-01

    The ability to screen new biomass pretreatments and advanced enzyme systems at process-relevant conditions is key to developing economically viable lignocellulosic ethanol. While much research is being invested in developing pretreatment technologies and enzyme systems that will more efficiently convert cellulosic biomass to sugars, the current standard reactor vessel, a shake flask, that is used for screening enzymatic saccharification of cellulosic biomass is inadequate at high-solids conditions. Shake flasks do not provide adequate mixing at high solids conditions. In this work, a roller bottle reactor was identified as a small-scale high-solids saccharification reaction vessel, and a method was developed for use in screening both pretreated biomass and enzyme systems at process-relevant conditions. This new method addresses mixing issues observed in high-solids saccharifications. In addition, yield calculations from sugar concentrations on a mass basis were used to account for the two-phase nature of the saccharification slurry, which eliminates discontinuities in comparing high-solids to low-solids saccharifications that occur when using concentrations on a volume basis. The roller bottle reactors out-performed the shake flasks by 5% for an initial insoluble solids loading of 15% and 140% for an initial soluble solids loading of 30%. The reactor system and method was compared at bench and floor scales and determined to be scalable for initial insoluble solids loading in the range of 15% to 30%. Pretreatment and enzyme screening results indicate that mid severity pretreated biomass is more digestible than the low and high severity biomass and GC220 is a superior enzyme to Spezyme CP.

  1. Generalized method of eigenoscillations for near-field optical microscopy

    NASA Astrophysics Data System (ADS)

    Jiang, Bor-Yuan; Zhang, Lingfeng; Castro Neto, Antonio; Basov, Dimitri; Fogler, Michael

    2015-03-01

    Electromagnetic interaction between a sub-wavelength particle (the ``probe'') and a material surface (the ``sample'') is studied theoretically. The interaction is shown to be governed by a series of resonances (eigenoscillations), corresponding to surface polariton modes localized near the probe. The resonance parameters depend on the dielectric function and geometry of the probe, as well as the surface reflectivity of the material. Calculation of such resonances is carried out for several axisymmetric particle shapes (spherical, spheroidal, and pear-shaped). For spheroids an efficient numerical method is proposed, capable of handling cases of large or strongly momentum-dependent surface reflectivity. The method is applied to modeling near-field spectroscopy studies of various materials. For highly resonant materials such as aluminum oxide (by itself or covered with graphene) a rich structure of the simulated signal is found, including multi-peak spectra and nonmonotonic approach curves. These features have a strong dependence on physical parameters, e.g., the probe shape. For less resonant materials such as silicon oxide the dependence is weaker, and the spheroid model is generally applicable.

  2. Evaluation of a Fluorescence-Based Method for Antibabesial Drug Screening

    PubMed Central

    Guswanto, Azirwan; Sivakumar, Thillaiampalam; Rizk, Mohamed Abdo; Elsayed, Shimaa Abd Elsalam; Youssef, Mohamed Ahmed; ElSaid, ElSaid El Shirbini; Yokoyama, Naoaki

    2014-01-01

    In vitro evaluation of chemotherapeutic agents against Babesia and Theileria parasites has become routine, and the effectiveness of these chemicals is usually determined by comparing the parasitemia dynamics of untreated and treated parasites. Although microscopy is widely used to calculate parasitemia, several disadvantages are associated with this technique. The present study evaluated a fluorescence-based method using SYBR green I stain (SG I) to screen antibabesial agents in in vitro cultures of Babesia bovis. The linearity between relative fluorescence units (RFU) and parasitemia was found to be well correlated with a 0.9944 goodness-of-fit (r2) value. Subsequently, 50% inhibitory concentration (IC50) values were calculated for 3 antiprotozoan agents, diminazene aceturate, nimbolide, and gedunin, by this method. For diminazene aceturate and nimbolide, the IC50s determined by the fluorescence-based method (408 nM and 8.13 μM, respectively) and microscopy (400.3 nM and 9.4 μM, respectively) were in agreement. Furthermore, the IC50 of gedunin determined by the fluorescence-based method (19 μM) was similar to the recently described microscopy-based value (21.7 μM) for B. bovis. Additionally, the Z′ factor (0.80 to 0.90), signal-to-noise (S/N) ratio (44.15 to 87.64), coefficient of variation at the maximum signal (%CVmax) (0.50 to 2.85), and coefficient of variation at the minimum signal (%CVmin) (1.23 to 2.21) calculated for the fluorescence method using diminazene aceturate were comparable to those previously determined in malaria research for this assay. These findings suggest that the fluorescence-based method might be useful for antibabesial drug screening and may have potential to be developed into a high-throughput screening (HTS) assay. PMID:24914124

  3. Evaluation of a fluorescence-based method for antibabesial drug screening.

    PubMed

    Guswanto, Azirwan; Sivakumar, Thillaiampalam; Rizk, Mohamed Abdo; Elsayed, Shimaa Abd Elsalam; Youssef, Mohamed Ahmed; ElSaid, ElSaid El Shirbini; Yokoyama, Naoaki; Igarashi, Ikuo

    2014-08-01

    In vitro evaluation of chemotherapeutic agents against Babesia and Theileria parasites has become routine, and the effectiveness of these chemicals is usually determined by comparing the parasitemia dynamics of untreated and treated parasites. Although microscopy is widely used to calculate parasitemia, several disadvantages are associated with this technique. The present study evaluated a fluorescence-based method using SYBR green I stain (SG I) to screen antibabesial agents in in vitro cultures of Babesia bovis. The linearity between relative fluorescence units (RFU) and parasitemia was found to be well correlated with a 0.9944 goodness-of-fit (r(2)) value. Subsequently, 50% inhibitory concentration (IC50) values were calculated for 3 antiprotozoan agents, diminazene aceturate, nimbolide, and gedunin, by this method. For diminazene aceturate and nimbolide, the IC(50)s determined by the fluorescence-based method (408 nM and 8.13 μM, respectively) and microscopy (400.3 nM and 9.4 μM, respectively) were in agreement. Furthermore, the IC50 of gedunin determined by the fluorescence-based method (19 μM) was similar to the recently described microscopy-based value (21.7 μM) for B. bovis. Additionally, the Z' factor (0.80 to 0.90), signal-to-noise (S/N) ratio (44.15 to 87.64), coefficient of variation at the maximum signal (%CVmax) (0.50 to 2.85), and coefficient of variation at the minimum signal (%CVmin) (1.23 to 2.21) calculated for the fluorescence method using diminazene aceturate were comparable to those previously determined in malaria research for this assay. These findings suggest that the fluorescence-based method might be useful for antibabesial drug screening and may have potential to be developed into a high-throughput screening (HTS) assay. PMID:24914124

  4. Depressed, anxious and breathless missing out: Weight screening in general practice in a regional catchment of New South Wales

    PubMed Central

    2015-01-01

    Abstract Objective To assess the recording status of weight management measures among adults presenting to general practices within regional catchments. Design Cross‐sectional; secondary data analysis. Setting Primary health care – 17 general practices located in the Illawarra Shoalhaven region of regional New South Wales. Participants A subset of the Sentinel Practices Data Sourcing project database (n = 118 709 adults) that included information on demographic indicators, chronic disease status, and obesity and overweight‐specific measurement indicators recorded from September 2011 to September 2013. Main outcome measures Proportions of coded recording of quantitative measures of overweight and obesity – body mass index (BMI) and waist circumference, and likelihood of BMI recording (odds ratios (ORs)) by various clinical diagnosis and counts of recorded conditions. Results Of the patients, 30.9% had a BMI recorded and only 8.0% had a waist circumference recorded in their electronic medical records. There were variations in BMI recording across age with those aged 45–64 years more likely (aOR = 1.25; 95% confidence interval (CI), 1.21–1.29; P‐value < 0.001) to have a recorded BMI. Patients with mental health conditions (a OR = 0.80; 95% CI, 0.76–0.84; P‐value < 0.001) and patients with respiratory conditions (aOR = 0.91; 95% CI, 0.86–0.96; P‐value = 0.001) were significantly less likely to have a BMI recorded. Conclusions Recording of measures of obesity and overweight in general practices within regional settings is much lower than optimal. More support and advocacy around weighing patients at all interactions is required for regional general practitioners to increase the weight screening in primary care. These findings have policy‐relevant implications for weight management in regional Australia. PMID:26694898

  5. A New Versatile Microarray-based Method for High Throughput Screening of Carbohydrate-active Enzymes*

    PubMed Central

    Vidal-Melgosa, Silvia; Pedersen, Henriette L.; Schückel, Julia; Arnal, Grégory; Dumon, Claire; Amby, Daniel B.; Monrad, Rune Nygaard; Westereng, Bjørge; Willats, William G. T.

    2015-01-01

    Carbohydrate-active enzymes have multiple biological roles and industrial applications. Advances in genome and transcriptome sequencing together with associated bioinformatics tools have identified vast numbers of putative carbohydrate-degrading and -modifying enzymes including glycoside hydrolases and lytic polysaccharide monooxygenases. However, there is a paucity of methods for rapidly screening the activities of these enzymes. By combining the multiplexing capacity of carbohydrate microarrays with the specificity of molecular probes, we have developed a sensitive, high throughput, and versatile semiquantitative enzyme screening technique that requires low amounts of enzyme and substrate. The method can be used to assess the activities of single enzymes, enzyme mixtures, and crude culture broths against single substrates, substrate mixtures, and biomass samples. Moreover, we show that the technique can be used to analyze both endo-acting and exo-acting glycoside hydrolases, polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. We demonstrate the potential of the technique by identifying the substrate specificities of purified uncharacterized enzymes and by screening enzyme activities from fungal culture broths. PMID:25657012

  6. Function-specific virtual screening for GPCR ligands using a combined scoring method

    PubMed Central

    Kooistra, Albert J.; Vischer, Henry F.; McNaught-Flores, Daniel; Leurs, Rob; de Esch, Iwan J. P.; de Graaf, Chris

    2016-01-01

    The ability of scoring functions to correctly select and rank docking poses of small molecules in protein binding sites is highly target dependent, which presents a challenge for structure-based drug discovery. Here we describe a virtual screening method that combines an energy-based docking scoring function with a molecular interaction fingerprint (IFP) to identify new ligands based on G protein-coupled receptor (GPCR) crystal structures. The consensus scoring method is prospectively evaluated by: 1) the discovery of chemically novel, fragment-like, high affinity histamine H1 receptor (H1R) antagonists/inverse agonists, 2) the selective structure-based identification of ß2-adrenoceptor (ß2R) agonists, and 3) the experimental validation and comparison of the combined and individual scoring approaches. Systematic retrospective virtual screening simulations allowed the definition of scoring cut-offs for the identification of H1R and ß2R ligands and the selection of an optimal ß-adrenoceptor crystal structure for the discrimination between ß2R agonists and antagonists. The consensus approach resulted in the experimental validation of 53% of the ß2R and 73% of the H1R virtual screening hits with up to nanomolar affinities and potencies. The selective identification of ß2R agonists shows the possibilities of structure-based prediction of GPCR ligand function by integrating protein-ligand binding mode information. PMID:27339552

  7. New multiplex PCR methods for rapid screening of genetically modified organisms in foods.

    PubMed

    Datukishvili, Nelly; Kutateladze, Tamara; Gabriadze, Inga; Bitskinashvili, Kakha; Vishnepolsky, Boris

    2015-01-01

    We present novel multiplex PCR methods for rapid and reliable screening of genetically modified organisms (GMOs). New designed PCR primers targeting four frequently used GMO specific sequences permitted identification of new DNA markers, in particular 141 bp fragment of cauliflower mosaic virus (CaMV) 35S promoter, 224 bp fragment of Agrobacterium tumefaciens nopaline synthase (NOS) terminator, 256 bp fragment of 5-enolppyruvylshikimate-phosphate synthase (epsps) gene and 258 bp fragment of Cry1Ab delta-endotoxin (cry1Ab) gene for GMO screening. The certified reference materials containing Roundup Ready soybean (RRS) and maize MON 810 were applied for the development and optimization of uniplex and multiplex PCR systems. Evaluation of amplification products by agarose gel electrophoresis using negative and positive controls confirmed high specificity and sensitivity at 0.1% GMO for both RRS and MON 810. The fourplex PCR was developed and optimized that allows simultaneous detection of three common transgenic elements, such as: CaMV 35S promoter, NOS terminator, epsps gene together with soybean-specific lectin gene. The triplex PCR developed enables simultaneous identification of transgenic elements, such as: 35S promoter and cry1Ab gene together with maize zein gene. The analysis of different processed foods demonstrated that multiplex PCR methods developed in this study are useful for accurate and fast screening of GM food products.

  8. A new versatile microarray-based method for high throughput screening of carbohydrate-active enzymes.

    PubMed

    Vidal-Melgosa, Silvia; Pedersen, Henriette L; Schückel, Julia; Arnal, Grégory; Dumon, Claire; Amby, Daniel B; Monrad, Rune Nygaard; Westereng, Bjørge; Willats, William G T

    2015-04-01

    Carbohydrate-active enzymes have multiple biological roles and industrial applications. Advances in genome and transcriptome sequencing together with associated bioinformatics tools have identified vast numbers of putative carbohydrate-degrading and -modifying enzymes including glycoside hydrolases and lytic polysaccharide monooxygenases. However, there is a paucity of methods for rapidly screening the activities of these enzymes. By combining the multiplexing capacity of carbohydrate microarrays with the specificity of molecular probes, we have developed a sensitive, high throughput, and versatile semiquantitative enzyme screening technique that requires low amounts of enzyme and substrate. The method can be used to assess the activities of single enzymes, enzyme mixtures, and crude culture broths against single substrates, substrate mixtures, and biomass samples. Moreover, we show that the technique can be used to analyze both endo-acting and exo-acting glycoside hydrolases, polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. We demonstrate the potential of the technique by identifying the substrate specificities of purified uncharacterized enzymes and by screening enzyme activities from fungal culture broths.

  9. New multiplex PCR methods for rapid screening of genetically modified organisms in foods.

    PubMed

    Datukishvili, Nelly; Kutateladze, Tamara; Gabriadze, Inga; Bitskinashvili, Kakha; Vishnepolsky, Boris

    2015-01-01

    We present novel multiplex PCR methods for rapid and reliable screening of genetically modified organisms (GMOs). New designed PCR primers targeting four frequently used GMO specific sequences permitted identification of new DNA markers, in particular 141 bp fragment of cauliflower mosaic virus (CaMV) 35S promoter, 224 bp fragment of Agrobacterium tumefaciens nopaline synthase (NOS) terminator, 256 bp fragment of 5-enolppyruvylshikimate-phosphate synthase (epsps) gene and 258 bp fragment of Cry1Ab delta-endotoxin (cry1Ab) gene for GMO screening. The certified reference materials containing Roundup Ready soybean (RRS) and maize MON 810 were applied for the development and optimization of uniplex and multiplex PCR systems. Evaluation of amplification products by agarose gel electrophoresis using negative and positive controls confirmed high specificity and sensitivity at 0.1% GMO for both RRS and MON 810. The fourplex PCR was developed and optimized that allows simultaneous detection of three common transgenic elements, such as: CaMV 35S promoter, NOS terminator, epsps gene together with soybean-specific lectin gene. The triplex PCR developed enables simultaneous identification of transgenic elements, such as: 35S promoter and cry1Ab gene together with maize zein gene. The analysis of different processed foods demonstrated that multiplex PCR methods developed in this study are useful for accurate and fast screening of GM food products. PMID:26257724

  10. Function-specific virtual screening for GPCR ligands using a combined scoring method.

    PubMed

    Kooistra, Albert J; Vischer, Henry F; McNaught-Flores, Daniel; Leurs, Rob; de Esch, Iwan J P; de Graaf, Chris

    2016-01-01

    The ability of scoring functions to correctly select and rank docking poses of small molecules in protein binding sites is highly target dependent, which presents a challenge for structure-based drug discovery. Here we describe a virtual screening method that combines an energy-based docking scoring function with a molecular interaction fingerprint (IFP) to identify new ligands based on G protein-coupled receptor (GPCR) crystal structures. The consensus scoring method is prospectively evaluated by: 1) the discovery of chemically novel, fragment-like, high affinity histamine H1 receptor (H1R) antagonists/inverse agonists, 2) the selective structure-based identification of ß2-adrenoceptor (ß2R) agonists, and 3) the experimental validation and comparison of the combined and individual scoring approaches. Systematic retrospective virtual screening simulations allowed the definition of scoring cut-offs for the identification of H1R and ß2R ligands and the selection of an optimal ß-adrenoceptor crystal structure for the discrimination between ß2R agonists and antagonists. The consensus approach resulted in the experimental validation of 53% of the ß2R and 73% of the H1R virtual screening hits with up to nanomolar affinities and potencies. The selective identification of ß2R agonists shows the possibilities of structure-based prediction of GPCR ligand function by integrating protein-ligand binding mode information. PMID:27339552

  11. New multiplex PCR methods for rapid screening of genetically modified organisms in foods

    PubMed Central

    Datukishvili, Nelly; Kutateladze, Tamara; Gabriadze, Inga; Bitskinashvili, Kakha; Vishnepolsky, Boris

    2015-01-01

    We present novel multiplex PCR methods for rapid and reliable screening of genetically modified organisms (GMOs). New designed PCR primers targeting four frequently used GMO specific sequences permitted identification of new DNA markers, in particular 141 bp fragment of cauliflower mosaic virus (CaMV) 35S promoter, 224 bp fragment of Agrobacterium tumefaciens nopaline synthase (NOS) terminator, 256 bp fragment of 5-enolppyruvylshikimate-phosphate synthase (epsps) gene and 258 bp fragment of Cry1Ab delta-endotoxin (cry1Ab) gene for GMO screening. The certified reference materials containing Roundup Ready soybean (RRS) and maize MON 810 were applied for the development and optimization of uniplex and multiplex PCR systems. Evaluation of amplification products by agarose gel electrophoresis using negative and positive controls confirmed high specificity and sensitivity at 0.1% GMO for both RRS and MON 810. The fourplex PCR was developed and optimized that allows simultaneous detection of three common transgenic elements, such as: CaMV 35S promoter, NOS terminator, epsps gene together with soybean-specific lectin gene. The triplex PCR developed enables simultaneous identification of transgenic elements, such as: 35S promoter and cry1Ab gene together with maize zein gene. The analysis of different processed foods demonstrated that multiplex PCR methods developed in this study are useful for accurate and fast screening of GM food products. PMID:26257724

  12. Pathophysiology, risk factors, and screening methods for prediabetes in women with polycystic ovary syndrome.

    PubMed

    Gourgari, Evgenia; Spanakis, Elias; Dobs, Adrian Sandra

    2016-01-01

    Polycystic ovary syndrome (PCOS) is a syndrome associated with insulin resistance (IR), obesity, infertility, and increased cardiometabolic risk. This is a descriptive review of several mechanisms that can explain the IR among women with PCOS, other risk factors for the development of diabetes, and the screening methods used for the detection of glucose intolerance in women with PCOS. Few mechanisms can explain IR in women with PCOS such as obesity, insulin receptor signaling defects, and inhibition of insulin-mediated glucose uptake in adipocytes. Women with PCOS have additional risk factors for the development of glucose intolerance such as family history of diabetes, use of oral contraceptives, anovulation, and age. The Androgen Society in 2007 and the Endocrine Society in 2013 recommended using oral glucose tolerance test as a screening tool for abnormal glucose tolerance in all women with PCOS. The approach to detection of glucose intolerance among women with PCOS varies among health care providers. Large prospective studies are still needed for the development of guidelines with strong evidence. When assessing risk of future diabetes in women with PCOS, it is important to take into account the method used for screening as well as other risk factors that these women might have. PMID:27570464

  13. Pathophysiology, risk factors, and screening methods for prediabetes in women with polycystic ovary syndrome

    PubMed Central

    Gourgari, Evgenia; Spanakis, Elias; Dobs, Adrian Sandra

    2016-01-01

    Polycystic ovary syndrome (PCOS) is a syndrome associated with insulin resistance (IR), obesity, infertility, and increased cardiometabolic risk. This is a descriptive review of several mechanisms that can explain the IR among women with PCOS, other risk factors for the development of diabetes, and the screening methods used for the detection of glucose intolerance in women with PCOS. Few mechanisms can explain IR in women with PCOS such as obesity, insulin receptor signaling defects, and inhibition of insulin-mediated glucose uptake in adipocytes. Women with PCOS have additional risk factors for the development of glucose intolerance such as family history of diabetes, use of oral contraceptives, anovulation, and age. The Androgen Society in 2007 and the Endocrine Society in 2013 recommended using oral glucose tolerance test as a screening tool for abnormal glucose tolerance in all women with PCOS. The approach to detection of glucose intolerance among women with PCOS varies among health care providers. Large prospective studies are still needed for the development of guidelines with strong evidence. When assessing risk of future diabetes in women with PCOS, it is important to take into account the method used for screening as well as other risk factors that these women might have. PMID:27570464

  14. Effects of semicore d-electrons in screened-exchange density functional methods

    NASA Astrophysics Data System (ADS)

    Lee, Byounghak; Wang, Lin-Wang

    2007-03-01

    We report a theoretical study on the role of shallow d states in the screened-exchange local density approximation (sX-LDA) band structure of binary semiconductor systems. We found that the inaccurate pseudo-wavefunctions can lead to 1) an overestimation of the screened-exchange interaction between the localized d states and the delocalized higher energy s and p states and 2) an underestimation of the screened-exchange interaction between the d states. The resulting sX-LDA band structures have substantially smaller band gaps compared with experiments. We correct the pseudo-wavefunctions of d states by including the s and p states of the same shell in the valence states. The correction of pseudo-wavefunctions yields band gaps and the d state binding energy in good agreement with experiments. Compared with the quasi-particle GW method, our sX-LDA results shows not only similar quality band gaps but also much better d state binding energy. As an example, we present sX-LDA results of s-d coupling in zinc-blende semiconductors and compare them with LDA+U results. We also present an efficient method to correct the pseudo-wavefunction exchange-integral error by using projection of wavefunctions onto atomic orbitals.

  15. Designing specific protein–protein interactions using computation, experimental library screening, or integrated methods

    PubMed Central

    Chen, T Scott; Keating, Amy E

    2012-01-01

    Given the importance of protein–protein interactions for nearly all biological processes, the design of protein affinity reagents for use in research, diagnosis or therapy is an important endeavor. Engineered proteins would ideally have high specificities for their intended targets, but achieving interaction specificity by design can be challenging. There are two major approaches to protein design or redesign. Most commonly, proteins and peptides are engineered using experimental library screening and/or in vitro evolution. An alternative approach involves using protein structure and computational modeling to rationally choose sequences predicted to have desirable properties. Computational design has successfully produced novel proteins with enhanced stability, desired interactions and enzymatic function. Here we review the strengths and limitations of experimental library screening and computational structure-based design, giving examples where these methods have been applied to designing protein interaction specificity. We highlight recent studies that demonstrate strategies for combining computational modeling with library screening. The computational methods provide focused libraries predicted to be enriched in sequences with the properties of interest. Such integrated approaches represent a promising way to increase the efficiency of protein design and to engineer complex functionality such as interaction specificity. PMID:22593041

  16. Trichrome staining for detection of intestinal protozoa a better screening method.

    PubMed

    Agrawal, Neerja; Sharma, Uma; Sharma, A K

    2006-12-01

    Intestinal protozoal infections are common in our country because of poor hygiene and tropical conditions. The efficacy of trichrome staining to screen stool smear was compared with commonly used methods i.e. concentrated iodine mount and direct wet mount to test its better effectiveness. All Stool samples were first examined by routine methods i.e. direct wet mount and iodine staining. A portion of stool sample was also inoculated in vial containing polyvinyl alcohol (PVA) fixative. From PVA preserved samples, slides were prepared and stained by modified wheately's trichrome method. The results of both methods were compared and relative accuracy was calculated. 1054 stool specimens were examined and 259 parasites detected, of which 20.7% were protozoa and 3.7% helminthde. Trichrome staining detected 19.1% protozoa while routine methods detected 12.9% protozoa. For identification of protozoa, accuracy was 91.8% in favor trichrome staining and 61.8% by wet mount and iodine staining. Trichrome stained smear alone can be used as screening method in those geographic areas where protozoa infections are common.

  17. Generalization of Youden index for multiple-class classification problems applied to the assessment of externally validated cognition in Parkinson disease screening.

    PubMed

    Nakas, Christos T; Dalrymple-Alford, John C; Anderson, Tim J; Alonzo, Todd A

    2013-03-15

    Routine cognitive screening in Parkinson disease (PD) has become essential for management, to track progression and to assess clinical status in therapeutic trials. Patients with mild cognitive impairment (PD-MCI) are more likely to progress to dementia and therefore need to be distinguished from patients with normal cognition and those with dementia. A three-class Youden index has been recently proposed to select cut-off points in three-class classification problems. In this article, we examine properties of a modification of the three-class Youden index and propose a generalization to k-class classification problems. Geometric and theoretical properties of the modified index J(k) are examined. It is shown that J(k) is equivalent to the sum of the k - 1 two-class Youden indices for the adjacent classes of the ordered alternative problem given that the ordering holds. Methods are applied in the assessment of the Montreal Cognitive Assessment test when screening cognition in PD.

  18. Analysis Of Volatile Fingerprints: A Rapid Screening Method For Antifungal Agents For Efficacy Against Dermatophytes

    NASA Astrophysics Data System (ADS)

    Naraghi, Kamran; Sahgal, Natasha; Adriaans, Beverley; Barr, Hugh; Magan, Naresh

    2009-05-01

    The potential of using an electronic nose (E. nose) for rapid screening dermatophytes to antifungal agents was studied. In vitro, the 50 and 90% effective concentration (EC) values of five antifungal agents for T. rubrum and T. mentagrophytes were obtained by mycelial growth assays. Then, the qualitative volatile production patterns of the growth responses of these fungi to these values were incorporated into solid medium were analysed after 96-120 hrs incubation at 25° C using headspace analyses. Overall, results, using PCA and CA demonstrated that it is possible to differentiate between various treatments within 96-120 hrs. This study showed that potential exists for using qualitative volatile patterns as a rapid screening method for antifungal agents for microorganism. This approach could also facilitate the monitoring of antimicrobial drug activities and infection control programmes and perhaps drug resistance build up in microbial species.

  19. Studies on bacterial cell wall inhibitors. VI. Screening method for the specific inhibitors of peptidoglycan synthesis.

    PubMed

    Omura, S; Tanaka, H; Oiwa, R; Nagai, T; Koyama, Y; Takahashi, Y

    1979-10-01

    A screening method was established for selecting new specific inhibitors of bacterial cell wall peptidoglycan synthesis. In the primary test, culture broths of soil isolates were selected based on relative microbial activity. A culture, to be retained, must be active against Bacillus subtilis and lack activities against Acholeplasma laidawii. In the secondary test, inhibitors of bacterial cell wall synthesis were identified by their ability to prevent the incorporation of meso-[3H]diaminopimelic acid but not to prevent the incorporation of L-[4C]leucine into the acid-insoluble macromolecular fraction of growing cells of Bacillus sp. ATCC 21206 (Dpm-). As the tertiary test, inhibitors with molecular weights under 1,000 were selected by passage through a Diaflo UM-2 membrane. By this screening procedure, six known antibiotics and one new one were picked out from ten thousand soil isolates. PMID:528376

  20. Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.

    PubMed

    Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

    2015-01-01

    Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. "analogue bias", "artificial enrichment" and "false negative". In addition, we introduce our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylases (HDACs) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The leave-one-out cross-validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased as measured by property matching, ROC curves and AUCs.

  1. New phenotyping methods for screening wheat and barley for beneficial responses to water deficit.

    PubMed

    Munns, Rana; James, Richard A; Sirault, Xavier R R; Furbank, Robert T; Jones, Hamlyn G

    2010-08-01

    This review considers stomatal conductance as an indicator of genotypic differences in the growth response to water stress. The benefits of using stomatal conductance are compared with photosynthetic rate and other indicators of genetic variation in water stress tolerance, along with the use of modern phenomics technologies. Various treatments for screening for genetic diversity in response to water deficit in controlled environments are considered. There is no perfect medium: there are pitfalls in using soil in pots, and in using hydroponics with ionic and non-ionic osmotica. Use of mixed salts or NaCl is recommended over non-ionic osmotica. Developments in infrared thermography provide new and feasible screening methods for detecting genetic variation in the stomatal response to water deficit in controlled environments and in the field.

  2. Benchmarking Data Sets for the Evaluation of Virtual Ligand Screening Methods: Review and Perspectives.

    PubMed

    Lagarde, Nathalie; Zagury, Jean-François; Montes, Matthieu

    2015-07-27

    Virtual screening methods are commonly used nowadays in drug discovery processes. However, to ensure their reliability, they have to be carefully evaluated. The evaluation of these methods is often realized in a retrospective way, notably by studying the enrichment of benchmarking data sets. To this purpose, numerous benchmarking data sets were developed over the years, and the resulting improvements led to the availability of high quality benchmarking data sets. However, some points still have to be considered in the selection of the active compounds, decoys, and protein structures to obtain optimal benchmarking data sets.

  3. A microtiter-plate screening method for biofilm disinfection and removal.

    PubMed

    Pitts, Betsey; Hamilton, Martin A; Zelver, Nicholas; Stewart, Philip S

    2003-08-01

    A quantitative spectrophotometric method was developed to measure the removal and killing efficacy of antibiofilm agents. Biofilms of Pseudomonas aeruginosa or Staphylococcus epidermidis were grown in 96-well plates, treated with an agent, then stained with either the biomass indicator crystal violet or the respiratory indicator 5-cyano-2,3-ditolyl tetrazolium chloride. This rapid screening method is sensitive enough to elucidate concentration-response relationships as well as differences between species responses to treatments. Using these assays, agents can be ranked by their ability to remove or kill biofilm. PMID:12782382

  4. A method to screen and evaluate tissue adhesives for joint repair applications

    PubMed Central

    2012-01-01

    Background Tissue adhesives are useful means for various medical procedures. Since varying requirements cause that a single adhesive cannot meet all needs, bond strength testing remains one of the key applications used to screen for new products and study the influence of experimental variables. This study was conducted to develop an easy to use method to screen and evaluate tissue adhesives for tissue engineering applications. Method Tissue grips were designed to facilitate the reproducible production of substrate tissue and adhesive strength measurements in universal testing machines. Porcine femoral condyles were used to generate osteochondral test tissue cylinders (substrates) of different shapes. Viability of substrates was tested using PI/FDA staining. Self-bonding properties were determined to examine reusability of substrates (n = 3). Serial measurements (n = 5) in different operation modes (OM) were performed to analyze the bonding strength of tissue adhesives in bone (OM-1) and cartilage tissue either in isolation (OM-2) or under specific requirements in joint repair such as filling cartilage defects with clinical applied fibrin/PLGA-cell-transplants (OM-3) or tissues (OM-4). The efficiency of the method was determined on the basis of adhesive properties of fibrin glue for different assembly times (30 s, 60 s). Seven randomly generated collagen formulations were analyzed to examine the potential of method to identify new tissue adhesives. Results Viability analysis of test tissue cylinders revealed vital cells (>80%) in cartilage components even 48 h post preparation. Reuse (n = 10) of test substrate did not significantly change adhesive characteristics. Adhesive strength of fibrin varied in different test settings (OM-1: 7.1 kPa, OM-2: 2.6 kPa, OM-3: 32.7 kPa, OM-4: 30.1 kPa) and was increasing with assembly time on average (2.4-fold). The screening of the different collagen formulations revealed a substance with significant higher adhesive

  5. Method for rapid screening analysis of Sr-90 in edible plant samples collected near Fukushima, Japan.

    PubMed

    Amano, Hikaru; Sakamoto, Hideaki; Shiga, Norikatsu; Suzuki, Kaori

    2016-06-01

    A screening method for measuring (90)Sr in edible plant samples by focusing on (90)Y in equilibrium with (90)Sr is reported. (90)Y was extracted from samples with acid, co-precipitated with iron hydroxide, and precipitated with oxalic acid. The dissolved oxalate precipitate was loaded on an extraction chromatography resin, and the (90)Y-enriched eluate was analyzed by Cherenkov counting with a TDCR liquid scintillation counter. (90)Sr ((90)Y) concentration was determined in plant samples collected near the damaged Fukushima Daiichi Nuclear Power Plants with this method. PMID:27043171

  6. General unknown screening, antioxidant and anti-inflammatory potential of Dendrobium macrostachyum Lindl.

    PubMed Central

    Sukumaran, Nimisha Pulikkal; Yadav, R. Hiranmai

    2016-01-01

    Context: D. macrostachyum is an epiphytic orchid abundant in Southern India and is reported for pain relief in folklore. Aims: The objective of the present study was to determine in vitro free radical scavenging and anti-inflammatory activity of D. macrostachyum and to perform LCMS based metabolic profiling of the plant. Settings and Design: Sequential stem and leaf extracts were assessed for its antioxidant and anti-inflammatory activity by in vitro methods. Materials and Methods: The antioxidant activity determined by assays based on the decolourization of the radical monocation of DPPH, ABTS and reducing power. Total amount of phenolics for quantitative analysis of antioxidative components was estimated. In vitro anti-inflammatory activity was evaluated using protein denaturation assay, membrane stabilization assay and proteinase inhibitory activity. Methanolic extract of plant was subjected to LCMS. Results: The stem ethanolic extracts exhibited significant IC50 value of 10.21, 31.54 and 142.97 μg/ml respectively for DPPH, ABTS radical scavenging and reducing power activity. The ethanol and water extract was highly effective as albumin denaturation inhibitors (IC50 = 114.13 and 135.818 μg/ml respectively) and proteinase inhibitors (IC50 = 72.49 and 129.681 μg/ml respectively). Membrane stabilization was also noticeably inhibited by the stem ethanolic extract among other extracts (IC50 = 89.33 μg/ml) but comparatively lower to aspirin standard (IC50 = 83.926 μg/ml). The highest total phenol content was exhibited by ethanolic stem and leaf extracts respectively at 20 and 16 mg of gallic acid equivalents of dry extract. On LCMS analysis 20 constituents were identified and it included chemotaxonomic marker for Dendrobium species. Conclusions: The results showed a relatively high concentration of phenolics, high scavenger activity and high anti-inflammatory activity of the stem extract compared to the leaf extract. The results indicate that the plant can be a

  7. General unknown screening, antioxidant and anti-inflammatory potential of Dendrobium macrostachyum Lindl.

    PubMed Central

    Sukumaran, Nimisha Pulikkal; Yadav, R. Hiranmai

    2016-01-01

    Context: D. macrostachyum is an epiphytic orchid abundant in Southern India and is reported for pain relief in folklore. Aims: The objective of the present study was to determine in vitro free radical scavenging and anti-inflammatory activity of D. macrostachyum and to perform LCMS based metabolic profiling of the plant. Settings and Design: Sequential stem and leaf extracts were assessed for its antioxidant and anti-inflammatory activity by in vitro methods. Materials and Methods: The antioxidant activity determined by assays based on the decolourization of the radical monocation of DPPH, ABTS and reducing power. Total amount of phenolics for quantitative analysis of antioxidative components was estimated. In vitro anti-inflammatory activity was evaluated using protein denaturation assay, membrane stabilization assay and proteinase inhibitory activity. Methanolic extract of plant was subjected to LCMS. Results: The stem ethanolic extracts exhibited significant IC50 value of 10.21, 31.54 and 142.97 μg/ml respectively for DPPH, ABTS radical scavenging and reducing power activity. The ethanol and water extract was highly effective as albumin denaturation inhibitors (IC50 = 114.13 and 135.818 μg/ml respectively) and proteinase inhibitors (IC50 = 72.49 and 129.681 μg/ml respectively). Membrane stabilization was also noticeably inhibited by the stem ethanolic extract among other extracts (IC50 = 89.33 μg/ml) but comparatively lower to aspirin standard (IC50 = 83.926 μg/ml). The highest total phenol content was exhibited by ethanolic stem and leaf extracts respectively at 20 and 16 mg of gallic acid equivalents of dry extract. On LCMS analysis 20 constituents were identified and it included chemotaxonomic marker for Dendrobium species. Conclusions: The results showed a relatively high concentration of phenolics, high scavenger activity and high anti-inflammatory activity of the stem extract compared to the leaf extract. The results indicate that the plant can be a

  8. [A double immunochemical method for detecting faecal haemoglobin and albumin in rectal screening].

    PubMed

    Tarpay, Adám; Szabadosné Németh, Mária; Orosz, Enikõ; Kásler, Miklós; Burai, Mária; Pap, Akos; Ottó, Szabolcs

    2011-11-01

    Undoubtedly, colonoscopy is the "gold standard" in the diagnosis of colorectal cancers. Sophisticated bowel preparation and risk of bowel perforation and bleeding, as well as the patient's discomfort during examination lead to low compliance in screening. Therefore, alternative non-invasive screening methods tend to come into the fore. In this study we compared the sensitivity and specificity of the double immunochemical FECA test for the haemoglobin + albumin content of the faeces with those of control colonoscopy in the detection of colorectal neoplasms. In a 3-year period 154 patients (69 males and 85 females) were scheduled for colonoscopy with previously collected stool samples. The sensitivity and specificity of the double immunochemical test for faecal haemoglobin + albumin content were determined in colorectal neoplasms of different severity. Colonoscopy served as a control examination. Colonoscopy identified in 77 cases benign lesions, and in 10 cases malignant tumours. The double immunochemical test for faecal blood and protein successfully used in model screening population showed in our present study 52.7% sensitivity and 92.3% specificity for significant neoplastic lesions (high-risk polyps and tumours). When the evaluation was limited to the high-risk polyps, the sensitivity was modified to 45.5% and the specificity to 92.3% and in case of invasive tumours to 90% and 100%, respectively. If only faecal haemoglobin content was measured, the overall sensitivity for polyps of any size and sort was 15.7% which, however, increased to 27.63% if faecal albumin was also measured. Based on relevant literature, the sensitivity of the FECA test for colorectal polyp and cancer is more favourable than that of other FITs. However, the increased sensitivity of the double faecal protein test falls short of the standard colonoscopy. Therefore, in certain cases the latter might be considered as a primary screening method.

  9. Development of colorimetric field screening methods for munitions compounds in soil

    NASA Astrophysics Data System (ADS)

    Jenkins, Thomas F.; Walsh, Marianne E.; Schumacher, Patricia W.; Thorne, Philip G.

    1995-10-01

    Simple colorimetric tests have been developed to screen for the presence of TNT, TNB, DNT, DNB, tetryl, RDX, HMX, nitroglycerine (NG), PETN, nitrocellulose (NC), nitroguanidine (NQ), picric acid and ammonium picrate in soil. Soils are extracted by manual shaking with acetone. For the nitroaromatics, the extracts are reacted with potassium hydroxide and sodium sulfite to form their colored Janowsky complexes. For RDX, HMX, NG, PETN, NC and NQ, extracts are passed through an anion exchange resin to remove nitrate, and then acidified with acetic acid; the nitramines and nitrate esters are reduced with zinc to form nitrous acid. The nitrous acid is detected by the Griess reaction using a Hach Nitriver 3 powder pillow, which produces a highly colored azo dye. Detection of these analytes can be obtained visually and concentrations estimated from absorbance measurements at 540 nm for TNT, TNB and tetryl, 570 nm for DNTs and DNB, and at 510 nm for RDX, HMX, NG, PETN, NC and NQ. For picric acid/ammonium picrate, the acetone extract is passed through a basic ion-exchange column that retains picrate ion. The column is rinsed with methanol to elute interferences, and the picrate is desorbed with acetone containing several drops of sulfuric acid. The extract is diluted with deionized water, and the concentration of picrate is obtained from the absorbance at 400 nm. Detection limits are about 1 (mu) g/g for all analytes except NG, NC and NQ, which are slightly higher. Results from field screening at a number of sites have been correlated with laboratory analyses for TNT and RDX. The results indicate that the field screening methods do not suffer from false negatives and the rate of false positives is low. Concentration estimates from field screening compared favorably with results from the standard laboratory methods.

  10. A screening method of oil-soluble synthetic dyes in chilli products based on multi-wavelength chromatographic fingerprints comparison.

    PubMed

    Zhu, Yonghong; Wu, Yanlei; Zhou, Chunjie; Zhao, Bo; Yun, Wen; Huang, Siyu; Tao, Peng; Tu, Dawei; Chen, Shiqi

    2016-02-01

    A multi-wavelength HPLC fingerprint comparison method was proposed for the screening of oil-soluble synthetic dyes in chilli products. The screening was based on the fingerprint differences of normal unadulterated chilli sample with tested chilli samples. The samples were extracted with acetone and fingerprinted by HPLC under four visible light wavelengths (450 nm, 490 nm, 520 nm, and 620 nm). It was found that the fingerprints of different chilli product samples had a relatively fixed number of peaks and stable retention time. When 16 kinds of known synthetic dyes were used as model analytes to assess the screening efficiency, 14 of them could be screened using fingerprint comparison method, with LOD of 0.40-2.41 mg/kg. The new screening method was simple and had the possibility of finding existence of the adulterated dyes which could not be identified using known standard analytes as control. PMID:26304371

  11. A screening method of oil-soluble synthetic dyes in chilli products based on multi-wavelength chromatographic fingerprints comparison.

    PubMed

    Zhu, Yonghong; Wu, Yanlei; Zhou, Chunjie; Zhao, Bo; Yun, Wen; Huang, Siyu; Tao, Peng; Tu, Dawei; Chen, Shiqi

    2016-02-01

    A multi-wavelength HPLC fingerprint comparison method was proposed for the screening of oil-soluble synthetic dyes in chilli products. The screening was based on the fingerprint differences of normal unadulterated chilli sample with tested chilli samples. The samples were extracted with acetone and fingerprinted by HPLC under four visible light wavelengths (450 nm, 490 nm, 520 nm, and 620 nm). It was found that the fingerprints of different chilli product samples had a relatively fixed number of peaks and stable retention time. When 16 kinds of known synthetic dyes were used as model analytes to assess the screening efficiency, 14 of them could be screened using fingerprint comparison method, with LOD of 0.40-2.41 mg/kg. The new screening method was simple and had the possibility of finding existence of the adulterated dyes which could not be identified using known standard analytes as control.

  12. A combinatorial chemistry method for fast screening of perovskite-based NO oxidation catalyst.

    PubMed

    Yoon, Dal Young; Lim, Eunho; Kim, Young Jin; Cho, Byong K; Nam, In-Sik; Choung, Jin Woo; Yoo, Seungbeom

    2014-11-10

    A fast parallel screening method based on combinatorial chemistry (combichem) has been developed and applied in the screening tests of perovskite-based oxide (PBO) catalysts for NO oxidation to hit a promising PBO formulation for the oxidation of NO to NO2. This new method involves three consecutive steps: oxidation of NO to NO2 over a PBO catalyst, adsorption of NOx onto the PBO and K2O/Al2O3, and colorimetric assay of the NOx adsorbed thereon. The combichem experimental data have been used for determining the oxidation activity of NO over PBO catalysts as well as three critical parameters, such as the adsorption efficiency of K2O/Al2O3 for NO2 (α) and NO (β), and the time-average fraction of NO included in the NOx feed stream (ξ). The results demonstrated that the amounts of NO2 produced over PBO catalysts by the combichem method under transient conditions correlate well with those from a conventional packed-bed reactor under steady-state conditions. Among the PBO formulations examined, La0.5Ag0.5MnO3 has been identified as the best chemical formulation for oxidation of NO to NO2 by the present combichem method and also confirmed by the conventional packed-bed reactor tests. The superior efficiency of the combichem method for high-throughput catalyst screening test validated in this study is particularly suitable for saving the time and resources required in developing a new formulation of PBO catalyst whose chemical composition may have an enormous number of possible variations.

  13. An in vitro screening method to evaluate chemicals as potential chemotherapeutants to control Aeromonas hydrophila infection in channel catfish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using catfish gill cells G1B and four chemicals (hydrogen peroxide, sodium chloride, potassium permanganate, and D-mannose), the feasibility of using an in vitro screening method to identify potential effective chemotherapeutants was evaluated in this study. In vitro screening results revealed that,...

  14. A Tree Based Method for the Rapid Screening of Chemical Fingerprints

    NASA Astrophysics Data System (ADS)

    Kristensen, Thomas G.; Nielsen, Jesper; Pedersen, Christian N. S.

    The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase for identifying novel drug candidates by screening large databases for molecules with fingerprints similar to a query fingerprint. In this paper, we present a method which efficiently finds all fingerprints in a database with Tanimoto coefficient to the query fingerprint above a user defined threshold. The method is based on two novel data structures for rapid screening of large databases: the kD grid and the Multibit tree. The kD grid is based on splitting the fingerprints into k shorter bitstrings and utilising these to compute bounds on the similarity of the complete bitstrings. The Multibit tree uses hierarchical clustering and similarity within each cluster to compute similar bounds. We have implemented our method and tested it on a large data set from the industry. Our experiments show that our method yields a three-fold speed-up over previous methods.

  15. Survey of South African fruit juices using a fast screening HILIC-MS method.

    PubMed

    Stander, Marietjie A; Kühn, Wernich; Hiten, Nicholas F

    2013-01-01

    Adulteration of fruit juices--by the addition of sugar or other less expensive fruit juices as well as preservatives, artificial sweeteners and colours--was tested for by using a developed screening method. The method employs hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) using electrospray ionisation in the negative mode and ultraviolet light detection. Different fruit juices can be differentiated by the content of marker compounds like sorbitol, certain phenolic molecules and their saccharide profile. This method was used to test 46 fruit juice samples from the retail market as well as 12 control samples. The study focused on the main types of fruit juices consumed on the South African market including apple, orange, grape and blends of these juices with other fruits like mango, pear and guava. Overall, the 46 samples tested mostly agreed with label claims. One grape juice sample was adulterated, probably with apple juice. Natamycin above the legal limits was found in two samples. In addition, two samples contained natamycin and one sample benzoate without it being indicated on the label. The method is well suited as a quick screening method for fruit juice adulteration and if used routinely would reduce fruit juice adulteration without the cost of the current array of tests needed for authenticity testing.

  16. Probing bulk defect energy bands using generalized charge pumping method

    NASA Astrophysics Data System (ADS)

    Masuduzzaman, Muhammad; Weir, Bonnie; Alam, Muhammad Ashraful

    2012-04-01

    The multifrequency charge pumping (CP) technique has long been used to probe the density of defects at the substrate-oxide interface, as well as in the bulk of the oxide of MOS transistors. However, profiling the energy levels of the defects has been more difficult due to the narrow scanning range of the voltage of a typical CP signal, and the uncertainty associated with the defect capture cross-section. In this paper, we discuss a generalized CP method that can identify defect energy bands within a bulk oxide, without requiring separate characterization of the defect capture cross-section. We use the new technique to characterize defects in both fresh and stressed samples of various dielectric compositions. By quantifying the way defects are generated as a function of time, we gain insight into the nature of defect generation in a particular gate dielectric. We also discuss the relative merits of voltage, time, and other variables of CP to probe bulk defect density, and compare the technique with related characterization approaches.

  17. A multidimensional screening method for the selection of two-photon enhanced fluorescent proteins

    NASA Astrophysics Data System (ADS)

    Stoltzfus, Caleb; Barnett, Lauren; Rebane, Aleksander; Hughes, Thomas; Drobizhev, Mikhail; Wicks, Geoffrey; Mikhailov, Alexandr

    2014-03-01

    Two-photon excitation of fluorescent proteins (FPs) is widely used in imaging whole organisms or living tissues. Many different FPs are now available but these proteins have only been optimized for their one-photon properties. We have developed a technique for screening entire libraries of E. coli colonies expressing FPs that utilizes multiple wavelengths of linear excitation as well as two-photon excitation. Single mutations in a particular protein that affect one or twophoton properties are easily identified, providing new views of structure/function relationships. An amplified femtosecond Ti:sapphire laser and a spectrally filtered lamp source are used to acquire the fluorescence signals of up to ~1000 E. coli colonies on a standard Petri dish. Automation of the analysis and acquisition of the fluorescent signals makes it feasible to rapidly screen tens of thousands of colonies. In a proof of principle experiment with the commonly used EGFP, we used two rounds of error prone PCR and selection to evolve new proteins with shifted absorption and increased two-photon cross sections at 790nm. This method of screening, coupled with careful measurements of photo bleaching dynamics and two-photon cross sections, should make it possible to optimize a wide variety of fluorescent proteins and biosensors for use in two-photon microscopes.

  18. Fast high-throughput screening of temoporfin-loaded liposomal formulations prepared by ethanol injection method.

    PubMed

    Yang, Kewei; Delaney, Joseph T; Schubert, Ulrich S; Fahr, Alfred

    2012-03-01

    A new strategy for fast, convenient high-throughput screening of liposomal formulations was developed, utilizing the automation of the so-called ethanol-injection method. This strategy was illustrated by the preparation and screening of the liposomal formulation library of a potent second-generation photosensitizer, temoporfin. Numerous liposomal formulations were efficiently prepared using a pipetting robot, followed by automated size characterization, using a dynamic light scattering plate reader. Incorporation efficiency of temoporfin and zeta potential were also detected in selected cases. To optimize the formulation, different parameters were investigated, including lipid types, lipid concentration in injected ethanol, ratio of ethanol to aqueous solution, ratio of drug to lipid, and the addition of functional phospholipid. Step-by-step small liposomes were prepared with high incorporation efficiency. At last, an optimized formulation was obtained for each lipid in the following condition: 36.4 mg·mL(-1) lipid, 13.1 mg·mL(-1) mPEG(2000)-DSPE, and 1:4 ethanol:buffer ratio. These liposomes were unilamellar spheres, with a diameter of approximately 50 nm, and were very stable for over 20 weeks. The results illustrate this approach to be promising for fast high-throughput screening of liposomal formulations.

  19. Kinase-interacting substrate screening is a novel method to identify kinase substrates

    PubMed Central

    Amano, Mutsuki; Hamaguchi, Tomonari; Shohag, Md. Hasanuzzaman; Kozawa, Kei; Kato, Katsuhiro; Zhang, Xinjian; Yura, Yoshimitsu; Matsuura, Yoshiharu; Kataoka, Chikako; Nishioka, Tomoki

    2015-01-01

    Protein kinases play pivotal roles in numerous cellular functions; however, the specific substrates of each protein kinase have not been fully elucidated. We have developed a novel method called kinase-interacting substrate screening (KISS). Using this method, 356 phosphorylation sites of 140 proteins were identified as candidate substrates for Rho-associated kinase (Rho-kinase/ROCK2), including known substrates. The KISS method was also applied to additional kinases, including PKA, MAPK1, CDK5, CaMK1, PAK7, PKN, LYN, and FYN, and a lot of candidate substrates and their phosphorylation sites were determined, most of which have not been reported previously. Among the candidate substrates for Rho-kinase, several functional clusters were identified, including the polarity-associated proteins, such as Scrib. We found that Scrib plays a crucial role in the regulation of subcellular contractility by assembling into a ternary complex with Rho-kinase and Shroom2 in a phosphorylation-dependent manner. We propose that the KISS method is a comprehensive and useful substrate screen for various kinases. PMID:26101221

  20. First screening method for the simultaneous detection of seven allergens by liquid chromatography mass spectrometry.

    PubMed

    Heick, J; Fischer, M; Pöpping, B

    2011-02-18

    The development of a multi-method for the detection of seven allergens based on liquid chromatography and triple-quadrupole tandem mass spectrometry in multiple reaction mode is described. It is based on extraction of the allergenic proteins from a food matrix, followed by enzymatic digestion with trypsin. The chosen marker peptides were implemented into one method that is capable of the simultaneous detection of milk, egg, soy, hazelnut, peanut, walnut and almond. This method has been used to detect all seven allergenic commodities from incurred reference bread material, which was baked according to a standard recipe from the baking industry. Detected concentrations ranged from 10 to 1000 μg/g, demonstrating that the mass spectrometric based method is a useful tool for allergen screening.

  1. Residual-driven online generalized multiscale finite element methods

    NASA Astrophysics Data System (ADS)

    Chung, Eric T.; Efendiev, Yalchin; Leung, Wing Tat

    2015-12-01

    The construction of local reduced-order models via multiscale basis functions has been an area of active research. In this paper, we propose online multiscale basis functions which are constructed using the offline space and the current residual. Online multiscale basis functions are constructed adaptively in some selected regions based on our error indicators. We derive an error estimator which shows that one needs to have an offline space with certain properties to guarantee that additional online multiscale basis function will decrease the error. This error decrease is independent of physical parameters, such as the contrast and multiple scales in the problem. The offline spaces are constructed using Generalized Multiscale Finite Element Methods (GMsFEM). We show that if one chooses a sufficient number of offline basis functions, one can guarantee that additional online multiscale basis functions will reduce the error independent of contrast. We note that the construction of online basis functions is motivated by the fact that the offline space construction does not take into account distant effects. Using the residual information, we can incorporate the distant information provided the offline approximation satisfies certain properties. In the paper, theoretical and numerical results are presented. Our numerical results show that if the offline space is sufficiently large (in terms of the dimension) such that the coarse space contains all multiscale spectral basis functions that correspond to small eigenvalues, then the error reduction by adding online multiscale basis function is independent of the contrast. We discuss various ways computing online multiscale basis functions which include a use of small dimensional offline spaces.

  2. Studies with the USF/NASA toxicity screening test method - Exercise wheels and oxygen replenishment

    NASA Technical Reports Server (NTRS)

    Hilado, C. J.; Cumming, H. J.

    1977-01-01

    Continuing efforts to improve the University of San Francisco/NASA toxicity screening test method have included the addition of exercise wheels to provide a different measure of incapacitation, and oxygen replenishment to offset any effect of oxygen depletion by the test animals. The addition of exercise wheels limited the number of animals in each test and doubled the required number of tests without any significant improvement in reproducibility. Oxygen replenishment appears to have an effect on survival in the last 5 minutes of the 30-minute test, but the effect is expected to be similar for most materials.

  3. Screening and selection of synthetic peptides for a novel and optimized endotoxin detection method.

    PubMed

    Mujika, M; Zuzuarregui, A; Sánchez-Gómez, S; Martínez de Tejada, G; Arana, S; Pérez-Lorenzo, E

    2014-09-30

    The current validated endotoxin detection methods, in spite of being highly sensitive, present several drawbacks in terms of reproducibility, handling and cost. Therefore novel approaches are being carried out in the scientific community to overcome these difficulties. Remarkable efforts are focused on the development of endotoxin-specific biosensors. The key feature of these solutions relies on the proper definition of the capture protocol, especially of the bio-receptor or ligand. The aim of the presented work is the screening and selection of a synthetic peptide specifically designed for LPS detection, as well as the optimization of a procedure for its immobilization onto gold substrates for further application to biosensors. PMID:25034430

  4. Improved statistical methods for hit selection in high-throughput screening.

    PubMed

    Brideau, Christine; Gunter, Bert; Pikounis, Bill; Liaw, Andy

    2003-12-01

    High-throughput screening (HTS) plays a central role in modern drug discovery, allowing the rapid screening of large compound collections against a variety of putative drug targets. HTS is an industrial-scale process, relying on sophisticated automation, control, and state-of-the art detection technologies to organize, test, and measure hundreds of thousands to millions of compounds in nano- to microliter volumes. Despite this high technology, hit selection for HTS is still typically done using simple data analysis and basic statistical methods. The authors discuss in this article some shortcomings of these methods and present alternatives based on modern methods of statistical data analysis. Most important, they describe and show numerous real examples from the biologist-friendly Stat Server HTS application (SHS), a custom-developed software tool built on the commercially available S-PLUS and StatServer statistical analysis and server software. This system remotely processes HTS data using powerful and sophisticated statistical methodology but insulates users from the technical details by outputting results in a variety of readily interpretable graphs and tables.

  5. Detection of Inorganic Arsenic in Rice Using a Field Test Kit: A Screening Method.

    PubMed

    Bralatei, Edi; Lacan, Severine; Krupp, Eva M; Feldmann, Jörg

    2015-11-17

    Rice is a staple food eaten by more than 50% of the world's population and is a daily dietary constituent in most South East Asian countries where 70% of the rice export comes from and where there is a high level of arsenic contamination in groundwater used for irrigation. Research shows that rice can take up and store inorganic arsenic during cultivation, and rice is considered to be one of the major routes of exposure to inorganic arsenic, a class I carcinogen for humans. Here, we report the use of a screening method based on the Gutzeit methodology to detect inorganic arsenic (iAs) in rice within 1 h. After optimization, 30 rice commodities from the United Kingdom market were tested with the field method and were compared to the reference method (high-performance liquid chromatography-inductively coupled plasma-mass spectrometry, HPLC-ICP-MS). In all but three rice samples, iAs compound can be determined. The results show no bias for iAs using the field method. Results obtained show quantification limits of about 50 μg kg(-1), a good reproducibility for a field method of ±12%, and only a few false positives and negatives (<10%) could only be recorded at the 2015 European Commission (EC) guideline for baby rice of 100 μg kg(-1), while none were recorded at the maximum level suggested by the World Health Organization (WHO) and implemented by the EC for polished and white rice of 200 μg kg(-1). The method is reliable, fast, and inexpensive; hence, it is suggested to be used as a screening method in the field for preselection of rice which violates legislative guidelines.

  6. Solution of Ambrosio-Tortorelli model for image segmentation by generalized relaxation method

    NASA Astrophysics Data System (ADS)

    D'Ambra, Pasqua; Tartaglione, Gaetano

    2015-03-01

    Image segmentation addresses the problem to partition a given image into its constituent objects and then to identify the boundaries of the objects. This problem can be formulated in terms of a variational model aimed to find optimal approximations of a bounded function by piecewise-smooth functions, minimizing a given functional. The corresponding Euler-Lagrange equations are a set of two coupled elliptic partial differential equations with varying coefficients. Numerical solution of the above system often relies on alternating minimization techniques involving descent methods coupled with explicit or semi-implicit finite-difference discretization schemes, which are slowly convergent and poorly scalable with respect to image size. In this work we focus on generalized relaxation methods also coupled with multigrid linear solvers, when a finite-difference discretization is applied to the Euler-Lagrange equations of Ambrosio-Tortorelli model. We show that non-linear Gauss-Seidel, accelerated by inner linear iterations, is an effective method for large-scale image analysis as those arising from high-throughput screening platforms for stem cells targeted differentiation, where one of the main goal is segmentation of thousand of images to analyze cell colonies morphology.

  7. Reprint of Solution of Ambrosio-Tortorelli model for image segmentation by generalized relaxation method

    NASA Astrophysics Data System (ADS)

    D'Ambra, Pasqua; Tartaglione, Gaetano

    2015-04-01

    Image segmentation addresses the problem to partition a given image into its constituent objects and then to identify the boundaries of the objects. This problem can be formulated in terms of a variational model aimed to find optimal approximations of a bounded function by piecewise-smooth functions, minimizing a given functional. The corresponding Euler-Lagrange equations are a set of two coupled elliptic partial differential equations with varying coefficients. Numerical solution of the above system often relies on alternating minimization techniques involving descent methods coupled with explicit or semi-implicit finite-difference discretization schemes, which are slowly convergent and poorly scalable with respect to image size. In this work we focus on generalized relaxation methods also coupled with multigrid linear solvers, when a finite-difference discretization is applied to the Euler-Lagrange equations of Ambrosio-Tortorelli model. We show that non-linear Gauss-Seidel, accelerated by inner linear iterations, is an effective method for large-scale image analysis as those arising from high-throughput screening platforms for stem cells targeted differentiation, where one of the main goal is segmentation of thousand of images to analyze cell colonies morphology.

  8. General adaptive guidance using nonlinear programming constraint solving methods (FAST)

    NASA Astrophysics Data System (ADS)

    Skalecki, Lisa; Martin, Marc

    An adaptive, general purpose, constraint solving guidance algorithm called FAST (Flight Algorithm to Solve Trajectories) has been developed by the authors in response to the requirements for the Advanced Launch System (ALS). The FAST algorithm can be used for all mission phases for a wide range of Space Transportation Vehicles without code modification because of the general formulation of the nonlinear programming (NLP) problem, ad the general trajectory simulation used to predict constraint values. The approach allows on board re-targeting for severe weather and changes in payload or mission parameters, increasing flight reliability and dependability while reducing the amount of pre-flight analysis that must be performed. The algorithm is described in general in this paper. Three degree of freedom simulation results are presented for application of the algorithm to ascent and reentry phases of an ALS mission, and Mars aerobraking. Flight processor CPU requirement data is also shown.

  9. Convenient, Sensitive and High-Throughput Method for Screening Botanic Origin

    NASA Astrophysics Data System (ADS)

    Yuan, Yuan; Jiang, Chao; Liu, Libing; Yu, Shulin; Cui, Zhanhu; Chen, Min; Lin, Shufang; Wang, Shu; Huang, Luqi

    2014-06-01

    In this work, a rapid (within 4-5 h), sensitive and visible new method for assessing botanic origin is developed by combining loop-mediated isothermal amplification with cationic conjugated polymers. The two Chinese medicinal materials (Jin-Yin-Hua and Shan-Yin-Hua) with similar morphology and chemical composition were clearly distinguished by gene SNP genotyping assays. The identification of plant species in Patented Chinese drugs containing Lonicera buds is successfully performed using this detection system. The method is also robust enough to be used in high-throughput screening. This new method is very helpful to identify herbal materials, and is beneficial for detecting safety and quality of botanic products.

  10. Precise method for investigation of Lissajous generalized figures

    NASA Astrophysics Data System (ADS)

    Bednarek, Stanisław

    2014-07-01

    This article describes the Lissajous generalized figure and the original instrument for its investigation. Two specially prepared electrodynamic loudspeakers—a horizontal and a vertical—cause oscillations in two mirrors. It is possible to precisely control the motion of the mirrors, achieve a high frequency of oscillation and investigate anharmonic vibrations because loudspeakers are powered by electronic generators. Eccentric mounting, and rotation of a vertical loudspeaker, also allow composition of the oscillations in inclined directions, which generates Lissajous’ generalized figures.

  11. Powered by DFT: Screening methods that accelerate materials development for hydrogen in metals applications.

    PubMed

    Nicholson, Kelly M; Chandrasekhar, Nita; Sholl, David S

    2014-11-18

    CONSPECTUS: Not only is hydrogen critical for current chemical and refining processes, it is also projected to be an important energy carrier for future green energy systems such as fuel cell vehicles. Scientists have examined light metal hydrides for this purpose, which need to have both good thermodynamic properties and fast charging/discharging kinetics. The properties of hydrogen in metals are also important in the development of membranes for hydrogen purification. In this Account, we highlight our recent work aimed at the large scale screening of metal-based systems with either favorable hydrogen capacities and thermodynamics for hydrogen storage in metal hydrides for use in onboard fuel cell vehicles or promising hydrogen permeabilities relative to pure Pd for hydrogen separation from high temperature mixed gas streams using dense metal membranes. Previously, chemists have found that the metal hydrides need to hit a stability sweet spot: if the compound is too stable, it will not release enough hydrogen under low temperatures; if the compound is too unstable, the reaction may not be reversible under practical conditions. Fortunately, we can use DFT-based methods to assess this stability via prediction of thermodynamic properties, equilibrium reaction pathways, and phase diagrams for candidate metal hydride systems with reasonable accuracy using only proposed crystal structures and compositions as inputs. We have efficiently screened millions of mixtures of pure metals, metal hydrides, and alloys to identify promising reaction schemes via the grand canonical linear programming method. Pure Pd and Pd-based membranes have ideal hydrogen selectivities over other gases but suffer shortcomings such as sensitivity to sulfur poisoning and hydrogen embrittlement. Using a combination of detailed DFT, Monte Carlo techniques, and simplified models, we are able to accurately predict hydrogen permeabilities of metal membranes and screen large libraries of candidate alloys

  12. Breast cancer in Iran: need for greater women awareness of warning signs and effective screening methods

    PubMed Central

    Montazeri, Ali; Vahdaninia, Mariam; Harirchi, Iraj; Harirchi, Amir Mahmood; Sajadian, Akram; Khaleghi, Fatemeh; Ebrahimi, Mandana; Haghighat, Shahpar; Jarvandi, Soghra

    2008-01-01

    Background Breast cancer remains an important public health problem. This study aimed to investigate about female knowledge of breast cancer and self-reported practice of breast self-examination in Iran. Methods This was a population-based survey carried out in Tehran, Iran. Data were collected via a structured questionnaire containing 15 questions on demographic status, history of personal and family breast problems, subjective knowledge about breast cancer covering its symptoms, the screening methods and practice of breast self-examination (BSE). A trained female nurse interviewed each respondent. Analysis included descriptive statistics and the Chi-squared test where necessary. Results A total of 1402 women were interviewed. The mean age of respondents was 43.4 (SD = 14.4) years; most were married (85%), and without any personal (94%) and family history (90%) of breast problems. It was found that 64% of the respondents were familiar with breast cancer and 61% (n = 851) believed that 'the disease is relatively common among women in Iran'. Most women (44%) perceived a painless mass as a breast cancer symptom. Overall, 61% of the respondents stated that they knew about breast cancer screening programs and most indicated that electronic media (television 34% and radio 14%) were their source of information. Only 17% of women said that 'they were conducting regular breast self-examination'. The main reason for women not doing breast self-examination was due to the fact that they did not know how to do it (64%). The findings indicated that performing breast self-examination is significantly related to: age, marital status, education, knowledge of breast cancer and knowledge about breast cancer screening programs (p < 0.05), but not to personal (P = 0.2) and family (P = 0.7) history of breast problems. Conclusion This descriptive study provides useful information that could be utilized by both researchers and those involved in public health programmes. The findings

  13. Microbial screening for quinolones residues in cow milk by bio-optical method.

    PubMed

    Appicciafuoco, Brunella; Dragone, Roberto; Frazzoli, Chiara; Bolzoni, Giuseppe; Mantovani, Alberto; Ferrini, Anna Maria

    2015-03-15

    The use of antibiotics on lactating cows should be monitored for the possible risk of milk contamination with residues. Accordingly, Maximum Residue Levels (MRLs) are established by the European Commission to guarantee consumers safety. As pointed out by Dec 2002/657/EC, screening is the first step in the strategy for antibiotic residue control, thus playing a key role in the whole control procedure. However, current routine screening methods applied in milk chain still fail to detect residues of quinolones at concentrations of interest. This paper reports the findings of a new bio-optical method for the screening of quinolones residues in bovine milk, based on E. coli ATCC 11303 growth inhibition. The effect of blank and spiked cow milk samples (aliquots equivalents to 0.8%, v/v) is evaluated in Mueller Hinton Broth (MHb) and MHb enriched with MgSO4 2% (MHb-Mg) inoculated with the test strain at the concentration of 10(4)CFU/mL. The presence of quinolones inhibits the cellular growth in MHb, while this effect is neutralized in MHb-Mg allowing both detection and presumptive identification of quinolones. Growth of the test strain is monitored at 37 °C in a Bioscreen C automated system, and Optical Density (OD) at 600 nm is recorded every 10 min after shaking for 10s. Growth curves (OD vs. time) of E. coli ATCC 11303 are assessed in milk samples, with and without quinolones, and their differences in terms of ΔOD (ΔOD600nm=ODMHb-Mg-ODMHb) are calculated. The presence of quinolones is detected by the cellular growth inhibition (OD vs time, none increase in the value OD) and presumptively identified through the increase of the slope of ΔOD600nm curve (ΔOD vs. time), after about 3h of incubation. The detection limit for ciprofloxacin and enrofloxacin is at the level of MRL, for marbofloxacin is at 2-fold the MRL whereas for danofloxacin is at 4-fold the MRL. Although the sensitivity of the method could be further improved and the procedure automated, it is a

  14. Establishing and sustaining a prospective screening program for breast cancer-related lymphedema at the massachusetts general hospital: lessons learned.

    PubMed

    Brunelle, Cheryl; Skolny, Melissa; Ferguson, Chantal; Swaroop, Meyha; O'Toole, Jean; Taghian, Alphonse G

    2015-01-01

    There has been an increasing call to prospectively screen patients with breast cancer for the development of breast cancer-related lymphedema (BCRL) following their breast cancer treatment. While the components of a prospective screening program have been published, some centers struggle with how to initiate, establish, and sustain a screening program of their own. The intent of this manuscript is to share our experience and struggles in establishing a prospective surveillance program within the infrastructure of our institution. It is our hope that by sharing our history other centers can learn from our mistakes and successes to better design their own prospective screening program to best serve their patient population. PMID:26011383

  15. Chronic kidney disease screening methods and its implication for Malaysia: an in depth review.

    PubMed

    Almualm, Yasmin; Zaman Huri, Hasniza

    2015-01-01

    Chronic Kidney Disease has become a public health problem, imposing heath, social and human cost on societies worldwide. Chronic Kidney Disease remains asymptomatic till late stage when intervention cannot stop the progression of the disease. Therefore, there is an urgent need to detect the disease early. Despite the high prevalence of Chronic Kidney Disease in Malaysia, screening is still lacking behind. This review discusses the strengths and limitations of current screening methods for Chronic Kidney Disease from a Malaysian point of view. Diabetic Kidney Disease was chosen as focal point as Diabetes is the leading cause of Chronic Kidney Disease in Malaysia. Screening for Chronic Kidney Disease in Malaysia includes a urine test for albuminuria and a blood test for serum creatinine. Recent literature indicates that albuminuria is not always present in Diabetic Kidney Disease patients and serum creatinine is only raised after substantial kidney damage has occurred.  Recently, cystatin C was proposed as a potential marker for kidney disease but this has not been studied thoroughly in Malaysia.  Glomerular Filtration Rate is the best method for measuring kidney function and is widely estimated using the Modification of Diet for Renal Disease equation. Another equation, the Chronic Kidney Disease Epidemiology Collaboration Creatinine equation was introduced in 2009. The new equation retained the precision and accuracy of the Modification of Diet for Renal Disease equation at GFR < 60ml/min/1.73m2, showed less bias and improved precision at GFR>60ml/min/1.73m2. In Asian countries, adding an ethnic coefficient to the equation enhanced its performance. In Malaysia, a multi-ethnic Asian population, the Chronic Kidney Disease Epidemiology Collaboration equation should be validated and the Glomerular Filtration Rate should be reported whenever serum creatinine is ordered. Reporting estimated Glomerular Filtration Rate will help diagnose patients who would have been

  16. Hydroxamate-based colorimetric method for direct screening of transglutaminase-producing bacteria.

    PubMed

    Bourneow, Chaiwut; Benjakul, Soottawat; H-Kittikun, Aran

    2012-05-01

    Microbial transglutaminase (MTGase) is a commercial enzyme that has been applied to many protein containing foods to improve their textural property. The screening of MTGase-producing microorganisms from various sources might lead to the discovery of a new MTGase with different characteristics. This report demonstrates the use of a direct detection method for MTGase-producing bacteria grown on an agar plate by filter paper disc (FPD) assay. The principle of the assay is the formation of a red burgundy color by the hydroxamate-ferric complex. The color developed intensity was linearly correlated by the concentration of hydroxamic acid in the range of 0.1-0.8 μM and was visually scored at 4 levels: 0, 1, 2 and 3. Streptoverticillium mobaraense DSM 40847, a positive MTGase-producer, was chosen for the verification and improving of the proposed method. The colonies grown on the nutrient agar plate at 37°C for 24 h were covered with FPDs and 30 μl of substrates (CBZ-Gln-Gly and hydroxylamine). After incubation, 10 μl of the ferric-TCA-HCl solution was placed on the FPD. The optimal time taken to catalyze the formation of CBZ-Gln-Gly-hydroxamic acid by the MTGase and the time taken for the hydroxamate-ferric complex to form color were 180 and 60 min, respectively. Using this assay, 30 of 189 colonies isolated from wastewater and floating-floc samples showed MTGase-positive colonies which were well correlated to the quantitative screening of MTGase activity (R(2) = 0.9758). The results revealed that the FPD assay could be used for the qualitative screening of MTGase-producing bacteria.

  17. Root-cubing and general root-powering methods for finding the zeros of polynomials

    NASA Technical Reports Server (NTRS)

    Bareiss, E. H.

    1969-01-01

    Mathematical analysis technique generalizes a root squaring and root cubing method into a general root powering method. The introduction of partitioned polynomials into this general root powering method simplifies the coding of the polynomial transformations into input data suitable for processing by computer. The method includes analytic functions.

  18. Screening method for selecting semiconductor substrates having defects below a predetermined level in an oxide layer

    DOEpatents

    Warren, W.L.; Vanheusden, K.J.R.; Schwank, J.R.; Fleetwood, D.M.; Shaneyfelt, M.R.; Winokur, P.S.; Devine, R.A.B.

    1998-07-28

    A method is disclosed for screening or qualifying semiconductor substrates for integrated circuit fabrication. The method comprises the steps of annealing at least one semiconductor substrate at a first temperature in a defect-activating ambient (e.g. hydrogen, forming gas, or ammonia) for sufficient time for activating any defects within on oxide layer of the substrate; measuring a defect-revealing electrical characteristic of at least a portion of the oxide layer for determining a quantity of activated defects therein; and selecting substrates for which the quantity of activated defects is below a predetermined level. The defect-revealing electrical characteristic may be a capacitance-versus voltage (C-V) characteristic or a current-versus-voltage (I-V) characteristic that is dependent on an electrical charge in the oxide layer generated by the activated defects. Embodiments of the present invention may be applied for screening any type of semiconductor substrate or wafer having an oxide layer formed thereon or therein. This includes silicon-on-insulator substrates formed by a separation by the implantation of oxygen (SIMOX) process or the bond and etch back silicon-on-insulator (BESOI) process, as well as silicon substrates having a thermal oxide layer or a deposited oxide layer. 5 figs.

  19. Screening method for selecting semiconductor substrates having defects below a predetermined level in an oxide layer

    DOEpatents

    Warren, William L.; Vanheusden, Karel J. R.; Schwank, James R.; Fleetwood, Daniel M.; Shaneyfelt, Marty R.; Winokur, Peter S.; Devine, Roderick A. B.

    1998-01-01

    A method for screening or qualifying semiconductor substrates for integrated circuit fabrication. The method comprises the steps of annealing at least one semiconductor substrate at a first temperature in a defect-activating ambient (e.g. hydrogen, forming gas, or ammonia) for sufficient time for activating any defects within on oxide layer of the substrate; measuring a defect-revealing electrical characteristic of at least a portion of the oxide layer for determining a quantity of activated defects therein; and selecting substrates for which the quantity of activated defects is below a predetermined level. The defect-revealing electrical characteristic may be a capacitance-versus-voltage (C-V) characteristic or a current-versus-voltage (I-V) characteristic that is dependent on an electrical charge in the oxide layer generated by the activated defects. Embodiments of the present invention may be applied for screening any type of semiconductor substrate or wafer having an oxide layer formed thereon or therein. This includes silicon-on-insulator substrates formed by a separation by the implantation of oxygen (SIMOX) process or the bond and etch back silicon-on-insulator (BESOI) process, as well as silicon substrates having a thermal oxide layer or a deposited oxide layer.

  20. [Establishment of the screening method and isolation of PQQ producing strains].

    PubMed

    Wang, Xin; Wang, Jian-Hua; Liu, Dang-Sheng; Zhang, Wei-Cai

    2007-12-01

    Pyrroloquinoline quinone (PQQ) is a cofactor of some oxido-reductases with many important physiological effects and potential pharmaceutical applications. The glucose dehydrogenase of Escherichia coli, being a candidate for enzymic detection of PQQ, is known to be a quinoprotein which is obligately dependant on PQQ as cofactor. The gdh gene of E. coli was amplified and cloned into plasmid pET28a. The recombinant GDH was overexpressed in soluble form in E. coli BL21 (DE3). A bioassay method was established for determination of PQQ by the purified GDH. A screening model was set up for the enrichment of methylotrophic bacteria. Together with the above bioassay method, over 2000 soil samples were screened for the isolation of high-yielding PQQ producing strains. A methylotrophic strain, named MP606, was thus isolated. The PQQ production of MP606 is determined to be 113mg/L without conditional optimization and genetic breeding. The PQQ crystal was obtained from the culture supernatant which has been identified by HPLC, absorption spectra assay, and enzymatic analysis. The 16S rDNA of MP606 was amplified and sequenced. According to the comparison of 16S rDNA sequences, overall similarity value between strain MP606 and 12 typical methylotrophic bacteria is above 95% . The highest value is with two strains of Methylovorus, which reached at 99%.

  1. Toward the discovery of functional transthyretin amyloid inhibitors: application of virtual screening methods.

    PubMed

    Simões, Carlos J V; Mukherjee, Trishna; Brito, Rui M M; Jackson, Richard M

    2010-10-25

    Inhibition of amyloid fibril formation by stabilization of the native form of the protein transthyretin (TTR) is a viable approach for the treatment of familial amyloid polyneuropathy that has been gaining momentum in the field of amyloid research. The TTR stabilizer molecules discovered to date have shown efficacy at inhibiting fibrilization in vitro but display impairing issues of solubility, affinity for TTR in the blood plasma and/or adverse effects. In this study we present a benchmark of four protein- and ligand-based virtual screening (VS) methods for identifying novel TTR stabilizers: (i) two-dimensional (2D) similarity searches with chemical hashed, pharmacophore, and UNITY fingerprints, (ii) 3D searches based on shape, chemical, and electrostatic similarity, (iii) LigMatch, a new ligand-based method which uses multiple templates and combines 3D geometric hashing with a 2D preselection process, and (iv) molecular docking to consensus X-ray crystal structures of TTR. We illustrate the potential of the best-performing VS protocols to retrieve promising new leads by ranking a tailored library of 2.3 million commercially available compounds. Our predictions show that the top-scoring molecules possess distinctive features from the known TTR binders, holding better solubility, fraction of halogen atoms, and binding affinity profiles. To the best of our knowledge, this is the first attempt to rationalize the utilization of a large battery of in silico screening techniques toward the identification of a new generation of TTR amyloid inhibitors.

  2. Investigation of screening effects on the shape resonances in the electron-hydrogen system using the complex-scaling method

    NASA Astrophysics Data System (ADS)

    Jiao, Li-Guang; Ho, Y. K.

    2013-05-01

    In the present work we study the effects of screened Coulomb potentials on shape resonances in the electron-hydrogen system. Here we concentrate on the 1Se and 1Po shape resonances associated with and lying above, respectively, the H (N = 2), (N =3), (N =4), and (N = 5) thresholds. The complex-scaling method is used to extract resonance poles, together with employing correlated Hylleraas-type wave functions up to 1078 and 1771 terms for the S- and P-wave states, respectively, to represent the two-electron system. To model the screening effect we replace the pure Coulomb interaction term for any pair of charged particles by a screened Coulomb (or Yukawa-type) interaction term. Our un-screened shape resonances agree well with those in the literature. We will present our latest results for the screened cases at the meeting. Supported by the National Science Council of Taiwan.

  3. A screening method for prioritizing non-target invertebrates for improved biosafety testing of transgenic crops.

    PubMed

    Todd, Jacqui H; Ramankutty, Padmaja; Barraclough, Emma I; Malone, Louise A

    2008-01-01

    We have developed a screening method that can be used during the problem formulation phase of risk assessment to identify and prioritize non-target invertebrates for risk analysis with any transgenic plant. In previously published protocols for this task, five criteria predominated. These criteria have been combined by our method in a simple model which assesses: (1) the possible level of risk presented by the plant to each invertebrate species (through measurements of potential hazard and exposure, the two principal criteria); (2) the hypothetical environmental impact of this risk (determined by the currently known status of the species' population in the ecosystem and its potential resilience to environmental perturbations); (3) the estimated economic, social and cultural value of each species; and (4) the assessed ability to conduct tests with the species. The screening method uses information on each of these criteria entered into a specially designed database that was developed using Microsoft Access 2003. The database holds biological and ecological information for each non-target species, as well as information about the transgenic plant that is the subject of the risk assessment procedure. Each piece of information is then ranked on the basis of the value of the information to each criterion being measured. This ranking system is flexible, allowing the method to be easily adapted for use in any agro-ecosystem and with any plant modification. A model is then used to produce a Priority Ranking of Non-Target Invertebrates (PRONTI) score for each species, which in turn allows the species to be prioritized for risk assessment. As an example, the method was used to prioritize non-target invertebrates for risk assessment of a hypothetical introduction of Bacillus thuringiensis (Bt) Cry1Ac-expressing Pinus radiata trees into New Zealand.

  4. Collaborative trial validation studies of real-time PCR-based GMO screening methods for detection of the bar gene and the ctp2-cp4epsps construct.

    PubMed

    Grohmann, Lutz; Brünen-Nieweler, Claudia; Nemeth, Anne; Waiblinger, Hans-Ulrich

    2009-10-14

    Polymerase Chain Reaction (PCR)-based screening methods targeting genetic elements commonly used in genetically modified (GM) plants are important tools for the detection of GM materials in food, feed, and seed samples. To expand and harmonize the screening capability of enforcement laboratories, the German Federal Office of Consumer Protection and Food Safety conducted collaborative trials for interlaboratory validation of real-time PCR methods for detection of the phosphinothricin acetyltransferase (bar) gene from Streptomyces hygroscopicus and a construct containing the 5-enolpyruvylshikimate-3-phosphate synthase gene from Agrobacterium tumefaciens sp. strain CP4 (ctp2-cp4epsps), respectively. To assess the limit of detection, precision, and accuracy of the methods, laboratories had to analyze two sets of 18 coded genomic DNA samples of events LLRice62 and MS8 with the bar method and NK603 and GT73 with the ctp2-cp4epsps method at analyte levels of 0, 0.02, and 0.1% GM content, respectively. In addition, standard DNAs were provided to the laboratories to generate calibration curves for copy number quantification of the bar and ctp2-cp4epsps target sequences present in the test samples. The study design and the results obtained are discussed with respect to the difficult issue of developing general guidelines and concepts for the collaborative trial validation of qualitative PCR screening methods.

  5. Collaborative trial validation studies of real-time PCR-based GMO screening methods for detection of the bar gene and the ctp2-cp4epsps construct.

    PubMed

    Grohmann, Lutz; Brünen-Nieweler, Claudia; Nemeth, Anne; Waiblinger, Hans-Ulrich

    2009-10-14

    Polymerase Chain Reaction (PCR)-based screening methods targeting genetic elements commonly used in genetically modified (GM) plants are important tools for the detection of GM materials in food, feed, and seed samples. To expand and harmonize the screening capability of enforcement laboratories, the German Federal Office of Consumer Protection and Food Safety conducted collaborative trials for interlaboratory validation of real-time PCR methods for detection of the phosphinothricin acetyltransferase (bar) gene from Streptomyces hygroscopicus and a construct containing the 5-enolpyruvylshikimate-3-phosphate synthase gene from Agrobacterium tumefaciens sp. strain CP4 (ctp2-cp4epsps), respectively. To assess the limit of detection, precision, and accuracy of the methods, laboratories had to analyze two sets of 18 coded genomic DNA samples of events LLRice62 and MS8 with the bar method and NK603 and GT73 with the ctp2-cp4epsps method at analyte levels of 0, 0.02, and 0.1% GM content, respectively. In addition, standard DNAs were provided to the laboratories to generate calibration curves for copy number quantification of the bar and ctp2-cp4epsps target sequences present in the test samples. The study design and the results obtained are discussed with respect to the difficult issue of developing general guidelines and concepts for the collaborative trial validation of qualitative PCR screening methods. PMID:19807158

  6. Evaluating the merits of using brief measures of PTSD or general mental health measures in two-stage PTSD screening.

    PubMed

    Steele, Nicole M; Benassi, Helen P; Chesney, Catherine J; Nicholson, Cherie; Fogarty, Gerard J

    2014-12-01

    Psychological screening of large numbers of personnel returning from deployments should be as brief as possible without sacrificing the ability to detect individuals who are experiencing serious psychological difficulties. This study focused on screening for posttraumatic stress disorder (PTSD) symptomatology in 421 deployed male members of the Australian Army while they were on deployment and again 3 to 6 months after they returned home. The first aim was to evaluate the performance of the Primary Care--Posttraumatic Stress Disorder Screen (PC-PTSD) and a 4-item version of the 17-item Posttraumatic Stress Disorder Checklist (PCL). A second aim was to evaluate the role of the Kessler-10 (K10) in psychological screening. The results indicated that the short form of the PCL was a better substitute for the full PCL than the PC-PTSD. Other results suggested that a more efficient screening process can be achieved using an initial K10 screening followed by more intensive PTSD screening for people identified as high risk. An additional advantage of an initial K10 filter is that other forms of mental illness could also be targeted in the second-stage screening. PMID:25469974

  7. Iterative methods for elliptic finite element equations on general meshes

    NASA Technical Reports Server (NTRS)

    Nicolaides, R. A.; Choudhury, Shenaz

    1986-01-01

    Iterative methods for arbitrary mesh discretizations of elliptic partial differential equations are surveyed. The methods discussed are preconditioned conjugate gradients, algebraic multigrid, deflated conjugate gradients, an element-by-element techniques, and domain decomposition. Computational results are included.

  8. Rapid determination of fluoroquinolone residues in honey by a microbiological screening method and liquid chromatography.

    PubMed

    Kanda, Maki; Kusano, Tomoto; Kanai, Setsuko; Hayashi, Hiroshi; Matushima, Yoko; Nakajima, Takayuki; Takeba, Kazue; Sasamoto, Takeo; Nagayma, Toshijiro

    2010-01-01

    A rapid and efficient method was developed for the simultaneous determination of seven fluoroquinolone (FQ) residues: norfloxacin, ciprofloxacin, danofloxacin, enrofloxacin, orbifloxacin, sarafloxacin, and difloxacin in honey. The samples were first screened with a microbiological method by using test plates made from metal-free purified agar seeded with Bacillus subtilis BGA. When a sample was found to contain FQ residues by using the microbiological method, it was analyzed by LC with fluorescence detection (LC/FL). FQs were extracted with Na2EDTA-McIlvaine buffer and purified by a dual SPE method in which a cation-exchange cartridge was connected to an anion-exchange cartridge. The overall recoveries of the seven FQs ranged from 70.0 to 92.1%. The intra-assay and interassay CVs were < or = 7.8 and < or = 5.1%, respectively. For the microbiological method, the LOD values ranged from 2 to 9 microg/kg. For LC/FL, the LOQ values ranged from 2 to 7 microg/kg. The developed method was used to analyze 70 honey samples. In 14 samples in which the microbiological method detected the presence of FQ residues, norfloxacin, ciprofloxacin, and enrofloxacin were identified by LC/FL.

  9. General unknown screening for pesticides in whole blood and Korean gastric contents by liquid chromatography-tandem mass spectrometry.

    PubMed

    Kim, Hyung-seung; Kim, Junghyun; Suh, Joon Hyuk; Han, Sang Beom

    2014-10-01

    A method of simultaneously screening 215 types of pesticides has been established by liquid chromatography with tandem mass spectrometry, quadrupole/time of flight mass spectrometry and triple quadrupole mass spectrometry. Samples of blood and gastric contents were prepared through the modified Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) method. A modified QuEChERS that uses dispersive solid phase extraction for a small amount of sample, mini-QuEChERS, was applied to blood and gastric contents for quick and convenient preparation of the sample and to reduce matrix effect. This method of simultaneous identification needs the upmost reliability because these results are employed by forensic toxicology and may lead to issues with the law. In this study, we incorporated the following two concepts to demonstrate its reliability: One concept is that two tandem mass spectrometers are applied for the confirmation and then a precise compound identification is conducted synchronously at the same retention time. The other concept for reliability adopts the approved criterion as identification points, defined by EU. Validation of the method was performed to assess selectivity, linearity, limit of quantification (LOQ), and recovery by standard addition procedure. The result of linearity was almost satisfactory, and the LOQ of pesticides detected in whole blood and Korean characteristic gastric contents was between 2.5-50 ng/mL. About 90 % of the pesticides had 80-120 % recovery in whole blood, and about 78 % of the pesticides had 80-120 % recovery in Korean gastric contents.

  10. A novel thin-layer chromatography method to screen 1,3-propanediol producers.

    PubMed

    Anand, Pinki; Saxena, Rajendra Kumar

    2012-11-01

    To date, there is no established protocol for the screening of 1,3-propanediol producers. The proposed method has a wide applicability to harness the commercial potential of microorganisms which produce 1,3-propanediol as the end product. Glycerol fermentation broth of 50 bacteria spotted on thin-layer chromatography plates and run by appropriate solvent systems followed by colour development using vanillin reagent gave different coloured spots with most of the compounds present in the fermentation broth. The appearance of a purple-coloured spot of 1,3-propanediol with a retention factor (R(f)) of 0.62 forms the basis for the selection of 1,3-propanediol producers. Apart from being a rapid detection system the proposed method is pH independent and its authenticity was reconfirmed by HPLC.

  11. Implementing a method of screening one-well hydraulic barrier design alternatives.

    PubMed

    Rubin, Hillel; Shoemaker, Christine A; Köngeter, Jürgen

    2009-01-01

    This article provides details of applying the method developed by the authors (Rubin et al. 2008b) for screening one-well hydraulic barrier design alternatives. The present article with its supporting information (manual and electronic spreadsheets with a case history example) provides the reader complete details and examples of solving the set of nonlinear equations developed by Rubin et al. (2008b). It allows proper use of the analytical solutions and also depicting the various charts given by Rubin et al. (2008b). The final outputs of the calculations are the required position and the discharge of the pumping well. If the contaminant source is nonaqueous phase liquid (NAPL) entrapped within the aquifer, then the method provides an estimate of the aquifer remediation progress (which is a by-product) due to operating the hydraulic barrier.

  12. 21 CFR 130.12 - General methods for water capacity and fill of containers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 2 2011-04-01 2011-04-01 false General methods for water capacity and fill of containers. 130.12 Section 130.12 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION FOOD STANDARDS: GENERAL General Provisions § 130.12 General methods for water capacity and...

  13. 21 CFR 130.12 - General methods for water capacity and fill of containers.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 2 2010-04-01 2010-04-01 false General methods for water capacity and fill of containers. 130.12 Section 130.12 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION FOOD STANDARDS: GENERAL General Provisions § 130.12 General methods for water capacity and...

  14. 21 CFR 130.12 - General methods for water capacity and fill of containers.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 2 2012-04-01 2012-04-01 false General methods for water capacity and fill of containers. 130.12 Section 130.12 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION FOOD STANDARDS: GENERAL General Provisions § 130.12 General methods for water capacity and...

  15. The weight method: a new screening method for estimating pesticide deposition from knapsack sprayers in developing countries.

    PubMed

    García-Santos, Glenda; Scheiben, Dominik; Binder, Claudia R

    2011-03-01

    Investigations of occupational and environmental risk caused by the use of agrochemicals have received considerable interest over the last decades. And yet, in developing countries, the lack of staff and analytical equipment as well the costs of chemical analyses make it difficult, if not impossible, to monitor pesticide contamination and residues in humans, air, water, and soils. A new and simple method is presented here for estimation of pesticide deposition in humans and soil after application. The estimate is derived on the basis of water mass balance measured in a given number of high absorbent papers under low evaporative conditions and unsaturated atmosphere. The method is presented as a suitable, rapid, low cost screening tool, complementary to toxicological tests, to assess occupational and environmental exposure caused by knapsack sprayers, where there is a lack of analytical instruments. This new method, called the "weight method", was tested to obtain drift deposition on the neighbouring field and the clothes of the applicator after spraying water with a knapsack sprayer in one of the largest areas of potato production in Colombia. The results were confirmed by experimental data using a tracer and the same set up used for the weight method. The weight method was able to explain 86% of the airborne drift and deposition variance.

  16. Precise Method for Investigation of Lissajous Generalized Figures

    ERIC Educational Resources Information Center

    Bednarek, Stanislaw

    2014-01-01

    This article describes the Lissajous generalized figure and the original instrument for its investigation. Two specially prepared electrodynamic loudspeakers--a horizontal and a vertical--cause oscillations in two mirrors. It is possible to precisely control the motion of the mirrors, achieve a high frequency of oscillation and investigate…

  17. Rapid methods for generalized transduction of Salmonella typhimurium mutants.

    PubMed

    Rosenfeld, S A; Brenchley, J

    1979-04-01

    A procedure has been developed that allows the propagation of generalized transducing phage directly on cells growing on solid media. After the donor cells are killed with chloroform, the phage can be transferred directly to recipient cells and transductants can be selected.

  18. A General Simulation Method for Multiple Bodies in Proximate Flight

    NASA Technical Reports Server (NTRS)

    Meakin, Robert L.

    2003-01-01

    Methods of unsteady aerodynamic simulation for an arbitrary number of independent bodies flying in close proximity are considered. A novel method to efficiently detect collision contact points is described. A method to compute body trajectories in response to aerodynamic loads, applied loads, and inter-body collisions is also given. The physical correctness of the methods are verified by comparison to a set of analytic solutions. The methods, combined with a Navier-Stokes solver, are used to demonstrate the possibility of predicting the unsteady aerodynamics and flight trajectories of moving bodies that involve rigid-body collisions.

  19. Ovarian Cancer Screening Method Fails to Reduce Deaths from the Disease

    Cancer.gov

    New results from the NCI-sponsored PLCO Cancer Screening Trial show that screening for ovarian cancer with transvaginal ultrasound (TVU) and the CA-125 blood test did not result in fewer deaths from the disease compared with usual care.

  20. Accelerated screening methods for determining chemical and thermal stability of refrigerant-lubricant mixtures, Part 1: Method assessment. Final report

    SciTech Connect

    Kauffman, R.

    1993-04-01

    This report presents results of a literature search performed to identify analytical techniques suitable for accelerated screening of chemical and thermal stabilities of different refrigerant/lubricant combinations. Search focused on three areas: Chemical stability data of HFC-134a and other non-chlorine containing refrigerant candidates; chemical stability data of CFC-12, HCFC-22, and other chlorine containing refrigerants; and accelerated thermal analytical techniques. Literature was catalogued and an abstract was written for each journal article or technical report. Several thermal analytical techniques were identified as candidates for development into accelerated screening tests. They are easy to operate, are common to most laboratories, and are expected to produce refrigerant/lubricant stability evaluations which agree with the current stability test ANSI/ASHRAE (American National Standards Institute/American Society of Heating, Refrigerating, and Air-Conditioning Engineers) Standard 97-1989, ``Sealed Glass Tube Method to Test the Chemical Stability of Material for Use Within Refrigerant Systems.`` Initial results of one accelerated thermal analytical candidate, DTA, are presented for CFC-12/mineral oil and HCFC-22/mineral oil combinations. Also described is research which will be performed in Part II to optimize the selected candidate.

  1. High throughput automated colorimetric method for the screening of l-lactic acid producing microorganisms.

    PubMed

    Liaud, Nadège; Navarro, David; Vidal, Nicolas; Sigoillot, Jean-Claude; Raouche, Sana

    2014-01-01

    Lactic acid is a valuable and fully degradable organic acid with promising applications in poly-lactic acid production (Taskila S and Ojamo, 2013 [1]). Despite their efficiency, the cost of the current lactic acid bio-processes is still an obstacle to this application (Miller et al., 2011 [2]). To ameliorate lactic acid producing strains, researchers are using mutations and metabolic engineering techniques, as well as medium optimization. All these studies necessitate a good and high throughput screening method. Currently, researchers mostly use HPLC methods which often necessitate sample preparation, are not stereospecific and do not allow high throughput. To help optimizing l-lactic acid production, we developed a high throughput colorimetric method inspired by the blood l-lactic acid detection method used for diagnosis (Lin et al., 1999 [3]).•Two sequential enzymatic reactions using l-lactate oxidase, peroxidase and ABTS (2,2'-azino-di-[3-ethylbenzthiazoine-sulfonate]), a chromogenic peroxidase substrate, are used to quantify l-lactate between 13.8 and 90 mg/l.•The accuracy of the method was ascertained before automation.•The method was successfully applied for the direct determination of l-lactate content in fungal culture supernatants.

  2. Current trends in virtual high throughput screening using ligand-based and structure-based methods.

    PubMed

    Sukumar, Nagamani; Das, Sourav

    2011-12-01

    High throughput in silico methods have offered the tantalizing potential to drastically accelerate the drug discovery process. Yet despite significant efforts expended by academia, national labs and industry over the years, many of these methods have not lived up to their initial promise of reducing the time and costs associated with the drug discovery enterprise, a process that can typically take over a decade and cost hundreds of millions of dollars from conception to final approval and marketing of a drug. Nevertheless structure-based modeling has become a mainstay of computational biology and medicinal chemistry, helping to leverage our knowledge of the biological target and the chemistry of protein-ligand interactions. While ligand-based methods utilize the chemistry of molecules that are known to bind to the biological target, structure-based drug design methods rely on knowledge of the three-dimensional structure of the target, as obtained through crystallographic, spectroscopic or bioinformatics techniques. Here we review recent developments in the methodology and applications of structure-based and ligand-based methods and target-based chemogenomics in Virtual High Throughput Screening (VHTS), highlighting some case studies of recent applications, as well as current research in further development of these methods. The limitations of these approaches will also be discussed, to give the reader an indication of what might be expected in years to come. PMID:21843144

  3. Screening for Depression in the General Population with the Center for Epidemiologic Studies Depression (CES-D): A Systematic Review with Meta-Analysis

    PubMed Central

    Vilagut, Gemma; Forero, Carlos G.; Barbaglia, Gabriela; Alonso, Jordi

    2016-01-01

    Objective We aimed to collect and meta-analyse the existing evidence regarding the performance of the Center for Epidemiologic Studies Depression (CES-D) for detecting depression in general population and primary care settings. Method Systematic literature search in PubMed and PsychINFO. Eligible studies were: a) validation studies of screening questionnaires with information on the accuracy of the CES-D; b) samples from general populations or primary care settings; c) standardized diagnostic interviews following standard classification systems used as gold standard; and d) English or Spanish language of publication. Pooled sensitivity, specificity, likelihood ratios and diagnostic odds ratio were estimated for several cut-off points using bivariate mixed effects models for each threshold. The summary receiver operating characteristic curve was estimated with Rutter and Gatsonis mixed effects models; area under the curve was calculated. Quality of the studies was assessed with the QUADAS tool. Causes of heterogeneity were evaluated with the Rutter and Gatsonis mixed effects model including each covariate at a time. Results 28 studies (10,617 participants) met eligibility criteria. The median prevalence of Major Depression was 8.8% (IQ range from 3.8% to 12.6%). The overall area under the curve was 0.87. At the cut-off 16, sensitivity was 0.87 (95% CI: 0.82–0.92), specificity 0.70 (95% CI: 0.65–0.75), and DOR 16.2 (95% CI: 10.49–25.10). Better trade-offs between sensitivity and specificity were observed (Sensitivity = 0.83, Specificity = 0.78, diagnostic odds ratio = 16.64) for cut-off 20. None of the variables assessed as possible sources of heterogeneity was found to be statistically significant. Conclusion The CES-D has acceptable screening accuracy in the general population or primary care settings, but it should not be used as an isolated diagnostic measure of depression. Depending on the test objectives, the cut-off 20 may be more adequate than the value

  4. A Finger-Stick Whole-Blood HIV Self-Test as an HIV Screening Tool Adapted to the General Public

    PubMed Central

    Prazuck, Thierry; Karon, Stephen; Gubavu, Camelia; Andre, Jerome; Legall, Jean Marie; Bouvet, Elisabeth; Kreplak, Georges; Teglas, Jean Paul; Pialoux, Gilles

    2016-01-01

    Background In 2013, the French Health Authority approved the use of HIV self-tests in pharmacies for the general public. This screening tool will allow an increase in the number of screenings and a reduction in the delay between infection and diagnosis, thus reducing the risk of further infections. We previously compared 5 HIV-self test candidates (4 oral fluid and one whole blood) and demonstrated that the whole blood HIV test exhibited the optimal level of performance (sensitivity/specificity). We studied the practicability of an easy-to-use finger-stick whole blood HIV self-test “autotest VIH®”, when used in the general public. Methods and Materials This multicenter cross-sectional study involved 411 participants from the Parisian region (AIDES and HF association) between April and July 2014 and was divided into 2 separate studies: one evaluating the capability of participants to obtain an interpretable result using only the information notice, and a second evaluating the interpretation of test results, using a provided chart. Results A total of 411 consenting participants, 264 in the first study and 147 in the second, were included. All participants were over 18 years of age. In the first study, 99.2% of the 264 participants correctly administered the auto-test, and 21.2% needed, upon their request, telephone assistance. Ninety-two percent of participants responded that the test was easy/very easy to perform, and 93.5% did not find any difficulty obtaining a sufficient good quantity of blood. In the second study, 98.1% of the 147 participants correctly interpreted the results. The reading/interpretation errors concerned the negative (2.1%) or the indeterminate (3.3%) auto-tests. Conclusions The success rate of handling and interpretation of this self-test is very satisfactory, demonstrating its potential for use by the general public and its utility to increase the number of opportunities to detect HIV patients. PMID:26882229

  5. Quantifying and monitoring overdiagnosis in cancer screening: a systematic review of methods

    PubMed Central

    Carter, Jamie L; Coletti, Russell J

    2015-01-01

    Objective To determine the optimal method for quantifying and monitoring overdiagnosis in cancer screening over time. Design Systematic review of primary research studies of any design that quantified overdiagnosis from screening for nine types of cancer. We used explicit criteria to critically appraise individual studies and assess strength of the body of evidence for each study design (double blinded review), and assessed the potential for each study design to accurately quantify and monitor overdiagnosis over time. Data sources PubMed and Embase up to 28 February 2014; hand searching of systematic reviews. Eligibility criteria for selecting studies English language studies of any design that quantified overdiagnosis for any of nine common cancers (prostate, breast, lung, colorectal, melanoma, bladder, renal, thyroid, and uterine); excluded case series, case reports, and reviews that only reported results of other studies. Results 52 studies met the inclusion criteria. We grouped studies into four methodological categories: (1) follow-up of a well designed randomized controlled trial (n=3), which has low risk of bias but may not be generalizable and is not suitable for monitoring; (2) pathological or imaging studies (n=8), drawing conclusions about overdiagnosis by examining biological characteristics of cancers, a simple design limited by the uncertain assumption that the measured characteristics are highly correlated with disease progression; (3) modeling studies (n=21), which can be done in a shorter time frame but require complex mathematical equations simulating the natural course of screen detected cancer, the fundamental unknown question; and (4) ecological and cohort studies (n=20), which are suitable for monitoring over time but are limited by a lack of agreed standards, by variable data quality, by inadequate follow-up time, and by the potential for population level confounders. Some ecological and cohort studies, however, have addressed these potential

  6. [Methicillin resistance detection in Staphylococcus aureus: comparison between conventional methods and MRSA-Screen latex agglutination technique].

    PubMed

    Soloaga, R; Corso, A; Gagetti, P; Faccone, D; Galas, M

    2004-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a significant pathogen that has emerged over the last four decades, causing both nosocomial and community-acquired infections. Rapid and accurate detection of methicillin resistance in S. aureus is important for the use of appropriate antimicrobial therapy and for the control of nosocomial spread of MRSA strains. We evaluated the efficiency of conventional methods for detection of methicillin resistance such as the disk diffusion, agar dilution, oxacillin agar screen test, and the latex agglutination test MRSA-Screen latex, in 100 isolates of S. aureus, 79 mecA positive and 21 mecA negative. The MRSA-Screen latex (Denka Seiken, Niigata, Japón), is a latex agglutination method that detects the presence of PLP-2a, product of mecA gene in S. aureus. The PCR of the mecA gene was used as the "gold standard" for the evaluation of the different methods tested. The percentages of sensitivity and specificity were as follows: disk difusión 97 and 100%, agar dilution 97 and 95%, oxacillin agar screen test 100 and 100%, and MRSA-Screen latex, 100 and 100 %. All methods presented high sensitivity and specificity, but MRSA-Screen latex had the advantage of giving a reliable result, equivalent to PCR, in only 15 minutes.

  7. A robust screening method for dietary agents that activate tumour-suppressor microRNAs

    PubMed Central

    Hagiwara, Keitaro; Gailhouste, Luc; Yasukawa, Ken; Kosaka, Nobuyoshi; Ochiya, Takahiro

    2015-01-01

    Certain dietary agents, such as natural products, have been reported to show anti-cancer effects. However, the underlying mechanisms of these substances in human cancer remain unclear. We recently found that resveratrol exerts an anti-cancer effect by upregulating tumour-suppressor microRNAs (miRNAs). In the current study, we aimed to identify new dietary products that have the ability to activate tumour-suppressor miRNAs and that therefore may serve as novel tools for the prevention and treatment of human cancers. We describe the generation and use of an original screening system based on a luciferase-based reporter vector for monitoring miR-200c tumour-suppressor activity. By screening a library containing 139 natural substances, three natural compounds — enoxolone, magnolol and palmatine chloride — were identified as being capable of inducing miR-200c expression in breast cancer cells at 10 μM. Moreover, these molecules suppressed the invasiveness of breast cancer cells in vitro. Next, we identified a molecular pathway by which the increased expression of miR-200c induced by natural substances led to ZEB1 inhibition and E-cadherin induction. These results indicate that our method is a valuable tool for a fast identification of natural molecules that exhibit tumour-suppressor activity in human cancer through miRNA activation. PMID:26423775

  8. OSO paradigm--A rapid behavioral screening method for acute psychosocial stress reactivity in mice.

    PubMed

    Brzózka, M M; Unterbarnscheidt, T; Schwab, M H; Rossner, M J

    2016-02-01

    Chronic psychosocial stress is an important environmental risk factor for the development of psychiatric diseases. However, studying the impact of chronic psychosocial stress in mice is time consuming and thus not optimally suited to 'screen' increasing numbers of genetically manipulated mouse models for psychiatric endophenotypes. Moreover, many studies focus on restraint stress, a strong physical stressor with limited relevance for psychiatric disorders. Here, we describe a simple and a rapid method based on the resident-intruder paradigm to examine acute effects of mild psychosocial stress in mice. The OSO paradigm (open field--social defeat--open field) compares behavioral consequences on locomotor activity, anxiety and curiosity before and after exposure to acute social defeat stress. We first evaluated OSO in male C57Bl/6 wildtype mice where a single episode of social defeat reduced locomotor activity, increased anxiety and diminished exploratory behavior. Subsequently, we applied the OSO paradigm to mouse models of two schizophrenia (SZ) risk genes. Transgenic mice with neuronal overexpression of Neuregulin-1 (Nrg1) type III showed increased risk-taking behavior after acute stress exposure suggesting that NRG1 dysfunction is associated with altered affective behavior. In contrast, Tcf4 transgenic mice displayed a normal stress response which is in line with the postulated predominant contribution of TCF4 to cognitive deficits of SZ. In conclusion, the OSO paradigm allows for rapid screening of selected psychosocial stress-induced behavioral endophenotypes in mouse models of psychiatric diseases.

  9. A fast and specific method to screen for intracellular amyloid inhibitors using bacterial model systems.

    PubMed

    Navarro, Susanna; Carija, Anita; Muñoz-Torrero, Diego; Ventura, Salvador

    2016-10-01

    The aggregation of a large variety of amyloidogenic proteins is linked to the onset of devastating human disorders. Therefore, there is an urgent need for effective molecules able to modulate the aggregative properties of these polypeptides in their natural environment, in order to prevent, delay or halt the progression of such diseases. On the one hand, the complexity and cost of animal models make them inefficient at early stages of drug discovery, where large chemical libraries are usually screened. On the other hand, in vitro aggregation assays in aqueous solutions hardly reproduce (patho)physiological conditions. In this context, because the formation of insoluble aggregates in bacteria shares mechanistic and functional properties with amyloid self-assembly in higher organisms, they have emerged as a promising system to model aggregation in the cell. Here we show that bacteria provide a powerful and cost-effective system to screen for amyloid inhibitors using fluorescence spectroscopy and flow cytometry, thanks to the ability of the novel red fluorescent ProteoStat dye to detect specifically intracellular amyloid-like aggregates. We validated the approach using the Alzheimer's linked Aβ40 and Aβ42 peptides and tacrine- and huprine-based aggregation inhibitors. Overall, the present method bears the potential to replace classical in vitro anti-aggregation assays.

  10. Benchmarking Methods and Data Sets for Ligand Enrichment Assessment in Virtual Screening

    PubMed Central

    Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

    2014-01-01

    Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. “analogue bias”, “artificial enrichment” and “false negative”. In addition, we introduced our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylase (HDAC) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The Leave-One-Out Cross-Validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased in terms of property matching, ROC curves and AUCs. PMID:25481478

  11. Screening and confirmatory methods for the analysis of macrocyclic lactone mycotoxins by CE with amperometric detection.

    PubMed

    Arribas, Alberto Sánchez; Bermejo, Esperanza; Zapardiel, Antonio; Téllez, Helena; Rodríguez-Flores, Juana; Zougagh, Mohammed; Ríos, Angel; Chicharro, Manuel

    2009-02-01

    A simple analytical scheme for the screening and quantification of zearalenone and its metabolites, alpha-zearalenol and beta-zearalenol, is reported. Extracts from maize flour samples were collected by supercritical fluid extraction and afterwards, they were analyzed by CE with amperometric detection. This scheme allowed a rapid and reliable identification of contaminated flour samples according to the reference value established for zearalenone by directive 2005/38/EC (200 microg/kg). The sample screening method was carried out by CZE using 25 mM borate separation buffer at pH 9.2 and 25.0 kV as separation voltage, monitoring the amperometric signal at +700 mV with a carbon paste electrode. In this way, total amount of mycotoxins was determined and samples were processed in 4 min with a detection limit of 12 microg/L, enough to discriminate between positive (more than 200 microg/L total mycotoxins) and negative samples (less than 200 microg/L total mycotoxins). Positive samples were then subjected to CZE separation and quantification of each analyte was done with 50 mM borate running buffer modified with 30% methanol at pH 9.7 and 17.5 kV as separation voltage. Under these conditions, separation was achieved in 15 min with detection limits from 20 to 35 microg/L for each analyte.

  12. Statistical and graphical methods for quality control determination of high-throughput screening data.

    PubMed

    Gunter, Bert; Brideau, Christine; Pikounis, Bill; Liaw, Andy

    2003-12-01

    High-throughput screening (HTS) is used in modern drug discovery to screen hundreds of thousands to millions of compounds on selected protein targets. It is an industrial-scale process relying on sophisticated automation and state-of-the-art detection technologies. Quality control (QC) is an integral part of the process and is used to ensure good quality data and mini mize assay variability while maintaining assay sensitivity. The authors describe new QC methods and show numerous real examples from their biologist-friendly Stat Server HTS application, a custom-developed software tool built from the commercially available S-PLUS and Stat Server statistical analysis and server software. This system remotely processes HTS data using powerful and sophisticated statistical methodology but insulates users from the technical details by outputting results in a variety of readily interpretable graphs and tables. It allows users to visualize HTS data and examine assay performance during the HTS campaign to quickly react to or avoid quality problems.

  13. Accuracy analysis of the Null-Screen method for the evaluation of flat heliostats

    NASA Astrophysics Data System (ADS)

    Cebrian-Xochihuila, P.; Huerta-Carranza, O.; Díaz-Uribe, R.

    2016-04-01

    In this work we develop an algorithm to determinate the accuracy of the Null-Screen Method, used for the testing of flat heliostats used as solar concentrators in a central tower configuration. We simulate the image obtained on a CCD camera when an orderly distribution of points are displayed on a Null-Screen perpendicular to the heliostat under test. The deformations present in the heliostat are represented as a cosine function of the position with different periods and amplitudes. As a resolution criterion, a deformation on the mirror can be detected when the differences in position between the spots on the image plane for the deformed surface as compared with those obtained for an ideally flat heliostat are equal to one pixel. For 6.4μm pixel size and 18mm focal length, the minimum deformation we can measure in the heliostat, correspond to amplitude equal a 122μm for a period equal to 1m; this is equivalent to 0.8mrad in slope. This result depends on the particular configuration used during the test and the size of the heliostat.

  14. Development of a screening method to identify regulators of MICA shedding.

    PubMed

    Kishikawa, Takahiro; Otsuka, Motoyuki; Ohno, Motoko; Yoshikawa, Takeshi; Sato, Masaya; Koike, Kazuhiko

    2015-10-01

    Immune cells, such as natural killer (NK) cells, recognize virally infected and transformed cells, and eliminate them through the interaction between NKG2D receptors on NK cells and NKG2D ligands on pathogenic cells. Shedding of NKG2D ligands is thought to be a type of counter-mechanism employed by pathogenic cells to evade from NKG2D-mediated immune surveillance. MHC class I polypeptide-related sequence A (MICA) is a prototypical NKG2D ligand. We previously reported that, in soluble form, MICA expression levels are significantly associated with hepatitis virus-induced hepatocellular carcinoma. Here, we report a MICA shedding assay that utilizes membrane-bound MICA tagged at its N-terminus with a nano-luciferase reporter to quantify MICA shedding into culture media. Using this method, we screened a compound library and identified putative regulators of MICA shedding that have the potential to enhance the immune reaction by simultaneously increasing cell surface MICA levels and decreasing soluble MICA levels. This shedding assay may be useful for screening regulators of cell surface molecule shedding.

  15. Development of Screening Method for an Frail Elderly by Measurement Quantitative Lower Limb Muscular Strength

    NASA Astrophysics Data System (ADS)

    Yamashita, Kazuhiko; Iwakami, Yumi; Imaizumi, Kazuya; Sato, Mitsuru; Nakajima, Sawako; Ino, Shuichi; Kawasumi, Masashi; Ifukube, Tohru

    Falling is one of the most serious problems for the elderly. The aim of this study was to develop a screening method for identifying factors that increase the risk of falling among the elderly, particularly with regard to lower limb muscular strength. Subjects were 48 elderly volunteers, including 25 classed as healthy and 23 classed as frail. All subjects underwent measurement of lower limb muscular strength via toe gap force and measurement of muscle strength of the hip joint adductor via knee gap force. In the frail group, toe gap force of the right foot was 20% lower than that in the healthy group; toe gap force of the left foot in the frail group was 23% lower than that in the healthy group, while knee gap force was 20% lower. Furthermore, we found that combining left toe gap force and knee gap force gave the highest odds ratio (6.05) with 82.6% sensitivity and 56.0% specificity when the toe gap force was 24 N and the knee gap force was 100 N. Thus, lower limb muscular strength can be used for simple and efficient screening, and approaches to prevent falls can be based on quantitative data such as lower limb muscular strength.

  16. Diabetes Screening Among Immigrants

    PubMed Central

    Creatore, Maria I.; Booth, Gillian L.; Manuel, Douglas G.; Moineddin, Rahim; Glazier, Richard H.

    2012-01-01

    OBJECTIVE To examine diabetes screening, predictors of screening, and the burden of undiagnosed diabetes in the immigrant population and whether these estimates differ by ethnicity. RESEARCH DESIGN AND METHODS A population-based retrospective cohort linking administrative health data to immigration files was used to follow the entire diabetes-free population aged 40 years and up in Ontario, Canada (N = 3,484,222) for 3 years (2004–2007) to determine whether individuals were screened for diabetes. Multivariate regression was used to determine predictors of having a diabetes test. RESULTS Screening rates were slightly higher in the immigrant versus the general population (76.0 and 74.4%, respectively; P < 0.001), with the highest rates in people born in South Asia, Mexico, Latin America, and the Caribbean. Immigrant seniors (age ≥65 years) were screened less than nonimmigrant seniors. Percent yield of new diabetes subjects among those screened was high for certain countries of birth (South Asia, 13.0%; Mexico and Latin America, 12.1%; Caribbean, 9.5%) and low among others (Europe, Central Asia, U.S., 5.1–5.2%). The number of physician visits was the single most important predictor of screening, and many high-risk ethnic groups required numerous visits before a test was administered. The proportion of diabetes that remained undiagnosed was estimated to be 9.7% in the general population and 9.0% in immigrants. CONCLUSIONS Overall diabetes-screening rates are high in Canada’s universal health care setting, including among high-risk ethnic groups. Despite this finding, disparities in screening rates between immigrant subgroups persist and multiple physician visits are often required to achieve recommended screening levels. PMID:22357181

  17. The Trial of Drug Discovery using the In-Silico Screening Methods Developed by Pharmaceutical Innovation Value Chain

    NASA Astrophysics Data System (ADS)

    Inoue, Tsuyoshi; Matsumura, Hiroyoshi; Adachi, Hiroaki; Mori, Yusuke; Takano, Kazufumi; Murakami, Satoshi; Fukunishi, Yoshifumi; Nakamura, Haruki; Kinoshita, Takayoshi; Nakanishi, Isao; Okuno, Yasushi; Minakata, Satoshi; Mikami, Yoshiaki; Sakuma, Toshihiro; Kitajima, Masato; Fukuoka, Yoshitada; Takada, Toshikazu; Sakata, Tsuneaki

    We have recently established Pharmaceutical Innovation Value Chain collaborated by The SOSHO project (http://www.so-sho.jp) and The BioGrid Project (http://www.biogrid.jp/) to accelerate new drug development. The in-silico group calculated the matrices on the interaction between the proteins and chemical compounds, and developed the novel in-silico screening methods, Multiple Target Screening (MTS) and Docking score index (DSI), improving the hit rate of screening a lead compound. We have applied these methods for the two target enzymes; human hematopoietic prostaglandin D synthase (H-PGDS) and orotidine 5’-monophosphate decarboxylase from human malaria parasite plasmodium falciparum (PfOMPDC). The optimizing of HQL-79, one of the known inhibitors for human H-PGDS and the screening of lead compounds for both enzymes are in study.

  18. [Contamination level of aflatoxin B1 in lotus seeds rapid screening by indirect competitive ELISA method].

    PubMed

    Chu, Xian-feng; Dou, Xiao-wen; Kong, Wei-jun; Yang, Mei-hua; Zhao, Chong; Zhao, Ming; Ouyang, Zhen

    2015-02-01

    A simple and cost-effective indirect competitive enzyme-linked immune sorbent assay (ic-ELISA) was developed to rapidly screen the content of aflatoxin B1 (AFB1) in lotus seeds, and the results were confirmed by ultra-fast liquid chromatography-tandem mass spectrometry( UFLC-MS/MS). Matrix-matched calibration expressed a good linearity ranging from 0. 171 to 7. 25 µg · L(-1) for AFB, with R2 > 0.978. The medium inhibitory concentration( IC50 ) for AFB1 was 1.29 µg · L(-1), the recovery for AFB1 was 74.73% to 126.9% with RSD < 5%, and the limit of detection (IC10) was 0.128 µg · L(-1). The developed ic-ELSIA method was applied to rapid analysis of AFB, in 20 lotus seeds samples and the results indicated that the contents of AFB, in samples 1-15 were in the range of 1. 19- 115. 3 µg · kg(-1) and in 40% of the samples exceeded the legal limit(5 µg · kg(-1)), while the contamination rate of AFB, in samples 16-20 was 40%. Pearson correlation coefficient(r) reached 0.997 for AFB1 content in the samples detected by ic-ELSIA and UFLC-MS/MS methods. The results proved that the developed ic-ELISA method is simple, sensitive and reliable, and can be used for rapid and high-throughput screening of AFB1 in lotus seeds

  19. An Improved Method for P2X7R Antagonist Screening

    PubMed Central

    Soares-Bezerra, Rômulo José; Ferreira, Natiele Carla da Silva; Alberto, Anael Viana Pinto; Bonavita, André Gustavo; Fidalgo-Neto, Antônio Augusto; Calheiros, Andrea Surrage; Frutuoso, Valber da Silva; Alves, Luiz Anastacio

    2015-01-01

    ATP physiologically activates the P2X7 receptor (P2X7R), a member of the P2X ionotropic receptor family. When activated by high concentrations of ATP (i.e., at inflammation sites), this receptor is capable of forming a pore that allows molecules of up to 900 Da to pass through. This receptor is upregulated in several diseases, particularly leukemia, rheumatoid arthritis and Alzheimer's disease. A selective antagonist of this receptor could be useful in the treatment of P2X7R activation-related diseases. In the present study, we have evaluated several parameters using in vitro protocols to validate a high-throughput screening (HTS) method to identify P2X7R antagonists. We generated dose-response curves to determine the EC50 value of the known agonist ATP and the ICs50 values for the known antagonists Brilliant Blue G (BBG) and oxidized ATP (OATP). The values obtained were consistent with those found in the literature (0.7 ± 0.07 mM, 1.3-2.6 mM and 173-285 μM for ATP, BBG and OATP, respectively). The Z-factor, an important statistical tool that can be used to validate the robustness and suitability of an HTS assay, was 0.635 for PI uptake and 0.867 for LY uptake. No inter-operator variation was observed, and the results obtained using our improved method were reproducible. Our data indicate that our assay is suitable for the selective and reliable evaluation of P2X7 activity in multiwell plates using spectrophotometry-based methodology. This method might improve the high-throughput screening of conventional chemical or natural product libraries for possible candidate P2X7R antagonist or agonist PMID:25993132

  20. A cell–ECM screening method to predict breast cancer metastasis

    PubMed Central

    Barney, L.E.; Dandley, E.C.; Jansen, L.E.; Reich, N.G.; Mercurio, A.M.

    2015-01-01

    Breast cancer preferentially spreads to the bone, brain, liver, and lung. The clinical patterns of this tissue-specific spread (tropism) cannot be explained by blood flow alone, yet our understanding of what mediates tropism to these physically and chemically diverse tissues is limited. While the microenvironment has been recognized as a critical factor in governing metastatic colonization, the role of the extracellular matrix (ECM) in mediating tropism has not been thoroughly explored. We created a simple biomaterial platform with systematic control over the ECM protein density and composition to determine if integrin binding governs how metastatic cells differentiate between secondary tissue sites. Instead of examining individual behaviors, we compiled large patterns of phenotypes associated with adhesion to and migration on these controlled ECMs. In combining this novel analysis with a simple biomaterial platform, we created an in vitro fingerprint that is predictive of in vivo metastasis. This rapid biomaterial screen also provided information on how β1, α2, and α6 integrins might mediate metastasis in patients, providing insights beyond a purely genetic analysis. We propose that this approach of screening many cell–ECM interactions, across many different heterogeneous cell lines, is predictive of in vivo behavior, and is much simpler, faster, and more economical than complex 3D environments or mouse models. We also propose that when specifically applied toward the question of tissue tropism in breast cancer, it can be used to provide insight into certain integrin subunits as therapeutic targets. Insight, innovation, integration We developed a high-throughput method to rapidly screen cell adhesion, motility, and growth factor responses on biomaterial surfaces. This approach is analogous to systems biology, relying on cell phenotypes in lieu of genetics. We used this technique to reveal patterns of phenotypes associated with breast cancer metastasis to

  1. Statistical Methods for Analysis of High-Throughput RNA Interference Screens

    PubMed Central

    Birmingham, Amanda; Selfors, Laura M.; Forster, Thorsten; Wrobel, David; Kennedy, Caleb J.; Shanks, Emma; Santoyo-Lopez, Javier; Dunican, Dara J.; Long, Aideen; Kelleher, Dermot; Smith, Queta; Beijersbergen, Roderick L.; Ghazal, Peter; Shamu, Caroline E.

    2009-01-01

    RNA interference (RNAi) has become a powerful technique for reverse genetics and drug discovery and, in both of these areas, large-scale high-throughput RNAi screens are commonly performed. The statistical techniques used to analyze these screens are frequently borrowed directly from small-molecule screening; however small-molecule and RNAi data characteristics differ in meaningful ways. We examine the similarities and differences between RNAi and small-molecule screens, highlighting particular characteristics of RNAi screen data that must be addressed during analysis. Additionally, we provide guidance on selection of analysis techniques in the context of a sample workflow. PMID:19644458

  2. Statistical methods for the analysis of a screening test for chronic beryllium disease

    SciTech Connect

    Frome, E.L.; Neubert, R.L.; Smith, M.H.; Littlefield, L.G.; Colyer, S.P.

    1994-10-01

    The lymphocyte proliferation test (LPT) is a noninvasive screening procedure used to identify persons who may have chronic beryllium disease. A practical problem in the analysis of LPT well counts is the occurrence of outlying data values (approximately 7% of the time). A log-linear regression model is used to describe the expected well counts for each set of test conditions. The variance of the well counts is proportional to the square of the expected counts, and two resistant regression methods are used to estimate the parameters of interest. The first approach uses least absolute values (LAV) on the log of the well counts to estimate beryllium stimulation indices (SIs) and the coefficient of variation. The second approach uses a resistant regression version of maximum quasi-likelihood estimation. A major advantage of the resistant regression methods is that it is not necessary to identify and delete outliers. These two new methods for the statistical analysis of the LPT data and the outlier rejection method that is currently being used are applied to 173 LPT assays. The authors strongly recommend the LAV method for routine analysis of the LPT.

  3. An automated mass spectrometry-based screening method for analysis of sulfated glycosaminoglycans.

    PubMed

    Kiselova, Nadezda; Dierker, Tabea; Spillmann, Dorothe; Ramström, Margareta

    2014-07-18

    Glycosaminoglycans (GAGs) are linear polysaccharides, consisting of repeated disaccharide units, attached to core proteins in all multicellular organisms. Chondroitin sulfate (CS) and dermatan sulfate (DS) constitute a subgroup of sulfated GAGs for which the degree of sulfation varies between species and tissues. One major goal in GAG characterization is to correlate structure to function. A common approach is to exhaustively degrade the GAG chains and thereafter determine the amount of component disaccharide units. In large-scale studies, there is a need for high-throughput screening methods since existing methods are either very time- or samples consuming. Here, we present a new strategy applying MALDI-TOF MS in positive ion mode for semi-qualitative and quantitative analysis of CS/DS derived disaccharide units. Only a few picomoles of sample are required per analysis and 10 samples can be analyzed in 25 min, which makes this approach an attractive alternative to many established assay methods. The total CS/DS concentration in 19 samples derived from Caenorhabditis elegans and mammalian tissues and cells was determined. The obtained results were well in accordance with concentrations determined by a standard liquid chromatography-based method, demonstrating the applicability of the method for samples from various biological matrices containing CS/DS of different sulfation degrees.

  4. Comparison of Adsorbed Mercury Screening Method With Cold-Vapor Atomic Absorption Spectrophotometry for Determination of Mercury in Soil

    NASA Technical Reports Server (NTRS)

    Easterling, Donald F.; Hovanitz, Edward S.; Street, Kenneth W.

    2000-01-01

    A field screening method for the determination of elemental mercury in environmental soil samples involves the thermal desorption of the mercury from the sample onto gold and then the thermal desorption from the gold to a gold-film mercury vapor analyzer. This field screening method contains a large number of conditions that could be optimized for the various types of soils encountered. In this study, the conditions were optimized for the determination of mercury in silty clay materials, and the results were comparable to the cold-vapor atomic absorption spectrophotometric method of determination. This paper discusses the benefits and disadvantages of employing the field screening method and provides the sequence of conditions that must be optimized to employ this method of determination on other soil types.

  5. Screening for adverse events.

    PubMed

    Karson, A S; Bates, D W

    1999-02-01

    Adverse events (AEs) in medical patients are common, costly, and often preventable. Development of quality improvement programs to decrease the number and impact of AEs demands effective methods for screening for AEs on a routine basis. Here we describe the impact, types, and potential causes of AEs and review various techniques for identifying AEs. We evaluate the use of generic screening criteria in detail and describe a recent study of the sensitivity and specificity of individual generic screening criteria and combinations of these criteria. In general, the most sensitive screens were the least specific and no small sub-set of screens identified a large percentage of adverse events. Combinations of screens that were limited to administrative data were the least expensive, but none were particularly sensitive, although in practice they might be effective since routine screening is currently rarely done. As computer systems increase in sophistication sensitivity will improve. We also discuss recent studies that suggest that programs that screen for and identify AEs can be useful in reducing AE rates. While tools for identifying AEs have strengths and weaknesses, they can play an important role in organizations' quality improvement portfolios. PMID:10468381

  6. A general, mass-preserving Navier-Stokes projection method

    NASA Astrophysics Data System (ADS)

    Salac, David

    2016-07-01

    The conservation of mass is a common issue with multiphase fluid simulations. In this work a novel projection method is presented which conserves mass both locally and globally. The fluid pressure is augmented with a time-varying component which accounts for any global mass change. The resulting system of equations is solved using an efficient Schur-complement method. Using the proposed method four numerical examples are performed: the evolution of a static bubble, the rise of a bubble, the breakup of a thin fluid thread, and the extension of a droplet in shear flow. The method is capable of conserving the mass even in situations with morphological changes such as droplet breakup.

  7. Rapid Methods for the Detection of General Fecal Indicators

    EPA Science Inventory

    Specified that EPA should develop: appropriate and effective indicators for improving detection in a timely manner of pathogens in coastal waters appropriate, accurate, expeditious and cost-effective methods for the timely detection of pathogens in coastal waters

  8. Composite method to quantify powder flow as a screening method in early tablet or capsule formulation development.

    PubMed

    Taylor, M K; Ginsburg, J; Hickey, A; Gheyas, F

    2000-06-24

    The flow properties of typical tablet and capsule formulation excipients, active compounds, and representative formulation blends were tested with current and novel flow measurement techniques to identify a reliable bench test to quantify powder flow as a screening method in early tablet and capsule formulation development. Test methods employed were vibrating spatula, critical orifice, angle of repose, compressibility index, and avalanching analysis. Powder flow results from each method were compiled in a database, sorted, and compared. An empirical composite index was established and powder flow was ranked in accordance with formulator experience. Principal components analyses of the angle of repose, percent compressibility, and critical orifice of the powder materials were also performed. The first principal component accounted for 72.8% of data variability; scores associated with this principal component score can serve as an index of flowability. Data generated from vibrating spatula and avalanching methods were not reproducible and were inconsistent with formulator experience and cited vendor references for flow. Improvements of test instruments and further studies are necessary for better assessment of these approaches.

  9. A new screening method for flunitrazepam in vodka and tequila by fluorescence spectroscopy.

    PubMed

    Leesakul, Nararak; Pongampai, Sirintip; Kanatharana, Proespichaya; Sudkeaw, Pravit; Tantirungrotechai, Yuthana; Buranachai, Chittanon

    2013-01-01

    A new screening method for flunitrazepam in colourless alcoholic beverages based on a spectroscopic technique is proposed. Absorption and steady-state fluorescence of flunitrazepam and its protonated form with various acids were investigated. The redshift of the wavelength of maximum absorption was distinctively observed in protonated flunitrazepam. An emissive fluorescence at 472 nm was detected in colourless spirits (vodka and tequila) at room temperature. 2-M perchloric acid was the most appropriated proton source. By using electron ionization mass spectrometry and time-dependent density functional theory calculations, the possible structure of protonated flunitrazepam was identified to be 2-nitro-N-methylacridone, an acridone derivative as opposed to 2-methylamino-5-nitro-2'-fluorobenzophenone, a benzophenone derivative.

  10. Studies with the USF/NASA toxicity screening test method - Oxygen concentrations with various test conditions

    NASA Technical Reports Server (NTRS)

    Hilado, C. J.; Cumming, H. J.; Solis, A. N.

    1977-01-01

    Continuing efforts to increase the versatility of the USF/NASA toxicity screening test method have included the use of different test conditions in order to simulate various fire environments. The use of air flow at flow rates of 16 to 48 ml/sec maintains oxygen concentrations above 19 percent throughout the 30 min exposure period, compared to above 16 percent without forced air flow. These levels of oxygen are well within the tolerance range of mice, and approach the oxygen levels found in many real fire situations. Proposed minimum oxygen levels based on experience with rats are unduly restrictive on the use of other species such as mice, and tend to eliminate the cost savings which may more than justify the selection of mice.

  11. Noninvasive Assessment of Excessive Erythrocytosis as a Screening Method for Chronic Mountain Sickness at High Altitude.

    PubMed

    Vyas, Kaetan J; Danz, David; Gilman, Robert H; Wise, Robert A; León-Velarde, Fabiola; Miranda, J Jaime; Checkley, William

    2015-06-01

    Vyas, Kaetan J., David Danz, Robert H. Gilman, Robert A. Wise, Fabiola León-Velarde, J. Jaime Miranda, and William Checkley. Noninvasive assessment of excessive erythrocytosis as a screening method for chronic mountain sickness at high altitude. High Alt Med Biol 16:162-168, 2015.--Globally, over 140 million people are at risk of developing chronic mountain sickness, a common maladaptation to life at high altitude (>2500 meters above sea level). The diagnosis is contingent upon the identification of excessive erythrocytosis (EE). Current best practices to identify EE require a venous blood draw, which is cumbersome for large-scale surveillance. We evaluated two point-of-care biomarkers to screen for EE: noninvasive spot-check tests of total hemoglobin and oxyhemoglobin saturation (Pronto-7, Masimo Corporation). We conducted paired evaluations of total serum hemoglobin from a venous blood draw and noninvasive, spot-check testing of total hemoglobin and oxyhemoglobin saturation with the Pronto-7 in 382 adults aged ≥35 years living in Puno, Peru (3825 meters above sea level). We used the Bland-Altman method to measure agreement between the noninvasive hemoglobin assessment and the gold standard lab hemoglobin analyzer. Mean age was 58.8 years and 47% were male. The Pronto-7 test was unsuccessful in 21 (5%) participants. Limits of agreement between total hemoglobin measured via venous blood draw and the noninvasive, spot-check test ranged from -2.8 g/dL (95% CI -3.0 to -2.5) to 2.5 g/dL (95% CI 2.2 to 2.7), with a bias of -0.2 g/dL (95% CI -0.3 to -0.02) for the difference between total hemoglobin and noninvasive hemoglobin concentrations. Overall, the noninvasive spot-check test of total hemoglobin had a better area under the receiver operating characteristic curve compared to oxyhemoglobin saturation for the identification of EE as measured by a gold standard laboratory hemoglobin analyzer (0.96 vs. 0.82; p<0.001). Best cut-off values to screen for EE with

  12. [Modern methods of early screening for preeclampsia and pregnancy-induced hypertension--a review].

    PubMed

    Poprawski, Grzegorz; Wender-Ozegowska, Ewa; Zawiejska, Agnieszka; Brazert, Jacek

    2012-09-01

    Preeclampsia remains to be a serious perinatal complication and early screening for this disease to identify the high risk population before the first symptoms develop constitutes a considerable clinical challenge. Modern methods of screening for preeclampsia and pregnancy-induced hypertension include patients history biochemical serum markers and foetal DNA and RNA in maternal serum. They aid the process of developing an optimal protocol to initiate treatment in early pregnancy and to reduce the rate of complications. Our review presents an overview of the novel methods and techniques used for early screening for preeclampsia and pregnancy-induced hypertension. Most of the research focuses on 11-13 weeks of gestation due to the fact that the first prenatal examination is performed at that time. The most important information seems to be: weight, mass, mean blood pressure, history of pregnancy-induced hypertension or preeclampsia at previous pregnancies as well as the ethnic origin. During an ultrasound scan, pulsatility index of the uterine arteries is measured. Blood samples are obtained during the last part of the examination. At the moment only a few markers seem to be strong predictors of hypertensive disorders during pregnancy: pregnancy-associated plasma protein-A (PAPP-A), placental growth factor (PIGF) and soluble fms-like tyrosine kinase-1 (sFlt-1). Also, fetal DNA and RNA in maternal plasma are helpful in the prediction of preeclampsia as they are markers of the trophoblast apoptosis. Researchers aim at identifying the population at high risk of pregnancy-induced hypertension and preeclampsia in order to offer appropriate antenatal care to these women. At the moment many drugs and diet supplements are investigated to reduce the prevalence of hypertensive disorders in pregnancy. These medications are usually administrated in early gestation (up to 16 week of gestation) before the first clinical symptoms present. Low doses of aspirin were found to decrease

  13. Strategies and applications of combinatorial methods and high throughput screening to the discovery of non-noble metal catalyst

    NASA Astrophysics Data System (ADS)

    Bricker, Maureen L.; Sachtler, J. W. Adriaan; Gillespie, Ralph D.; McGonegal, Charles P.; Vega, Honorio; Bem, Dave S.; Holmgren, Jennifer S.

    2004-02-01

    The integrated End-to-End™ combinatorial process for catalyst preparation and screening, with emphasis on its capability to vary both process and compositional parameters will be demonstrated. Additionally, each step of the combinatorial screening process has been validated against results from traditional screening methods. The greatest challenge of all has been the adherence to the core concepts of the combinatorial approach. Catalyst libraries have been made and tested for naphthalene dehydrogenation chemistry. The preparation of these libraries has included the application of high throughput techniques for: metal impregnation; catalyst finishing; catalyst screening. The catalyst screening system has been used to find a non-noble metal catalyst system that can replace Pt in dehydrogenation applications in the petroleum industry. A proprietary catalytic composition was developed for the dehydrogenation of methylcyclohexane (MCH) to toluene starting with four non-noble metals of different proportions and four different supports (alumina, titania, zirconia and silica) prepared in different ways and applying a statistical design of experiments. These data demonstrate that all steps of catalyst preparation and screening are performed in a rapid, useful, high throughput manner. Data will be presented from the catalyst screening efforts will demonstrate that optimized metal composition is dependent on the support type.

  14. Micellar electrokinetic chromatographic screening method for common sexual assault drugs administered in beverages.

    PubMed

    Bishop, Sandra C; Lerch, Margaret; McCord, Bruce R

    2004-04-20

    Recently, much attention has been given to benzodiazepines and gamma-hydroxybutyric acid (GHB) related compounds owing to their alleged widespread use as date-rape drugs. Toxicologists would greatly benefit from a screening method that allows for the simultaneous detection of both groups of substances. A new capillary electrophoresis (CE) method has been developed in the micellar mode to accomplish this separation in under 16 min using a sodium dodecyl sulfate (SDS)/sodium tetraborate/boric acid buffer with an acetonitrile organic modifier. Optimization of SDS and organic modifier concentration, along with pH, were performed on a set of standards containing eight benzodiazepines, GHB, gamma-butyrolactone, and the internal standard, sulfanilic acid. The method was shown to have a detection limit of less than 2 microg/ml for five out of eight benzodiazepines with a linear range of 2.5-100 microg/ml. The detection limit for GHB was 32 mg/ml with a linear range to 2500 microg/ml. This method was applied to the rapid analysis of spiked beverages. GHB spiked beverages were monitored after using a series of simple dilutions to determine the effects of time on the drug analysis. Possible interfering peaks from drugs of abuse and artifacts from a variety of different drink combinations were also studied in detail. A one-step liquid-liquid extraction was the only necessary sample pretreatment. PMID:15066708

  15. A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

    PubMed

    Hu, Xiaohua; Chen, Nana; Li, Weichen

    2016-07-01

    Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide. PMID:27365051

  16. A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

    PubMed

    Hu, Xiaohua; Chen, Nana; Li, Weichen

    2016-07-01

    Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.

  17. Health Screenings and Immunizations

    MedlinePlus

    ... your primary doctor. Blood Tests – A Common Screening Method (Source: National Heart, Lung, and Blood Institute) Click ... tests, see What Are Blood Tests? Other Screening Methods Doctors can't screen for all diseases and ...

  18. Mass screening for celiac disease from the perspective of newly diagnosed adolescents and their parents: A mixed-method study

    PubMed Central

    2011-01-01

    Background Mass screening for celiac disease (CD) as a public health intervention is controversial. Prior to implementation, acceptability to the targeted population should be addressed. We aimed at exploring adolescents' and parents' experiences of having the adolescents' CD detected through mass screening, and their attitudes towards possible future mass screening. Methods All adolescents (n = 145) with screening-detected CD found in a Swedish school-based screening study, and their parents, were invited to this study about one year after diagnosis. In all, 14 focus group discussions were conducted with 31 adolescents and 43 parents. Written narrative was completed by 91 adolescents (63%) and 105 parents (72%), and questionnaires returned by 114 parents (79%). Data were analyzed using qualitative content analysis. In addition, narratives and questionnaire data allowed for quantified measures. Results Adolescents and parents described how they agreed to participate "for the good of others," without considering consequences for themselves. However, since the screening also introduced a potential risk of having the disease, the invitation was regarded as "an offer hard to resist." For the majority, receiving the diagnosis was described as "a bolt of lightning," but for some it provided an explanation for previous health problems, and "suddenly everything made sense." Looking back at the screening, the predominant attitude was "feeling grateful for being made aware," but some adolescents and parents also expressed "ambivalent feelings about personal benefits." Among parents, 92% supported future CD screening. The most common opinion among both adolescents and parents was that future CD mass screening should be "a right for everyone" and should be offered as early as possible. However, some argued that it should be "only for sufferers" with symptoms, whereas others were "questioning the benefits" of CD mass screening. Conclusions Although the incentives to participate

  19. General Method for Functionalized Polyaryl Synthesis via Aryne Intermediates

    PubMed Central

    2015-01-01

    A method for base-promoted arylation of arenes and heterocycles by aryl halides and aryl triflates is described. Additionally, in situ electrophilic trapping of ArLi intermediates generated in the reaction of benzyne with deprotonated arenes or heterocycles has been developed, providing rapid and easy access to a wide range of highly functionalized polyaryls. Base-promoted arylation methodology complements transition-metal-catalyzed direct arylation and allows access to structures that are not easily accessible via other direct arylation methods. The reactions are highly functional-group tolerant, with alkene, ether, dimethylamino, trifluoromethyl, ester, cyano, halide, hydroxyl, and silyl functionalities compatible with reaction conditions. PMID:24893069

  20. UV-visible spectroscopy method for screening the chemical stability of potential antioxidants for proton exchange membrane fuel cells

    NASA Astrophysics Data System (ADS)

    Banham, Dustin; Ye, Siyu; Knights, Shanna; Stewart, S. Michael; Wilson, Mahlon; Garzon, Fernando

    2015-05-01

    A novel method based on UV-visible spectroscopy is reported for screening the chemical stability of potential antioxidant additives for proton exchange membrane fuel cells, and the chemical stabilities of three CeOx samples of varying crystallite sizes (6, 13, or 25 nm) are examined. The chemical stabilities predicted by this new screening method are compared to in-situ membrane electrode assembly (MEA) accelerated stress testing, with the results confirming that this rapid and inexpensive method can be used to accurately predict performance impacts of antioxidants.

  1. Scalable Kernel Methods and Algorithms for General Sequence Analysis

    ERIC Educational Resources Information Center

    Kuksa, Pavel

    2011-01-01

    Analysis of large-scale sequential data has become an important task in machine learning and pattern recognition, inspired in part by numerous scientific and technological applications such as the document and text classification or the analysis of biological sequences. However, current computational methods for sequence comparison still lack…

  2. A General Linear Method for Equating with Small Samples

    ERIC Educational Resources Information Center

    Albano, Anthony D.

    2015-01-01

    Research on equating with small samples has shown that methods with stronger assumptions and fewer statistical estimates can lead to decreased error in the estimated equating function. This article introduces a new approach to linear observed-score equating, one which provides flexible control over how form difficulty is assumed versus estimated…

  3. FMM-Yukawa: An adaptive fast multipole method for screened Coulomb interactions

    NASA Astrophysics Data System (ADS)

    Huang, Jingfang; Jia, Jun; Zhang, Bo

    2009-11-01

    A Fortran program package is introduced for the rapid evaluation of the screened Coulomb interactions of N particles in three dimensions. The method utilizes an adaptive oct-tree structure, and is based on the new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related packages are also available at http://www.fastmultipole.org/. This paper is a brief review of the program and its performance. Catalogue identifier: AEEQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 12 385 No. of bytes in distributed program, including test data, etc.: 79 222 Distribution format: tar.gz Programming language: Fortran77 and Fortran90 Computer: Any Operating system: Any RAM: Depends on the number of particles, their distribution, and the adaptive tree structure Classification: 4.8, 4.12 Nature of problem: To evaluate the screened Coulomb potential and force field of N charged particles, and to evaluate a convolution type integral where the Green's function is the fundamental solution of the modified Helmholtz equation. Solution method: An adaptive oct-tree is generated, and a new version of fast multipole method is applied in which the "multipole-to-local" translation operator is diagonalized. Restrictions: Only three and six significant digits accuracy options are provided in this version. Unusual features: Most of the codes are written in

  4. Utilization of breast cancer screening methods in a developing nation: results from a nationally representative sample of Malaysian households.

    PubMed

    Dunn, Richard A; Tan, Andrew K G

    2011-01-01

    As is the case in many developing nations, previous studies of breast cancer screening behavior in Malaysia have used relatively small samples that are not nationally representative, thereby limiting the generalizability of results. Therefore, this study uses nationally representative data from the Malaysia Non-Communicable Disease Surveillance-1 to investigate the role of socio-economic status on breast cancer screening behavior in Malaysia, particularly differences in screening behaviour between ethnic groups. The decisions of 816 women above age 40 in Malaysia to screen for breast cancer using mammography, clinical breast exams (CBE), and breast self-exams (BSE) are modeled using logistic regression. Results indicate that after adjusting for differences in age, education, household income, marital status, and residential location, Malay women are less likely than Chinese and Indian women to utilize mammography, but more likely to perform BSE. Education level and urban residence are positively associated with utilization of each method, but these relationships vary across ethnicity. Higher education levels are strongly related to using each screening method among Chinese women, but have no statistically significant relationship to screening among Malays. PMID:21615819

  5. Utilization of breast cancer screening methods in a developing nation: results from a nationally representative sample of Malaysian households.

    PubMed

    Dunn, Richard A; Tan, Andrew K G

    2011-01-01

    As is the case in many developing nations, previous studies of breast cancer screening behavior in Malaysia have used relatively small samples that are not nationally representative, thereby limiting the generalizability of results. Therefore, this study uses nationally representative data from the Malaysia Non-Communicable Disease Surveillance-1 to investigate the role of socio-economic status on breast cancer screening behavior in Malaysia, particularly differences in screening behaviour between ethnic groups. The decisions of 816 women above age 40 in Malaysia to screen for breast cancer using mammography, clinical breast exams (CBE), and breast self-exams (BSE) are modeled using logistic regression. Results indicate that after adjusting for differences in age, education, household income, marital status, and residential location, Malay women are less likely than Chinese and Indian women to utilize mammography, but more likely to perform BSE. Education level and urban residence are positively associated with utilization of each method, but these relationships vary across ethnicity. Higher education levels are strongly related to using each screening method among Chinese women, but have no statistically significant relationship to screening among Malays.

  6. Density-functional expansion methods: Generalization of the auxiliary basis

    PubMed Central

    Giese, Timothy J.; York, Darrin M.

    2011-01-01

    The formulation of density-functional expansion methods is extended to treat the second and higher-order terms involving the response density and spin densities with an arbitrary single-center auxiliary basis. The two-center atomic orbital products are represented by the auxiliary functions centered about those two atoms, and the mapping coefficients are determined from a local constrained variational procedure. This two-center variational procedure allows the mapping coefficients to be pretabulated and splined as a function of internuclear separation for efficient look up. The splines of mapping coefficients have a range no longer than that of the overlap integrals, and the auxiliary density appears as a single point-multipole expansion to all nonoverlapping atoms, thus allowing for the trivial implementation of a linear-scaling algorithm. The method is tested using Gaussian multipole expansions, and the effect of angular and radial completeness is explored. Several auxiliary basis sets are parametrized and compared to an auxiliary basis analogous to that used in the self-consistent-charge density-functional tight-binding model, and the method is demonstrated to greatly improve the representation of the density response with respect to a reference expansion model that does not use an auxiliary basis. PMID:21599040

  7. A general method to determine the stability of compressible flows

    NASA Technical Reports Server (NTRS)

    Guenther, R. A.; Chang, I. D.

    1982-01-01

    Several problems were studied using two completely different approaches. The initial method was to use the standard linearized perturbation theory by finding the value of the individual small disturbance quantities based on the equations of motion. These were serially eliminated from the equations of motion to derive a single equation that governs the stability of fluid dynamic system. These equations could not be reduced unless the steady state variable depends only on one coordinate. The stability equation based on one dependent variable was found and was examined to determine the stability of a compressible swirling jet. The second method applied a Lagrangian approach to the problem. Since the equations developed were based on different assumptions, the condition of stability was compared only for the Rayleigh problem of a swirling flow, both examples reduce to the Rayleigh criterion. This technique allows including the viscous shear terms which is not possible in the first method. The same problem was then examined to see what effect shear has on stability.

  8. Methods for transforming and expression screening of filamentous fungal cells with a DNA library

    SciTech Connect

    Teter, Sarah; Lamsa, Michael; Cherry, Joel; Ward, Connie

    2015-06-02

    The present invention relates to methods for expression screening of filamentous fungal transformants, comprising: (a) isolating single colony transformants of a DNA library introduced into E. coli; (b) preparing DNA from each of the single colony E. coli transformants; (c) introducing a sample of each of the DNA preparations of step (b) into separate suspensions of protoplasts of a filamentous fungus to obtain transformants thereof, wherein each transformant contains one or more copies of an individual polynucleotide from the DNA library; (d) growing the individual filamentous fungal transformants of step (c) on selective growth medium, thereby permitting growth of the filamentous fungal transformants, while suppressing growth of untransformed filamentous fungi; and (e) measuring activity or a property of each polypeptide encoded by the individual polynucleotides. The present invention also relates to isolated polynucleotides encoding polypeptides of interest obtained by such methods, to nucleic acid constructs, expression vectors, and recombinant host cells comprising the isolated polynucleotides, and to methods of producing the polypeptides encoded by the isolated polynucleotides.

  9. DART-MS as a preliminary screening method for "herbal incense": chemical analysis of synthetic cannabinoids.

    PubMed

    Lesiak, Ashton D; Musah, Rabi A; Domin, Marek A; Shepard, Jason R E

    2014-03-01

    Direct analysis in real time mass spectrometry (DART-MS) served as a method for rapid high-throughput screening of six commercially available "Spice" products, detecting various combinations of five synthetic cannabinoids. Direct analysis in real time is an ambient ionization process that, along with high mass accuracy time-of-flight (TOF)-MS to 0.0001 Da, was employed to establish the presence of cannabinoids. Mass spectra were acquired by simply suspending a small portion of sample between the ion source and the mass spectrometer inlet. The ability to test minute amounts of sample is a major advantage when very limited amounts of evidentiary material are available. In addition, reports are widespread regarding the testing backlogs that now exist because of the large influx of designer drugs. This method circumvents time-consuming sample extraction, derivatization, chromatographic, and other sample preparative steps required for analysis by more conventional mass spectrometric methods. Accordingly, the synthetic cannabinoids AM-2201, JWH-122, JWH-203, JWH-210, and RCS-4 were identified in commercially available herbal Spice products, singly and in tandem, at concentrations within the range of 4-141 mg/g of material. Direct analysis in real time mass spectrometry decreases the time necessary to triage analytical evidence, and therefore, it has the potential to contribute to backlog reduction and more timely criminal prosecution.

  10. Red cell antibody screening and identification: a comparison of two column technology methods.

    PubMed

    Bromilow, I M; Eggington, J A; Owen, G A; Duguid, J K

    1993-12-01

    Two commercial column techniques for use in antibody screening and identification procedures were tested in parallel with 1000 random samples sent for ante-natal serological investigation. The DiaMed ID microtyping system uses a sephadex gel contained in microtubes, either neutral or impregnated with anti-human globulin (AHG), for use in two-stage enzyme methods and LISS indirect antiglobulin testing (IAT) respectively. The Ortho Biovue technique consists of a slurry of micro glass spheres which act as the filter to retain haemagglutination reactions within the matrix. Columns containing AHG also possess a macromolecular density barrier to prevent test serum from passing into the column and neutralising the AHG. Both systems offer the advantage of 'no-wash' IAT, which minimises the potential for problems and errors associated with conventional spin-tube techniques. In this comparison of the two column methods, antibody detection rates were found to be similar and the sensitivity of both methods was comparable, although the Biovue technique was prone to exhibit equivocal results, particularly in the IAT.

  11. A fluorescence high throughput screening method for the detection of reactive electrophiles as potential skin sensitizers.

    PubMed

    Avonto, Cristina; Chittiboyina, Amar G; Rua, Diego; Khan, Ikhlas A

    2015-12-01

    Skin sensitization is an important toxicological end-point in the risk assessment of chemical allergens. Because of the complexity of the biological mechanisms associated with skin sensitization, integrated approaches combining different chemical, biological and in silico methods are recommended to replace conventional animal tests. Chemical methods are intended to characterize the potential of a sensitizer to induce earlier molecular initiating events. The presence of an electrophilic mechanistic domain is considered one of the essential chemical features to covalently bind to the biological target and induce further haptenation processes. Current in chemico assays rely on the quantification of unreacted model nucleophiles after incubation with the candidate sensitizer. In the current study, a new fluorescence-based method, 'HTS-DCYA assay', is proposed. The assay aims at the identification of reactive electrophiles based on their chemical reactivity toward a model fluorescent thiol. The reaction workflow enabled the development of a High Throughput Screening (HTS) method to directly quantify the reaction adducts. The reaction conditions have been optimized to minimize solubility issues, oxidative side reactions and increase the throughput of the assay while minimizing the reaction time, which are common issues with existing methods. Thirty-six chemicals previously classified with LLNA, DPRA or KeratinoSens™ were tested as a proof of concept. Preliminary results gave an estimated 82% accuracy, 78% sensitivity, 90% specificity, comparable to other in chemico methods such as Cys-DPRA. In addition to validated chemicals, six natural products were analyzed and a prediction of their sensitization potential is presented for the first time.

  12. A fluorescence high throughput screening method for the detection of reactive electrophiles as potential skin sensitizers.

    PubMed

    Avonto, Cristina; Chittiboyina, Amar G; Rua, Diego; Khan, Ikhlas A

    2015-12-01

    Skin sensitization is an important toxicological end-point in the risk assessment of chemical allergens. Because of the complexity of the biological mechanisms associated with skin sensitization, integrated approaches combining different chemical, biological and in silico methods are recommended to replace conventional animal tests. Chemical methods are intended to characterize the potential of a sensitizer to induce earlier molecular initiating events. The presence of an electrophilic mechanistic domain is considered one of the essential chemical features to covalently bind to the biological target and induce further haptenation processes. Current in chemico assays rely on the quantification of unreacted model nucleophiles after incubation with the candidate sensitizer. In the current study, a new fluorescence-based method, 'HTS-DCYA assay', is proposed. The assay aims at the identification of reactive electrophiles based on their chemical reactivity toward a model fluorescent thiol. The reaction workflow enabled the development of a High Throughput Screening (HTS) method to directly quantify the reaction adducts. The reaction conditions have been optimized to minimize solubility issues, oxidative side reactions and increase the throughput of the assay while minimizing the reaction time, which are common issues with existing methods. Thirty-six chemicals previously classified with LLNA, DPRA or KeratinoSens™ were tested as a proof of concept. Preliminary results gave an estimated 82% accuracy, 78% sensitivity, 90% specificity, comparable to other in chemico methods such as Cys-DPRA. In addition to validated chemicals, six natural products were analyzed and a prediction of their sensitization potential is presented for the first time. PMID:26455772

  13. From CBCL to DSM: A Comparison of Two Methods to Screen for DSM-IV Diagnoses Using CBCL Data

    ERIC Educational Resources Information Center

    Krol, Nicole P. C. M.; De Bruyn, Eric E. J.; Coolen, Jolanda C.; van Aarle, Edward J. M.

    2006-01-01

    The screening efficiency of 2 methods to convert Child Behavior Checklist (CBCL) assessment data into Diagnostic and Statistical Manual of Mental Disorders (4th ed. [DSM-IV]; American Psychiatric Association, 1994) diagnoses was compared. The Machine-Aided Diagnosis (MAD) method converts CBCL input data directly into DSM-IV symptom criteria. The…

  14. Public awareness of colon cancer screening among the general population: A study from the Western Region of Saudi Arabia

    PubMed Central

    Khayyat, Yasir Mohammed; Ibrahim, Ezzeldin Mostafa

    2014-01-01

    Background: Screening for colon cancer aims at early detection and prompt treatment of the disease. Prior knowledge of the disease will contribute to increased participation. However, barriers to performing screening are not known. Methods: A survey using a questionnaire was presented to patients attending the Outpatient Department of a tertiary hospital in the Western Region of Saudi Arabia, to evaluate the background knowledge of colon cancer screening, the diagnostic methods used for that purpose, and the barriers that may resist the implementation of screening. Results: Six hundred and nineteen questionnaires were distributed. Completed questionnaires that were included in the final analysis numbered 321 (51.9%). Age and gender had no statistically significant association with increased awareness of screening options (p = 0.526 and p = 0.2). However, education played a significant role (p = 0.045). Among the group that agreed to undergo screening, there were 55.3% who were willing to undergo colonoscopy or sigmoidoscopy. Contrary to that, among the group that did not agree to undergo screening, 77.4% of them would undergo radiological screening using barium enema and/or a computed tomography (CT) scan of the abdomen. Conclusion: There is a deficiency of knowledge of colorectal cancer (CRC) screening influenced by an individual's level of education, yet unrelated to age or gender. The endoscopic modality was usually chosen by individuals who were aware of CRC screening. However, the fear of undergoing this investigation, for the same reason, would likely make them decide to choose less invasive testing, using barium enema or a CT of the abdomen. الوعي العام بفحوصات الكشف عن سرطان القولون بين عامة السكان دراسة من المنطقة الغربية في المملكة السعودية العربية الملخص الأهداف: يهدف الكشف المبكر عن سرطان القولون إلى

  15. Costs and methods of preventive visual screening and the relation between esotropia and increasing hypermetropia.

    PubMed

    Simonsz, H J; Grosklauser, B; Leuppi, S

    1992-01-01

    Atkinson has shown that early correction of hypermetropia reduces the incidence of esotropia. If esotropia is reduced by prescribing glasses early, the rate of esotropia-induced amblyopia can be similarly reduced; this would have important economic consequences. We have studied (1) how costs compare to benefits in early visual screening, (2) how videorefraction as used by Atkinson compares to retinoscopy, and (3) whether esotropia is more likely to occur in children who have increasing as opposed to decreasing hypermetropia. The costs of the study so far have been high. It was exceedingly difficult to get all infants invited, come to the clinic and examined. Videorefraction did not compare favourably with retinoscopy in terms of costs and precision, whereas the amount of skill and time needed was approximately equal. The third question, whether esotropia is more likely to occur in children who have increasing as opposed to decreasing hypermetropia, arose from the controversy whether, in the general population, refraction increases or decreases during the first years of life. We found that papers reporting a decrease of hypermetropia in early childhood were studies of large cross-sections of the general population, whereas papers that reported an initial increase originated from ophthalmological practices or strabismus departments. These conflicting results could be reconciled by assuming a population bias: if esotropia is more likely to occur in children with increasing hypermetropia, children with increasing hypermetropia will preferentially be seen by ophthalmologists. It seems natural that children with increasing hypermetropia are more likely to squint, because additional accommodation, needed to overcome increasing hypermetropia, will inevitably confer additional convergence. This relationship has meanwhile been confirmed by others. PMID:1305031

  16. LC-MS/MS screening method for designer amphetamines, tryptamines, and piperazines in serum.

    PubMed

    Wohlfarth, Ariane; Weinmann, Wolfgang; Dresen, Sebastian

    2010-04-01

    Since the late 1990s and early 2000s, derivatives of well-known designer drugs as well as new psychoactive compounds have been sold on the illicit drug market and have led to intoxications and fatalities. The LC-MS/MS screening method presented covers 31 new designer drugs as well as cathinone, methcathinone, phencyclidine, and ketamine which were included to complete the screening spectrum. All but the last two are modified molecular structures of amphetamine, tryptamine, or piperazine. Among the amphetamine derivatives are cathinone, methcathinone, 3,4-DMA, 2,5-DMA, DOB, DOET, DOM, ethylamphetamine, MDDMA, 4-MTA, PMA, PMMA, 3,4,5-TMA, TMA-6 and members of the 2C group: 2C-B, 2C-D, 2C-H, 2C-I, 2C-P, 2C-T-2, 2C-T-4, and 2C-T-7. AMT, DPT, DiPT, MiPT, DMT, and 5MeO-DMT are contained in the tryptamine group, BZP, MDBP, TFMPP, mCPP, and MeOPP in the piperazine group. Using an Applied Biosystems LC-MS/MS API 365 TurboIonSpray it is possible to identify all 35 substances. After addition of internal standards and mixed-mode solid-phase extraction the analytes are separated using a Synergi Polar RP column and gradient elution with 1 mM ammonium formate and methanol/0.1% formic acid as mobile phases A and B. Data acquisition is performed in MRM mode with positive electro spray ionization. The assay is selective for all tested substances. Limits of detection were determined by analyzing S/N-ratios and are between 1.0 and 5.0 ng/mL. Matrix effects lie between 65% and 118%, extraction efficiencies range from 72% to 90%.

  17. Choosing the optimal method in programmatic colorectal cancer screening: current evidence and controversies.

    PubMed

    Castells, Antoni

    2015-07-01

    Colorectal cancer (CRC) is an important health problem all over the world, being the third most common cancer and the second leading cause of cancer-related death in Western countries. The most important strategy for CRC prevention is screening (i.e. secondary prevention). Since it is widely accepted that adenomas and serrated polyps are the precursors of the vast majority of CRC, early detection and removal of these lesions is associated with a reduction of CRC incidence and, consequently, mortality. Moreover, cancers detected by screening are usually diagnosed at early stages and, therefore, curable by endoscopic or surgical procedures. This review will be address CRC screening strategies in average-risk population, which is defined by those individuals, men and women, 50 years of age or older, without any additional personal or familial predisposing risk factor. In order to maximize the impact of screening and ensure high coverage and equity of access, only organized screening programs (i.e. programmatic screening) should be implemented, as opposed to case-finding or opportunistic screening. For that reason and considering that the optimal approach for colorectal screening may differ depending on the scenario, this review will be focused on the advantages and limitations of each screening strategy in an organized setting.

  18. Choosing the optimal method in programmatic colorectal cancer screening: current evidence and controversies

    PubMed Central

    2015-01-01

    Colorectal cancer (CRC) is an important health problem all over the world, being the third most common cancer and the second leading cause of cancer-related death in Western countries. The most important strategy for CRC prevention is screening (i.e. secondary prevention). Since it is widely accepted that adenomas and serrated polyps are the precursors of the vast majority of CRC, early detection and removal of these lesions is associated with a reduction of CRC incidence and, consequently, mortality. Moreover, cancers detected by screening are usually diagnosed at early stages and, therefore, curable by endoscopic or surgical procedures. This review will be address CRC screening strategies in average-risk population, which is defined by those individuals, men and women, 50 years of age or older, without any additional personal or familial predisposing risk factor. In order to maximize the impact of screening and ensure high coverage and equity of access, only organized screening programs (i.e. programmatic screening) should be implemented, as opposed to case-finding or opportunistic screening. For that reason and considering that the optimal approach for colorectal screening may differ depending on the scenario, this review will be focused on the advantages and limitations of each screening strategy in an organized setting. PMID:26136839

  19. [Hydrogen (H2) exhalation tests--methods for general practice].

    PubMed

    Bornschein, W

    1988-04-01

    According to the literature as well as to own experience hydrogen breath tests seem to be suitable for a gastroenterologist's practice because of their practicability (this means non invasive and cheap methods) and their diagnostic relevance (sensitivity, specificity). Although hydrogen breath test with lactose is now the best way for diagnosis of lactose intolerance, hydrogen breath test with glucose as a mean of investigation of small bowel bacterial overgrowth still is subject to discussion. Lactulose hydrogen breath test in order to estimate small bowel transit time is of minor importance in gastroenterologist's practice. Yet at special questions it still may be of relevance (e.g. suspicion of functional diarrhea).

  20. Accelerated screening methods for determining chemical and thermal stability of refreigerant-lubricant mixtures. Part II: Experimental comparison and verification of methods. Final report, volume I

    SciTech Connect

    Kauffman, R.

    1995-09-01

    The research reported herein was performed to develop an accelerated screening method for determining the chemical and thermal stabilities of refrigerant/lubricant mixtures. The developed screening method was designed to be safe and to produce accelerated stability rankings that are in agreement with the rankings determined by the current test, Sealed Glass Tube Method to Test the Chemical Stability of Material for Use Within Refrigerant Systems, ANSI/ASHRAE Method 97-1989. The accelerated screening test developed was designed to be independent of refrigerant and lubricant compositions and to be used with a wide variety of construction materials. The studied refrigerants included CFC-11, CFC-12, HCFC-22, HFC-134a, and HFC-32/HFC-134a (zeotrope 30:70 by weight). The studied lubricants were selected from the chemical classes of mineral oil, alkylbenzene oil, polyglycols, and polyolesters. The work reported herein was performed in three phases. In the first phase, previously identified thermal analytical techniques were evaluated for development into an accelerated screening method for refrigerant/lubricant mixtures. The identified thermal analytical techniques used in situ measurements of color, temperature, or conductivity to monitor the degradation of the heated refrigerant/lubricant mixtures. The identified thermal analytical techniques also used catalysts such as ferric fluoride to accelerate the degradation of the heated refrigerant/lubricant mixtures. The thermal analytical technique employing in situ conductivity measurements was determined to be the most suitable for development into an accelerated screening method.

  1. A Generalized, Likelihood-Free Method for Posterior Estimation

    PubMed Central

    Turner, Brandon M.; Sederberg, Per B.

    2014-01-01

    Recent advancements in Bayesian modeling have allowed for likelihood-free posterior estimation. Such estimation techniques are crucial to the understanding of simulation-based models, whose likelihood functions may be difficult or even impossible to derive. However, current approaches are limited by their dependence on sufficient statistics and/or tolerance thresholds. In this article, we provide a new approach that requires no summary statistics, error terms, or thresholds, and is generalizable to all models in psychology that can be simulated. We use our algorithm to fit a variety of cognitive models with known likelihood functions to ensure the accuracy of our approach. We then apply our method to two real-world examples to illustrate the types of complex problems our method solves. In the first example, we fit an error-correcting criterion model of signal detection, whose criterion dynamically adjusts after every trial. We then fit two models of choice response time to experimental data: the Linear Ballistic Accumulator model, which has a known likelihood, and the Leaky Competing Accumulator model whose likelihood is intractable. The estimated posterior distributions of the two models allow for direct parameter interpretation and model comparison by means of conventional Bayesian statistics – a feat that was not previously possible. PMID:24258272

  2. Generalized spectral method for near-field optical microscopy

    NASA Astrophysics Data System (ADS)

    Jiang, B.-Y.; Zhang, L. M.; Castro Neto, A. H.; Basov, D. N.; Fogler, M. M.

    2016-02-01

    Electromagnetic interaction between a sub-wavelength particle (the "probe") and a material surface (the "sample") is studied theoretically. The interaction is shown to be governed by a series of resonances corresponding to surface polariton modes localized near the probe. The resonance parameters depend on the dielectric function and geometry of the probe as well as on the surface reflectivity of the material. Calculation of such resonances is carried out for several types of axisymmetric probes: spherical, spheroidal, and pear-shaped. For spheroids, an efficient numerical method is developed, capable of handling cases of large or strongly momentum-dependent surface reflectivity. Application of the method to highly resonant materials, such as aluminum oxide (by itself or covered with graphene), reveals a rich structure of multi-peak spectra and nonmonotonic approach curves, i.e., the probe-sample distance dependence. These features also strongly depend on the probe shape and optical constants of the model. For less resonant materials such as silicon oxide, the dependence is weak, so that the spheroidal model is reliable. The calculations are done within the quasistatic approximation with radiative damping included perturbatively.

  3. Collaborative study of a microbiological screening method (three-plate) for the banned antimicrobial growth promotors tylosin, virginiamycin, spiramycin, zinc bacitracin and avoparcin in animal feed.

    PubMed

    Pol-Hofstad, I; Driessen-Van Lankveld, W; Tomassen, M; De Jong, J; Van Egmond, H

    2008-12-01

    A microbiological screening method (three-plate) for the detection of the antimicrobial growth promoters tylosin, spiramycin, virginiamycin, zinc bacitracin, and avoparcin in animal feed has been developed and validated successfully. A collaborative study involving 18 laboratories receiving 172 samples was carried out to verify the performance characteristics. The detection level for tylosin/virginiamycin/spiramycin, expressed in microbiological activity, was 1 mg kg(-1) (false-positives, 2%; false-negatives, 3, 0, and 6%, respectively). Avoparcin could be detected at 1 mg kg(-1) in feed in general (false-positives, 2%; false-negatives, 0%). However, in calf feed the sensitivity was lower. The percentages of false-negatives were found to be 12%, 7%, and 0% at 1, 3, and 5 mg kg(-1), respectively (false-positives, 4%). The limit of detection for zinc bacitracin was 3-5 mg kg(-1) (false-positives, 5-10%; false-negatives, 77% at 1 mg kg(-1), 45% at 2 mg kg(-1), 12% at 3 mg kg(-1), and 4% at 5 mg kg(-1)). The method allowed for a distinction to be made between the groups of antibiotics: avoparcin/zinc bacitracin versus tylosin/virginiamycin/spiramycin. This definitely gives added value to the method in the framework of a follow-up of positive screening results by post-screening and confirmatory analysis. PMID:19680856

  4. Initial periodontal screening and radiographic findings - A comparison of two methods to evaluate the periodontal situation

    PubMed Central

    2011-01-01

    Background The periodontal screening index (PSI) is an element of the initial dental examination. The PSI provides information on the periodontal situation and allows a first estimation of the treatment required. The dental panoramic tomography (DPT) indicates the proximal bone loss, thus also allowing conclusions on the periodontal situation. In this study, the results of both methods in determining the periodontal situation are compared. Methods The clinical examination covered DMF-T, QHI, and PSI scores at four proximal sites per tooth; the examining dentist was unaware of the radiographic finding. Based on the PSI scores, the findings were diagnosed as follows: score 0 - 2 "no periodontitis", score 3 and 4 "periodontitis". Independent of the locality and time of the clinical evaluation, two dentists examined the DPTs of the subjects. The results were classified as follows: no bone loss = "no periodontitis", and bone loss = "periodontitis". Results 112 male subjects (age 18 to 58, Ø 37.7 ± 8 years) were examined. Regarding the PSI, 17 subjects were diagnosed "no periodontitis" and 95 subjects "periodontitis". According to the evaluation of the DPTs, 70 subjects were diagnosed "no periodontitis" and 42 "periodontitis". A comparison of both methods revealed that the diagnosis "no periodontitis" corresponded in 17 cases and "periodontitis" in 42 cases (53%). In 47% (53 cases) the results were not congruent. The difference between both methods was statistically significant (p < 0.001; kappa = 0.194). Conclusion The present study shows that the initial assessment of the periodontal situation significantly depends on the method of evaluation. PMID:21235747

  5. A general method for modeling biochemical and biomedical response

    NASA Astrophysics Data System (ADS)

    Ortiz, Roberto; Lerd Ng, Jia; Hughes, Tyler; Abou Ghantous, Michel; Bouhali, Othmane; Arredouani, Abdelilah; Allen, Roland

    2012-10-01

    The impressive achievements of biomedical science have come mostly from experimental research with human subjects, animal models, and sophisticated laboratory techniques. Additionally, theoretical chemistry has been a major aid in designing new drugs. Here we introduce a method which is similar to others already well known in theoretical systems biology, but which specifically addresses biochemical changes as the human body responds to medical interventions. It is common in systems biology to use first-order differential equations to model the time evolution of various chemical concentrations, and we as physicists can make a significant impact through designing realistic models and then solving the resulting equations. Biomedical research is rapidly advancing, and the technique presented in this talk can be applied in arbitrarily large models containing tens, hundreds, or even thousands of interacting species, to determine what beneficial effects and side effects may result from pharmaceuticals or other medical interventions.

  6. A general method for exploiting QSAR models in lead optimization.

    PubMed

    Lewis, Richard A

    2005-03-10

    Computer-aided drug design tools can generate many useful and powerful models that explain structure-activity relationship (SAR) observations in a quantitative manner. These models can use many different descriptors, functional forms, and methods from simple linear equations through to multilayer neural nets. Using a model, a medicinal chemist can compute an activity, given a structure, but it is much harder to work out what changes are needed to make a structure more active. The impact of a model on the design process would be greatly enhanced if the model were more interpretable to the bench chemist. This paper describes a new protocol for performing automated iterative quantitative structure-activity relationship (QSAR) studies and presents the results of experiments on two QSAR sets from the literature. The fundamental goal of this work is to try to assist the chemist in his search for what to make next.

  7. A general method for sifting linguistic knowledge from structured terminologies.

    PubMed

    Grabar, N; Zweigenbaum, P

    2000-01-01

    Morphological knowledge is useful for medical language processing, information retrieval and terminology or ontology development. We show how a large volume of morphological associations between words can be learnt from existing medical terminologies by taking advantage of the semantic relations already encoded between terms in these terminologies: synonymy, hierarchy and transversal relations. The method proposed relies on no a priori linguistic knowledge. Since it can work with different relations between terms, it can be applied to any structured terminology. Tested on SNOMED and ICD in French and English, it proves to identify fairly reliable morphological relations (precision > 90%) with a good coverage (over 88% compared to the UMLS lexical variant generation program). For English words with a stem longer than 3 characters, recall reaches 98.8% for inflection and 94.7% for derivation.

  8. Strategies to Overcome Barriers to Implementation of Alcohol Screening and Brief Intervention in General Practice: a Delphi Study Among Healthcare Professionals and Addiction Prevention Experts.

    PubMed

    Abidi, L; Oenema, A; Nilsen, P; Anderson, P; van de Mheen, D

    2016-08-01

    Despite the evidence base, alcohol screening and brief intervention (ASBI) have rarely been integrated into routine clinical practice. The aim of this study is to identify strategies that could tackle barriers to ASBI implementation in general practice by involving primary healthcare professionals and addiction prevention experts. A three-round online Delphi study was carried out in the Netherlands. The first-round questionnaire consisted of open-ended questions to generate ideas about strategies to overcome barriers. In the second round, participants were asked to indicate how applicable they found each strategy. Items without consensus were systematically fed back with group median ratings and interquartile range (IQR) scores in the third-round questionnaire. In total, 39 out of 69 (57 %) invited participants enrolled in the first round, 214 participants completed the second round, and 144 of these (67 %) completed the third-round questionnaire. Results show that participants reached consensus on 59 of 81 strategies, such as the following: (1) use of E-learning technology, (2) symptom-specific screening by general practitioners (GPs) and/or universal screening by practice nurses, (3) reimbursement incentives, (4) supportive materials, (5) clear guidelines, (6) service provision of addiction care centers, and (7) more publicity in the media. This exploratory study identified a broad set of strategies that could potentially be used for overcoming barriers to ASBI implementation in general practice and paves the way for future research to experimentally test the identified implementation strategies using multifaceted approaches. PMID:27167074

  9. A fast screening MALDI method for the detection of cocaine and its metabolites in hair.

    PubMed

    Vogliardi, Susanna; Favretto, Donata; Frison, Giampietro; Ferrara, Santo Davide; Seraglia, Roberta; Traldi, Pietro

    2009-01-01

    Matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry was used for the rapid detection of cocaine, benzoylecgonine and cocaethylene in hair. Different MALDI sample preparation procedures have been tested and the employment of a multi-layer 'graphite-sample-electrosprayed alpha-cyano-4-hydroxycinnamic acid (HCCA)' yielded the best results for standard solutions of the target analytes. The same approach was subsequently applied to hair samples that were known to contain cocaine, benzoylecgonine and cocaethylene, as determined by a classical GC-MS method. It was however necessary to extract hair samples by incubating them in methanol/trifluoroacetic acid for a short time (15 min) at 45 degrees C; 1 microl of the obtained supernatant was deposed on a metal surface treated with graphite, and HCCA was electrosprayed on it. This procedure successfully suppressed matrix peaks and was effective in detecting all the target analytes as their protonated species. The results obtained give further confirmation of the effectiveness of the MALDI for detecting drugs and their metabolites in complex biological matrices. The method can be useful as a fast screening procedure to detect the presence of cocaine and metabolites in hair samples. PMID:18698561

  10. A rapid sample screening method for authenticity control of whiskey using capillary electrophoresis with online preconcentration.

    PubMed

    Heller, Melina; Vitali, Luciano; Oliveira, Marcone Augusto Leal; Costa, Ana Carolina O; Micke, Gustavo Amadeu

    2011-07-13

    The present study aimed to develop a methodology using capillary electrophoresis for the determination of sinapaldehyde, syringaldehyde, coniferaldehyde, and vanillin in whiskey samples. The main objective was to obtain a screening method to differentiate authentic samples from seized samples suspected of being false using the phenolic aldehydes as chemical markers. The optimized background electrolyte was composed of 20 mmol L(-1) sodium tetraborate with 10% MeOH at pH 9.3. The study examined two kinds of sample stacking, using a long-end injection mode: normal sample stacking (NSM) and sample stacking with matrix removal (SWMR). In SWMR, the optimized injection time of the samples was 42 s (SWMR42); at this time, no matrix effects were observed. Values of r were >0.99 for the both methods. The LOD and LOQ were better than 100 and 330 mg mL(-1) for NSM and better than 22 and 73 mg L(-1) for SWMR. The CE-UV reliability in the aldehyde analysis in the real sample was compared statistically with LC-MS/MS methodology, and no significant differences were found, with a 95% confidence interval between the methodologies.

  11. Grading the Functional Movement Screen: A Comparison of Manual (Real-Time) and Objective Methods.

    PubMed

    Whiteside, David; Deneweth, Jessica M; Pohorence, Melissa A; Sandoval, Bo; Russell, Jason R; McLean, Scott G; Zernicke, Ronald F; Goulet, Grant C

    2016-04-01

    Although intertester and intratester reliability have been common themes in Functional Movement Screen (FMS) research, the criterion validity of manual grading is yet to be comprehensively examined. This study compared the FMS scores assigned by a certified FMS tester to those measured by an objective inertial-based (IMU) motion capture system. Eleven female division I collegiate athletes performed 6 FMS exercises and were manually graded by a certified tester. Explicit kinematic thresholds were formulated to correspond to each of the grading criteria for each FMS exercise and then used to grade athletes objectively using the IMU data. The levels of agreement between the 2 grading methods were poor in all 6 FMS exercises and implies that manual grading of the FMS may be confounded by vague grading criteria. Evidently, more explicit grading guidelines are needed to improve the uniformity and accuracy of manual FMS grading and also facilitate the use of objective measurement systems in the grading process. Contrary to the approach that has been adopted in several previous studies, the potential for subjective and/or inaccurate FMS grading intimates that it may be inappropriate to assume that manual FMS grading provides a valid measurement tool. Consequently, the development and criterion validation of uniform grading procedures must precede research attempting to link FMS performance and injury rates. With manual grading methods seemingly susceptible to error, the FMS should be used cautiously to direct strength and/or conditioning programs. PMID:25162646

  12. A modified bioautographic method for antibacterial component screening against anaerobic and microaerophilic bacteria.

    PubMed

    Kovács, Judit K; Horváth, Györgyi; Kerényi, Monika; Kocsis, Béla; Emődy, Levente; Schneider, György

    2016-04-01

    Direct bioautography is a useful method to identify antimicrobial compounds with potential therapeutic importance. Because of technical limitations till now, it has been applied only for aerobic bacteria. In this work we present the modification of the original method by which antimicrobial screening of bacteria requiring modified atmosphere became feasible by direct bioautography. Here we demonstrate its applicability by testing three anaerobic Clostridium perfringens and three microaerophilic Campylobacter jejuni strains against two essential oils, clove and thyme. Antimicrobial component profiles of clove and thyme essential oils against these two medically important pathogenic bacteria were compared and significant differences were revealed in their inhibition capacities. Linalool, a component of thyme essential oil exerted a more expressed antibacterial activity against C. perfringens than against C. jejuni. Our results demonstrate that direct bioautography is not only suitable for testing aerobic bacteria, but by applying the presently described modified version it can also contribute to the quest to find novel antimicrobial agents against multidrug resistant anaerobic and microaerophilic bacteria. PMID:26853123

  13. Penile xenon (/sup 133/Xe) washout: a rapid method of screening for vasculogenic impotence

    SciTech Connect

    Nseyo, U.O.; Wilbur, H.J.; Kang, S.A.; Flesh, L.; Bennett, A.H.

    1984-01-01

    The radioactive inert gas xenon (/sup 133/Xe) is a well-established isotopic indicator used to assess vascular status in many organ systems. Xenon-133 was used to evaluate male impotence. Xenon-133 was injected subcutaneously at the level of the coronal sulcus in the detumescent state. Using the gamma camera, sequential images were obtained and computer-generated curves calculated. The clearance time for 50 per cent washout of the injected /sup 133/Xe (T1/2) was then calculated for each patient, as well as a control group. Preliminary findings indicate a correlation with such established techniques of evaluating erectile impotence as history, physical examination, penile pulse Doppler tracings, and brachial-penile blood pressure index. The xenon-133 washout study was a rapid, minimally invasive, reproducible, and cost-effective method of screening those impotent patients for vasculogenic etiology of their erectile impotence. We recommend the addition of this method to the surgeon engaged in the care of impotent males.

  14. Examining Standing Turnout with Two Measurement Methods During Dance Wellness Screening.

    PubMed

    Harmon-Matthews, Lindsay E; Davis-Coen, J Hope; Nierman, Mariah; Willigenburg, Nienke W; Hewett, Timothy E

    2016-01-01

    This study describes trends in mean standing functional turnout angles measured on a floor protractor (FP) and the Functional Footprint(®) rotational instrument (RI) during routine clinical screens. Twenty-three professional ballet dancers, 26 collegiate modern students, and 46 ballet academy dancers participated in the study. All dancers demonstrated greater total turnout on the FP compared to the RI (p < 0.001), and the collegiate dancers had significantly smaller total turnout angles compared to both of the other groups (p < 0.001). A significant interaction between measurement method and training group (p = 0.047) on lower extremity asymmetry indicated that only in professionals left turnout angle was greater than right turnout angle on the RI (4.30° ± 6.64°) but not on the FP (0.17° ± 4.57°). It is concluded that turnout can be measured using either the FP or the RI measurement method, with recognition that FP measurements will be an average of 10° greater than those on the RI. Lower extremity asymmetries in turnout angles may be better detected on the RI than the FP. PMID:27661623

  15. A volumetric method for estimation of breast density on digitized screen-film mammograms.

    PubMed

    Pawluczyk, Olga; Augustine, Bindu J; Yaffe, Martin J; Rico, Dan; Yang, Jiwei; Mawdsley, Gordon E; Boyd, Norman F

    2003-03-01

    A method is described for the quantitative volumetric analysis of the mammographic density (VBD) from digitized screen-film mammograms. The method is based on initial calibration of the imaging system with a tissue-equivalent plastic device and the subsequent correction for variations in exposure factors and film processing characteristics through images of an aluminum step wedge placed adjacent to the breast during imaging. From information about the compressed breast thickness and technique factors used for taking the mammogram as well as the information from the calibration device, VBD is calculated. First, optical sensitometry is used to convert images to Log relative exposure. Second, the images are corrected for x-ray field inhomogeneity using a spherical section PMMA phantom image. The effectiveness of using the aluminum step wedge in tracking down the variations in exposure factors and film processing was tested by taking test images of the calibration device, aluminum step wedge and known density phantoms at various exposure conditions and also at different times over one year. Results obtained on known density phantoms show that VBD can be estimated to within 5% accuracy from the actual value. A first order thickness correction is employed to correct for inaccuracy in the compression thickness indicator of the mammography units. Clinical studies are ongoing to evaluate whether VBD can be a better indicator for breast cancer risk. PMID:12674236

  16. A rapid sample screening method for authenticity control of whiskey using capillary electrophoresis with online preconcentration.

    PubMed

    Heller, Melina; Vitali, Luciano; Oliveira, Marcone Augusto Leal; Costa, Ana Carolina O; Micke, Gustavo Amadeu

    2011-07-13

    The present study aimed to develop a methodology using capillary electrophoresis for the determination of sinapaldehyde, syringaldehyde, coniferaldehyde, and vanillin in whiskey samples. The main objective was to obtain a screening method to differentiate authentic samples from seized samples suspected of being false using the phenolic aldehydes as chemical markers. The optimized background electrolyte was composed of 20 mmol L(-1) sodium tetraborate with 10% MeOH at pH 9.3. The study examined two kinds of sample stacking, using a long-end injection mode: normal sample stacking (NSM) and sample stacking with matrix removal (SWMR). In SWMR, the optimized injection time of the samples was 42 s (SWMR42); at this time, no matrix effects were observed. Values of r were >0.99 for the both methods. The LOD and LOQ were better than 100 and 330 mg mL(-1) for NSM and better than 22 and 73 mg L(-1) for SWMR. The CE-UV reliability in the aldehyde analysis in the real sample was compared statistically with LC-MS/MS methodology, and no significant differences were found, with a 95% confidence interval between the methodologies. PMID:21662238

  17. Novel method for screening microbes for application in microbial fuel cell.

    PubMed

    Szöllősi, Attila; Rezessy-Szabó, Judit M; Hoschke, Ágoston; Nguyen, Quang D

    2015-03-01

    The ability to produce and to transport exo-electrons by microbes either to external acceptors or to electrodes are reported in our study. All investigated microorganisms (exception of Lactobacillus plantarum) exhibited strong iron-reducing capabilities in the absence of mediator meaning production and secretion of exo-electrons to the growth medium. L.plantarum, Saccharomyces cerevisiae and Escherichia coli need an electron shuttle molecule to reduce Fe(3+) ion. Significant correlation was observed between growth and iron-reducing capacity, as well as between initial cell counts and iron-reducing capacity. Changes of bio-current generated in MFC and iron-reduction were experimentally monitored, and a mathematical model was established by regression analysis. Based on these results, a novel and rapid screening method was developed for the selection of microorganisms for potential application in MFC. The method is based on the measurement of absorbance of bacterial and yeast cultures at 460 nm, providing a robust and high sample throughput approach.

  18. Type 2 Diabetes Biomarkers of Human Gut Microbiota Selected via Iterative Sure Independent Screening Method

    PubMed Central

    Li, Dongfang; Zhou, Ke; Zou, Fuhao

    2015-01-01

    Type 2 diabetes, which is a complex metabolic disease influenced by genetic and environment, has become a worldwide problem. Previous published results focused on genetic components through genome-wide association studies that just interpret this disease to some extent. Recently, two research groups published metagenome-wide association studies (MGWAS) result that found meta-biomarkers related with type 2 diabetes. However, One key problem of analyzing genomic data is that how to deal with the ultra-high dimensionality of features. From a statistical viewpoint it is challenging to filter true factors in high dimensional data. Various methods and techniques have been proposed on this issue, which can only achieve limited prediction performance and poor interpretability. New statistical procedure with higher performance and clear interpretability is appealing in analyzing high dimensional data. To address this problem, we apply an excellent statistical variable selection procedure called iterative sure independence screening to gene profiles that obtained from metagenome sequencing, and 48/24 meta-markers were selected in Chinese/European cohorts as predictors with 0.97/0.99 accuracy in AUC (area under the curve), which showed a better performance than other model selection methods, respectively. These results demonstrate the power and utility of data mining technologies within the large-scale and ultra-high dimensional genomic-related dataset for diagnostic and predictive markers identifying. PMID:26479726

  19. Generalized method for constructing the atomic coordinates of nanotube caps

    NASA Astrophysics Data System (ADS)

    Robinson, M.; Suarez-Martinez, I.; Marks, N. A.

    2013-04-01

    A practical numerical method for the rapid construction of nanotube caps is proposed. Founded upon the notion of lattice duality, the algorithm considers the face dual representation of a given nanotube which is used to solve an energy minimization problem analogous to The Thomson Problem. Not only does this produce caps for nanotubes of arbitrary chirality, but the caps generated will be physically sensible and in most cases the lowest energy structure. To demonstrate the applicability of the technique, caps of the (5,5) and the (10,0) nanotubes are investigated by means of density-functional tight binding (DFTB). The calculation of cap energies highlights the ability of the algorithm to produce lowest energy caps. Due to the preferential construction of spherical caps, the technique is particularly well suited for the construction of capped multiwall nanotubes (MWNTs). To validate this proposal and the overall robustness of the algorithm, a MWNT is constructed containing the chiralities (9,2)@(15,6)@(16,16). The algorithm presented paves the way for future computational investigations into the physics and chemistry of capped nanotubes.

  20. Current and emerging screening methods to identify post-head-emergence frost adaptation in wheat and barley.

    PubMed

    Frederiks, T M; Christopher, J T; Harvey, G L; Sutherland, M W; Borrell, A K

    2012-09-01

    Cereal crops can suffer substantial damage if frosts occur at heading. Identification of post-head-emergence frost (PHEF) resistance in cereals poses a number of unique and difficult challenges. Many decades of research have failed to identify genotypes with PHEF resistance that could offer economically significant benefit to growers. Research and breeding gains have been limited by the available screening systems. Using traditional frost screening systems, genotypes that escape frost injury in trials due to spatial temperature differences and/or small differences in phenology can be misidentified as resistant. We believe that by improving techniques to minimize frost escapes, such 'false-positive' results can be confidently identified and eliminated. Artificial freezing chambers or manipulated natural frost treatments offer many potential advantages but are not yet at the stage where they can be reliably used for frost screening in breeding programmes. Here we describe the development of a novel photoperiod gradient method (PGM) that facilitates screening of genotypes of different phenology under natural field frosts at matched developmental stages. By identifying frost escapes and increasing the efficiency of field screening, the PGM ensures that research effort can be focused on finding genotypes with improved PHEF resistance. To maximize the likelihood of identifying PHEF resistance, we propose that the PGM form part of an integrated strategy to (i) source germplasm;(ii) facilitate high throughput screening; and (iii) permit detailed validation. PGM may also be useful in other studies where either a range of developmental stages and/or synchronized development are desired. PMID:22888127

  1. Current and emerging screening methods to identify post-head-emergence frost adaptation in wheat and barley.

    PubMed

    Frederiks, T M; Christopher, J T; Harvey, G L; Sutherland, M W; Borrell, A K

    2012-09-01

    Cereal crops can suffer substantial damage if frosts occur at heading. Identification of post-head-emergence frost (PHEF) resistance in cereals poses a number of unique and difficult challenges. Many decades of research have failed to identify genotypes with PHEF resistance that could offer economically significant benefit to growers. Research and breeding gains have been limited by the available screening systems. Using traditional frost screening systems, genotypes that escape frost injury in trials due to spatial temperature differences and/or small differences in phenology can be misidentified as resistant. We believe that by improving techniques to minimize frost escapes, such 'false-positive' results can be confidently identified and eliminated. Artificial freezing chambers or manipulated natural frost treatments offer many potential advantages but are not yet at the stage where they can be reliably used for frost screening in breeding programmes. Here we describe the development of a novel photoperiod gradient method (PGM) that facilitates screening of genotypes of different phenology under natural field frosts at matched developmental stages. By identifying frost escapes and increasing the efficiency of field screening, the PGM ensures that research effort can be focused on finding genotypes with improved PHEF resistance. To maximize the likelihood of identifying PHEF resistance, we propose that the PGM form part of an integrated strategy to (i) source germplasm;(ii) facilitate high throughput screening; and (iii) permit detailed validation. PGM may also be useful in other studies where either a range of developmental stages and/or synchronized development are desired.

  2. Evaluation of screening methods for demulsifying bacteria and characterization of lipopeptide bio-demulsifier produced by Alcaligenes sp.

    PubMed

    Huang, Xiang-Feng; Liu, Jia; Lu, Li-Jun; Wen, Yue; Xu, Jing-Cheng; Yang, Dian-Hai; Zhou, Qi

    2009-02-01

    In this paper, surface tension measurement, oil-spreading test and blood-plate hemolysis test were attempted in the screening of demulsifying bacteria. After the comparison to the screening results obtained in demulsification test, 50 mN/m of surface tension of culture was proposed as a preliminary screening standard for potential demulsifying bacteria. For the identification of efficient demulsifying strains, surface tension level was set at 40 mN/m. The detected strains were further verified in demulsification test. Compared to using demulsification test alone as screening method, the proposed screening protocol would be more efficient. From the screening, a highly efficient demulsifying stain, S-XJ-1, was isolated from petroleum-contaminated soil and identified as Alcaligenes sp. by 16S rRNA gene and physiological test. It achieved 96.5% and 49.8% of emulsion breaking ratio in W/O and O/W kerosene emulsion within 24h, respectively, and also showed 95% of water separation ratio in oilfield petroleum emulsion within 2h. The bio-demulsifier was found to be cell-wall combined. After soxhlet extraction and purification through silicon-gel column, the bio-demulsifier was then identified as lipopeptide biosurfactant by TLC and FT-IR. PMID:18799309

  3. Ovarian Cancer Screening Method Fails to Reduce Deaths from the Disease | Division of Cancer Prevention

    Cancer.gov

    New results from the NCI-sponsored Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial show that screening for ovarian cancer with transvaginal ultrasound (TVU) and the CA-125 blood test did not result in fewer deaths from the disease compared with usual care. |

  4. School-Based BMI and Body Composition Screening and Parent Notification in California: Methods and Messages

    ERIC Educational Resources Information Center

    Madsen, Kristine A.; Linchey, Jennifer

    2012-01-01

    Background: School-based body mass index (BMI) or body composition screening is increasing, but little is known about the process of parent notification. Since 2001, California has required annual screening of body composition via the FITNESSGRAM, with optional notification. This study sought to identify the prevalence of parental notification…

  5. Analysis of three strategies to increase screening coverage for cervical cancer in the general population of women aged 60 to 70 years: the CRICERVA study

    PubMed Central

    2014-01-01

    Background Cervical cancer is a frequently diagnosed cancer in women worldwide. Despite having easy preventive and therapeutic approaches, it is an important cause of mortality among women. Methods The CRICERVA study is a cluster clinical trial which assigned one of three interventions to the target population registered in Cerdanyola, Barcelona. Among the 5,707 resident women aged 60 to 70 years in the study area, women with no record of cervical cytology over the last three years were selected. The study included four arms: three interventions all including a pre-assigned date for screening visit and i) personalized invitation letter; ii) adding to i) an informative leaflet; and, iii) in addition to ii) a personalized appointment reminder phone call, and iv) no specific action taken (control group). Participants were offered a personal interview about social-demographic characteristics and about screening attitudes. Cervical cytology and HPV DNA test (HC2) were offered as screening tests. In the case of screening positive in any of these tests, the women were followed up until a full diagnosis could be obtained. The effect size of each study arm was estimated as the absolute gain in coverage between the original coverage and the final coverage. Results From the intervention groups (4,775 women), we identified 3,616 who were not appropriately screened, of which 2,560 women answered the trial call and 1,376 were amenable to screening. HPV was tested in 920 women and cervical cytology in all 1,376. Overall, there was an absolute gain in coverage of 28.8% in the intervention groups compared to 6% in the control group. Coverage increased from 51.2% to 76.0% in strategy i); from 47.4% to 79.0% in strategy ii) and from 44.5% to 74.6% in strategy iii). Lack of information about the relevance of screening was the most important factor for not attending the screening program. Conclusions The study confirms that actively contacting women and including a date for a screening

  6. Screening and confirmatory method for multiclass determination of 62 antibiotics in meat.

    PubMed

    Moretti, Simone; Dusi, Guglielmo; Giusepponi, Danilo; Pellicciotti, Simona; Rossi, Rosanna; Saluti, Giorgio; Cruciani, Gabriele; Galarini, Roberta

    2016-01-15

    A multiclass method for screening and confirmatory analysis of antimicrobial residues in muscle has been developed and validated, according to Commission Decision 2002/657/EC. Sixty-two antibiotics belonging to ten different drug families (amphenicols, beta-lactams, diamino-pyrimidine, lincosamides, macrolides, pleuromutilins, quinolones, rifamycins, sulfonamides and tetracyclines) have been included in the method. After the addition of an aqueous solution of EDTA, the minced muscle was extracted with acetonitrile/water mixture and, later, with pure acetonitrile. The extract was evaporated and redissolved in ammonium acetate buffer prior to LC injection. Instrumental determination was performed by liquid chromatography coupled to hybrid high resolution mass analyser (LC-HRMS/MS) operating in positive electrospray ionization mode. Chromatographic separation was optimized on a Poroshell 120 EC-C18 column (100 × 3.0 mm, 2.7 μm) with gradient using methanol and water containing 0.1% of formic acid as mobile phases. The method was validated in bovine muscle in the range 3.3-150 μg kg(-1) for all antibiotics; for some compounds with MRL higher than 100 μg kg(-1), the validation interval has been extended until 1500 μg kg(-1). The studied performance characteristics were selectivity, linearity, precision, trueness (recovery), decision limits, detection capabilities, detection and quantification limits. Satisfactory quantitative performances were obtained for all the analytes. Ruggedness tests demonstrated the applicability to swine and poultry muscle, too. Finally the wide participation in proficiency tests allowed to investigate in deep the method performances. PMID:26726937

  7. GC/MS screening method for phthalate esters in children's toys.

    PubMed

    Ting, Keh-Chuh; Gill, Modan; Garbin, Orlando

    2009-01-01

    Phthalate esters are commonly added into polyvinyl chloride (PVC) as softeners to make the plastic material flexible. Phthalates are suspected cancer-causing agents and possible teratogens; they have been linked to liver and kidney damage, as well as the underdevelopment of reproductive organs in humans and animals. Public safety concerns about human exposure to phthalates are on the rise because they do not chemically bond to PVC and leach from the material over time. Following the lead of the European Union and Japan in restricting the use of certain phthalates, a legal limit of 0.1% in children's toys was established by the California State Legislature (AB-1108). In addition to its mission to protect public health and the environment from toxic harm, the California Department of Toxic Substances Control (DTSC) has been delegated the role of lead agency for consumer product safety. To support DTSC's Green Chemistry activities, the Environmental Chemistry Laboratory Mobile Laboratory Team has developed an on-site screening method to monitor phthalates in children's toys. This method is simple, fast, and effective, with ample sensitivity to quantify the 6 restricted phthalates in children's toys at 100 ppm (limit of quantitation = 100 microg/g) which is 10 times lower than the legal allowable level of 0.1%. Additionally, the method has a high throughput capability and enables testing of approximately 6-10 samples per day, depending on the complexity of the sample matrix and concentration. This method is designed to survey the 6 phthalates in children's toys and other consumer products for compliance with the threshold of 0.1% (1000 ppm).

  8. General unknown screening in hair by liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS).

    PubMed

    Broecker, Sebastian; Herre, Sieglinde; Pragst, Fritz

    2012-05-10

    The retrospective investigation of the exposure to toxic substances by general unknown screening of hair is still a difficult task because of the large number of possible poisons, the low sample amount and the difficult sample matrix. In this study the use of liquid chromatography-hybrid quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) was tested as a promising technique for this purpose. In the optimized procedure, 20mg hair were decontaminated with water and acetone and two times extracted by 18h incubation with 0.5ml of a mixture of methanol/acetonitrile/H(2)O/ammonium formate at 37°C. A mixture of deuterated standards from different drug groups was added for quantification and method control. The united extracts were evaporated to a residue of 0.5ml and 5μl were injected without clean-up for LC-QTOF-MS measurement (instrument Agilent 6530) with positive electrospray ionization and in data dependent acquisition mode. For peak identification the accurate mass data base and spectral library of the authors was used which contains accurate mass CID spectra of more than 2500 and theoretically calculated accurate mass data of more than 7500 toxicologically relevant substances. Validation at the example of 24 illegal drugs, their metabolites and benzodiazepines resulted in limits of detection of 0.003-0.015ng/mg, and limits of quantification of 0.006-0.021ng/mg with good accuracy and intra- and interday reproducibility. The matrix effect by ion suppression/enhancement was 72-107% for basic drugs and 42-75% for benzodiazepines. Yields of the hair extraction above 90% were determined for 59 drugs or metabolites. The method was applied to hair samples from 30 drug fatalities and from 60 death cases with known therapeutic drug intake at life time. Altogether 212 substances were identified with a frequency per drug of 1-40 (mean 4.2) and per case of 2-33 (mean 10.2), between them 35 illegal drug related substances and 154 therapeutic drugs. Comparison with the

  9. The Polish language version of the Confusion Assessment Method - a questionnaire for the screening of consciousness disorders.

    PubMed

    Świerzy, Krzysztof A; Pudlo, Robert; Wesołowski, Bartosz; Garbacz, Marcin; Morawski, Michał; Jaworska, Izabela; Sołtysik, Mariusz; Zembala, Marian

    2016-06-01

    Confusion on a somatic basis is a dangerous problem mainly related with aging of the population. Data says that consciousness disorders concern 10-15% of patients in general wards, and up to 50% of patients admitted to geriatric wards. The persistence of the symptoms of confusion results in increase of agitation, disorganization, fear, which increases the risk of self-injuries of patients, it causes the need for parenteral feeding and hydratation, as well as maintaining water balance, and also disturbs cooperation, worsening the course and prognosis of the primary disease. It is believed that consciousness disorders are one of the most difficult diagnostic problems and the most difficult therapy problem among psychotic disorders. So far in Poland there have been no screening evaluation tools to assess the occurrence of confusion on the somatic basis. The purpose of this paper is to introduce the Polish translation of the widely used scale to assess consciousness disorders, intended also for middle personnel of health care - Confusion Assessment Method (CAM). Numerous studies over 16 years established the position of CAM as an exceptionally effective standardized diagnostic test, specifying the sensitivity of 94-100%, specificity from 90-95%, positive predictive value of 91-94%, negative predictive value of 90-100%. The questionnaire and instructions of its interpretation have been translated by doctors with active help from the original creators of CAM. Further studies are required in order to validate and determine the effectiveness of the newly formed diagnostic tool. PMID:27516799

  10. The Polish language version of the Confusion Assessment Method – a questionnaire for the screening of consciousness disorders

    PubMed Central

    Pudlo, Robert; Wesołowski, Bartosz; Garbacz, Marcin; Morawski, Michał; Jaworska, Izabela; Sołtysik, Mariusz; Zembala, Marian

    2016-01-01

    Confusion on a somatic basis is a dangerous problem mainly related with aging of the population. Data says that consciousness disorders concern 10-15% of patients in general wards, and up to 50% of patients admitted to geriatric wards. The persistence of the symptoms of confusion results in increase of agitation, disorganization, fear, which increases the risk of self-injuries of patients, it causes the need for parenteral feeding and hydratation, as well as maintaining water balance, and also disturbs cooperation, worsening the course and prognosis of the primary disease. It is believed that consciousness disorders are one of the most difficult diagnostic problems and the most difficult therapy problem among psychotic disorders. So far in Poland there have been no screening evaluation tools to assess the occurrence of confusion on the somatic basis. The purpose of this paper is to introduce the Polish translation of the widely used scale to assess consciousness disorders, intended also for middle personnel of health care – Confusion Assessment Method (CAM). Numerous studies over 16 years established the position of CAM as an exceptionally effective standardized diagnostic test, specifying the sensitivity of 94-100%, specificity from 90-95%, positive predictive value of 91-94%, negative predictive value of 90-100%. The questionnaire and instructions of its interpretation have been translated by doctors with active help from the original creators of CAM. Further studies are required in order to validate and determine the effectiveness of the newly formed diagnostic tool. PMID:27516799

  11. Model-based clustered-dot screening

    NASA Astrophysics Data System (ADS)

    Kim, Sang Ho

    2006-01-01

    I propose a halftone screen design method based on a human visual system model and the characteristics of the electro-photographic (EP) printer engine. Generally, screen design methods based on human visual models produce dispersed-dot type screens while design methods considering EP printer characteristics generate clustered-dot type screens. In this paper, I propose a cost function balancing the conflicting characteristics of the human visual system and the printer. By minimizing the obtained cost function, I design a model-based clustered-dot screen using a modified direct binary search algorithm. Experimental results demonstrate the superior quality of the model-based clustered-dot screen compared to a conventional clustered-dot screen.

  12. Noninvasive Assessment of Excessive Erythrocytosis as a Screening Method for Chronic Mountain Sickness at High Altitude

    PubMed Central

    Vyas, Kaetan J.; Danz, David; Gilman, Robert H.; Wise, Robert A.; León-Velarde, Fabiola; Jaime Miranda, J.

    2015-01-01

    Abstract Vyas, Kaetan J., David Danz, Robert H. Gilman, Robert A. Wise, Fabiola León-Velarde, J. Jaime Miranda, and William Checkley. Noninvasive assessment of excessive erythrocytosis as a screening method for chronic mountain sickness at high altitude. High Alt Med Biol 16:162–168, 2015.—Globally, over 140 million people are at risk of developing chronic mountain sickness, a common maladaptation to life at high altitude (>2500 meters above sea level). The diagnosis is contingent upon the identification of excessive erythrocytosis (EE). Current best practices to identify EE require a venous blood draw, which is cumbersome for large-scale surveillance. We evaluated two point-of-care biomarkers to screen for EE: noninvasive spot-check tests of total hemoglobin and oxyhemoglobin saturation (Pronto-7, Masimo Corporation). We conducted paired evaluations of total serum hemoglobin from a venous blood draw and noninvasive, spot-check testing of total hemoglobin and oxyhemoglobin saturation with the Pronto-7 in 382 adults aged ≥35 years living in Puno, Peru (3825 meters above sea level). We used the Bland-Altman method to measure agreement between the noninvasive hemoglobin assessment and the gold standard lab hemoglobin analyzer. Mean age was 58.8 years and 47% were male. The Pronto-7 test was unsuccessful in 21 (5%) participants. Limits of agreement between total hemoglobin measured via venous blood draw and the noninvasive, spot-check test ranged from −2.8 g/dL (95% CI −3.0 to −2.5) to 2.5 g/dL (95% CI 2.2 to 2.7), with a bias of −0.2 g/dL (95% CI −0.3 to −0.02) for the difference between total hemoglobin and noninvasive hemoglobin concentrations. Overall, the noninvasive spot-check test of total hemoglobin had a better area under the receiver operating characteristic curve compared to oxyhemoglobin saturation for the identification of EE as measured by a gold standard laboratory hemoglobin analyzer (0.96 vs. 0.82; p<0.001). Best cut-off values

  13. Multiparameter Screening on SlipChip Used for Nanoliter Protein Crystallization Combining Free Interface Diffusion and Microbatch Methods

    SciTech Connect

    Li, Liang; Du, Wenbin; Ismagilov, Rustem F.

    2010-08-04

    This paper describes two SlipChip-based approaches to protein crystallization: a SlipChip-based free interface diffusion (FID) method and a SlipChip-based composite method that simultaneously performs microbatch and FID crystallization methods in a single device. The FID SlipChip was designed to screen multiple reagents, each at multiple diffusion equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis, against 48 different reagents at five different equilibration times each, consuming 12 {micro}L of each protein for a total of 480 experiments using three SlipChips. The composite SlipChip was designed to screen multiple reagents, each at multiple mixing ratios and multiple equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis. To prevent cross-contamination while keeping the solution in the neck channels for FID stable, the plates of the SlipChip were etched with a pattern of nanowells. This nanopattern was used to increase the contact angle of aqueous solutions on the surface of the silanized glass. The composite SlipChip increased the number of successful crystallization conditions and identified more conditions for crystallization than separate FID and microbatch screenings. Crystallization experiments were scaled up in well plates using conditions identified during the SlipChip screenings, and X-ray diffraction data were obtained to yield the protein structure of dihydrofolate reductase/thymidylate synthase at 1.95 {angstrom} resolution. This free-interface diffusion approach provides a convenient and high-throughput method of setting up gradients in microfluidic devices and may find additional applications in cell-based assays.

  14. Rapid Screening Method for Detecting Ethinyl Estradiol in Natural Water Employing Voltammetry

    PubMed Central

    2016-01-01

    17α-Ethinyl estradiol (EE2), which is used worldwide in the treatment of some cancers and as a contraceptive, is often found in aquatic systems and is considered a pharmaceutically active compound (PhACs) in the environment. Current methods for the determination of this compound, such as chromatography, are expensive and lengthy and require large amounts of toxic organic solvents. In this work, a voltammetric procedure is developed and validated as a screening tool for detecting EE2 in water samples without prior extraction, clean-up, or derivatization steps. Application of the method we elaborate here to EE2 analysis is unprecedented. EE2 detection was carried out using differential pulse adsorptive cathodic stripping voltammetry (DP AdCSV) with a hanging mercury drop electrode (HMDE) in pH 7.0 Britton-Robinson buffer. The electrochemical process of EE2 reduction was investigated by cyclic voltammetry at different scan rates. Electroreduction of the hormone on a mercury electrode exhibited a peak at −1.16 ± 0.02 V versus Ag/AgCl. The experimental parameters were as follows: −0.7 V accumulation potential, 150 s accumulation time, and 60 mV s−1 scan rate. The limit of detection was 0.49 μg L−1 for a preconcentration time of 150 s. Relative standard deviations were less than 13%. The method was applied to the detection of EE2 in water samples with recoveries ranging from 93.7 to 102.5%. PMID:27738548

  15. Production of monoclonal antibodies specific for Haemophilus ducreyi: a screening method to discriminate specific and cross-reacting antibodies.

    PubMed

    Odumeru, J A; Alfa, M J; Martin, C F; Ronald, A R; Jay, F T

    1989-06-01

    Haemophilus ducreyi is the etiological agent of chancroid. The organism shares extensive immunological cross-reactivity with other Haemophilus species. This presents substantial difficulties for the production of specific monoclonal antibodies (MAbs). A competition ELISA was devised for hybridoma screening which allowed the detection of H. ducreyi-specific antibody-producing hybridoma cultures during the initial screening process. With this screening method, seven MAbs specific for H. ducreyi were obtained in a single cell fusion exercise. The specificities of the 7 MAbs were demonstrated by direct ELISA and dot immunobinding assays against several strains each of H. influenzae, H. parainfluenzae and Neisseria gonorrhoeae. Five of the MAbs reacted against all ten strains of H. ducreyi. These MAbs may permit the development of rapid and efficient immunodiagnostics for chancroid. The principle of the competition ELISA for hybridoma screening should be widely applicable to the development of specific MAbs to other organisms in which immunological cross-reactivity is an impediment to hybridoma screening by conventional methods. PMID:2787274

  16. Label-free high-throughput screening via mass spectrometry: a single cystathionine quantitative method for multiple applications.

    PubMed

    Holt, Tom G; Choi, Bernard K; Geoghagen, Neil S; Jensen, Kristian K; Luo, Qi; LaMarr, William A; Makara, Gergely M; Malkowitz, Lorraine; Ozbal, Can C; Xiong, Yusheng; Dufresne, Claude; Luo, Ming-Juan

    2009-10-01

    Label-free mass spectrometric (MS) technologies are particularly useful for enzyme assay design for drug discovery screens. MS permits the selective detection of enzyme substrates or products in a wide range of biological matrices without need for derivatization, labeling, or capture technologies. As part of a cardiovascular drug discovery effort aimed at finding modulators of cystathionine beta-synthase (CBS), we used the RapidFire((R)) label-free high-throughput MS (HTMS) technology to develop a high-throughput screening (HTS) assay for CBS activity. The in vitro assay used HTMS to quantify the unlabeled product of the CBS reaction, cystathionine. Cystathionine HTMS analyses were carried out with a throughput of 7 s per sample and quantitation over a linear range of 80-10,000 nM. A compound library of 25,559 samples (or 80 384-well plates) was screened as singlets using the HTMS assay in a period of 8 days. With a hit rate of 0.32%, the actives showed a 90% confirmation rate. The in vitro assay was applied to secondary screens in more complex matrices with no additional analytical development. Our results show that the HTMS method was useful for screening samples containing serum, for cell-based assays, and for liver explants. The novel extension of the in vitro analytical method, without modification, to secondary assays resulted in a significant and advantageous economy of development time for the drug discovery project.

  17. PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation.

    PubMed

    Shin, Woong-Hee; Christoffer, Charles W; Wang, Jibo; Kihara, Daisuke

    2016-09-26

    Virtual screening has become an indispensable procedure in drug discovery. Virtual screening methods can be classified into two categories: ligand-based and structure-based. While the former have advantages, including being quick to compute, in general they are relatively weak at discovering novel active compounds because they use known actives as references. On the other hand, structure-based methods have higher potential to find novel compounds because they directly predict the binding affinity of a ligand in a target binding pocket, albeit with substantially lower speed than ligand-based methods. Here we report a novel structure-based virtual screening method, PL-PatchSurfer2. In PL-PatchSurfer2, protein and ligand surfaces are represented by a set of overlapping local patches, each of which is represented by three-dimensional Zernike descriptors (3DZDs). By means of 3DZDs, the shapes and physicochemical complementarities of local surface regions of a pocket surface and a ligand molecule can be concisely and effectively computed. Compared with the previous version of the program, the performance of PL-PatchSurfer2 is substantially improved by the addition of two more features, atom-based hydrophobicity and hydrogen-bond acceptors and donors. Benchmark studies showed that PL-PatchSurfer2 performed better than or comparable to popular existing methods. Particularly, PL-PatchSurfer2 significantly outperformed existing methods when apo-form or template-based protein models were used for queries. The computational time of PL-PatchSurfer2 is about 20 times shorter than those of conventional structure-based methods. The PL-PatchSurfer2 program is available at http://www.kiharalab.org/plps2/ . PMID:27500657

  18. PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation.

    PubMed

    Shin, Woong-Hee; Christoffer, Charles W; Wang, Jibo; Kihara, Daisuke

    2016-09-26

    Virtual screening has become an indispensable procedure in drug discovery. Virtual screening methods can be classified into two categories: ligand-based and structure-based. While the former have advantages, including being quick to compute, in general they are relatively weak at discovering novel active compounds because they use known actives as references. On the other hand, structure-based methods have higher potential to find novel compounds because they directly predict the binding affinity of a ligand in a target binding pocket, albeit with substantially lower speed than ligand-based methods. Here we report a novel structure-based virtual screening method, PL-PatchSurfer2. In PL-PatchSurfer2, protein and ligand surfaces are represented by a set of overlapping local patches, each of which is represented by three-dimensional Zernike descriptors (3DZDs). By means of 3DZDs, the shapes and physicochemical complementarities of local surface regions of a pocket surface and a ligand molecule can be concisely and effectively computed. Compared with the previous version of the program, the performance of PL-PatchSurfer2 is substantially improved by the addition of two more features, atom-based hydrophobicity and hydrogen-bond acceptors and donors. Benchmark studies showed that PL-PatchSurfer2 performed better than or comparable to popular existing methods. Particularly, PL-PatchSurfer2 significantly outperformed existing methods when apo-form or template-based protein models were used for queries. The computational time of PL-PatchSurfer2 is about 20 times shorter than those of conventional structure-based methods. The PL-PatchSurfer2 program is available at http://www.kiharalab.org/plps2/ .

  19. Screening instruments for a population of older adults: The 10-item Kessler Psychological Distress Scale (K10) and the 7-item Generalized Anxiety Disorder Scale (GAD-7).

    PubMed

    Vasiliadis, Helen-Maria; Chudzinski, Veronica; Gontijo-Guerra, Samantha; Préville, Michel

    2015-07-30

    Screening tools that appropriately detect older adults' mental disorders are of great public health importance. The present study aimed to establish cutoff scores for the 10-item Kessler Psychological Distress (K10) and the 7-item Generalized Anxiety Disorder (GAD-7) scales when screening for depression and anxiety. We used data from participants (n = 1811) in the Enquête sur la Santé des Aînés-Service study. Depression and anxiety were measured using DSM-V and DSM-IV criteria. Receiver operating characteristic (ROC) curve analysis provided an area under the curve (AUC) of 0.767 and 0.833 for minor and for major depression when using K10. A cutoff of 19 was found to balance sensitivity (0.794) and specificity (0.664) for minor depression, whereas a cutoff of 23 was found to balance sensitivity (0.692) and specificity (0.811) for major depression. When screening for an anxiety with GAD-7, ROC analysis yielded an AUC of 0.695; a cutoff of 5 was found to balance sensitivity (0.709) and specificity (0.568). No significant differences were found between subgroups of age and gender. Both K10 and GAD-7 were able to discriminate between cases and non-cases when screening for depression and anxiety in an older adult population of primary care service users. PMID:25956759

  20. A simple, novel and high efficiency sap inoculation method to screen for tobacco streak virus.

    PubMed

    Sundaresha, S; Sreevathsa, Rohini; Balol, Gurupada B; Keshavareddy, G; Rangaswamy, K T; Udayakumar, M

    2012-10-01

    A rapid and efficient sap inoculation method for tobacco streak virus (TSV) was developed in sunflower. Sap from TSV-infected sunflower plants was freshly extracted in phosphate buffer and diluted serially from 10(-1) to 10(-8). Two-day old seedlings of sunflower were injured at the meristem and immersed in the sap for 10 min, maintained at 20 °C for 2-3 days and shifted to greenhouse. The surviving seedlings in the respective sap dilution were scored for symptoms of sunflower necrosis disease (SND). SND symptoms were seen in 80 % of the seedlings inoculated with a sap dilution of 10(-5). ELISA and RT-PCR analysis of coat protein and movement protein of TSV confirmed SND symptoms. The methodology was also found to be reproducible when the sap from the infected plants was inoculated onto healthy plants. The main aim of the study was to develop a primary screening strategy for the selection of transgenics developed for SND resistance. This methodology can also be extended for the analysis of resistance against other viruses.

  1. Prion protein-coated magnetic beads: synthesis, characterization and development of a new ligands screening method.

    PubMed

    de Moraes, Marcela Cristina; Santos, Juliana Bosco; Dos Anjos, Daniel Meira; Rangel, Luciana Pereira; Vieira, Tuane Cristine Ramos Gonçalves; Moaddel, Ruin; da Silva, Jerson Lima

    2015-01-30

    Prion diseases are characterized by protein aggregation and neurodegeneration. Conversion of the native prion protein (PrP(C)) into the abnormal scrapie PrP isoform (PrP(Sc)), which undergoes aggregation and can eventually form amyloid fibrils, is a critical step leading to the characteristic path morphological hallmark of these diseases. However, the mechanism of conversion remains unclear. It is known that ligands can act as cofactors or inhibitors in the conversion mechanism of PrP(C) into PrP(Sc). Within this context, herein, we describe the immobilization of PrP(C) onto the surface of magnetic beads and the morphological characterization of PrP(C)-coated beads by fluorescence confocal microscopy. PrP(C)-coated magnetic beads were used to identify ligands from a mixture of compounds, which were monitored by UHPLC-ESI-MS/MS. This affinity-based method allowed the isolation of the anti-prion compound quinacrine, an inhibitor of PrP aggregation. The results indicate that this approach can be applied to not only "fish" for anti-prion compounds from complex matrixes, but also to screening for and identify possible cellular cofactors involved in the deflagration of prion diseases. PMID:25576041

  2. Prion protein-coated magnetic beads: synthesis, characterization and development of a new ligands screening method.

    PubMed

    de Moraes, Marcela Cristina; Santos, Juliana Bosco; Dos Anjos, Daniel Meira; Rangel, Luciana Pereira; Vieira, Tuane Cristine Ramos Gonçalves; Moaddel, Ruin; da Silva, Jerson Lima

    2015-01-30

    Prion diseases are characterized by protein aggregation and neurodegeneration. Conversion of the native prion protein (PrP(C)) into the abnormal scrapie PrP isoform (PrP(Sc)), which undergoes aggregation and can eventually form amyloid fibrils, is a critical step leading to the characteristic path morphological hallmark of these diseases. However, the mechanism of conversion remains unclear. It is known that ligands can act as cofactors or inhibitors in the conversion mechanism of PrP(C) into PrP(Sc). Within this context, herein, we describe the immobilization of PrP(C) onto the surface of magnetic beads and the morphological characterization of PrP(C)-coated beads by fluorescence confocal microscopy. PrP(C)-coated magnetic beads were used to identify ligands from a mixture of compounds, which were monitored by UHPLC-ESI-MS/MS. This affinity-based method allowed the isolation of the anti-prion compound quinacrine, an inhibitor of PrP aggregation. The results indicate that this approach can be applied to not only "fish" for anti-prion compounds from complex matrixes, but also to screening for and identify possible cellular cofactors involved in the deflagration of prion diseases.

  3. Detection and screening of bovine leukocyte adhesion deficiency in Pakistan using molecular methods.

    PubMed

    Nasreen, Fozia; Altaf Malik, Naveed; Naeem Riaz, Muhammad; Anver Qureshi, Javed

    2009-05-01

    Bovine leukocyte adhesion deficiency (BLAD) is an autosomal recessive disease. Affected animals die because of extreme susceptibility to infections caused by the lack of a membrane glycoprotein called the leukocyte integrin beta-2 subunit of CD18. The present study was planned to standardize a technique for the diagnosis of BLAD and to get an estimation of BLAD allele in the Pakistani cattle population. The study was performed on 700 animals including Holstein-Friesian (HF) (n=280), Friesian-Sahiwal (FS) (n=120) Sahiwal (n=100) cows and HF calves (n=59) from Government as well as private farms. Similarly 141 bulls of Sahiwal (n=100), HF (n=18) and FS (n=23) from the Semen Production Unit Qadirabad and Kherimorat were also sampled. The identification of normal, carrier and affected animals were made by the PCR-RFLP method. No animal was found homozygous for BLAD while 10 animals including HF calve (n=1), FS bull (n=1), HF (n=6) and FS (n=2) cows were BLAD carrier. The Hardy-Weinberg frequency of the mutant allele in HF and FS population in Pakistan was calculated to 0.01. Thus there is a need of regular screening of the bulls used for artificial insemination to avoid the risk of spreading BLAD in the cattle population of Pakistan. PMID:19490168

  4. Temperature-induced fluorescence changes : a screening method for frost tolerance of potato (solanum sp.).

    PubMed

    Sundbom, E; Strand, M; Hällgren, J E

    1982-11-01

    Field-grown tuber-bearing potatoes were screened for frost tolerance in a late stage of development. Three different clones of Solanum tuberosum L. and two interspecific crosses between clones of S. tuberosum and the wild potato species S. demissum Lindl. were studied. Two different methods were used. (a) Temperature-induced fluorescence changes of intact leaves were measured in freeze-thaw cycles between 20 degrees C and -10 degrees C. The variable fluorescence pattern was characterized in relation to frost tolerance. (b) Controlled freezings of plants in a climate chamber with successively increased low temperature stress, of 1 to 2 hours duration during the dark period. Freezing damages were classified visually.The short-term frost during the fluorescence measurement was compared with the long-term frost treatments in the climate chamber. The results of the two were identical to ranking of the different clones for frost tolerance. The temperature-induced fluorescence changes also monitored progressive damages to the chloroplast membranes when plants were exposed to successively lower temperatures in a controlled climate chamber freezing test. It was deduced from the fluorescence measurements that the freezing injury of potato occurs on the water splitting side of photosystem II. PMID:16662670

  5. Device and method for screening crystallization conditions in solution crystal growth

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C. (Inventor)

    1995-01-01

    A device and method for detecting optimum protein crystallization conditions and for growing protein crystals in either 1g or microgravity environments comprising a housing, defining at least one pair of chambers for containing crystallization solutions is presented. The housing further defines an orifice therein for providing fluid communication between the chambers. The orifice is adapted to receive a tube which contains a gelling substance for limiting the rate of diffusive mixing of the crystallization solutions. The solutions are diffusively mixed over a period of time defined by the quantity of gelling substance sufficient to achieve equilibration and to substantially reduce density driven convection disturbances therein. The device further includes endcaps to seal the first and second chambers. One of the endcaps includes a dialysis chamber which contains protein solution in which protein crystals are grown. Once the endcaps are in place, the protein solution is exposed to the crystallization solutions wherein the solubility of the protein solution is reduced at a rate responsive to the rate of diffusive mixing of the crystallization solutions. This allows for a controlled approach to supersaturation and allows for screening of crystal growth conditions at preselected intervals.

  6. Device and Method for Screening Crystallization Conditions in Solution Crystal Growth

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C. (Inventor)

    1997-01-01

    A device and method for detecting optimum protein crystallization conditions and for growing protein crystals in either 1 g or microgravity environments comprising a housing defining at least one pair of chambers for containing crystallization solutions. The housing further defines an orifice therein for providing fluid communication between the chambers. The orifice is adapted to receive a tube which contains a gelling substance for limiting the rate of diffusive mixing of the crystallization solutions. The solutions are diffusively mixed over a period of time defined by the quantity of gelling substance sufficient to achieve equilibration and to substantially reduce density driven convection disturbances therein. The device further includes endcaps to seal the first and second chambers. One of the endcaps includes a dialysis chamber which contains protein solution in which protein crystals are grown. Once the endcaps are in place. the protein solution is exposed to the crystallization solutions wherein the solubility of the protein solution is reduced at a rate responsive to the rate of diffusive mixing of the crystallization solutions. This allows for a controlled approach to supersaturation and allows for screening of crystal growth conditions at preselected intervals.

  7. [The Reliability of Measurement Methods for Medical Examinations and Health Screening].

    PubMed

    Hosogaya, Shigemi

    2016-03-01

    Clinical laboratory data used in medical examinations and health screening need to have a guaranteed analytical reliability. To ensure the reliability of measurement data, each constituent is required to be compatible with its traceability chain, and any constituent whose traceability chain has yet to be established is required to be appropriately harmonized in the current measurement system. The inter-laboratory reproducibility of standardized measurement values obtained from the external quality assessments conducted by the Japan Medical Association and Japanese Association of Medical Technologists was estimated to evaluate the analytical reliability of clinical tests in Japan. The estimated inter-laboratory reproducibility was then compared with the permissible error limits which have been reported domestically and internationally based on inter- and intra-individual biological variations of healthy subjects. The results showed that most of the measurement uncertainties were sufficiently lower than the permissible limits. This study proposes that the measurement uncertainty of the standardized measurement method has the potential to be a new assessment standard for analytical reliability. PMID:27363220

  8. Method with high-throughput screening potential for antioxidative substances using Escherichia coli biosensor katG'::lux.

    PubMed

    Tienaho, Jenni; Sarjala, Tytti; Franzén, Robert; Karp, Matti

    2015-11-01

    A new method is described for the rapid real-time screening of antioxidative properties using a recombinant Escherichia coli DPD2511 biosensor. This microplate technique, without time-consuming pre-incubations and handling, has potential for a high-throughput search of bioactive compounds. Special emphasis was given to obtaining highly reliable and repeatable results.

  9. Rapid screening of anti-infective drug products for counterfeits using Raman spectral library-based correlation methods.

    PubMed

    Loethen, Yvette L; Kauffman, John F; Buhse, Lucinda F; Rodriguez, Jason D

    2015-11-01

    A new spectral library-based approach that is capable of screening a diverse set of finished drug products using only an active pharmaceutical ingredient spectral library is described in this paper. This approach obviates the need for a comprehensive drug product library, thereby streamlining the use of spectral library-based tests for anti-counterfeiting efforts, specifically to target finished drug products containing the wrong active ingredient or no active ingredient at all. Both laboratory-based and portable spectrometers are used in the study to demonstrate the usefulness and transferability of the spectral correlation method for field screening. The spectral correlation between the active pharmaceutical ingredient and finished drug product spectra is calculated using both full spectral analysis and targeted spectral regions analysis of six types of antimalarial, antibiotic and antiviral products. The spectral regions were determined using a moving window spectral correlation algorithm, and the use of specific spectral regions is shown to be crucial in screening finished drug products using only the active pharmaceutical ingredient spectrum. This comprehensive screening spectral correlation method is tested on seven different validation samples from different manufacturers as those used to develop the method, as well as simulated counterfeits which were prepared to mimic falsified drugs containing no active ingredient. The spectral correlation method is successful in correctly identifying 100% of the authentic products and simulated counterfeit samples tested. PMID:26401527

  10. Determination of Tolerance to Internal Shorts and Its Screening in Lithium-ion Cells NASA - JSC Method

    NASA Technical Reports Server (NTRS)

    Jeevarajan, Judith

    2009-01-01

    This slide presentation reviews the method developed by the NASA Johnson Space Center (JSC) to determine tolerances to internal shorts and screening for problems in commercial off the shelf (COTS) Lithium-ion batteries. The test apparatus is shown and several examples of the usage and results of the test are discussed.

  11. LC-ESI/MS/MS method for rapid screening and confirmation of 44 exogenous anabolic steroids in human urine.

    PubMed

    Jeon, Byoung Wook; Yoo, Hye Hyun; Jeong, Eun Sook; Kim, Ho Jun; Jin, Changbae; Kim, Dong Hyun; Lee, Jaeick

    2011-09-01

    A sensitive and rapid method based on liquid chromatography-triple-quadrupole tandem mass spectrometry (LC-MS/MS) with electrospray ionization (ESI) has been developed and validated for the screening and confirmation of 44 exogenous anabolic steroids (29 parent steroids and 15 metabolites) in human urine. The method involves an enzymatic hydrolysis, liquid-liquid extraction, and detection by LC-MS/MS. A triple-quadrupole mass spectrometer was operated in positive ESI mode with selected reaction monitoring (SRM) mode for the screening and product ion scan mode for the confirmation. The protonated molecular ions were used as precursor ions for the SRM analysis and product ion scan. The intraday and interday precisions of the target analytes at concentrations of the minimum required performance levels for the screening were 2-14% and 2-15%, respectively. The limits of detection for the screening and confirmation method were 0.1-10 ng/mL and 0.2-10 ng/mL, respectively, for 44 steroids. This method was successfully applied to analysis of urine samples from suspected anabolic steroid abusers.

  12. Rapid screening of anti-infective drug products for counterfeits using Raman spectral library-based correlation methods.

    PubMed

    Loethen, Yvette L; Kauffman, John F; Buhse, Lucinda F; Rodriguez, Jason D

    2015-11-01

    A new spectral library-based approach that is capable of screening a diverse set of finished drug products using only an active pharmaceutical ingredient spectral library is described in this paper. This approach obviates the need for a comprehensive drug product library, thereby streamlining the use of spectral library-based tests for anti-counterfeiting efforts, specifically to target finished drug products containing the wrong active ingredient or no active ingredient at all. Both laboratory-based and portable spectrometers are used in the study to demonstrate the usefulness and transferability of the spectral correlation method for field screening. The spectral correlation between the active pharmaceutical ingredient and finished drug product spectra is calculated using both full spectral analysis and targeted spectral regions analysis of six types of antimalarial, antibiotic and antiviral products. The spectral regions were determined using a moving window spectral correlation algorithm, and the use of specific spectral regions is shown to be crucial in screening finished drug products using only the active pharmaceutical ingredient spectrum. This comprehensive screening spectral correlation method is tested on seven different validation samples from different manufacturers as those used to develop the method, as well as simulated counterfeits which were prepared to mimic falsified drugs containing no active ingredient. The spectral correlation method is successful in correctly identifying 100% of the authentic products and simulated counterfeit samples tested.

  13. Effects of Scanning—Routine Health Information Exposure—on Cancer Screening and Prevention Behaviors in the General Population

    PubMed Central

    Hornik, Robert; Parvanta, Sarah; Mello, Susan; Freres, Derek; Kelly, Bridget; Schwartz, J. Sanford

    2014-01-01

    Research on health information exposure focuses primarily on deliberate information seeking behavior and its effects on health. By contrast, this study explores the complementary and perhaps more influential role of health information acquired through exposure to routinely used sources, called scanning. We hypothesized that scanning from non-medical sources, both mediated and interpersonal, affects cancer screening and prevention decisions. A nationally representative longitudinal survey of adults 40 to 70 years (N=2,489) was used to analyze the effects of scanning on three cancer screening behaviors (mammography, PSA, colonoscopy) and three prevention behaviors (exercising, eating fruits and vegetables, dieting to lose weight). After adjustment for baseline behaviors and covariates, scanning at baseline predicted one year later weekly exercise days overall, as well as daily fruits and vegetables servings for those already higher on baseline consumption. Also among those reporting timely screening mammogram behavior at baseline, scanning predicted repeat mammography. Scanning was marginally predictive of PSA uptake among those not reporting a PSA at baseline. While there were strong cross-sectional associations, scanning did not predict dieting or colonoscopy uptake in longitudinal analyses. These analyses provide substantial support for a claim that routine exposure to health content from non-medical sources affects specific health behaviors. PMID:24083417

  14. Phene Plate (PhP) biochemical fingerprinting. A screening method for epidemiological typing of enterococcal isolates.

    PubMed

    Saeedi, B; Tärnberg, M; Gill, H; Hällgren, A; Jonasson, J; Nilsson, L E; Isaksson, B; Kühn, I; Hanberger, H

    2005-09-01

    Pulsed-field gel electrophoresis (PFGE) is currently considered the gold standard for genotyping of enterococci. However, PFGE is both expensive and time-consuming. The purpose of this study was to investigate whether the PhP system can be used as a reliable clinical screening method for detection of genetically related isolates of enterococci. If so, it should be possible to minimize the number of isolates subjected to PFGE typing, which would save time and money. Ninety-nine clinical enterococcal isolates were analysed by PhP (similarity levels 0.90-0.975) and PFGE (similarity levels < or =3 and < or =6 bands) and all possible pairs of isolates were cross-classified as matched or mismatched. We found that the probability that a pair of isolates (A and B) belonging to the same type according to PhP also belong to the same cluster according to PFGE, i.e. p(A(PFGE)=B(PFGE) * A(PhP)=B(PhP)), and the probability that a pair of isolates of different types according to PhP also belong to different clusters according to PFGE, i.e. p(A(PFGE) not equalB(PFGE) * A(PhP) not equalB(PhP)), was relatively high for E. faecalis (0.86 and 0.96, respectively), but was lower for E. faecium (0.51 and 0.77, respectively). The concordance which shows the probability that PhP and PFGE agree on match or mismatch was 86%-93% for E. faecalis and 54%-66% for E. faecium, which indicates that the PhP method may be useful for epidemiological typing of E. faecalis in the current settings but not for E. faecium.

  15. Comparison Between a Rapid Biological Screening Method (EPA 4425) for TCDDs/TCDFs and Chemical Analytical Methods

    SciTech Connect

    Anderson, Jack W.; Jones, Jennifer M.; McCoy, Daniel L.; Fujita, Akira; Yamamoto, Taichi; Iijima, Satoshi

    2003-08-01

    Seven polychlorinated dibenzo-p-dioxins (PCDDs), ten polychlorinated dibenzofurans (PCDFs) as well as twelve polychlorinated biphenyls (PCBs) are collectively referred to as dioxin-like compounds. The World Health Organization toxic equivalency factors (TEFs) for these persistent chlorinated organic compounds and their measured concentrations are used to produce the toxic equivalency quotient (TEQ) of a sample. TEF values are partially based on a common mechanism involving binding of the chemical to the aryl hydrocarbon receptor (AhR). Biological methods for the determination of TEQs are based on the assumption that all dioxin-related compounds act through the Ah receptor signal transduction pathway. Based on the biochemical response of CYP1A activation via the AhR, in vitro systems that utilize a reporter gene under transcriptional control of CYP1A have been developed. Several investigations have reported on the success of utilizing biological test systems to detect PCDDs, PCDFs, PCBs in environmental samples. The P450 Human Reporter Gene System assay (EPA Method 4425) utilizes a human hepatoma cell line (HepG2) in which a plasmid containing the human CYP1A1 promoter and 5'-flanking sequences with three xenobiotic responsive elements (XREs) fused to the luciferase reporter gene. The enzyme luciferase is produced in the presence of compounds that bind the XREs, and can be detected by a simple assay that measures relative light units with a luminometer. Method 4425, used by Columbia Analytical Services (CAS), has gained acceptance as a rapid and inexpensive approach for screening solvent extracts of environmental samples of soil, sediment, tissue, and water to detect compounds that activate the AhR. Investigations in the U. S. and Japan comparing the results of 4425 and standard high-resolution GC/MS (HRGC/HRMS) will be reported here. The purpose of making these comparisons is to determine if risk assessments for large dioxin sites both before and after remediation

  16. Health economic analysis of the Swedish neonatal metabolic screening programme. A method of optimizing routines.

    PubMed

    Alm, J; Larsson, A; Rosenqvist, U

    1982-01-01

    A benefit-cost analysis was carried out to optimize the routines for neonatal metabolic screening. The basis of the study was provided by results of the Swedish neonatal screening programme from 1965 to 1979. During this period over one million infants were screened by the Guthrie test for phenylketonuria and galactosaemia, and for limited periods also for tyrosinaemia, homocystinuria and histidinaemia. The benefit-cost ratio was calculated for combinations of different screening tests, recall routines, and varying degrees of coverage. The largest benefit-cost ratio was obtained with combined screening for phenylketonuria and galactosaemia, using a borderline blood phenylalanine level of 0.50 mmol/L in the Guthrie test for phenylketonuria. However, the inaccuracy of this test necessitated the use of a lower blood phenylalanine level of 0.25 mmol/L and the acceptance of a lower benefit-cost ratio. An increase in the present 98% coverage of newborns by the screening programme was found to be an effective means of improving the benefit-cost ratio in the present programme.

  17. The existence results and Tikhonov regularization method for generalized mixed variational inequalities in Banach spaces

    NASA Astrophysics Data System (ADS)

    Wang, Min

    2016-04-01

    This paper aims to establish the Tikhonov regularization method for generalized mixed variational inequalities in Banach spaces. For this purpose, we firstly prove a very general existence result for generalized mixed variational inequalities, provided that the mapping involved has the so-called mixed variational inequality property and satisfies a rather weak coercivity condition. Finally, we establish the Tikhonov regularization method for generalized mixed variational inequalities. Our findings extended the results for the generalized variational inequality problem (for short, GVIP(F, K)) in R^n spaces (He in Abstr Appl Anal, 2012) to the generalized mixed variational inequality problem (for short, GMVIP(F,φ , K) ) in reflexive Banach spaces. On the other hand, we generalized the corresponding results for the generalized mixed variational inequality problem (for short, GMVIP(F,φ ,K) ) in R^n spaces (Fu and He in J Sichuan Norm Univ (Nat Sci) 37:12-17, 2014) to reflexive Banach spaces.

  18. Generalization of the residual cutting method based on the Krylov subspace

    NASA Astrophysics Data System (ADS)

    Abe, Toshihiko; Sekine, Yoshihito; Kikuchi, Kazuo

    2016-06-01

    The residual cutting (RC) method has been reported to have superior converging characteristics in numerically solving elliptic partial differential equations. However, its application is limited to linear problems with diagonal-dominant matrices in general, for which convergence of a relaxation method such as SOR is guaranteed. In this study, we propose the generalized residual cutting (GRC) method, which is based on the Krylov subspace and applicable to general unsymmetric linear problems. Also, we perform numerical experiments with various coefficient matrices, and show that the GRC method has some desirable properties such as convergence characteristics and memory usage, in comparison to the conventional RC, BiCGSTAB and GMRES methods.

  19. The generalized order-k Fibonacci-Pell sequence by matrix methods

    NASA Astrophysics Data System (ADS)

    Kilic, Emrah

    2007-12-01

    In this paper, we consider the usual and generalized order-k Fibonacci and Pell recurrences, then we define a new recurrence, which we call generalized order-k F-P sequence. Also we present a systematic investigation of the generalized order-k F-P sequence. We give the generalized Binet formula, some identities and an explicit formula for sums of the generalized order-k F-P sequence by matrix methods. Further, we give the generating function and combinatorial representations of these numbers. Also we present an algorithm for computing the sums of the generalized order-k Pell numbers, as well as the Pell numbers themselves.

  20. A Protocolised Once a Day Modified Early Warning Score (MEWS) Measurement Is an Appropriate Screening Tool for Major Adverse Events in a General Hospital Population

    PubMed Central

    Ludikhuize, Jeroen; Kramer, Mark H. H.

    2016-01-01

    Background The Modified Early Warning Score (MEWS) was developed to timely recognise clinically deteriorating hospitalised patients. However, the ability of the MEWS in predicting serious adverse events (SAEs) in a general hospital population has not been examined prospectively. The aims were to (1) analyse protocol adherence to a MEWS protocol in a real-life setting and (2) to determine the predictive value of protocolised daily MEWS measurement on SAEs: death, cardiac arrests, ICU-admissions and readmissions. Methods All adult patients admitted to 6 hospital wards in October and November 2015 were included. MEWS were checked each morning by the research team. For each critical score (MEWS ≥ 3), the clinical staff was inquired about the actions performed. 30-day follow-up for SAEs was performed to compare between patients with and without a critical score. Results 1053 patients with 3673 vital parameter measurements were included, 200 (19.0%) had a critical score. The protocol adherence was 89.0%. 18.2% of MEWS were calculated wrongly. Patients with critical scores had significant higher rates of unplanned ICU admissions [7.0% vs 1.3%, p < 0.001], in-hospital mortality [6.0% vs 0.8%, p < 0.001], 30-day readmission rates [18.6% vs 10.8%, p < 0.05], and a longer length of stay [15.65 (SD: 15.7 days) vs 6.09 (SD: 6.9), p < 0.001]. Specificity of MEWS related to composite adverse events was 83% with a negative predicting value of 98.1%. Conclusions Protocol adherence was high, even though one-third of the critical scores were calculated wrongly. Patients with a MEWS ≥ 3 experienced significantly more adverse events. The negative predictive value of early morning MEWS < 3 was 98.1%, indicating the reliability of this score as a screening tool. PMID:27494719

  1. Development and interlaboratory validation of quantitative polymerase chain reaction method for screening analysis of genetically modified soybeans.

    PubMed

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

    2013-01-01

    A novel real-time polymerase chain reaction (PCR)-based quantitative screening method was developed for three genetically modified soybeans: RRS, A2704-12, and MON89788. The 35S promoter (P35S) of cauliflower mosaic virus is introduced into RRS and A2704-12 but not MON89788. We then designed a screening method comprised of the combination of the quantification of P35S and the event-specific quantification of MON89788. The conversion factor (Cf) required to convert the amount of a genetically modified organism (GMO) from a copy number ratio to a weight ratio was determined experimentally. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDR), respectively. The determined RSDR values for the method were less than 25% for both targets. We consider that the developed method would be suitable for the simple detection and approximate quantification of GMO.

  2. Development and interlaboratory validation of quantitative polymerase chain reaction method for screening analysis of genetically modified soybeans.

    PubMed

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

    2013-01-01

    A novel real-time polymerase chain reaction (PCR)-based quantitative screening method was developed for three genetically modified soybeans: RRS, A2704-12, and MON89788. The 35S promoter (P35S) of cauliflower mosaic virus is introduced into RRS and A2704-12 but not MON89788. We then designed a screening method comprised of the combination of the quantification of P35S and the event-specific quantification of MON89788. The conversion factor (Cf) required to convert the amount of a genetically modified organism (GMO) from a copy number ratio to a weight ratio was determined experimentally. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDR), respectively. The determined RSDR values for the method were less than 25% for both targets. We consider that the developed method would be suitable for the simple detection and approximate quantification of GMO. PMID:23302646

  3. Fast mouse PK (Fast PK): a rapid screening method to increase pharmacokinetic throughput in pre-clinical drug discovery.

    PubMed

    Reddy, Jitendar; Madishetti, Sreedhar; Vachaspati, Prakash R

    2012-09-29

    We describe a rapid screening methodology for performing pharmacokinetic (PK) studies in mice called Fast PK. In this Fast PK method, two mice were used per compound and four blood samples were collected from each mouse. The sampling times were staggered (sparse sampling) between the two mice, thus yielding complete PK profile in singlicate across eight time points. The plasma PK parameters from Fast PK were comparable to that obtained from conventional PK methods. This method has been used to rapidly screen compounds in the early stages of drug discovery and about 600 compounds have been profiled in the last 3 years, which has resulted in reduction in the usage of mice by 800 per year in compliance with the 3R principles of animal ethics. In addition, this Fast PK method can also help in evaluating the PK parameters from the same set of animals used in safety/toxicology/efficacy studies without the need for satellite groups. PMID:22789493

  4. Awareness of colonoscopy as a screening method for colorectal cancer and its uptake in Spain.

    PubMed

    Ricardo-Rodrigues, Isa; Hernandez-Barrera, Valentin; Jiménez-García, Rodrigo

    2014-09-01

    The objective of this study was to describe awareness levels of colonoscopy as a screening procedure for colorectal cancer (CRC), to study its uptake and analyze possible associated factors in Spain. This was a cross-sectional study using data from the Oncobarómetro survey, carried out by face-to-face interviews with a representative national sample of the Spanish population aged 18 years and older. Awareness was assessed using the following questions: 'Do you know of any examination procedures or medical technique used to detect cancer?' and 'I'm going to list some screening procedures (including colonoscopy) to see if you know of them as a cancer screening test or whether this is the first time you have heard of them'. To evaluate colonoscopy uptake, participants were asked whether they had undergone a colonoscopy in the past 2 years. The independent variables included sociodemographic, socioeconomic, and health-related factors. 65.7% of the study population was aware of colonoscopy as a screening tool. Individuals from lower socioeconomic groups or those who only had primary education showed a lower level of awareness. 12.8% of participants had undergone a colonoscopy in the past 2 years. This number increased to 45% in the Spanish Autonomous Communities, where screening programs are in place. Colonoscopy screening rates are 10.28 times higher among those who had fecal occult blood testing during the previous 2 years. There is an inverse relationship between social inequality and both awareness and uptake of colonoscopy. Consequently, for screening to be more effective, interventions that reduce barriers to access for target populations should be implemented. PMID:24681532

  5. Detection of indoor PCB contamination by thermal desorption of dust. A rapid screening method?

    PubMed

    Wilkins, Ken; Bøwadt, Søren; Larsen, Kjeld; Sporring, Sune

    2002-01-01

    Although PCB in caulking materials has been forbidden for many years in most of Europe, including Denmark, there has been continued interest to measure PCB levels in the air of contaminated buildings and blood of the occupants (Mengon and Schlatter 1993, Fromme et al. 1996, Ewers et al. 1998, Currado and Harrad 1998, Gabrio et al. 2000). The relatively low priority for investigations of this contamination is probably due to the small quantities inhaled compared to exposure via food, and the rapid metabolism of the most volatile congeners demonstrated by low concentrations of all congeners in the blood of exposed persons (Ewers et al. 1998, Gabrio et al. 2000). There is, however, evidence that PCB containing caulking materials have been used even during the '90s (Fromme et al. 1996). In Denmark, it is estimated that 75 t PCB is still in buildings (Organization of Sealant Branch's Manufacturers and Distributors 2000). During an investigation of dust from buildings with excessive microbial growth (including 35 rooms from 9 buildings), the analysis of semivolatile compounds by thermal desorption-GC/MS of samples from a single building surprisingly revealed large amounts of PCBs containing 3, 4 and 5 chlorine atoms, 10-20 times the amounts found in samples from other buildings. Extraction of the dust by SFE followed by GC/ECD analysis for 12 PCB congeners showed that there was approximately 20 times the total PCB concentrations in dust from the polluted building compared to the levels in the other buildings. Subsequent headspace analysis of caulking material from the polluted building revealed this to be the source. Shelf dust functions as a passive sampling medium and, thus, can be used as a screening method to detect PCB and other semivolatile pollution indoors.

  6. Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods.

    PubMed

    Wu, Yuhua; Wang, Yulei; Li, Jun; Li, Wei; Zhang, Li; Li, Yunjing; Li, Xiaofei; Li, Jun; Zhu, Li; Wu, Gang

    2014-01-01

    The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported detection methods, targeting different regions of the P35S promoter. Initial assessment revealed that due to the absence of primer binding sites in the P35S sequence, 19 of the 24 reported methods failed to detect P35S in MON88913 cotton, and the other two methods could only be applied to certain GMOs. The rest three reported methods were not suitable for measurement of P35S in some testing events, because SNPs in binding sites of the primer/probe would result in abnormal amplification plots and poor linear regression parameters. In this study, we discovered a conserved region in the P35S sequence through sequencing of P35S promoters from multiple transgenic events, and developed new qualitative and quantitative detection systems targeting this conserved region. The qualitative PCR could detect the P35S promoter in 23 unique GMO events with high specificity and sensitivity. The quantitative method was suitable for measurement of P35S promoter, exhibiting good agreement between the amount of template and Ct values for each testing event. This study provides a general P35S screening method, with greater coverage than existing methods. PMID:25483893

  7. Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods

    PubMed Central

    Wu, Yuhua; Wang, Yulei; Li, Jun; Li, Wei; Zhang, Li; Li, Yunjing; Li, Xiaofei; Li, Jun; Zhu, Li; Wu, Gang

    2014-01-01

    The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported detection methods, targeting different regions of the P35S promoter. Initial assessment revealed that due to the absence of primer binding sites in the P35S sequence, 19 of the 24 reported methods failed to detect P35S in MON88913 cotton, and the other two methods could only be applied to certain GMOs. The rest three reported methods were not suitable for measurement of P35S in some testing events, because SNPs in binding sites of the primer/probe would result in abnormal amplification plots and poor linear regression parameters. In this study, we discovered a conserved region in the P35S sequence through sequencing of P35S promoters from multiple transgenic events, and developed new qualitative and quantitative detection systems targeting this conserved region. The qualitative PCR could detect the P35S promoter in 23 unique GMO events with high specificity and sensitivity. The quantitative method was suitable for measurement of P35S promoter, exhibiting good agreement between the amount of template and Ct values for each testing event. This study provides a general P35S screening method, with greater coverage than existing methods. PMID:25483893

  8. Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods.

    PubMed

    Wu, Yuhua; Wang, Yulei; Li, Jun; Li, Wei; Zhang, Li; Li, Yunjing; Li, Xiaofei; Li, Jun; Zhu, Li; Wu, Gang

    2014-01-01

    The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported detection methods, targeting different regions of the P35S promoter. Initial assessment revealed that due to the absence of primer binding sites in the P35S sequence, 19 of the 24 reported methods failed to detect P35S in MON88913 cotton, and the other two methods could only be applied to certain GMOs. The rest three reported methods were not suitable for measurement of P35S in some testing events, because SNPs in binding sites of the primer/probe would result in abnormal amplification plots and poor linear regression parameters. In this study, we discovered a conserved region in the P35S sequence through sequencing of P35S promoters from multiple transgenic events, and developed new qualitative and quantitative detection systems targeting this conserved region. The qualitative PCR could detect the P35S promoter in 23 unique GMO events with high specificity and sensitivity. The quantitative method was suitable for measurement of P35S promoter, exhibiting good agreement between the amount of template and Ct values for each testing event. This study provides a general P35S screening method, with greater coverage than existing methods.

  9. [Current state of studies on screening method for sensitinogens in injections for traditional Chinese medicine and synthetic immunity method].

    PubMed

    He, Fu-yuan; Deng, Kai-wen; Zeng, Jiao-li; Dai, Ru-wen; Xia, Zan-shao; Liu, Weng-long; Shi, Ji-lian

    2012-10-01

    Injections for traditional Chinese medicine have over 60 years of history of development and application. In recent years, however, their adverse reactions have been reported one after another. Consequently, studies on screening sensitinogens (sensibiligens) from injections for traditional Chinese medicine have drawn people's attention and become a tough problem all over the world. This essay analyzes the current state of studies on screening techniques of sensitinogens in injections for traditional Chinese medicine according their mechanism of immunotoxicity, and then proposes to adopt the synthetic immunoassay combining immunity bottle chip, immunity cover chip and immunity chromatographic fingerprint to screen sensitinogens from injections for traditional Chinese medicine, in order to build a safety evaluation barrier for development and clinical application of injections for traditional Chinese medicine.

  10. Cultural adaptation into Spanish of the generalized anxiety disorder-7 (GAD-7) scale as a screening tool

    PubMed Central

    2010-01-01

    Background Generalized anxiety disorder (GAD) is a prevalent mental health condition which is underestimated worldwide. This study carried out the cultural adaptation into Spanish of the 7-item self-administered GAD-7 scale, which is used to identify probable patients with GAD. Methods The adaptation was performed by an expert panel using a conceptual equivalence process, including forward and backward translations in duplicate. Content validity was assessed by interrater agreement. Criteria validity was explored using ROC curve analysis, and sensitivity, specificity, predictive positive value and negative value for different cut-off values were determined. Concurrent validity was also explored using the HAM-A, HADS, and WHO-DAS-II scales. Results The study sample consisted of 212 subjects (106 patients with GAD) with a mean age of 50.38 years (SD = 16.76). Average completion time was 2'30''. No items of the scale were left blank. Floor and ceiling effects were negligible. No patients with GAD had to be assisted to fill in the questionnaire. The scale was shown to be one-dimensional through factor analysis (explained variance = 72%). A cut-off point of 10 showed adequate values of sensitivity (86.8%) and specificity (93.4%), with AUC being statistically significant [AUC = 0.957-0.985); p < 0.001]. The scale significantly correlated with HAM-A (0.852, p < 0.001), HADS (anxiety domain, 0.903, p < 0.001), and WHO-DAS II (0.696, p > 0.001). Limitations Elderly people, particularly those very old, may need some help to complete the scale. Conclusion After the cultural adaptation process, a Spanish version of the GAD-7 scale was obtained. The validity of its content and the relevance and adequacy of items in the Spanish cultural context were confirmed. PMID:20089179

  11. Why 24-h Urine Albumin Excretion Rate Method Still is Used for Screening of Diabetic Nephropathy in Isfahan Laboratories?

    PubMed Central

    Teimoury, Azam; Iraj, Bijan; Heidari-Beni, Motahar; Amini, Massoud; Hosseiny, Seyed-Mohsen

    2014-01-01

    Background: The first step in diagnosis of diabetic nephropathy is measurement of albumin in a spot urine sample. The aim of this study was assessment of the accuracy of urinary albumin to creatinine ratio (UACR) in random urine specimens (RUS) for microalbuminuria and macroalbuminuria screening in Iranian diabetic patients. Methods: A total of 200 diabetic patients participated to our study. 24 h timed urine specimens followed by RUS were collected. 24-h urine albumin excretion (24-h urinary albumin excretion (UAE)) and UACR in RUS were measured. Data were analyzed by Pearson's correlation, receiver operating characteristic (ROC) curve and McNemar test. Results: A total of 165 patients finalized the study. Pearson's correlation of coefficient for 24-h UAE versus UACR was 0.64. The area under ROC curve for UACR was 0.83 in microalbuminuria and 0.91 in macroalbuminuria. The cutoff point of 30 mg/g in UACR method had 86% sensitivity and 60% specificity for microalbuminuria screening and cut-off point of 300 mg/g had 75% sensitivity and 99% specificity for macroalbuminuria screening respectively. Conclusions: UACR in RUS showed acceptable performance as a screening test for diagnosis of both micro and macroalbuminuria in Iranian diabetic patients. PMID:24829719

  12. Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios.

    PubMed

    Hristozov, Dimitar P; Oprea, Tudor I; Gasteiger, Johann

    2007-01-01

    Four different ligand-based virtual screening scenarios are studied: (1) prioritizing compounds for subsequent high-throughput screening (HTS); (2) selecting a predefined (small) number of potentially active compounds from a large chemical database; (3) assessing the probability that a given structure will exhibit a given activity; (4) selecting the most active structure(s) for a biological assay. Each of the four scenarios is exemplified by performing retrospective ligand-based virtual screening for eight different biological targets using two large databases--MDDR and WOMBAT. A comparison between the chemical spaces covered by these two databases is presented. The performance of two techniques for ligand--based virtual screening--similarity search with subsequent data fusion (SSDF) and novelty detection with Self-Organizing Maps (ndSOM) is investigated. Three different structure representations--2,048-dimensional Daylight fingerprints, topological autocorrelation weighted by atomic physicochemical properties (sigma electronegativity, polarizability, partial charge, and identity) and radial distribution functions weighted by the same atomic physicochemical properties--are compared. Both methods were found applicable in scenario one. The similarity search was found to perform slightly better in scenario two while the SOM novelty detection is preferred in scenario three. No method/descriptor combination achieved significant success in scenario four.

  13. A genome-scale CRISPR-Cas9 screening method for protein stability reveals novel regulators of Cdc25A

    PubMed Central

    Wu, Yuanzhong; Zhou, Liwen; Wang, Xin; Lu, Jinping; Zhang, Ruhua; Liang, Xiaoting; Wang, Li; Deng, Wuguo; Zeng, Yi-Xin; Huang, Haojie; Kang, Tiebang

    2016-01-01

    The regulation of stability is particularly crucial for unstable proteins in cells. However, a convenient and unbiased method of identifying regulators of protein stability remains to be developed. Recently, a genome-scale CRISPR-Cas9 library has been established as a genetic tool to mediate loss-of-function screening. Here, we developed a protein stability regulators screening assay (Pro-SRSA) by combining the whole-genome CRISPR-Cas9 library with a dual-fluorescence-based protein stability reporter and high-throughput sequencing to screen for regulators of protein stability. Using Cdc25A as an example, Cul4B-DDB1DCAF8 was identified as a new E3 ligase for Cdc25A. Moreover, the acetylation of Cdc25A at lysine 150, which was acetylated by p300/CBP and deacetylated by HDAC3, prevented the ubiquitin-mediated degradation of Cdc25A by the proteasome. This is the first study to report that acetylation, as a novel posttranslational modification, modulates Cdc25A stability, and we suggest that this unbiased CRISPR-Cas9 screening method at the genome scale may be widely used to globally identify regulators of protein stability. PMID:27462461

  14. Incorporating Virtual Reactions into a Logic-based Ligand-based Virtual Screening Method to Discover New Leads

    PubMed Central

    Reynolds, Christopher R; Muggleton, Stephen H; Sternberg, Michael J E

    2015-01-01

    The use of virtual screening has become increasingly central to the drug development pipeline, with ligand-based virtual screening used to screen databases of compounds to predict their bioactivity against a target. These databases can only represent a small fraction of chemical space, and this paper describes a method of exploring synthetic space by applying virtual reactions to promising compounds within a database, and generating focussed libraries of predicted derivatives. A ligand-based virtual screening tool Investigational Novel Drug Discovery by Example (INDDEx) is used as the basis for a system of virtual reactions. The use of virtual reactions is estimated to open up a potential space of 1.21×1012 potential molecules. A de novo design algorithm known as Partial Logical-Rule Reactant Selection (PLoRRS) is introduced and incorporated into the INDDEx methodology. PLoRRS uses logical rules from the INDDEx model to select reactants for the de novo generation of potentially active products. The PLoRRS method is found to increase significantly the likelihood of retrieving molecules similar to known actives with a p-value of 0.016. Case studies demonstrate that the virtual reactions produce molecules highly similar to known actives, including known blockbuster drugs. PMID:26583052

  15. A genome-scale CRISPR-Cas9 screening method for protein stability reveals novel regulators of Cdc25A.

    PubMed

    Wu, Yuanzhong; Zhou, Liwen; Wang, Xin; Lu, Jinping; Zhang, Ruhua; Liang, Xiaoting; Wang, Li; Deng, Wuguo; Zeng, Yi-Xin; Huang, Haojie; Kang, Tiebang

    2016-01-01

    The regulation of stability is particularly crucial for unstable proteins in cells. However, a convenient and unbiased method of identifying regulators of protein stability remains to be developed. Recently, a genome-scale CRISPR-Cas9 library has been established as a genetic tool to mediate loss-of-function screening. Here, we developed a protein stability regulators screening assay (Pro-SRSA) by combining the whole-genome CRISPR-Cas9 library with a dual-fluorescence-based protein stability reporter and high-throughput sequencing to screen for regulators of protein stability. Using Cdc25A as an example, Cul4B-DDB1(DCAF8) was identified as a new E3 ligase for Cdc25A. Moreover, the acetylation of Cdc25A at lysine 150, which was acetylated by p300/CBP and deacetylated by HDAC3, prevented the ubiquitin-mediated degradation of Cdc25A by the proteasome. This is the first study to report that acetylation, as a novel posttranslational modification, modulates Cdc25A stability, and we suggest that this unbiased CRISPR-Cas9 screening method at the genome scale may be widely used to globally identify regulators of protein stability. PMID:27462461

  16. A genome-scale CRISPR-Cas9 screening method for protein stability reveals novel regulators of Cdc25A.

    PubMed

    Wu, Yuanzhong; Zhou, Liwen; Wang, Xin; Lu, Jinping; Zhang, Ruhua; Liang, Xiaoting; Wang, Li; Deng, Wuguo; Zeng, Yi-Xin; Huang, Haojie; Kang, Tiebang

    2016-01-01

    The regulation of stability is particularly crucial for unstable proteins in cells. However, a convenient and unbiased method of identifying regulators of protein stability remains to be developed. Recently, a genome-scale CRISPR-Cas9 library has been established as a genetic tool to mediate loss-of-function screening. Here, we developed a protein stability regulators screening assay (Pro-SRSA) by combining the whole-genome CRISPR-Cas9 library with a dual-fluorescence-based protein stability reporter and high-throughput sequencing to screen for regulators of protein stability. Using Cdc25A as an example, Cul4B-DDB1(DCAF8) was identified as a new E3 ligase for Cdc25A. Moreover, the acetylation of Cdc25A at lysine 150, which was acetylated by p300/CBP and deacetylated by HDAC3, prevented the ubiquitin-mediated degradation of Cdc25A by the proteasome. This is the first study to report that acetylation, as a novel posttranslational modification, modulates Cdc25A stability, and we suggest that this unbiased CRISPR-Cas9 screening method at the genome scale may be widely used to globally identify regulators of protein stability.

  17. Field seasonal influenza vaccine effectiveness: evaluation of the screening method using different sources of data during the 2010/2011 French influenza season.

    PubMed

    Falchi, Alessandra; Souty, Cecile; Grisoni, Marie-Lise; Mosnier, Anne; Hanslik, Thomas; Daviaud, Isabelle; Varesi, Laurent; Kerneis, Solen; Carrat, Fabrice; Blanchon, Thierry

    2013-11-01

    Thanks to the screening method, we estimated among target groups the 2010/2011 field vaccine effectiveness (FVE) against laboratory confirmed influenza cases seen in general practice. We also compared the values of FVE estimations obtained by using three sources of the population vaccination coverage (VC) based on three different methodologies: (1) administrative data from the main social security scheme (Caisse Nationale d'Assurance Maladie des Travailleurs Salariés--CNAMTS) covering about 85% of the French population, (2) a cross-sectional national telephone survey in the general population, and (3) a declarative survey in the population seen in a one-day general practitioner (GP) consultations. The FVE estimates among target groups were stratified by age (< 65 y old with reported chronic illness; ≥65 y old and overall). Using the VC of the CNAMTS, the FVE of the 2010/2011 seasonal trivalent vaccine against laboratory confirmed infection with any influenza virus was 59% (95% Confidence Interval, 17 to 81). It was 85% (17 to 99) and 50% (-16 to 80) for A(H1N1)pdm09 and B influenza infections, respectively. The values of FVE using the influenza VC obtained in a sample of the general population and of the population of GPs' patients were 73% (45 to 87) and 82% (63 to 92), respectively. We estimated a moderate influenza FVE in preventing confirmed influenza viruses in target groups by using the VC of the CNAMTS. We also observed that the screening method generates FVE values dependent on the choice of the source of VC and thus should be used cautiously. PMID:23811610

  18. Screening fungicides for use in fish culture: Evaluation of the agar plug transfer, cellophane transfer, and agar dilution methods

    USGS Publications Warehouse

    Bailey, Tom A.

    1983-01-01

    The reliability, reproducibility, and usefulness of three screening methods -- the cellophane transfer, the agar plug transfer, and the agar dilution -- to screen aquatic fungicides were evaluated. Achlya flagellata and Saprolegnia hypogyna were exposed to 1, 10, and 100 mg/L of malachite green to test each method. The cellophane transfer and agar plug transfer techniques had similar reliability and reproducibility in rating fungicidal activity, and were both superior to the agar dilution technique. The agar plug transfer and agar dilution techniques adequately projected in vivo activity of malachite green, but the cellophane transfer technique overestimated its activity. Overall, the agar plug transfer technique most accurately rated the activity of malachite green and was the easiest test to perform. It therefore appears to be the method of choice for testing aquatic fungicides.

  19. Validation of radioimmunoassay screening methods for beta-agonists in bovine liver according to Commission Decision 2002/657/EC.

    PubMed

    Granja, R H M M; Montes Niño, A M; Rabone, F; Montes Niño, R E; Cannavan, A; Salerno, A Gonzalez

    2008-12-01

    Validation studies were carried out on a multi-residue screening method for anilinic type beta-agonists (clenbuterol, mabuterol, brombuterol, cimaterol, cimbuterol, mapenterol, clenpenterol) and a method for the phenolic type beta-agonist, salbutamol, in bovine liver. The validation was performed according to the European Union Commission Decision 2002/657/EC (European Commission 2002), which establishes criteria and procedures for the determination of parameters such as the detection capability (CCbeta), specificity, stability of standard solutions and stability of the analyte in matrix. CCbeta values for the eight target compounds were between 0.25 and 0.5 microg kg(-1). The stability of standard solutions and analytes in matrix and the specificity of the antibody were characterized. The methods are applicable for qualitative screening of beta-agonists for regulatory programmes according to European Union performance requirements, or as a semi-quantitative research tool for known target compounds.

  20. Lipid monolayer and sparse matrix screening for growing two-dimensional crystals for electron crystallography: methods and examples.

    PubMed

    Yeager, Mark; Dryden, Kelly A; Ganser-Pornillos, Barbie K

    2013-01-01

    Electron microscopy provides an efficient method for rapidly assessing whether a solution of macromolecules is homogeneous and monodisperse. If the macromolecules can be induced to form two-dimensional crystals that are a single layer in thickness, then electron crystallography of frozen-hydrated crystals has the potential of achieving three-dimensional density maps at sub-nanometer or even atomic resolution. Here we describe the lipid monolayer and sparse matrix screening methods for growing two-dimensional crystals and present successful applications to soluble macromolecular complexes: carboxysome shell proteins and HIV CA, respectively. Since it is common to express recombinant proteins with poly-His tags for purification by metal affinity chromatography, the monolayer technique using bulk lipids doped with Ni(2+) lipids has the potential for broad application. Likewise, the sparse matrix method uses screening conditions for three-dimensional crystallization and is therefore of broad applicability.