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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. 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

  3. 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.

  4. 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.

  5. 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.

  6. Cardiovascular screening in general practice in a low SES area

    PubMed Central

    2012-01-01

    Background Lower social economic status (SES) is related to an elevated cardiovascular (CV) risk. A pro-active primary prevention CV screening approach in general practice (GP) might be effective in a region with a low mean SES. This approach, supported by a regional GP laboratory, was investigated on feasibility, attendance rate and proportion of persons identified with an elevated risk. Methods In a region with a low mean SES, men and women aged ≥50/55 years, respectively, were invited for cardiovascular risk profiling, based on SCORE 10-year risk of fatal cardiovascular disease and additional risk factors (family history, weight and end organ damage). Screening was performed by laboratory personnel, at the GP practice. Treatment advice was based on Dutch GP guidelines for cardiovascular risk management. Response rates were compared to those in five other practices, using the same screening method. Results 521 persons received invitations, 354 (68%) were interested, 33 did not attend and 43 were not further analysed because of already known diabetes/cardiovascular disease. Eventually 278 risk profiles were analysed, of which 60% had a low cardiovascular risk (SCORE-risk <5%). From the 40% participants with a SCORE-risk ≥5%, 60% did not receive medication yet for hypertension/hypercholesterolemia. In the other five GPs response rates were comparable to the currently described GP. Conclusion Screening in GP in a low SES area, performed by a laboratory service, was feasible, resulted in high attendance, and identification and treatment advice of many new persons at risk for cardiovascular disease. PMID:23228012

  7. 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.

  8. 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.

  9. Prenatal Screening Methods for Aneuploidies

    PubMed Central

    Dey, Madhusudan; Sharma, Sumedha; Aggarwal, Sumita

    2013-01-01

    Aneuploidies are a major cause of perinatal morbidity and mortality. Therefore, it is the most common indication for invasive prenatal diagnosis. Initially, screening for aneuploidies started with maternal age risk estimation. Later on, serum testing for biochemical markers and ultrasound markers were added. Women detected to be at high-risk for aneuploidies were offered invasive testing. New research is now focusing on non-invasive prenatal testing using cell-free fetal DNA in maternal circulation. The advantage of this technique is the ability to reduce the risk of miscarriage associated with invasive diagnostic procedures. However, this new technique has its own set of technical limitations and ethical issues at present and careful consideration is required before broad implementation PMID:23626953

  10. DHAD variants and methods of screening

    DOEpatents

    Kelly, Kristen J.; Ye, Rick W.

    2017-02-28

    Methods of screening for dihydroxy-acid dehydratase (DHAD) variants that display increased DHAD activity are disclosed, along with DHAD variants identified by these methods. Such enzymes can result in increased production of compounds from DHAD requiring biosynthetic pathways. Also disclosed are isolated nucleic acids encoding the DHAD variants, recombinant host cells comprising the isolated nucleic acid molecules, and methods of producing butanol.

  11. 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

  12. Development and application of a general plasmid reference material for GMO screening.

    PubMed

    Wu, Yuhua; Li, Jun; Wang, Yulei; Li, Xiaofei; Li, Yunjing; Zhu, Li; Li, Jun; Wu, Gang

    The use of analytical controls is essential when performing GMO detection through screening tests. Additionally, the presence of taxon-specific sequences is analyzed mostly for quality control during GMO detection. In this study, 11 commonly used genetic elements involving three promoters (P-35S, P-FMV35S and P-NOS), four marker genes (Bar, NPTII, HPT and Pmi), and four terminators (T-NOS, T-35S, T-g7 and T-e9), together with the reference gene fragments from six major crops of maize, soybean, rapeseed, rice, cotton and wheat, were co-integrated into the same single plasmid to construct a general reference plasmid pBI121-Screening. The suitability test of pBI121-Screening plasmid as reference material indicated that the non-target sequence on the pBI121-Screening plasmid did not affect the PCR amplification efficiencies of screening methods and taxon-specific methods. The sensitivity of screening and taxon-specific assays ranged from 5 to 10 copies of pBI121-Screening plasmid, meeting the sensitivity requirement of GMO detection. The construction of pBI121-Screening solves the lack of a general positive control for screening tests, thereby reducing the workload and cost of preparing a plurality of the positive control.

  13. Thermography is not a feasible method for breast cancer screening.

    PubMed

    Brkljacić, Boris; Miletić, Damir; Sardanelli, Francesco

    2013-06-01

    Breast cancer is a common malignancy causing high mortality in women especially in developed countries. Due to the contribution of mammographic screening and improvements in therapy, the mortality rate from breast cancer has decreased considerably. An imaging-based early detection of breast cancer improves the treatment outcome. Mammography is generally established not only as diagnostic but also as screening tool, while breast ultrasound plays a major role in the diagnostic setting in distinguishing solid lesions from cysts and in guiding tissue sampling. Several indications are established for contrast-enhanced magnetic resonance imaging. Thermography was not validated as a screening tool and the only study performed long ago for evaluating this technology in the screening setting demonstrated very poor results. The conclusion that thermography might be feasible for screening cannot be derived from studies with small sample size, unclear selection of patients, and in which mammography and thermography were not blindly compared as screening modalities. Thermography can not be used to aspirate, biopsy or localize lesions preoperatively since no method so far was described to accurately transpose the thermographic location of the lesion to the mammogram or ultrasound and to surgical specimen. Thermography cannot be proclaimed as a screening method, without any evidence whatsoever.

  14. Generalized James' effective Hamiltonian method

    NASA Astrophysics Data System (ADS)

    Shao, Wenjun; Wu, Chunfeng; Feng, Xun-Li

    2017-03-01

    James' effective Hamiltonian method has been extensively adopted to investigate largely detuned interacting quantum systems. This method only corresponds to the second-order perturbation theory and cannot be exploited to treat problems which should be solved by using the third- or higher-order perturbation theory. In this paper, we generalize James' effective Hamiltonian method to the higher-order case. Using the method developed here, we reexamine two recently published examples [L. Garziano et al., Phys. Rev. Lett. 117, 043601 (2016), 10.1103/PhysRevLett.117.043601; Ken K. W. Ma and C. K. Law, Phys. Rev. A 92, 023842 (2015), 10.1103/PhysRevA.92.023842]; our results turn out to be the same as the original ones derived from the third-order perturbation theory and adiabatic elimination method, respectively. For some specific problems, this method can simplify the calculating procedure and the resultant effective Hamiltonian is more general.

  15. Cervical cytology screening: experience of a general hospital.

    PubMed Central

    Sargeant, E. J.; Qizilbash, A. H.; Johnson, F. L.

    1977-01-01

    At Henderson General Hospital, Hamilton, a program was introduced whereby cervical smears were taken routinely for cytologic study from all women admitted aged 17 years or older. The procedure was performed by a specially trained nurse. In a 5-year period 53% of eligible patients were screened. Of these, 32% had not had a cervical smear taken before. In 7681 smears nine instances of invasive disease were discovered: three of the cervix, three of the endometrium and three metastatic. There were 20 cases of carcinoma in situ and 2 of severe dysplasia. Evidence of infection was present in a high percentage of the smears. Hospital admission affords an excellent opportunity of applying this valuable screening procedure. PMID:912627

  16. Impact of general practice endorsement on the social gradient in uptake in bowel cancer screening

    PubMed Central

    Raine, Rosalind; Duffy, Stephen W; Wardle, Jane; Solmi, Francesca; Morris, Stephen; Howe, Rosemary; Kralj-Hans, Ines; Snowball, Julia; Counsell, Nicholas; Moss, Sue; Hackshaw, Allan; von Wagner, Christian; Vart, Gemma; McGregor, Lesley M; Smith, Samuel G; Halloran, Stephen; Handley, Graham; Logan, Richard F; Rainbow, Sandra; Smith, Steve; Thomas, Mary C; Atkin, Wendy

    2016-01-01

    Background: There is a socioeconomic gradient in the uptake of screening in the English NHS Bowel Cancer Screening Programme (BCSP), potentially leading to inequalities in outcomes. We tested whether endorsement of bowel cancer screening by an individual's general practice (GP endorsement; GPE) reduced this gradient. Methods: A cluster-randomised controlled trial. Over 20 days, individuals eligible for screening in England from 6480 participating general practices were randomly allocated to receive a GP-endorsed or the standard invitation letter. The primary outcome was the proportion of people adequately screened and its variation by quintile of Index of Multiple Deprivation. Results: We enrolled 265 434 individuals. Uptake was 58.2% in the intervention arm and 57.5% in the control arm. After adjusting for age, sex, hub and screening episode, GPE increased the overall odds of uptake (OR=1.07, 95% CI 1.04–1.10), but did not affect its socioeconomic gradient. We estimated that implementing GPE could result in up to 165 more people with high or intermediate risk colorectal adenomas and 61 cancers detected, and a small one-off cost to modify the standard invitation (£78 000). Conclusions: Although GPE did not improve its socioeconomic gradient, it offers a low-cost approach to enhancing overall screening uptake within the NHS BCSP. PMID:26742011

  17. 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.

  18. General health screening as part of a periodontal examination

    PubMed Central

    Raphael, Sarah L.

    2010-01-01

    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. PMID:21523218

  19. 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.

  20. 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.

  1. A general topology, Godunov method

    SciTech Connect

    Addessio, F.; Cline, M.; Dukowicz, J.

    1987-01-01

    A numerical technique that utilizes a general topology mesh is described. The method employs the arbitrary Lagrangian-Eulerian procedure and explicit, finite-volume, Godunov numerics. Material interfaces are resolved to eliminate fictitious mixing and nonphysical shear impedance. Cell-centered variables, including velocity, are used to provide consistent control volumes for the advection of mass, momentum, and energy, and to allow arbitrary slip between material regions. The computational mesh is composed of arbitrary polygonal cells. The constraint of a fixed logical connectivity for the mesh is removed. Consequently, geometrical mesh limitations, which are responsible for inaccuracies and code failure during the evolution of region boundaries, are absent. Arbitrary boundaries can be resolved, and the mesh is capable of changing smoothly and rapidly from regions of high to low resolution. Lack of a coherent mesh orientation minimizes numerical anisotropy. A mesh rezoning approach, based on a dual triangulation and coupled with a global remapping algorithm, allows the mesh to evolve dynamically. 9 refs., 6 figs.

  2. 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.

  3. 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.…

  4. 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.

  5. 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.

  6. 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.

  7. Risk Stratification in Cervical Cancer Screening by Complete Screening History- Applying Bioinformatics to a General Screening Population.

    PubMed

    Baltzer, Nicholas; Sundström, Karin; Nygård, Jan F; Dillner, Joakim; Komorowski, Jan

    2017-04-06

    Women screened for cervical cancer in Sweden are currently treated under a one-size-fits-all programme, which has been successful in reducing the incidence of cervical cancer but does not use all of the participants' available medical information. This study aimed to use women's complete cervical screening histories to identify diagnostic patterns that may indicate an increased risk of developing cervical cancer. A nationwide case-control study was performed where cervical cancer screening data from 125,476 women with a maximum follow-up of 10 years were evaluated for patterns of SNOMED diagnoses. The cancer development risk was estimated for a number of different screening history patterns and expressed as Odds Ratios (OR), with a history of 4 benign cervical tests as reference, using logistic regression. The overall performance of the model was moderate (64% accuracy, 71% Area Under Curve (AUC)) with 61-62% of the study population showing no specific patterns associated with risk. However, predictions for high-risk groups as defined by screening history patterns were highly discriminatory with ORs ranging from 8 to 36. The model for computing risk performed consistently across different screening history lengths, and several patterns predicted cancer outcomes. The results show the presence of risk-increasing and risk-decreasing factors in the screening history. Thus it is feasible to identify subgroups based on their complete screening histories. Several high-risk subgroups identified might benefit from an increased screening density. Some low-risk subgroups identified could likely have a moderately reduced screening density without additional risk. This article is protected by copyright. All rights reserved.

  8. Current and potential providers of blood pressure self-screening: a mixed methods study in Oxfordshire

    PubMed Central

    Tompson, A C; Heneghan, C J; Greenfield, S M; Hobbs, F D R; Ward, A M

    2017-01-01

    Objectives To (1) establish the extent of opportunities for members of the public to check their own blood pressure (BP) outside of healthcare consultations (BP self-screening), (2) investigate the reasons for and against hosting such a service and (3) ascertain how BP self-screening data are used in primary care. Design A mixed methods, cross-sectional study. Setting Primary care and community locations in Oxfordshire, UK. Participants 325 sites were surveyed to identify where and in what form BP self-screening services were available. 23 semistructured interviews were then completed with current and potential hosts of BP self-screening services. Results 18/82 (22%) general practices offered BP self-screening and 68/110 (62%) pharmacies offered professional-led BP screening. There was no evidence of permanent BP self-screening activities in other community settings. Healthcare professionals, managers, community workers and leaders were interviewed. Those in primary care generally felt that practice-based BP self-screening was a beneficial activity that increased the attainment of performance targets although there was variation in its perceived usefulness for patient care. The pharmacists interviewed provided BP checking as a service to the community but were unable to develop self-screening services without a clear business plan. Among potential hosts, barriers to providing a BP self-screening service included a perceived lack of healthcare commissioner and public demand, and a weak—if any—link to their core objectives as an organisation. Conclusions BP self-screening currently occurs in a minority of general practices. Any future development of community BP self-screening programmes will require (1) public promotion and (2) careful consideration of how best to support—and reward—the community hosts who currently perceive little if any benefit. PMID:28336742

  9. 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 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL ASSISTANCE PROGRAMS PROGRAM INTEGRITY: MEDICAID Provider Screening and Enrollment §...

  10. Heavy quarkonia description from a generalized screened potential model

    SciTech Connect

    González, P.

    2016-01-22

    The spectral effect of open flavor meson-meson thresholds in heavy quarkonia is analyzed by using a Non Relativistic Quark Model. The proposed form of the effective quark-antiquark potential, based on lattice indications, incorporates implicitly screening effects from meson-meson configurations. The application of the model to heavy quarkonia provides a resonable description of unconventional J{sup ++} charmonium states and a definite prediction for unconventional J{sup ++} states in bottomonium.

  11. High-throughput bubble screening method for combinatorial discovery of electrocatalysts for water splitting.

    PubMed

    Xiang, Chengxiang; Suram, Santosh K; Haber, Joel A; Guevarra, Dan W; Soedarmadji, Ed; Jin, Jian; Gregoire, John M

    2014-02-10

    Combinatorial synthesis and screening for discovery of electrocatalysts has received increasing attention, particularly for energy-related technologies. High-throughput discovery strategies typically employ a fast, reliable initial screening technique that is able to identify active catalyst composition regions. Traditional electrochemical characterization via current-voltage measurements is inherently throughput-limited, as such measurements are most readily performed by serial screening. Parallel screening methods can yield much higher throughput and generally require the use of an indirect measurement of catalytic activity. In a water-splitting reaction, the change of local pH or the presence of oxygen and hydrogen in the solution can be utilized for parallel screening of active electrocatalysts. Previously reported techniques for measuring these signals typically function in a narrow pH range and are not suitable for both strong acidic and basic environments. A simple approach to screen the electrocatalytic activities by imaging the oxygen and hydrogen bubbles produced by the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) is reported here. A custom built electrochemical cell was employed to record the bubble evolution during the screening, where the testing materials were subject to desired electrochemical potentials. The transient of the bubble intensity obtained from the screening was quantitatively analyzed to yield a bubble figure of merit (FOM) that represents the reaction rate. Active catalysts in a pseudoternary material library, (Ni-Fe-Co)Ox, which contains 231 unique compositions, were identified in less than one minute using the bubble screening method. An independent, serial screening method on the same material library exhibited excellent agreement with the parallel bubble screening. This general approach is highly parallel and is independent of solution pH.

  12. 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...

  13. 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

  14. A Triangulation Method for Identifying Hydrostratigraphic Locations of Well Screens

    SciTech Connect

    Whiteside, T. S.

    2015-01-31

    A method to identify the hydrostratigraphic location of well screens was developed using triangulation with known locations. This method was applied to all of the monitor wells being used to develop the new GSA groundwater model. Results from this method are closely aligned with those from an alternate method which uses a mesh surface.

  15. A composite screening tool for medication reviews of outpatients: general issues with specific examples.

    PubMed

    De Smet, Peter A G M; Denneboom, Wilma; Kramers, Cees; Grol, Richard

    2007-01-01

    Regular performance of medication reviews is prominent among methods that have been advocated to reduce the extent and seriousness of drug-related problems, such as adverse drug reactions, drug-disease interactions, drug-drug interactions, drug ineffectiveness and cost ineffectiveness. Several screening tools have been developed to guide practising healthcare professionals and researchers in reviewing the medication patterns of elderly patients; however, each of these tools has its own limitations. This review discusses a wide range of general prescription-, treatment- and patient-related issues that should be taken into account when reviewing medication patterns by implicit screening. These include generic and therapeutic substitution; potentially superfluous or inappropriate medications; potentially inappropriate dosages or duration of treatment; drug-disease and drug-drug interactions; under-treatment; making use of laboratory test results; patient adherence, experiences and habits; appropriate dosage forms and packaging. A broad selection of specific examples and references that can be used as a basis for explicit screening of medication patterns in outpatients is also offered.

  16. Generalized model screening potentials for Fermi-Dirac plasmas

    NASA Astrophysics Data System (ADS)

    Akbari-Moghanjoughi, M.

    2016-04-01

    In this paper, some properties of relativistically degenerate quantum plasmas, such as static ion screening, structure factor, and Thomson scattering cross-section, are studied in the framework of linearized quantum hydrodynamic theory with the newly proposed kinetic γ-correction to Bohm term in low frequency limit. It is found that the correction has a significant effect on the properties of quantum plasmas in all density regimes, ranging from solid-density up to that of white dwarf stars. It is also found that Shukla-Eliasson attractive force exists up to a few times the density of metals, and the ionic correlations are seemingly apparent in the radial distribution function signature. Simplified statically screened attractive and repulsive potentials are presented for zero-temperature Fermi-Dirac plasmas, valid for a wide range of quantum plasma number-density and atomic number values. Moreover, it is observed that crystallization of white dwarfs beyond a critical core number-density persists with this new kinetic correction, but it is shifted to a much higher number-density value of n0 ≃ 1.94 × 1037 cm-3 (1.77 × 1010 gr cm-3), which is nearly four orders of magnitude less than the nuclear density. It is found that the maximal Thomson scattering with the γ-corrected structure factor is a remarkable property of white dwarf stars. However, with the new γ-correction, the maximal scattering shifts to the spectrum region between hard X-ray and low-energy gamma-rays. White dwarfs composed of higher atomic-number ions are observed to maximally Thomson-scatter at slightly higher wavelengths, i.e., they maximally scatter slightly low-energy photons in the presence of correction.

  17. Some general methods of preparing affinity columns

    PubMed Central

    Sundaram, P.V.

    1974-01-01

    Some general methods of covalent coupling of nucleotides, especially derivatized nucleotides, polynucleotides and cofactors to insoluble polymers are described in this paper. Wherever necessary individual methods also carry some information on the binding of enzymes to the same polymers to serve as a guide to the efficiency of the coupling methods. PMID:10793714

  18. Generalization of the ERIT principle and method.

    SciTech Connect

    Ruggiero,A.G.

    2007-11-04

    The paper describes the generalization of the method to produce secondary particles with a low-energy and low-intensity primary beam circulating in a Storage Ring with the Emittance-Recovery by Internal-Target (ERIT).

  19. Is there evidence that we should screen the general population for Lynch syndrome with genetic testing? A systematic review

    PubMed Central

    Prince, Anya E R; Cadigan, R Jean; Henderson, Gail E; Evans, James P; Adams, Michael; Coker-Schwimmer, Emmanuel; Penn, Dolly C; Van Riper, Marcia; Corbie-Smith, Giselle; Jonas, Daniel E

    2017-01-01

    Background The emerging dual imperatives of personalized medicine and technologic advances make population screening for preventable conditions resulting from genetic alterations a realistic possibility. Lynch syndrome is a potential screening target due to its prevalence, penetrance, and the availability of well-established, preventive interventions. However, while population screening may lower incidence of preventable conditions, implementation without evidence may lead to unintentional harms. We examined the literature to determine whether evidence exists that screening for Lynch-associated mismatch repair (MMR) gene mutations leads to improved overall survival, cancer-specific survival, or quality of life. Documenting evidence and gaps is critical to implementing genomic approaches in public health and guiding future research. Materials and methods Our 2014–2015 systematic review identified studies comparing screening with no screening in the general population, and controlled studies assessing analytic validity of targeted next-generation sequencing, and benefits or harms of interventions or screening. We conducted meta-analyses for the association between early or more frequent colonoscopies and health outcomes. Results Twelve studies met our eligibility criteria. No adequate evidence directly addressed the main question or the harms of screening in the general population. Meta-analyses found relative reductions of 68% for colorectal cancer incidence (relative risk: 0.32, 95% confidence interval: 0.23–0.43, three cohort studies, 590 participants) and 78% for all-cause mortality (relative risk: 0.22, 95% confidence interval: 0.09–0.56, three cohort studies, 590 participants) for early or more frequent colonoscopies among family members of people with cancer who also had an associated MMR gene mutation. Conclusion Inadequate evidence exists examining harms and benefits of population-based screening for Lynch syndrome. Lack of evidence highlights the need

  20. 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.

  1. 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 ...

  2. 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

  3. 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.

  4. Adherence to guidelines on cervical cancer screening in general practice: programme elements of successful implementation.

    PubMed Central

    Hermens, R P; Hak, E; Hulscher, M E; Braspenning, J C; Grol, R P

    2001-01-01

    BACKGROUND: There is still only limited understanding of whether and why interventions to facilitate the implementation of guidelines for improving primary care are successful. It is therefore important to look inside the 'black box' of the intervention, to ascertain which elements work well or less well. AIM: To assess the associations of key elements of a nationwide multifaceted prevention programme with the successful implementation of cervical screening guidelines in general practice. DESIGN OF STUDY: A nationwide prospective cohort study. SETTING: A random sample of one-third of all 4,758 general practices in The Netherlands (n = 1,586). METHOD: General practitioners (GPs) in The Netherlands were exposed to a two-and-a-half-year nationwide multifaceted prevention programme to improve the adherence to national guidelines for cervical cancer screening. Adherence to guidelines at baseline and after the intervention and actual exposure to programme elements were assessed in the sample using self-administered questionnaires. RESULTS: Both baseline and post-measurement questionnaires were returned by 988 practices (response rate = 62%). No major differences in baseline practice characteristics between study population, non-responders, and all Netherlands practices were observed. After the intervention all practices improved markedly (P<0.001) in their incorporation of nine out of 10 guideline indicators for effective cervical screening into practice. The most important elements for successful implementation were: specific software modules (odds ratios and 95% confidence intervalsfor all nine indicators ranged from OR = 1.85 [95% CI = 1.24-2.77] to OR = 10.2 [95% CI = 7.58-14.1]); two or more 'practice visits' by outreach visitors (ORs and 95% CIs for six indicators ranged from OR = 1.46 [95% CI= 1.01-2.12] to OR = 2.35 [95% CI = 1.63-3.38]); and an educational programme for practice assistants (ORs and 95% CIs for four indicators ranged from OR = 1.57 [95% CI = 1

  5. 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.

  6. 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.

  7. 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...

  8. A spectrophotometric screening method for avermectin oxidizing microorganisms.

    PubMed

    Wang, Yuan-Shan; Hu, Qi-Wei; Zheng, Xing-Chang; Zhang, Jian-Fen; Zheng, Yu-Guo

    2017-04-01

    A spectrophotometric screening method for avermectin oxidizing microbes by determination of 4″-oxo-avermectin was established based on the reaction between 4″-oxo-avermectin and 2,4-dinitrophenylhydrazine. Combined with a gradient HPLC assay, microorganisms capable of regioselectively oxidizing avermectin to 4″-oxo-avermectin were successfully obtained by this method.

  9. 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.

  10. Integrating oral and general health screening at senior centers for minority elders.

    PubMed

    Marshall, Stephen E; Cheng, Bin; Northridge, Mary E; Kunzel, Carol; Huang, Catherine; Lamster, Ira B

    2013-06-01

    Racial/ethnic and socioeconomic disparities regarding untreated oral disease exist for older adults, and poor oral health diminishes quality of life. The ElderSmile program integrated screening for diabetes and hypertension into its community-based oral health activities at senior centers in northern Manhattan. The program found a willingness among minority seniors (aged ≥ 50 years) to be screened for primary care sensitive conditions by dental professionals and a high level of unrecognized disease (7.8% and 24.6% of ElderSmile participants had positive screening results for previously undiagnosed diabetes and hypertension, respectively). Dental professionals may screen for primary care-sensitive conditions and refer patients to health care providers for definitive diagnosis and treatment. The ElderSmile program is a replicable model for community-based oral and general health screening.

  11. The slide centrifuge gram stain as a urine screening method.

    PubMed

    Olson, M L; Shanholtzer, C J; Willard, K E; Peterson, L R

    1991-10-01

    A slide centrifuge Gram stain procedure was performed to screen for bacteriuria 4161 urine specimens submitted in urine preservative tubes for routine culture. For slide centrifuge Gram staining, each urine sample was mixed well. Thereafter, 0.2 mL of each sample was placed, using a pipette, into a slide centrifuge chamber and centrifuged at 2,000 rpm for 5 minutes. The slides were heat fixed, Gram stained, and read by laboratory personnel who scanned 12 consecutive oil-immersion fields using a set pattern. The presence of the same organism in six or more fields was defined as a positive urine screen. Urine samples were cultured using a 0.001-mL loop and a comparison of culture growth with slide centrifuge screening was made. When growth of 100,000 or more colony-forming units per milliliter (CFU/mL) was the reference for comparison, the screen had a sensitivity rate of 98%, a specificity rate of 90%, a negative predictive value of 99%, and a positive predictive value of 65%. When a lower colony count of 10,000 or more CFU/mL was the reference for comparison, the screen had a sensitivity rate of 88%, a specificity rate of 95%, a negative predictive value of 96%, and a positive predictive value of 84%. The slide centrifuge Gram stain is a very sensitive screening method to detect bacteriuria in an adult male population.

  12. Attitudes of general practitioners and midwives towards ethnicity-based haemoglobinopathy-carrier screening

    PubMed Central

    Jans, Suze MPJ; de Jonge, Ank; Henneman, Lidewij; Cornel, Martina C; Lagro-Janssen, Antoinette LM

    2012-01-01

    Haemoglobinopathies (HbP) are severe autosomal recessive disorders with high prevalence among certain ethnic groups. World Health Organisation (WHO) advises implementing screening programmes for risk groups. Research in the Netherlands has shown that general practitioners and midwives do not perceive ethnicity as a risk factor for HbP. Moreover, registration of ethnicity is a controversial societal issue, which may complicate the introduction of a national preconception or antenatal carrier screening programme. This study investigates attitudes, intention and behaviour of general practitioners and midwives towards ethnicity-based HbP-carrier screening in general. A structured questionnaire based on the Theory of Planned Behaviour was sent by mail to a random selection of 2100 general practitioners and 1800 primary care midwives. Response was 35% (midwives 44.2% GPs 27.6%). Although 45% of respondents thought that offering a carrier test on the basis of ethnicity alone should become national policy, it is currently not carried out. The main factor explaining lack of intention towards ethnicity-based HbP-carrier screening was subjective norm, the perception that their peers do not think they should offer screening (52.2% variance explained). If ethnicity-based HbP-carrier screening would become national policy, most professionals report that they would carry this out. Most respondents favoured ethnicity registration for health purposes. As most practitioners look for role models among peers, debate among general practitioners and midwives should be encouraged when new policy is to be developed, articulating the voices of colleagues who already actively offer HbP-carrier screening. Moreover, primary care professionals and professional organisations need support of policy at national level. PMID:22549405

  13. 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…

  14. 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...

  15. Carotenoid analysis using the puree absorbance method for germplasm screening

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many fruits and vegetables contain health-promoting compounds which require labor intensive analyses to detect. This is the case with quantifying carotenoids in fresh fruits and vegetables. Carotenoid content can vary significantly between varieties; therefore a method to rapidly screen germplasm ...

  16. Multislope MUSCL method for general unstructured meshes

    NASA Astrophysics Data System (ADS)

    Le Touze, C.; Murrone, A.; Guillard, H.

    2015-03-01

    The multislope concept has been recently introduced in the literature to deal with MUSCL reconstructions on triangular and tetrahedral unstructured meshes in the finite volume cell-centered context. Dedicated scalar slopes are used to compute the interpolations on each face of a given element, in opposition to the monoslope methods in which a unique limited gradient is used. The multislope approach reveals less expensive and potentially more accurate than the classical gradient techniques. Besides, it may also help the robustness when dealing with hyperbolic systems involving complex solutions, with large discontinuities and high density ratios. However some important limitations on the mesh topology still have to be overcome with the initial multislope formalism. In this paper, a generalized multislope MUSCL method is introduced for cell-centered finite volume discretizations. The method is freed from constraints on the mesh topology, thereby operating on completely general unstructured meshes. Moreover optimal second-order accuracy is reached at the faces centroids. The scheme can be written with nonnegative coefficients, which makes it L∞-stable. Special attention has also been paid to equip the reconstruction procedure with well-adapted dedicated limiters, potentially CFL-dependent. Numerical tests are provided to prove the ability of the method to deal with completely general meshes, while exhibiting second-order accuracy.

  17. Impact of general practitioners' sex and age on systematic recommendation for cancer screening.

    PubMed

    Eisinger, François; Pivot, Xavier; Coscas, Yvan; Viguier, Jérôme; Calazel-Benque, Anne; Blay, Jean-Yves; Roussel, Claire; Morère, Jean-François

    2011-01-01

    Characteristics of primary-care providers have been associated with their patients' participation in breast cancer screening. A nationwide observational survey, 'EDIFICE', was conducted by telephone from December 2007 to January 2008 on a representative sample of 600 general practitioners (GPs) working in France, to investigate how a GP's characteristics may influence patient participation in screening for breast, colorectal and prostate cancer. For breast cancer screening, systematic recommendation was associated with female physicians [odds ratio (OR) =1.9; 95% confidence interval (CI) 1.2-3.1]. This systematic recommendation was also correlated with systematic referral for colorectal cancer (OR=1.5; 95% CI=1.0-2.5) and prostate cancer screening (OR=2.7; 95% CI=1.8-4.1). For colorectal cancer screening, the sex of the GP had no significant impact. However, systematic recommendation for both breast and prostate cancer screening was shown to be associated with systematic recommendation for colorectal cancer screening (OR=2.7; 95% CI=1.6-4.7 and OR=1.8; 95% CI=1.1-3.0, respectively). For prostate cancer screening, there was no significant sex specificity. However, systematic recommendation for both breast and colorectal cancer screening was associated with an advice on prostate cancer screening (OR=2.9; 95% CI=2.0-4.4 and OR=2.0; 95% CI=1.3-3.2, respectively). The age of the GP was not associated with a higher rate of systematic recommendation for screening for the three types of cancer. Male GPs were more likely than female GPs to perform digital rectal examinations on male patients (69 vs. 54%; OR=1.86; 95% CI=1.31-2.63). There is a global pattern of physicians being screening-prone (as suggested by the cross impact of recommendations from one cancer type to another). Although the frequency of systematic recommendation for breast cancer screening is higher with female GPs, systematic recommendation for prostate cancer is not higher among male GPs. The factors

  18. 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

  19. Sensitivity of endoscopic screening for gastric cancer by the incidence method.

    PubMed

    Hamashima, Chisato; Okamoto, Mikizo; Shabana, Michiko; Osaki, Yoneatsu; Kishimoto, Takuji

    2013-08-01

    Although radiographic screening for gastric cancer has been conducted in Japan, it is anticipated that endoscopy will become a new screening method because of its high detection rate. The sensitivities of endoscopic and radiographic screening were calculated by the detection method and the incidence method based on the results of community-based screening in Japan. There were 56,676 screenings for gastric cancer using endoscopy and radiography from April 2002 to March 2007 in Yonago, Japan. The target age group was from 40 to 79 years. Screen-detected and interval cancers were investigated based on a screening database linked to the Tottori Cancer Registry. All gastric cancers diagnosed within 1 year after a negative screen were considered interval cancers. Based on the screening history, these were divided into prevalence screening and incidence screening. Prevalence screenings included 7,388 for endoscopic screening and 5,410 for radiographic screening, whereas incidence screenings included 18,021 for endoscopic screening and 11,417 for radiographic screening. The sensitivity of prevalence screening calculated by the incidence method was 0.886 (95% confidence interval [CI] = 0.698-0.976) for endoscopic screening and 0.831 (95% CI = 0.586-0.964) for radiographic screening; however, the difference was not significant (p = 0.626). The sensitivity of incidence screening calculated by the incidence method was 0.954 (95% CI = 0.842-0.994) for endoscopic screening and 0.855 (95% CI = 0.637-0.970) for radiographic screening (p = 0.177). Endoscopic screening for gastric cancer had a higher sensitivity than radiographic screening by the incidence method in both screening rounds. However, further study is needed to evaluate mortality reduction and to estimate overdiagnosis with endoscopic screening for gastric cancer.

  20. 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.

  1. 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

  2. General relativistic neutrino transport using spectral methods

    NASA Astrophysics Data System (ADS)

    Peres, Bruno; Penner, Andrew Jason; Novak, Jérôme; Bonazzola, Silvano

    2014-02-01

    We present a new code, Lorene's Ghost (for Lorene's gravitational handling of spectral transport) developed to treat the problem of neutrino transport in supernovae with the use of spectral methods. First, we derive the expression for the nonrelativistic Liouville operator in doubly spherical coordinates (r, θ, ϕ, ɛ, Θ, Φ), and further its general relativistic counterpart. We use the 3 + 1 formalism with the conformally flat approximation for the spatial metric, to express the Liouville operator in the Eulerian frame. Our formulation does not use any approximations when dealing with the angular arguments (θ, ϕ, Θ, Φ), and is fully energy-dependent. This approach is implemented in a spherical shell, using either Chebyshev polynomials or Fourier series as decomposition bases. It is here restricted to simplified collision terms (isoenergetic scattering) and to the case of a static fluid. We finish this paper by presenting test results using basic configurations, including general relativistic ones in the Schwarzschild metric, in order to demonstrate the convergence properties, the conservation of particle number and correct treatment of some general relativistic effects of our code. The use of spectral methods enables to run our test cases in a six-dimensional setting on a single processor.

  3. A Generalized Slave-Particle Method

    NASA Astrophysics Data System (ADS)

    Georgescu, Alexandru Bogdan; Ismail-Beigi, Sohrab

    2015-03-01

    Two slave-particle methods, namely the slave-rotor and the slave-spin approaches, have been of recent interest in the computational correlated electron community. Both methods solve Hubbard-type models and go beyond the single-particle approximations by describing aspects of correlated electron behavior in a computationally efficient manner. We present a generalized slave-particle formalism that connects the the two while reproducing the results of each method in the appropriate limit. The framework automatically corrects the problematic small U behavior of the slave-rotor approach while reproducing its behavior in situations where it has been found physically relevant (e.g., for nickelate heterostructures). This work is supported by the National Science Foundation through Grant MRSEC NSF DMR-1119826.

  4. Synthesizing High-Frequency (1-25 HZ) Regional Phases at Large Distances (>1000 KM) Using Generalized Screen Propagators (GSP)

    DTIC Science & Technology

    2004-09-01

    seismology and earthquake seismology . The generalized screen propagator (GSP) is based on the one-way wave equation and the one-return approximation. The...High-Frequency (1-25 HZ) Regional Phases at Large Distances O (>1000 KM) Using Generalized Screen Propagators (GSP) SApproved for public release...DTRA 01-97-1-0004 Synthesizing High-Freguency (1-25 HZ) Regional Phases at Large Distances (1 > 1000 KM) Using Generalized Screen Propagators (GSP) 5b

  5. Cognitive screening for children and adolescents: general limits or ceiling effects?

    PubMed

    Bornholt, Laurel J; Ajersch, Susan; Fisher, Ian H; Markham, Roslyn H; Ouvrier, Robert A

    2010-05-01

    Cognitive screening tools designed for children can also be used with adolescents. However, early studies suggest that scores can approach a maximum at about age 10 or 11 years. The initial hypothesis was this apparent ''ceiling effect'' is due to limits in the materials, where items can be insufficiently challenging for some adolescents. The alternative hypothesis is that general cognitive screening has a true limit by early adolescence. Participants (N = 85) were 10 to 15-year-old girls and boys, with a database (N = 1249) of 4 to 12-year-old children. The School-Years Screening Test for the Evaluation of Mental Status (SYSTEMS) cognitive screening was extended by more difficult items. Results show that scores increase rapidly for young children and tend toward a maximum in early adolescence. This characteristic asymptotic curve explained a substantial proportion of the variance. We can conclude that, although specific functions continue to develop, there is an upper limit in early adolescence for such general cognitive functioning. The findings support cognitive screening across a broad age range and suggest worthwhile research and clinical applications.

  6. New high throughput screening method for drug release measurements.

    PubMed

    Pelczarska, Aleksandra; Delie, Florence; Domańska, Urszula; Carrupt, Pierre-Alain; Martel, Sophie

    2013-09-01

    In the field of drug delivery systems, microparticles made of polymeric matrix appear as an attractive approach. The in vitro release kinetic profile is crucial information when developing new particulate formulations. These data are essential for batch to batch comparison, quality control as well as for anticipation of in vivo behavior to select the best formulation to go further in preclinical investigations. The methods available present common drawbacks such as the time- and compound-consumption that does not fit with formulation screening requirements in early development stages. In this study, a new microscale high throughput screening (HTS) method has been developed to investigate drug release kinetic from piroxicam-loaded polylactic acid (PLA) and polylactic-co-glycolic acid (PLGA) microparticles. The method is a sample- and separation-based method where separation is performed by filtration using 96-well micro filter plates. 96 experiments can therefore be performed on one plate in one time in a fully automated way and with a very low sample and particle consumption. The influence of different parameters controlling release profiles was also investigated using this technique. The HTS method gave the same release profile than the standard dialysis method. Shaking, particle concentration, and the nature of the release medium were found to be of influence. The HTS method appears as a reliable method to evaluate drug release from particles with smaller standard deviation and less consumption of material.

  7. A general method to determine twinning elements

    PubMed Central

    Zhang, Yudong; Li, Zongbin; Esling, Claude; Muller, Jacques; Zhao, Xiang; Zuo, Liang

    2010-01-01

    The fundamental theory of crystal twinning has been long established, leading to a significant advance in understanding the nature of this physical phenomenon. However, there remains a substantial gap between the elaborate theory and the practical determination of twinning elements. This paper proposes a direct and simple method – valid for any crystal structure and based on the minimum shear criterion – to calculate various twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. Without additional efforts, it is generally applicable to identify and predict possible twinning modes occurring in a variety of crystalline solids. Therefore, the present method is a promising tool to characterize twinning elements, especially for those materials with complex crystal structure. PMID:22477779

  8. 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.

  9. A general strategy for antibody library screening via conversion of transient target binding into permanent reporter deposition.

    PubMed

    Maaß, Alexander; Heiseler, Tim; Maaß, Franziska; Fritz, Janine; Hofmeyer, Thomas; Glotzbach, Bernhard; Becker, Stefan; Kolmar, Harald

    2014-02-01

    We report here a generally applicable method for the selective covalent attachment of a reporter molecule to a replicating entity that allows one to obtain specific binders from a single round of library screening. We show that selective biotinylation of phage particles displaying a binder to any given target can be achieved by application of a coupled enzyme reaction on the surface of the target-binding phage particles that includes a peroxidase, an oxidase and a catalase. Due to the covalent linkage of biotin together with the tight and stable interaction of biotin with streptavidin, very stringent wash conditions for removal of nonspecific binders can be applied. The method termed (3)CARD (triple catalytic reporter deposition) was successfully applied to single-round screening of a phage display library of camelid single-domain antibodies against three different target proteins.

  10. Two-Electron System in the Field of Generalized Screened Potential

    NASA Astrophysics Data System (ADS)

    Ghoshal, Arijit; Ho, Y. K.

    Ground states of a two-electron system in generalized screened potential (GSP) with screening parameter λ: $$ V(r)=\\frac{1}{r}e^{-\\lambda r}\\cos(\\epsilon \\lambda r)\\,\\, {\\rm (in\\, a.u.)}, $$ where ɛ is a constant, have been investigated. Employing highly correlated and extensive wave functions in Ritz's variational principle, we have been able to determine accurate ground state energies and wave functions of a two-electron system for different values of the screening parameter λ and the constant ɛ. Convergence of the ground state energies with the increase of the number of terms in the wave function are shown. We also report various geometrical expectation values associated with the system, ground state energies of the corresponding one-electron system and the ionization potentials of the system. Such a calculation for the ground state of a two-electron system in GSP is carried out for first time in the literature.

  11. Screening method for assessing verbal learning efficiency using the Cognistat.

    PubMed

    Fouty, H Edward; Smith, Cassandra R; Briceno, Karen Y; Brown, Katelyn D; Guzman, Daniel; Ailes, Erica L; DeVries, Christopher T; Diluccia, Christina M; McLarnan, Kristy M; Betancourt, Stephanie C; Catoe, Whitney L

    2017-04-07

    The Cognistat is a widely used neurobehavioral screening instrument that addresses functioning across multiple domains. Unlike many popular neuropsychological tests, the Cognistat does not currently assess learning efficiency for verbal material. The purpose of this study was to develop a screening method for assessing verbal learning efficiency with the Cognistat, investigate the effects of two demographic variables (age and gender) on performance, and to establish cutoff scores for impairment. Participants were 253 volunteers between the ages of 18 and 96 years. Participants were classified into two age groups: 18-64 years and 65 + years. The data revealed a significant age and gender performance difference. Implications for the present findings and for future research are presented.

  12. Screening methods for assessment of biodegradability of chemicals in seawater--results from a ring test.

    PubMed

    Nyholm, N; Kristensen, P

    1992-04-01

    An international ring test involving 14 laboratories was organized on behalf of the Commission of the European Economic Communities (EEC) with the purpose of evaluating two proposed screening methods for assessment of biodegradability in seawater: (a) a shake flask die-away test based primarily on analysis of dissolved organic carbon and (b) a closed bottle test based on determination of dissolved oxygen. Both tests are performed with nutrient-enriched natural seawater as the test medium and with no inoculum added other than the natural seawater microflora. The test methods are seawater versions of the modified OECD screening test and the closed bottle test, respectively, adopted by the Organization for Economic Cooperation and Development (OECD) and by the EEC as tests for "ready biodegradability." The following five chemicals were examined: sodium benzoate, aniline, diethylene glycol, pentaerythritol, and 4-nitrophenol. Sodium benzoate and aniline, which are known to be generally readily biodegradable consistently degraded in practically all tests, thus demonstrating the technical feasibility of the methods. Like in previous ring tests with freshwater screening methods variable results were obtained with the other three compounds, which is believed primarily to be due to site-specific differences between the microflora of the different seawater samples used and to some extent also to differences in the applied concentrations of test material. A positive result with the screening methods indicates that the test substance will most likely degrade relatively rapidly in seawater from the site of collection, while a negative test result does not preclude biodegradability under environmental conditions where the concentrations of chemicals are much lower than the concentrations applied for analytical reasons in screening tests. Nevertheless, the screening tests are considered useful and cost-effective tools for an initial assessment of biodegradability in marine

  13. Review of the Generalized Least Squares Method

    NASA Astrophysics Data System (ADS)

    Menke, William

    2014-09-01

    The generalized least squares (GLS) method uses both data and prior information to solve for a best-fitting set of model parameters. We review the method and present simplified derivations of its essential formulas. Concepts of resolution and covariance—essential in all of inverse theory—are applicable to GLS, but their meaning, and especially that of resolution, must be carefully interpreted. We introduce derivations that show that the quantity being resolved is the deviation of the solution from the prior model and that the covariance of the model depends on both the uncertainty in the data and the uncertainty in the prior information. On face value, the GLS formulas for resolution and covariance seem to require matrix inverses that may be difficult to calculate for the very large (but often sparse) linear systems encountered in practical inverse problems. We demonstrate how to organize the computations in an efficient manner and present MATLAB code that implements them. Finally, we formulate the well-understood problem of interpolating data with minimum curvature splines as an inverse problem and use it to illustrate the GLS method.

  14. Review of the Generalized Least Squares Method

    NASA Astrophysics Data System (ADS)

    Menke, William

    2015-01-01

    The generalized least squares (GLS) method uses both data and prior information to solve for a best-fitting set of model parameters. We review the method and present simplified derivations of its essential formulas. Concepts of resolution and covariance—essential in all of inverse theory—are applicable to GLS, but their meaning, and especially that of resolution, must be carefully interpreted. We introduce derivations that show that the quantity being resolved is the deviation of the solution from the prior model and that the covariance of the model depends on both the uncertainty in the data and the uncertainty in the prior information. On face value, the GLS formulas for resolution and covariance seem to require matrix inverses that may be difficult to calculate for the very large (but often sparse) linear systems encountered in practical inverse problems. We demonstrate how to organize the computations in an efficient manner and present MATLAB code that implements them. Finally, we formulate the well-understood problem of interpolating data with minimum curvature splines as an inverse problem and use it to illustrate the GLS method.

  15. 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.

  16. Rapid and alternative screening methods for microbiological analysis.

    PubMed

    van der Zee, H; Huis in't Veld, J H

    1997-01-01

    Automated analytical instruments for enumerating indicator organisms and diagnostic test kits for pathogens can be used in food microbiology to screen samples and to replace conventional cultural and confirmation steps. Such methods are now available for rapid detection or estimation of groups of (indicator) organisms, pathogenic micro-organisms, bacterial toxins and mycotoxins, and molds. These alternative methods can be classified by the principles on which they are based: modified conventional methods, instrumental measurement of bacterial metabolism, bioluminescence, immunological techniques, DNA techniques, and combinations of these techniques. To meet user expectations, test kits must be accurate, sensitive, specific, rapid (24 h or less), easy to use, and labor-saving. They must also offer the possibility of computerization, a low detection limit, and low investment and running costs. The paper compares the ability of alternative methods to meet these criteria. Variations were found, depending on the techniques used and the target organism of the analysis. Economic reasons can determine whether alternative methods can be used routinely. Adoption of these screening systems also can be hampered by lack of internationally coordinated and accepted validation protocols.

  17. 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

  18. Potential screening and early diagnosis method for cancer: Tongue diagnosis

    PubMed Central

    HAN, SHUWEN; YANG, XI; QI, QUAN; PAN, YUEFEN; CHEN, YONGCHAO; SHEN, JUNJUN; LIAO, HAIHONG; JI, ZHAONING

    2016-01-01

    Tongue diagnosis, as a unique method of traditional Chinese medicine (TCM), was used to discriminate physiological functions and pathological conditions by observing the changes of the tongue and tongue coating. The aims of the present study were to explore a potential screening and early diagnosis method of cancer through evaluating the differences of the images of tongue and tongue coating and the microbiome on the tongue coating. The DS01-B tongue diagnostic information acquisition system was used to photograph and analyze the tongue and tongue coating. The next-generation sequencing technology was used to determine the V2-V4 hypervariable regions of 16S rDNA to investigate the microbiome on the tongue coating. Bioinformatics and statistical methods were used to analyze the microbial community structure and diversity. Comparing with the healthy people, the number of mirror-like tongue, thick tongue coating and the moisture of tongue were increased in cancers. The dominant color of the tongue in the healthy people was reddish while it was purple in the cancers. The relative abundance of Neisseria, Haemophilus, Fusobacterium and Porphyromonas in the healthy people were higher than that in the cancers. We also found 6 kinds of special microorganisms at species level in cancers. The study suggested that tongue diagnosis may provide potential screening and early diagnosis method for cancer. PMID:27035407

  19. [Simultaneous screening method for Bordetella species by conventional PCR assay].

    PubMed

    Akiyama, Yumi; Saito, Etsuko; Enomoto, Miki; Tsuji, Hidetaka; Chikahira, Masatsugu; Yoshida, Masashi

    2013-11-01

    A simultaneous screening method using conventional PCR was developed for the detection and discrimination of Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii. A formulated multiprex method employing 4 kinds of paired primers on amplification of 4 corresponding different insertion sequences (IS481, IS1001, IS1002 and hIS1001) enabled rapid screening and identification. The detection limits of each DNA extracted from 3 kinds of Bordetella species were 5fg/microL for each. Obscure existences of B. pertussis and B. holmesii at low levels were confirmed with the LAMP method. This multiplex assay was applied to the clinical specimens obtained from patients with pertussis-like symptoms at sentinel clinics under the epidemiological surveillance of infectious diseases of Hyogo prefecture in FY2012. Among 42 nasopharyngeal swabs, B. pertussis was detected from 12 samples including 8 samples collected at outbreak in nursery school. The use of this method for the surveillance of infectious agents enabled us to search for 3 kinds of Bordetella species at once with low costs.

  20. 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.

  1. Potential screening and early diagnosis method for cancer: Tongue diagnosis.

    PubMed

    Han, Shuwen; Yang, Xi; Qi, Quan; Pan, Yuefen; Chen, Yongchao; Shen, Junjun; Liao, Haihong; Ji, Zhaoning

    2016-06-01

    Tongue diagnosis, as a unique method of traditional Chinese medicine (TCM), was used to discriminate physiological functions and pathological conditions by observing the changes of the tongue and tongue coating. The aims of the present study were to explore a potential screening and early diagnosis method of cancer through evaluating the differences of the images of tongue and tongue coating and the microbiome on the tongue coating. The DS01-B tongue diagnostic information acquisition system was used to photograph and analyze the tongue and tongue coating. The next-generation sequencing technology was used to determine the V2-V4 hypervariable regions of 16S rDNA to investigate the microbiome on the tongue coating. Bioinformatics and statistical methods were used to analyze the microbial community structure and diversity. Comparing with the healthy people, the number of mirror-like tongue, thick tongue coating and the moisture of tongue were increased in cancers. The dominant color of the tongue in the healthy people was reddish while it was purple in the cancers. The relative abundance of Neisseria, Haemophilus, Fusobacterium and Porphyromonas in the healthy people were higher than that in the cancers. We also found 6 kinds of special microorganisms at species level in cancers. The study suggested that tongue diagnosis may provide potential screening and early diagnosis method for cancer.

  2. 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.

  3. Treecode-based generalized Born method

    NASA Astrophysics Data System (ADS)

    Xu, Zhenli; Cheng, Xiaolin; Yang, Haizhao

    2011-02-01

    We have developed a treecode-based O(Nlog N) algorithm for the generalized Born (GB) implicit solvation model. Our treecode-based GB (tGB) is based on the GBr6 [J. Phys. Chem. B 111, 3055 (2007)], an analytical GB method with a pairwise descreening approximation for the R6 volume integral expression. The algorithm is composed of a cutoff scheme for the effective Born radii calculation, and a treecode implementation of the GB charge-charge pair interactions. Test results demonstrate that the tGB algorithm can reproduce the vdW surface based Poisson solvation energy with an average relative error less than 0.6% while providing an almost linear-scaling calculation for a representative set of 25 proteins with different sizes (from 2815 atoms to 65456 atoms). For a typical system of 10k atoms, the tGB calculation is three times faster than the direct summation as implemented in the original GBr6 model. Thus, our tGB method provides an efficient way for performing implicit solvent GB simulations of larger biomolecular systems at longer time scales.

  4. Screening in brief intervention trials targeting excessive drinkers in general practice: systematic review and meta-analysis

    PubMed Central

    Beich, Anders; Thorsen, Thorkil; Rollnick, Stephen

    2003-01-01

    Objective To determine the effectiveness of programmes of screening in general practice for excessive alcohol use and providing brief interventions. Design Systematic review and meta-analysis of randomised controlled trials that used screening as a precursor to brief intervention. Setting General practice. Main outcome measures Number needed to treat, proportion of patients positive on screening, proportion given brief interventions, and effect of screening. Results The eight studies included for meta-analysis all used health questionnaires for screening, and the brief interventions included feedback, information, and advice. The studies contained several sources of bias that might lead to overestimates of the effects of intervention. External validity was compromised because typically three out of four people identified by screening as excessive users of alcohol did not qualify for the intervention after a secondary assessment. Overall, in 1000 screened patients, 90 screened positive and required further assessment, after which 25 qualified for brief intervention; after one year 2.6 (95% confidence interval 1.7 to 3.4) reported they drank less than the maximum recommended level. Conclusions Although even brief advice can reduce excessive drinking, screening in general practice does not seem to be an effective precursor to brief interventions targeting excessive alcohol use. This meta-analysis raises questions about the feasibility of screening in general practice for excessive use of alcohol. PMID:12958114

  5. Screening for inhibitors of histone deacetylase by incorporating a spraying method to micro-arrayed compound screening.

    PubMed

    Sabet, R S; Marcotte, P; Glaser, K; Burns, D J; Warrior, U; Groebe, D R

    2004-03-01

    We have developed a method of spraying assay reagents onto a target gel in the Micro-Arrayed Compound Screening ( micro ARCS) format. After application of target gels to compound sheets, subsequent reagents can be applied by spraying onto the target gel. The spraying method conserves on assay reagents by up to 10-fold, eliminates the need for casting additional agarose gels, and increases the throughput of a screen by 3-fold. To demonstrate the efficacy of applying the spraying method to micro ARCS, we screened over 600,000 compounds for inhibitors of histone deacetylase (HDAC). Commercially available HDAC substrate and reaction developer were sprayed directly onto the gel to initiate the reaction and to amplify the signal, respectively. Picks in the primary screen were retested at a density of 384 compounds per sheet in the micro ARCS format. IC(50) values for active compounds were confirmed in a 96-well plate assay. The screen identified several small molecule inhibitors of the enzyme, including members of several classes of known HDAC inhibitors. The combination of the high-density format of micro ARCS, the efficiency of the spraying method, and a timed sequence of adding assay reagents permitted a screening throughput of 200,000 tests an hour. We present the details of the screening format and the analysis of the hits from the screen.

  6. Generalized integral-screening for efficient calculations of nonlinear optical properties of large molecules

    NASA Astrophysics Data System (ADS)

    Ruud, Kenneth; Jonsson, Dan; Norman, Patrick; A˚Gren, Hans; Saue, Trond; Jensen, Hans Jørgen Aa.; Dahle, Pa˚L.; Helgaker, Trygve

    1998-05-01

    We describe the implementation of integral screening in the integral-direct SCF calculation of cubic response functions. The screening is applied to all computational steps that involve the construction of Fock matrices or one-index transformed Fock matrices. We apply this implementation to study the length dependence of the polarizability and second hyperpolarizability of diphenylpolyenes. It is demonstrated that calculations of the second hyperpolarizability of molecules containing more than 140 atoms are now accessible by ab initio methods on a time scale that makes it of interest in real applications.

  7. Screening, prevention and treatment of cervical cancer -- a global and regional generalized cost-effectiveness analysis.

    PubMed

    Ginsberg, Gary Michael; Edejer, Tessa Tan-Torres; Lauer, Jeremy A; Sepulveda, Cecilia

    2009-10-09

    The paper calculates regional generalized cost-effectiveness estimates of screening, prevention, treatment and combined interventions for cervical cancer. Using standardised WHO-CHOICE methodology, a cervical cancer model was employed to provide estimates of screening, vaccination and treatment effectiveness. Intervention effectiveness was determined via a population state-transition model (PopMod) that simulates the evolution of a sub-regional population accounting for births, deaths and disease epidemiology. Economic costs of procedures and treatment were estimated, including programme overhead and training costs. In regions characterized by high income, low mortality and high existing treatment coverage, the addition of any screening programme to the current high treatment levels is very cost-effective. However, based on projections of the future price per dose (representing the economic costs of the vaccination excluding monopolistic rents and vaccine development cost) vaccination is the most cost-effective intervention. In regions characterized by low income, low mortality and existing treatment coverage around 50%, expanding treatment with or without combining it with screening appears to be cost-effective or very cost-effective. Abandoning treatment in favour of screening in a no-treatment scenario would not be cost-effective. Vaccination is usually the most cost-effective intervention. Penta or tri-annual PAP smears appear to be cost-effective, though when combined with HPV-DNA testing they are not cost-effective. In regions characterized by low income, high mortality and low treatment levels, expanding treatment with or without adding screening would be very cost-effective. A one off vaccination plus expanding treatment was usually very cost-effective. One-off PAP or VIA screening at age 40 are more cost-effective than other interventions though less effective overall. From a cost-effectiveness perspective, consideration should be given to implementing

  8. 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.

  9. Autoradiographic method to screen for soil microorganisms which accumulate zinc

    SciTech Connect

    Zamani, B.; Knezek, B.D.; Flegler, S.L.; Beneke, E.S.; Dazzo, F.B.

    1985-01-01

    An autoradiographic method was developed to screen for and isolate soil microorganisms which accumulate zinc (ZN). Diluted soil samples (pH 5.9) were plated on soil extract-glucose agar containing radioactive /sup 65/Zn. After 7 days of incubation, individual colonies which accumulated sufficient /sup 65/Zn could be detected by autoradiography. These colonies were isolated and confirmed as Zn accumulators in pure culture by using the autoradiographic plate technique. Most Zn accumulators were filamentous fungi, identified as Penicillium janthinellum, Aspergillus fumigatus, and Paecilomyces sp. Isolates of Penicillium janthinellum were the most common Zn accumulators. The most abundant Zn-accumulating bacteria were Bacillus spp. The validity of the autoradiographic plate technique to differentiate soil microbes which accumulate Zn was examined independently by energy dispersive X-ray analysis in a scanning electron microscope. This method confirmed that fungal isolates which gave positive autoradiographic responses in the plate assay bioaccumulated more Zn in their biomass than fungal isolates from the same soil sample which gave negative autoradiographic responses. Thus, this technique can be applied to specifically screen for and isolate microbes from the environment which bioaccumulate Zn.

  10. A RCT of three training and support strategies to encourage implementation of screening and brief alcohol intervention by general practitioners.

    PubMed Central

    Kaner, E F; Lock, C A; McAvoy, B R; Heather, N; Gilvarry, E

    1999-01-01

    BACKGROUND: Providing doctors with new research findings or clinical guidelines is rarely sufficient to promote changes in clinical practice. An implementation strategy is required to provide clinicians with the skills and encouragement needed to alter established routines. AIM: To evaluate the effectiveness and cost-effectiveness of different training and support strategies in promoting implementation of screening and brief alcohol intervention (SBI) by general practitioners (GPs). METHOD: Subjects were 128 GPs, one per practice, from the former Northern and Yorkshire Regional Health Authority, who agreed to use the 'Drink-Less' SBI programme in an earlier dissemination trial. GPs were stratified by previous marketing conditions and randomly allocated to three intensities of training and support: controls (n = 43) received the programme with written guidelines only, trained GPs (n = 43) received the programme plus practice-based training in programme usage, trained and supported GPs (n = 42) received the programme plus practice-based training and a support telephone call every two weeks. GPs were requested to use the programme for three months. Outcome measures included proportions of GPs implementing the programme and numbers of patients screened and intervened with. RESULTS: Seventy-three (57%) GPs implemented the programme and screened 11,007 patients for risk drinking. Trained and supported GPs were significantly more likely to implement the programme (71%) than controls (44%) or trained GPs (56%); they also screened, and intervened with, significantly more patients. Costs per patient screened were: trained and supported GPs, 1.05 Pounds; trained GPs, 1.08 Pounds; and controls, 1.47 Pounds. Costs per patient intervened with were: trained and supported GPs, 5.43 Pounds; trained GPs, 6.02 Pounds; and controls, 8.19 Pounds. CONCLUSION: Practice-based training plus support telephone calls was the most effective and cost-effective strategy to encourage

  11. 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.

  12. General method for plasmid construction using homologous recombination.

    PubMed

    Raymond, C K; Pownder, T A; Sexson, S L

    1999-01-01

    We describe a general method for plasmid assembly that uses yeast and extends beyond yeast-specific research applications. This technology exploits the homologous recombination, double-stranded break repair pathway in Saccharomyces cerevisiae to join DNA fragments. Synthetic, double-stranded "recombination linkers" were used to "subclone" a DNA fragment into a plasmid with > 80% efficiency. Quantitative data on the influence of DNA concentration and overlap length on the efficiency of recombination are presented. Using a simple procedure, plasmids were shuttled from yeast into E. coli for subsequent screening and large-scale plasmid preps. This simple method for plasmid construction has several advantages. (i) It bypasses the need for extensive PCR amplification and for purification, modification and/or ligation techniques routinely used for plasmid constructions. (ii) The method does not rely on available restriction sites, thus fragment and vector DNA can be joined within any DNA sequence. This enables the use of multifunctional cloning vectors for protein expression in mammalian cells, other yeast species, E. coli and other expression systems as discussed. (iii) Finally, the technology exploits yeast strains, plasmids and microbial techniques that are inexpensive and readily available.

  13. Screening for Autistic Spectrum Disorder in Children Aged 14-15 Months. II: Population Screening with the Early Screening of Autistic Traits Questionnaire (ESAT). Design and General Findings

    ERIC Educational Resources Information Center

    Dietz, Claudine; Swinkels, Sophie; van Daalen, Emma; van Engeland, Herman; Buitelaar, Jan K.

    2006-01-01

    A two-stage protocol for screening for autistic spectrum disorders (ASD) was evaluated in a random population of 31,724 children aged 14-15 months. Children were first pre-screened by physicians at well-baby clinics using a 4-item screening instrument. Infants that screened positive were then evaluated during a 1.5-h home visit by a trained…

  14. 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.

  15. 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.

  16. 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

    2010-07-05

    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)).

  17. Screening for prediabetes in the general child population: maternal attitude to participation.

    PubMed

    Ludvigsson, J; Ludvigsson, M; Sepa, A

    2001-12-01

    Screening to predict serious diseases in the general population has been regarded as unethical as it is supposed to make people anxious. Therefore we have evaluated whether mothers become anxious when their babies participate in a project to predict diabetes in the general child population. Out of 21 700 newborn children, 16 300 (75%) entered the ABIS project (All Babies in South-east Sweden). The parents (usually the mothers) answered a questionnaire at the child's birth and then again after 1 yr. A total of 10 868 representative birth questionnaires had been analyzed. To the question, 'How do you feel when you know that your child is participating in this study?', only 2.5% of mothers of children with type 1 diabetes in the family answered 'more anxious/much more anxious', and even fewer (1.5%) of the mothers in the general population (p < 0.01). A total of 52.5% of the general population answered 'calmer/more reassured' (29.3% 'calmer' and 23.2% 'much calmer'), while 43.3% felt unaffected. Those 1.5% of mothers who reported becoming more anxious were more likely to be in an unstable social situation (unemployed, p < 0.001; born abroad, p < 0.001; low education, p < 0.001). At the 1-yr follow-up, 4948 unselected questionnaires had been analyzed. Only 1.2% of the mothers felt 'more anxious', while the overwhelming majority felt either unaffected (58.7%) or calmer (38.6%). At this follow-up, most of those who had felt 'more anxious' at birth did not feel that way any longer, and none of those with diabetes in the family. We conclude that large-scale screening studies for the prediction of diabetes in the general population can be performed without causing increased anxiety. A few parents, most often found in the group with known social problems, might need extra information and support.

  18. A Desktop Screen Sharing System based on Various Connection Methods

    NASA Astrophysics Data System (ADS)

    Negishi, Yuya; Kawaguchi, Nobuo

    Recently it became very common to use information devices such as PCs during presentations and discussions. In these situations, a need arises for techniques that allow a smooth switch of presenters without changing cables, or an easy screen sharing in case of remote videoconferences. In this paper, we propose a desktop screen sharing system that can be used for such purposes and situations. For that, we designed an automatic control of connections in the VNC system that can be operated remotely over the network. We also suggested an interface that assigns a role such as “Screen sender" or “Screen receiver" to each terminal. In the proposed system, while sharing a screen between multiple terminals, one can easily display and browse the screen without having to understand how the others are connected. We also implemented a “role card" using contactless IC card, where roles are assigned only by placing the card in the IC reader.

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

    PubMed

    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

    2015-06-01

    This study aims 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. 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. To increase OCS by dentists in PR, the FG participants proposed a 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 re-licensure, improving OCS dentist-patient communication skills, and establishment of an oral lesion referral center were also viewed favorably. In conclusion, 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.

  20. [General concepts and study methods in pharmacogenetics].

    PubMed

    Lubomirov, Rubin; Telenti, Amalio; Rotger, Margalida

    2008-05-01

    Pharmacogenetics, the study of how individual genetic profiles influence the response to drugs, is an important topic. Results from pharmacogenetics studies in various clinical settings may lead to personalized medicine. Herein, we present the most important concepts of this discipline, as well as currently-used study methods.

  1. Generalized summability methods of functions using ideals

    NASA Astrophysics Data System (ADS)

    Savaş, Ekrem

    2015-09-01

    In this paper, we shall make a new approach to two well known summability methods by using ideals and introduce new notions, namely, ℐ-statistical convergence and ℐ-lacunary statistical convergence by taking a nonnegative real-valued Lebesque measurable function in the interval (1, ∞) and mainly investigate their relationship and also make some observations about these classes.

  2. Superconvergence in the Generalized Finite Element Method

    DTIC Science & Technology

    2005-01-01

    Galerkin method for elliptic equations based on tensor products of piecewise polynomials. RAIRO Anal. Numer., 8:61– 66, 1974. [19] M. Kř́ıžek...London, 1986. [22] P. Lesaint and M. Zlámal. Superconvergence of the gradient of finite ele- ment solutions. RAIRO Anal. Numer., 13:139–166, 1979. [23] Q

  3. Discovery of a Novel General Anesthetic Chemotype Using High-throughput Screening

    PubMed Central

    McKinstry-Wu, Andrew R.; Bu, Weiming; Rai, Ganesha; Lea, Wendy A.; Weiser, Brian P.; Liang, David F.; Simeonov, Anton; Jadhav, Ajit; Maloney, David J.; Eckenhoff, Roderic G.

    2014-01-01

    Background The development of novel anesthetics has historically been a process of combined serendipity and empiricism, with most recent new anesthetics developed via modification of existing anesthetic structures. Methods Using a novel high-throughput screen employing the fluorescent anesthetic 1-aminoanthracene (1-AMA) and apoferritin as a surrogate for on-pathway anesthetic protein target(s), we screened a 350,000 compound library for competition with 1-AMA-apoferritin binding. Hit compounds meeting structural criteria had their binding affinities for apoferritin quantified with isothermal titration calorimetry and were tested for γ-aminobutyric acid type A-receptor binding using a flunitrazepam binding assay. Chemotypes with a strong presence in the top 700 and exhibiting activity via isothermal titration calorimetry were selected for medicinal chemistry optimization including testing for anesthetic potency and toxicity in an in vivo Xenopus laevis tadpole assay. Compounds with low toxicity and high potency were tested for anesthetic potency in mice. Results From an initial chemical library of over 350,000 compounds, we identified 2,600 compounds that potently inhibited 1-AMA binding to apoferritin. A subset of compounds chosen by structural criteria (700) was successfully reconfirmed using the initial assay. Based upon a strong presence in both the initial and secondary screens the 6-phenylpyridazin-3(2H)-one chemotype was assessed for anesthetic activity in tadpoles. Medicinal chemistry efforts identified four compounds with high potency and low toxicity in tadpoles, two were found to be effective novel anesthetics in mice. Conclusions We demonstrate the first use of a high-throughput screen to successfully identify a novel anesthetic chemotype and show mammalian anesthetic activity for members of that chemotype. PMID:25603205

  4. Generalized direct Lyapunov method for the analysis of stability and attraction in general time systems

    SciTech Connect

    Druzhinina, O V; Shestakov, A A

    2002-10-31

    A generalized direct Lyapunov method is put forward for the study of stability and attraction in general time systems of the following types: the classical dynamical system in the sense of Birkhoff, the general system in the sense of Zubov, the general system in the sense of Seibert, the general system with delay, and the general 'input-output' system. For such systems, with the help of generalized Lyapunov functions with respect to two filters, two quasifilters, or two filter bases, necessary and sufficient conditions for stability and attraction are obtained under minimal assumptions about the mathematical structure of the general system.

  5. Recombinant methods for screening human DNA excision repair proficiency

    SciTech Connect

    Athas, W.F.

    1988-01-01

    A method for measuring DNA excision repair in response to ultraviolet radiation (UV)-induced DNA damage has been developed, validated, and field-tested in cultured human lymphocytes. The methodology is amenable to population-based screening and should facilitate future epidemiologic studies seeking to investigate associations between excision repair proficiency and cancer susceptibility. The impetus for such endeavors derives from the belief that the high incidence of skin cancer in the genetic disorder xeroderma pigmentosum (XP) primarily is a result of the reduced capacity of patients cells to repair UV-induced DNA damage. For assay, UV-irradiated non-replicating recombinant plasmid DNA harboring a chloramphenicol acetyltransferase (CAT) indicator gene is introduced into lymphocytes using DEAE-dextran short-term transfection conditions. Exposure to UV induces transcriptionally-inactivating DNA photoproducts in the plasmid DNA which inactivate CAT gene expression. Excision repair of the damaged CAT gene is monitored indirectly as a function of reactivated CAT enzyme activity following a 40 hour repair/expression incubation period.

  6. 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.

  7. Thermography--a feasible method for screening breast cancer?

    PubMed

    Kolarić, Darko; Herceg, Zeljko; Nola, Iskra Alexandra; Ramljak, Vesna; Kulis, Tomislav; Holjevac, Jadranka Katancić; Deutsch, Judith A; Antonini, Svetlana

    2013-06-01

    Potential use of thermography for more effective detection of breast carcinoma was evaluated on 26 patients scheduled for breast carcinoma surgery. Ultrasonographic scan, mammography and thermography were performed at the University Hospital for Tumors. Thermographic imaging was performed using a new generation of digital thermal cameras with high sensitivity and resolution (ThermoTracer TH7102WL, NEC). Five images for each patient were recorded: front, right semi-oblique, right oblique, left- semi oblique and left oblique. While mammography detected 31 changes in 26 patients, thermography was more sensitive and detected 6 more changes in the same patients. All 37 changes were subjected to the cytological analysis and it was found that 16 of samples were malignant, 8 were suspected malignant and 11 were benign with atypia or proliferation while only 2 samples had benign findings. The pathohistological method (PHD) recorded 75.75% malignant changes within the total number of samples. Statistical analysis of the data has shown a probability of a correct mammographic finding in 85% of the cases (sensitivity of 85%, specificity of 84%) and a probability of a correct thermographic finding in 92% of the cases (sensitivity of 100%, specificity of 79%). As breast cancer remains the most prevalent cancer in women and thermography exhibited superior sensitivity, we believe that thermography should immediately find its place in the screening programs for early detection of breast carcinoma, in order to reduce the sufferings from this devastating disease.

  8. Generalization of the Engineering Method to the UNIVERSAL METHOD.

    ERIC Educational Resources Information Center

    Koen, Billy Vaughn

    1987-01-01

    Proposes that there is a universal method for all realms of knowledge. Reviews Descartes's definition of the universal method, the engineering definition, and the philosophical basis for the universal method. Contends that the engineering method best represents the universal method. (ML)

  9. Screening of GABRB3 in French-Canadian families with idiopathic generalized epilepsy.

    PubMed

    Lachance-Touchette, Pamela; Martin, Caroline; Poulin, Chantal; Gravel, Micheline; Carmant, Lionel; Cossette, Patrick

    2010-09-01

    Mutations in the GABRB3 have been recently associated with childhood absence epilepsy (CAE) in families from Honduras and Mexico. In this study, we aimed to determine the frequency of mutation in this gene in our cohort of families with CAE and other related idiopathic generalized epilepsy (IGE) syndromes. We screened the open reading frame of GABRB3 in 183 French-Canadian individuals with IGE, including 88 with CAE. A total of nine single nucleotide polymorphisms (SNPs) have been identified,five of which are novel. The previously described P11S missense mutation was found in three affected and one unaffected individuals from a French-Canadian family. However, the P11S variant was also found in one of our 190 control individuals of French-Canadian origin, suggesting that this variant is rather a rare polymorphism in this population. Further screening of other IGE cohorts from various ethnic origins would help to confirm the association between this rare functional variant and epilepsy.

  10. Virtual screening methods as tools for drug lead discovery from large chemical libraries.

    PubMed

    Ma, X H; Zhu, F; Liu, X; Shi, Z; Zhang, J X; Yang, S Y; Wei, Y Q; Chen, Y Z

    2012-01-01

    Virtual screening methods have been developed and explored as useful tools for searching drug lead compounds from chemical libraries, including large libraries that have become publically available. In this review, we discussed the new developments in exploring virtual screening methods for enhanced performance in searching large chemical libraries, their applications in screening libraries of ~ 1 million or more compounds in the last five years, the difficulties in their applications, and the strategies for further improving these methods.

  11. A Rapid Spectrophotometric Screening Method for 2,4-dinitroanisole in Laboratory Water

    DTIC Science & Technology

    2014-07-01

    Approved for public release; distribution is unlimited. ERDC/EL TN-14-3 July 2014 A Rapid Spectrophotometric Screening Method for 2,4-dinitroanisole...REPORT TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE A Rapid Spectrophotometric Screening Method for 2,4-dinitroanisole in...D., A. J. Kennedy, A. R. Poda, and A. L. Russell. 2014. A rapid spectrophotometric screening method for 2,4-dinitroanisole in laboratory water

  12. A luciferase-based screening method for inhibitors of alphavirus replication applied to nucleoside analogues.

    PubMed

    Pohjala, Leena; Barai, Vladimir; Azhayev, Alex; Lapinjoki, Seppo; Ahola, Tero

    2008-06-01

    Several members of the widespread alphavirus group are pathogenic, but no therapy is available to treat these RNA virus infections. We report here a quantitative assay to screen for inhibitors of Semliki Forest virus (SFV) replication, and demonstrate the effects of 29 nucleosides on SFV and Sindbis virus replication. The anti-SFV assay developed is based on a SFV strain containing Renilla luciferase inserted after the nsP3 coding region, yielding a marker virus in which the luciferase is cleaved out during polyprotein processing. The reporter-gene assay was miniaturized, automated and validated, resulting in a Z' value of 0.52. [3H]uridine labeling for 1 h at the maximal viral RNA synthesis time point was used as a comparative method. Anti-SFV screening and counter-screening for cell viability led to the discovery of several new SFV inhibitors. 3'-amino-3'-deoxyadenosine was the most potent inhibitor in this set, with an IC50 value of 18 microM in the reporter-gene assay and 2 microM in RNA synthesis rate detection. Besides the 3'-substituted analogues, certain N6-substituted nucleosides had similar IC50 values for both SFV and Sindbis replication, suggesting the applicability of this methodology to alphaviruses in general.

  13. 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.

  14. 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.

  15. 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.

  16. System and method for obtaining wide screen Schlieren photographs

    NASA Technical Reports Server (NTRS)

    Parthasarathy, S. P. (Inventor)

    1979-01-01

    A system for use in Schlieren photography includes (1) a viewing screen adjacently related to a large grating; (2) a small grating disposed in spaced relation with the large grating; (3) a transparent retainer for confining a transparent medium between the gratings; and (4) optics for imaging the small grating on the large grating. A light source and optically aligned lens are used to project a beam of light along axes extending through the small grating and strike the large grating, subsequent to passing through the medium. A Schlieren image of striations resulting from distortions of light rays proposed by the medium are formed on the screen. A camera is used to photograph the Schlieren image projected on the large screen.

  17. Screening of Nutritional Risk and Nutritional Support in General Surgery Patients: A Survey from Shanghai, China

    PubMed Central

    Jia, Zhen-Yi; Yang, Jun; Tong, Da-Nian; Peng, Jia-Yuan; Zhang, Zhong-Wei; Liu, Wei-Jie; Xia, Yang; Qin, Huan-long

    2015-01-01

    To determine the prevalence of nutritional risk in surgical departments and to evaluate the impact of nutritional support on clinical outcomes. The nutritional risk in different surgical diseases and the different way of nutritional support on clinical outcomes in patients at nutritional risk remain unclear. Hospitalized patients from general surgical departments were screened using the Nutritional Risk Screening (NRS) 2002 questionnaire on admission. Data were collected on nutritional risk, complications, and length of stay (LOS). Overall, 5034 patients were recruited; the overall prevalence of nutritional risk on admission were 19.2%. The highest prevalence was found among patients with gastric cancer. At-risk patients had more complications and longer LOS than nonrisk patients. Of the at-risk patients, the complication rate was significantly lower and LOS was significantly shorter in the nutritional-support group than in the no-support group (20.9 versus 30.0%, P < 0.05). Subgroup analysis showed reduced complication rates and LOS only in patients with gastric cancer, colorectal cancer, and hepato-pancreato-biliary (HPB) cancer. Significantly lower complication rates relative to nonsupported patients were found among patients who received enteral nutrition or who received support for 5 to 7 days, or daily support entailing 16 to 25 kcal/kg of nonprotein energy. Different surgical diseases have different levels of nutritional risk. The provision of nutritional support was associated with a lower complication rate and a shorter LOS for gastric, colorectal, and HPB cancer patients at nutritional risk. The improper use of nutritional support may not improve outcomes for at-risk patients. PMID:26011204

  18. 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.

  19. 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.

  20. An improved method for rapid generation and screening of Bacillus thuringiensis phage-resistant mutants.

    PubMed

    Gillis, Annika; Mahillon, Jacques

    2014-11-01

    A simple method to isolate, screen and select phage-resistant mutants of Bacillus thuringiensis was developed. The traditional double-layer agar method was improved by a combination of the spotting assay using a lytic phage, to generate the bacterial-resistant mutants, with an inverted spotting assay (ISA), to rapidly screen the candidate-resistant mutants.

  1. 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.

  2. 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

  3. A highly cost effective method of mass screening for thalassaemia.

    PubMed Central

    Silvestroni, E; Bianco, I

    1983-01-01

    A simple, fast, and reliable two step procedure for the detection of non-alpha-thalassaemias in mass screening programmes is presented. Step 1 consists of a study of red cell morphology and a one tube red cell osmotic fragility tests. This step eliminates the non-thalassaemic samples; the rest are processed through step 2, consisting of determination of red cell indices and haemoglobin studies. Over the past seven years this procedure has been used at this centre in mass screening secondary school students in Latium. Blood samples from 289 763 students were examined, and 6838 cases of thalassaemia detected. It is estimated that 0.35 +/- 0.25% of subjects with thalassaemia escaped detection by this procedure. PMID:6403170

  4. Evaluation of Quantitative Environmental Stress Screening (ESS) Methods. Volume 1

    DTIC Science & Technology

    1991-11-01

    muu4 The objective of this study was to evaluate Environmental Stress Screening (ESS) techniques contained in DOD-HDBK-344,’ by applying the methodology...to several electronic products during actual factor production. Validation of the techniques , the develop- ment of improved, qi•p’lified,_ad...automated procedures and subsequent revisions to the Handbook were the objectives, qf the evaluation. The Rome Laboratory has developed techniques which

  5. A choice-based screening method for compulsive drug users in rats.

    PubMed

    Lenoir, Magalie; Augier, Eric; Vouillac, Caroline; Ahmed, Serge H

    2013-07-01

    We describe a protocol for screening compulsive drug users among cocaine self-administering rats, the most frequently used animal model in addiction research. Rats are first trained on several alternating days to self-administer either cocaine (i.v.) or saccharin-sweetened water (by mouth)--a potent, albeit nonessential, nondrug reward. Then rats are allowed to choose between the two rewards over several days until the preference stabilizes. Most rats choose to stop using cocaine and pursue the alternative reward. Only a minority of Wistar strain rats (generally 15%) persist in taking the drug, regardless of the severity of past cocaine use and even when made hungry and offered the possibility to relieve their physiological need. Persistence of cocaine use in the face of a high-stakes choice is a core defining feature of compulsion. This choice-based screening method for compulsive drug users is easy to implement, has several important applications, and compares well with other methods in the field.

  6. Clinical value of whole-body magnetic resonance imaging in health screening of general adult population

    PubMed Central

    Tarnoki, David Laszlo; Tarnoki, Adam Domonkos; Richter, Antje; Karlinger, Kinga; Berczi, Viktor; Pickuth, Dirk

    2015-01-01

    Background Whole-body magnetic resonance imaging (WB-MRI) and angiography (WB-MRA) has become increasingly popular in population-based research. We evaluated retrospectively the frequency of potentially relevant incidental findings throughout the body. Materials and methods 22 highly health-conscious managers (18 men, mean age 47±9 years) underwent WB-MRI and WB-MRA between March 2012 and September 2013 on a Discovery MR750w wide bore 3 Tesla device (GE Healthcare) using T1 weighted, short tau inversion recovery (STIR) and diffusion weighted imaging (DWI) acquisitions according to a standardized protocol. Results A suspicious (pararectal) malignancy was detected in one patient which was confirmed by an endorectal sonography. Incidental findings were described in 20 subjects, including hydrocele (11 patients), benign bony lesion (7 patients) and non-specific lymph nodes (5 patients). Further investigations were recommended in 68% (ultrasound: 36%, computed tomography: 28%, mammography: 9%, additional MRI: 9%). WB-MRA were negative in 16 subjects. Vascular normal variations were reported in 23%, and a 40% left proximal common carotid artery stenosis were described in one subject. Conclusions WB-MRI and MRA lead to the detection of clinically relevant diseases and unexpected findings in a cohort of healthy adults that require further imaging or surveillance in 68%. WB-MR imaging may play a paramount role in health screening, especially in the future generation of (epi)genetic based screening of malignant and atherosclerotic disorders. Our study is the first which involved a highly selected patient group using a high field 3-T wide bore magnet system with T1, STIR, MRA and whole-body DWI acquisitions as well. PMID:25810696

  7. Effect of reminders mailed to general practitioners on colorectal cancer screening adherence: a cluster-randomized trial.

    PubMed

    Le Breton, Julien; Ferrat, Émilie; Attali, Claude; Bercier, Sandrine; Le Corvoisier, Philippe; Brixi, Zahida; Veerabudun, Kalaivani; Renard, Vincent; Bastuji-Garin, Sylvie

    2016-09-01

    Reminders have been used in various settings, but failed to produce convincing evidence of benefits on patient adherence to colorectal cancer (CRC) screening. The aim of this study was to assess the effectiveness of sending general practitioners (GPs) printed reminders about CRC screening. We conducted a cluster-randomized controlled trial involving 144 GPs in the Val-de-Marne district (France), who provided care for any reason to 20 778 patients eligible for CRC screening between June 2010 and November 2011. Data were collected from the main statutory health-insurance programme and local cancer screening agency. GPs were randomly assigned in a 1 : 1 proportion to the intervention or the control group. Every 4 months, intervention-group GPs received a computer-generated printed list of patients who had not performed scheduled faecal occult blood test (FOBT) screening. The primary outcome was patient adherence to FOBT screening or exclusion from CRC screening for medical reasons. The screening adherence rate was 31.2% [95% confidence interval (CI) 30.3-32.1] in the control group and 32.9% (95% CI 32.0-33.8) in the intervention group [crude relative risk, 1.05 (95% CI 1.01-1.09), P<0.01]. This rate was not significantly different between groups by multilevel modelling accounting for clustering and confounding variables [adjusted relative risk, 1.07 (95% CI 0.95-1.20), P=0.27]. Computer-generated printed reminders sent to GPs did not significantly improve patient adherence to organized CRC screening by the FOBT.

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

    DOEpatents

    Kim, Sung-Hou [Moraga, CA; Kim, Rosalind [Moraga, CA; Jancarik, Jamila [Walnut Creek, CA

    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.

  9. 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...

  10. 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 ...

  11. Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries.

    PubMed

    Ma, Xiao H; Jia, Jia; Zhu, Feng; Xue, Ying; Li, Ze R; Chen, Yu Z

    2009-05-01

    Machine learning methods have been explored as ligand-based virtual screening tools for facilitating drug lead discovery. These methods predict compounds of specific pharmacodynamic, pharmacokinetic or toxicological properties based on their structure-derived structural and physicochemical properties. Increasing attention has been directed at these methods because of their capability in predicting compounds of diverse structures and complex structure-activity relationships without requiring the knowledge of target 3D structure. This article reviews current progresses in using machine learning methods for virtual screening of pharmacodynamically active compounds from large compound libraries, and analyzes and compares the reported performances of machine learning tools with those of structure-based and other ligand-based (such as pharmacophore and clustering) virtual screening methods. The feasibility to improve the performance of machine learning methods in screening large libraries is discussed.

  12. Integrating Multiple Teaching Methods into a General Chemistry Classroom.

    ERIC Educational Resources Information Center

    Francisco, Joseph S.; Nicoll, Gayle; Trautmann, Marcella

    1998-01-01

    Four different methods of teaching--cooperative learning, class discussions, concept maps, and lectures--were integrated into a freshman-level general chemistry course to compare students' levels of participation. Findings support the idea that multiple modes of learning foster the metacognitive skills necessary for mastering general chemistry.…

  13. Tangential and sagittal curvature from the normals computed by the null screen method in corneal topography

    NASA Astrophysics Data System (ADS)

    Estrada-Molina, Amilcar; Díaz-Uribe, Rufino

    2011-08-01

    A new method for computing the tangential and sagittal curvatures from the normals to a cornea is proposed. The normals are obtained through a Null Screen method from the coordinates of the drops shaped spots at the null screen, the coordinates on a reference approximating surface and the centroids on the image plane. This method assumes that the cornea has rotational symmetry and our derivations will be carried out in the meridional plane that contains the symmetry axis. Experimental results are shown for a calibration spherical surface, using cylindrical null screens with radial point arrays.

  14. Performance Comparison of Student-Athletes and General College Students on the Functional Movement Screen and the Y Balance Test.

    PubMed

    Engquist, Katherine D; Smith, Craig A; Chimera, Nicole J; Warren, Meghan

    2015-08-01

    Although various studies have assessed performance of athletes on the Functional Movement Screen (FMS) and the Y Balance Test (YBT), no study to date has directly evaluated a comparison of performance between athletes and members of the general population. Thus, to better understand the application of the FMS and the YBT to general college students, this study examined whether or not general college students performed similarly to student-athletes on the FMS (composite and movement pattern scores) and the YBT (composite and reach directions). This study evaluated 167 Division I student-athletes and 103 general college students from the same university on the FMS and the YBT. No difference was found in FMS composite scores between student-athletes and general college students. For FMS movement patterns, female student-athletes scored higher than general college students in the deep squat. No difference was found for men in any FMS movement pattern. Female student-athletes scored higher than female general college students in YBT composite scores; no difference was found for men in YBT composite scores. In analysis of YBT reach directions, female student-athletes scored higher than female general college students in all reach directions, whereas no difference was found in men. Existing research on the FMS composite score in athletic populations may apply to a general college population for the purposes of preparticipation screening, injury prediction, etc. Existing research on the YBT in male athletic populations is expected to apply equally to general college males for the purposes of preparticipation screening, injury prediction, etc.

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

    DOEpatents

    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.

  16. Electrical Bioimpedance Analysis: A New Method in Cervical Cancer Screening

    PubMed Central

    Das, Soumen; Chatterjee, Jyotirmoy

    2015-01-01

    Cervical cancer is the second most common female cancer worldwide and a disease of concern due to its high rate of incidence of about 500,000 women annually and is responsible for about 280,000 deaths in a year. The mortality and morbidity of cervical cancer are reduced through mass screening via Pap smear, but this technique suffers from very high false negativity of around 30% to 40% and hence the sensitivity of this technique is not more than 60%. Electrical bioimpedance study employing cytosensors over a frequency range offers instantaneous and quantitative means to monitor cellular events and is an upcoming technique in real time to classify cells as normal and abnormal ones. This technology is exploited for label-free detection of diseases by identifying and measuring nonbiological parameters of the cell which may carry the disease signature. PMID:27006939

  17. [Detection of early forms of keratoconus - current screening methods].

    PubMed

    Goebels, S; Eppig, T; Seitz, B; Langenbucher, A

    2013-10-01

    The detection of early forms of keratoconus is still a challenge for clinicians. Beside clinical examination and diagnosis of keratoconus, a series of examination techniques has been established in clinical routine to assist in the diagnosis of early forms of keratoconus: corneal topography for measuring the geometry of the corneal front surface, tomography for measuring the geometry of structures of the anterior segment of the eye, aberrometers for evaluation of optical aberrations of the entire eye, and a system for investigation of the biomechanical properties of the cornea. These instruments provide software tools which are designed for diagnostic support in keratoconus. In this review article, we provide an overview over the spectrum of measurement systems currently on the market focussing on their performance for detecting (early forms of) keratoconus. In detail, we focus on dedicated keratoconus screening software modules of topography, tomography, aberrometry and biomechanics.

  18. [Barrett's esophagus: new screening methods and new endoscopic therapy].

    PubMed

    Nguyen-Tang, Thai; Frossard, Jean-Louis; Dumonceau, Jean-Marc

    2011-09-07

    New endoscopic techniques allow, for the diagnosis, to better identify dysplastic lesions using "virtual" chromoendoscopy (without replacing systematic biopsies), and for the treatment, to resect large superficial lesions or ablate the entire Barrett's mucosa (the latter technique uses radiofrequency and does not provide any specimen). Endoscopic resection allows (1) to more accurately stage the lesion than biopsies, (2) to be curative in case of high grade dysplasia or intramucosal carcinoma. Radiofrequency ablation of the entire metaplastic mucosa is recommended after resection of neoplastic lesions with a curative intent (to avoid recurrences) or as first line treatment in case of dysplasia without visible lesion. In practical, if neoplasia is detected during screening endoscopy, a careful (chromoendoscopy) examination is required to orient patient's management (resection and/or radiofrequency ablation).

  19. 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.

  20. General image method in a plane-layered elastostatic medium

    NASA Technical Reports Server (NTRS)

    Fares, N.; Li, V. C.

    1988-01-01

    The general-image method presently used to obtain the elastostatic fields in plane-layered media relies on the use of potentials in order to represent elastic fields. For the case of a single interface, this method yields the displacement field in closed form, and is applicable to antiplane, plane, and three-dimensional problems. In the case of multiplane interfaces, the image method generates the displacement fields in terms of infinite series whose convergences can be accelerated to improve method efficiency.

  1. 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...

  2. 77 FR 4544 - CPSC Symposium on Phthalates Screening and Testing Methods

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-30

    ...(a)(2)) defines a ``children's product'' as a consumer product designed or intended primarily for... From the Federal Register Online via the Government Publishing Office CONSUMER PRODUCT SAFETY COMMISSION CPSC Symposium on Phthalates Screening and Testing Methods AGENCY: Consumer Product...

  3. 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.

  4. 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.

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

    DOEpatents

    Warner, Benjamin P [Los Alamos, NM; Havrilla, George J [Los Alamos, NM; Miller, Thomasin C [Bartlesville, OK; Lewis, Cris [Los Alamos, NM; Mahan, Cynthia A [Los Alamos, NM; Wells, Cyndi A [Los Alamos, NM

    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.

  6. 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…

  7. A General Method for Modeling Macromolecular Shape in Solution

    PubMed Central

    Harding, Stephen E.

    1987-01-01

    A general method for modeling macromolecular shape in solution is described involving measurements of viscosity, radius of gyration, and the second thermodynamic virial coefficient. The method, which should be relatively straightforward to apply, does not suffer from uniqueness problems, involves shape functions that are independent of hydration, and models the gross conformation of the macromolecule in solution as a general triaxial ellipsoid. The method is illustrated by application to myosin, and the relevance and applicability of ellipsoid modeling to biological structures is discussed. PMID:19431695

  8. Multi wave method for the generalized form of BBM equation

    NASA Astrophysics Data System (ADS)

    Bildik, Necdet; Tandogan, Yusuf Ali

    2014-12-01

    In this paper, we apply the multi-wave method to find new multi wave solutions for an important nonlinear physical model. This model is well known as generalized form of Benjamin Bona Mahony (BBM) equation. Using the mathematics software Mathematica, we compute the traveling wave solutions. Then, the multi wave solutions including periodic wave solutions, bright soliton solutions and rational function solutions are obtained by the multi wave method. It is seen that this method is very useful mathematical approach for generalized form of BBM equation.

  9. 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.

  10. Dynamically screened local correlation method using enveloping localized orbitals.

    PubMed

    Auer, Alexander A; Nooijen, Marcel

    2006-07-14

    In this paper we present a local coupled cluster approach based on a dynamical screening scheme, in which amplitudes are either calculated at the coupled cluster level (in this case CCSD) or at the level of perturbation theory, employing a threshold driven procedure based on MP2 energy increments. This way, controllable accuracy and smooth convergence towards the exact result are obtained in the framework of an a posteriori approximation scheme. For the representation of the occupied space a new set of local orbitals is presented with the size of a minimal basis set. This set is atom centered, is nonorthogonal, and has shapes which are fairly independent of the details of the molecular system of interest. Two slightly different versions of combined local coupled cluster and perturbation theory equations are considered. In the limit both converge to the untruncated CCSD result. Benchmark calculations for four systems (heptane, serine, water hexamer, and oxadiazole-2-oxide) are carried out, and decay of the amplitudes, truncation error, and convergence towards the exact CCSD result are analyzed.

  11. Dynamically screened local correlation method using enveloping localized orbitals

    NASA Astrophysics Data System (ADS)

    Auer, Alexander A.; Nooijen, Marcel

    2006-07-01

    In this paper we present a local coupled cluster approach based on a dynamical screening scheme, in which amplitudes are either calculated at the coupled cluster level (in this case CCSD) or at the level of perturbation theory, employing a threshold driven procedure based on MP2 energy increments. This way, controllable accuracy and smooth convergence towards the exact result are obtained in the framework of an a posteriori approximation scheme. For the representation of the occupied space a new set of local orbitals is presented with the size of a minimal basis set. This set is atom centered, is nonorthogonal, and has shapes which are fairly independent of the details of the molecular system of interest. Two slightly different versions of combined local coupled cluster and perturbation theory equations are considered. In the limit both converge to the untruncated CCSD result. Benchmark calculations for four systems (heptane, serine, water hexamer, and oxadiazole-2-oxide) are carried out, and decay of the amplitudes, truncation error, and convergence towards the exact CCSD result are analyzed.

  12. 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.

  13. Development and Evaluation of Nursing User Interface Screens Using Multiple Methods

    PubMed Central

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

    2009-01-01

    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. PMID:19460464

  14. A rapid and general method for measurement of protein in micro-algal biomass.

    PubMed

    Slocombe, Stephen P; Ross, Michael; Thomas, Naomi; McNeill, Sharon; Stanley, Michele S

    2013-02-01

    A convenient small-scale extraction method for lyophilized micro-algae is described that dispenses with labor-intensive homogenization and is widely applicable to algae from different phyla. The procedure employs an optimized sequential extraction in trichloroacetic acid (TCA) and NaOH to achieve chemical lysis. Conditions were tested using several micro-algal strains to develop a method that was generally applicable. Incubation of lyophilized material in 24% (w/v) TCA at 95 °C followed by a hot alkaline treatment was found to be effective for strains that are resistant to conventional extraction approaches, such as the Chlorella and the Eustigmatophycean species. The single-tube extraction procedure can be complete in 4h and is conveniently followed by the Lowry assay, requiring a further 30 min. Overall, this method proved to be generally applicable and ideal either for single samples or for high-throughput screening of multiple algal strains for protein content.

  15. A fast method for a generalized nonlocal elastic model

    NASA Astrophysics Data System (ADS)

    Du, Ning; Wang, Hong; Wang, Che

    2015-09-01

    We develop a numerical method for a generalized nonlocal elastic model, which is expressed as a composition of a Riesz potential operator with a fractional differential operator, by composing a collocation method with a finite difference discretization. By carefully exploring the structure of the coefficient matrix of the numerical method, we develop a preconditioned fast Krylov subspace method, which reduces the computations to (Nlog ⁡ N) per iteration and the memory to O (N). The use of the preconditioner significantly reduces the number of iterations, and the preconditioner can be inverted in O (Nlog ⁡ N) computations. Numerical results show the utility of the method.

  16. 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.

  17. 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.

  18. [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.

  19. Chemical Safety Alert: Identifying Chemical Reactivity Hazards Preliminary Screening Method

    EPA Pesticide Factsheets

    Introduces small-to-medium-sized facilities to a method developed by Center for Chemical Process Safety (CCPS), based on a series of twelve yes-or-no questions to help determine hazards in warehousing, repackaging, blending, mixing, and processing.

  20. Concurrent validation of Hutt's Bender Gestalt screening method for schizophrenia, depression, and brain damage.

    PubMed

    Lownsdale, W S; Rogers, B J; McCall, J N

    1989-01-01

    The effectiveness of Hutt's Bender Gestalt scoring system in screening for schizophrenia, depression, and brain damage was investigated in a sample of mixed, psychiatric inpatients. Fifteen patients represented each diagnostic category. After an examination of each patient's Bender Gestalt protocol according to Hutt's criteria, it was found that the true positive and true negative success rates of the screening procedures for depression and brain damage were significantly higher than corresponding base rates. The Lacks Bender Gestalt screening method for brain damage was no more successful than the Hutt method in identifying true positives and true negatives. With the brain-damaged patients excluded, Hutt's screening procedures for both depression and schizophrenia resulted in significantly high rates of successful identification of true positives and true negatives. Moreover, these rates did not significantly differ from those determined by patients' Minnesota Multiphasic Personality Inventory (MMPI) T scores on corresponding scales.

  1. [A Decrease in Lung Cancer Mortality Following the Implementation of CT Screening for General Population].

    PubMed

    Nawa, Takeshi

    2015-01-01

    In Hitachi Medical Area, a large-scale lung cancer screening program using low-dose CT has been underway in two medical facilities since its introduction in 1998 and 2001. A total of 61,914 tests were performed among 25,385 participants until 2006. Two hundred and ten lung cancer patients had been identified on CT screening. The estimated 5-year survival rate for all patients was 90%. Among residents in Hitachi City, nearly 40% of inhabitants aged 50-69 years were estimated to have participated in the screening from 1998 through 2009. Cancer mortality data were obtained from a regional cancer registry and the standardized mortality ratio (SMR) of lung cancer was calculated for each 5-year period during 1995-2009. For residents aged 50-79 years, SMR was nearly unity between 1995 and 2004; however, there was a significant decrease during 2005-2009, with SMR (95% confidence interval) being 0.76 (0.67-0.86). These results suggest that the wide implementation of CT screening may reduce lung cancer mortality in the community, 4-8 years after introduction. It is desirable to continue to focus on future developments, including original research in Japan.

  2. A new mass screening method for methylmercury poisoning using mercury-volatilizing bacteria from Minamata Bay.

    PubMed

    Nakamura, K; Naruse, I; Takizawa, Y

    1999-09-01

    A simplified mass screening method for methylmercury exposure was developed using methylmercury-volatilizing bacteria from Minamata Bay. Some bacteria can transform methylmercury into mercury vapor. Most mercury in the hair is methylmercury, which is readily extracted with HCl solution. Black spots are formed on X-ray film due to the reduction of Ag(+) emulsion with mercury vapor produced by methylmercury-volatilizing bacteria. By exploiting these characteristics, a screening method was developed, whereby the fur of rats injected with methylmercury chloride formed clear black spots on X-ray film, whereas the fur of rats injected with saline did not. Subsequently, 50 human hair samples were examined using this mass screening method. The method identified people who had high mercury concentration, over 20 microg/g. A few thousand hair samples may be screened in a day using this method because it is rapid, simple, and economical. This method, therefore, enables screening of persons with methylmercury poisoning in mercury-polluted areas.

  3. [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.

  4. A simple DNA recombination screening method by RT-PCR as an alternative to Southern blot.

    PubMed

    Albers, Eliene; Sbroggiò, Mauro; Martin-Gonzalez, Javier; Avram, Alexandra; Munk, Stephanie; Lopez-Contreras, Andres J

    2017-01-19

    The generation of genetically engineered mouse models (GEMMs), including knock-out (KO) and knock-in (KI) models, often requires genomic screening of many mouse ES cell (mESC) clones by Southern blot. The use of large targeting constructs facilitates the recombination of exogenous DNA in a specific genomic locus, but limits the detection of its correct genomic integration by standard PCR methods. Genomic Long Range PCR (LR-PCR), using primers adjacent to the homology arms, has been used as an alternative to radioactive-based Southern blot screenings. However, LR-PCRs are often difficult and render many false positive and false negative results. Here, we propose an alternative screening method based on the detection of a genetic modification at the mRNA level, which we successfully optimized in two mouse models. This screening method consists of a reverse-transcription PCR (RT-PCR) using primers that match exons flanking the targeting construct. The detection of the expected modification in this PCR product confirms the integration at the correct genomic location and shows that the mutant mRNA is expressed. This is a simple and sensitive strategy to screen locus-specific recombination of targeting constructs which can also be useful to screen KO and KI mutant mice or cell lines including those generated by CRISPR/Cas9.

  5. 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...

  6. Methods for Factor Screening in Computer Simulation Experiments

    DTIC Science & Technology

    1979-03-01

    of the dat-a In a-space, impacto the variable selection problem s ign if Lrast ly. S-arch-type variable selection methods include the all-po"sible...i.iv 41.1 ti * n wt- -iu’pt-v c C it st’vt’re mu It ico11 inear it v is pro-crtnt Lind. , ii;.qt4pai tlv * Iti’lt- c- j c. tic j icivnt, art, verv

  7. Screening for serious mental illness in the general population with the K6 screening scale: results from the WHO World Mental Health (WMH) survey initiative.

    PubMed

    Kessler, Ronald C; Green, Jennifer Greif; Gruber, Michael J; Sampson, Nancy A; Bromet, Evelyn; Cuitan, Marius; Furukawa, Toshi A; Gureje, Oye; Hinkov, Hristo; Hu, Chi-Yi; Lara, Carmen; Lee, Sing; Mneimneh, Zeina; Myer, Landon; Oakley-Browne, Mark; Posada-Villa, Jose; Sagar, Rajesh; Viana, Maria Carmen; Zaslavsky, Alan M

    2010-06-01

    Data are reported on the background and performance of the K6 screening scale for serious mental illness (SMI) in the World Health Organization (WHO) World Mental Health (WMH) surveys. The K6 is a six-item scale developed to provide a brief valid screen for Diagnostic and Statistical Manual of Mental Disorders 4th edition (DSM-IV) SMI based on the criteria in the US ADAMHA Reorganization Act. Although methodological studies have documented good K6 validity in a number of countries, optimal scoring rules have never been proposed. Such rules are presented here based on analysis of K6 data in nationally or regionally representative WMH surveys in 14 countries (combined N = 41,770 respondents). Twelve-month prevalence of DSM-IV SMI was assessed with the fully-structured WHO Composite International Diagnostic Interview. Nested logistic regression analysis was used to generate estimates of the predicted probability of SMI for each respondent from K6 scores, taking into consideration the possibility of variable concordance as a function of respondent age, gender, education, and country. Concordance, assessed by calculating the area under the receiver operating characteristic curve, was generally substantial (median 0.83; range 0.76-0.89; inter-quartile range 0.81-0.85). Based on this result, optimal scaling rules are presented for use by investigators working with the K6 scale in the countries studied.

  8. Novel method for screening of enteric film coatings properties with magnetic resonance imaging.

    PubMed

    Dorożyński, Przemysław; Jamróz, Witold; Niwiński, Krzysztof; Kurek, Mateusz; Węglarz, Władysław P; Jachowicz, Renata; Kulinowski, Piotr

    2013-11-18

    The aim of the study is to present the concept of novel method for fast screening of enteric coating compositions properties without the need of preparation of tablets batches for fluid bed coating. Proposed method involves evaluation of enteric coated model tablets in specially designed testing cell with application of MRI technique. The results obtained in the testing cell were compared with results of dissolution studies of mini-tablets coated in fluid bed apparatus. The method could be useful in early stage of formulation development for screening of film coating properties that will shorten and simplify the development works.

  9. General Method for Describing Three-Dimensional Magnetic Reconnection

    NASA Astrophysics Data System (ADS)

    Titov, Viacheslav; Forbes, Terry; Priest, Eric; Mikic, Zoran; Linker, Jon

    2009-11-01

    A general method for describing magnetic reconnection in arbitrary three-dimensional magnetic configurations is proposed. The method is based on the field-line mapping technique previously used only for the analysis of magnetic structure at a given time. This technique is extended here so as to analyze the evolution of magnetic structure. Such a generalization is made with the help of new dimensionless quantities called ``slip-squashing factors''. Their large values define the surfaces that border the reconnected or to-be-reconnected magnetic flux tubes for a given period of time during the magnetic evolution. The proposed method is universal, since it assumes only that the time sequence of evolving magnetic field and the tangential boundary flows are known. We illustrate our method for several examples and compare it with the general magnetic reconnection theory, proposed previously by Hesse and coworkers. The new method admits a straightforward numerical implementation and provides a powerful tool for the diagnostics of numerical data obtained in theoretical or experimental studies of magnetic reconnection in space and laboratory plasmas.

  10. 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

  11. A parallel Lanczos method for symmetric generalized eigenvalue problems

    SciTech Connect

    Wu, K.; Simon, H.D.

    1997-12-01

    Lanczos algorithm is a very effective method for finding extreme eigenvalues of symmetric matrices. It requires less arithmetic operations than similar algorithms, such as, the Arnoldi method. In this paper, the authors present their parallel version of the Lanczos method for symmetric generalized eigenvalue problem, PLANSO. PLANSO is based on a sequential package called LANSO which implements the Lanczos algorithm with partial re-orthogonalization. It is portable to all parallel machines that support MPI and easy to interface with most parallel computing packages. Through numerical experiments, they demonstrate that it achieves similar parallel efficiency as PARPACK, but uses considerably less time.

  12. Parental concerns based general developmental screening tool and autism risk: the Taiwan National Birth cohort study.

    PubMed

    Lung, For-Wey; Shu, Bih-Ching; Chiang, Tung-Liang; Lin, Shio-Jean

    2010-02-01

    Early detection of developmental delay and childhood disorders are important for early intervention. This study aimed to describe the distribution of responses in a large population-based survey, identify cutoff points for the parent concern checklist (PCC) suitable for the Chinese language and culture, and explore how many children were identified as having evidence of problems at age 18 mo different from those at age 6 mo. Using a national randomly selected sample, the overall development of 21,248 children was investigated using the Taiwan Birth Cohort study instrument, and the PCC, a problem-oriented screening instrument. The Newton-Raphson iteration showed that the PCC should be separated into three groups, those scoring 1-2 in the first group, 3- 6 in the second group, and 7- 8 in the third group.Structural equation models showed that 6-mo development was predictive of 18-mo development; additionally, 18-mo development and the PCC showed good concurrent validity. This study identified three groups with distinct developmental trajectories and two cutoff points of 2/3 and 6/7. Thus, the PCC can be used as a first-stage screening instrument in a two-stage window screening procedure. Further studies are needed to investigate the factors, which contribute to the differences among these groups;follow-up on the typical and atypical development of these children is necessary.

  13. [Screening for risk of child abuse and neglect. A practicable method?].

    PubMed

    Kindler, H

    2010-10-01

    Selective primary prevention programs for child abuse and neglect depend on risk screening instruments that have the goal of systematically identifying families who can profit most from early help. Based on a systematic review of longitudinal studies, a set of established risk factors for early child abuse and neglect is presented. Nearly half of the items included in screening instruments can be seen as validated. Available studies indicate a high sensitivity of risk screening instruments. Positive predictive values, however, are low. Overall, the use of risk screening instruments in the area of primary prevention for families at risk represents a feasible method, as long as stigmatizing effects can be avoided and participating families also benefit beyond preventing endangerment.

  14. Cystic fibrosis: need for mass deployable screening methods.

    PubMed

    Sengar, Aditya Singh; Agarwal, Anirudh; Singh, Manish K

    2014-10-01

    Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR is a member of the adenosine triphosphate (ATP)-binding cassette superfamily of proteins and it functions as a chloride channel. CFTR largely controls the working of epithelial cells of the airways, the gastrointestinal tract, exocrine glands, and genitourinary system. Cystic fibrosis is responsible for severe chronic pulmonary disorders in children. Other maladies in the spectrum of this life-limiting disorder include nasal polyposis, pansinusitis, rectal prolapse, pancreatitis, cholelithiasis, insulin-dependent hyperglycemia, and cirrhosis. This review summarizes the recent state of art in the field of cystic fibrosis diagnostic methods with the help of CF literature published so far and proposes new research domains in the field of cystic fibrosis diagnosis.

  15. 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.

  16. 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.

  17. 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...

  18. 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...

  19. Assessing the feasibility of screening and providing brief advice for alcohol misuse in general dental practice: a clustered randomised control trial protocol for the DART study

    PubMed Central

    Ntouva, Antiopi; Porter, Jessie; Crawford, Mike J; Britton, Annie; Gratus, Christine; Newton, Tim; Tsakos, Georgios; Heilmann, Anja; Pikhart, Hynek; Watt, Richard G

    2015-01-01

    Introduction Alcohol misuse is a significant public health problem with major health, social and economic consequences. Systematic reviews have reported that brief advice interventions delivered in various health service settings can reduce harmful drinking. Although the links between alcohol and oral health are well established and dentists come into contact with large numbers of otherwise healthy patients regularly, no studies have been conducted in the UK to test the feasibility of delivering brief advice about alcohol in general dental settings. Methods and analysis The Dental Alcohol Reduction Trial (DART) aims to assess the feasibility and acceptability of screening for alcohol misuse and delivering brief advice in patients attending National Health Service (NHS) general dental practices in North London. DART is a cluster randomised control feasibility trial and uses a mixed methods approach throughout the development, design, delivery and evaluation of the intervention. It will be conducted in 12 NHS general dental practices across North London and will include dental patients who drink above the recommended guidance, as measured by the Alcohol Use Disorders Identification Test (AUDIT-C) screening tool. The intervention involves 5 min of tailored brief advice delivered by dental practitioners during the patient's appointment. Feasibility and acceptability measures as well as suitability of proposed primary outcomes of alcohol consumption will be assessed. Initial economic evaluation will be undertaken. Recruitment and retention rates as well as acceptability of the study procedures from screening to follow-up will be measured. Ethics and dissemination Ethical approval was obtained from the Camden and Islington Research Ethics Committee. Study outputs will be disseminated via scientific publications, newsletters, reports and conference presentations to a range of professional and patient groups and stakeholders. Based on the results of the trial

  20. 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.

  1. 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.

  2. A randomized trial of three marketing strategies to disseminate a screening and brief alcohol intervention programme to general practitioners.

    PubMed Central

    Lock, C A; Kaner, E F; Heather, N; McAvoy, B R; Gilvarry, E

    1999-01-01

    BACKGROUND: Research findings are of little benefit to patients or society if they do not reach the audience they are intended to influence. A dissemination strategy is needed to target new findings at its user group and encourage a process of consideration and adoption or rejection. AIM: To evaluate the effectiveness and cost-effectiveness of different marketing strategies for the dissemination of a screening and brief alcohol intervention (SBI) programme to general practitioners (GPs). METHOD: Seven hundred and twenty-nine GPs, one per practice, from the former Northern and Yorkshire Regional Health Authority were randomly assigned to one of three marketing strategies: postal marketing (mailing a promotional brochure to GPs), telemarketing (following a script to market the programme over the telephone), and personal marketing (following the same script during face-to-face marketing at GPs' practices). GPs who took up the programme were asked if they would agree to use it. Outcome measures included the proportions of GPs who took up the programme and agreement to use it. RESULTS: Of the 614 GPs eligible for the study, 321 (52%) took the programme. There was a significant difference in the proportions of GPs from the three marketing strategies who took the programme (82% telemarketing, 68% personal marketing, and 22% postal marketing). Of the 315 GPs who took the programme and were eligible to use it, 128 (41%) agreed to use the programme for three months. GPs in the postal marketing group were more likely to agree to use the programme (55% postal marketing, 44% personal marketing, and 34% telemarketing). Personal marketing was the most effective overall dissemination strategy; however, economic analysis revealed that telemarketing was the most cost-effective strategy. Costs for dissemination per GP were: 13 Pounds telemarketing, 15 Pounds postal marketing, and 88 Pounds personal marketing. CONCLUSION: Telemarketing appeared to be the most cost-effective strategy

  3. 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.

  4. 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. . Center for Environmental Health and Injury Control)

    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.

  5. 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

  6. Efficiency and cost-effectiveness of dyslipidemia screening methods among workers in Bangkok.

    PubMed

    Sanguantrakul, Unchalee; Jiamjarasrangsi, Wiroj; Vimolket, Thosporn

    2010-01-01

    Dyslipidemia is now a worldwide health problem. Secondary prevention in the form of early detection of dyslipidemia and risk modification via drug and non-drug procedures, particularly among the high-risk group, is thus imperative. The objective of this study was to determine the sensitivity and specificity, cost, and cost-effectiveness of dyslipidemia screening methods which were proposed by the Royal Thai Medical Association (RTMA), the United States National Cholesterol Education Program (NCEP), British Hyperlipidemia Association (BHA), and our modified screening instrument (MSI). A cross-sectional descriptive study was conducted among 2,000 workers aged > or = 35 years taking annual health examination from a university hospital during July-September, 2008. Sensitivity and specificity of the screening methods were analyzed using the universal serum lipid testing as the gold standard. Their total and unit costs, and cost-effectiveness were then calculated. Overall, the sensitivities for detecting any type of serum lipid abnormalities ranged between 29.9-99.4 %, while the specificities ranged between 0.5-74.1%. The total costs per 1,000 people screened ranged between THB 88,742 - 184,750. No screening method was obviously more cost-effective when using the cost per case detected of the universal blood test as the reference.

  7. High-Order Integral Equation Methods for Diffraction Problems Involving Screens and Apertures

    NASA Astrophysics Data System (ADS)

    Lintner, Stephane K.

    This thesis presents a novel approach for the numerical solution of problems of diffraction by infinitely thin screens and apertures. The new methodology relies on combination of weighted versions of the classical operators associated with the Dirichlet and Neumann open-surface problems. In the two-dimensional case, a rigorous proof is presented, establishing that the new weighted formulations give rise to second-kind Fredholm integral equations, thus providing a generalization to open surfaces of the classical closed-surface Calderon formulae. High-order quadrature rules are introduced for the new weighted operators, both in the two-dimensional case as well as the scalar three-dimensional case. Used in conjunction with Krylov subspace iterative methods, these rules give rise to efficient and accurate numerical solvers which produce highly accurate solutions in small numbers of iterations, and whose performance is comparable to that arising from efficient high-order integral solvers recently introduced for closed-surface problems. Numerical results are presented for a wide range of frequencies and a variety of geometries in two- and three-dimensional space, including complex resonating structures as well as, for the first time, accurate numerical solutions of classical diffraction problems considered by the 19th-century pioneers: diffraction of high-frequency waves by the infinitely thin disc, the circular aperture, and the two-hole geometry inherent in Young's experiment.

  8. A General Method to Discover Epitopes from Sera

    PubMed Central

    Whittemore, Kurt; Johnston, Stephen Albert; Sykes, Kathryn; Shen, Luhui

    2016-01-01

    Antigen-antibody complexes are central players in an effective immune response. However, finding those interactions relevant to a particular disease state can be arduous. Nonetheless many paths to discovery have been explored since deciphering these interactions can greatly facilitate the development of new diagnostics, therapeutics, and vaccines. In silico B cell epitope mapping approaches have been widely pursued, though success has not been consistent. Antibody mixtures in immune sera have been used as handles for biologically relevant antigens, but these and other experimental approaches have proven resource intensive and time consuming. In addition, these methods are often tailored to individual diseases or a specific proteome, rather than providing a universal platform. Most of these methods are not able to identify the specific antibody’s epitopes from unknown antigens, such as un-annotated neo antigens in cancer. Alternatively, a peptide library comprised of sequences unrestricted by naturally-found protein space provides for a universal search for mimotopes of an antibody’s epitope. Here we present the utility of such a non-natural random sequence library of 10,000 peptides physically addressed on a microarray for mimotope discovery without sequence information of the specific antigen. The peptide arrays were probed with serum from an antigen-immunized rabbit, or alternatively probed with serum pre-absorbed with the same immunizing antigen. With this positive and negative screening scheme, we identified the library-peptides as the mimotopes of the antigen. The unique library peptides were successfully used to isolate antigen-specific antibodies from complete immune serum. Sequence analysis of these peptides revealed the epitopes in the immunized antigen. We present this method as an inexpensive, efficient method for identifying mimotopes of any antibody’s targets. These mimotopes should be useful in defining both components of the antigen

  9. 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.

  10. A comparative rapid and sensitive method to screen l-asparaginase producing fungi.

    PubMed

    Dhale, Mohan A; Mohan-Kumari, H Puttananjaiah

    2014-07-01

    Fungi are well known to produce various industrial enzymes and secondary metabolites with different colours. Fungi producing l-asparaginase enzyme are conventionally screened on medium containing phenol red (PR). The contrast between enzyme-hydrolysed zone and unhydrolysed l-asparagine is not very evident and distinct in medium containing PR and bromothymol blue (BB) due to coloured secondary metabolite production. Thus, PR and BB limit and affect the detection and screening method. In the present investigation, an improved method for screening is reported by comparing with PR and BB, wherein methyl red (MR) is incorporated as pH indicator. The enzyme activity was distinctly observed (red and light-yellow) in MR incorporated medium compared to PR and BB.

  11. A fast and easy screening method for voice disorders among teacher students.

    PubMed

    Simberg, S; Sala, E; Laine, A; Rönnemaa, A M

    2001-01-01

    A recent study concerning voice disorders among future teachers showed that about 20% of the students had a voice disorder. Most of the disorders were organic. In the current study, we describe a voice-screening method that can be administered by the health care personnel in order to select students for further examination by the speech language therapist and/or phoniatrician. The screening method consists of a perceptual assessment of voice quality and a questionnaire concerning vocal symptoms. As criterion for further medical investigation and voice therapy, we selected a score of 35 mm or above on a visual analogue scale assessing Grade, i.e. overall grade of hoarseness and/or two or more weekly or more often occurring vocal symptoms. The results showed that health care personnel with some training in assessing voices using the questionnaire are competent to perform a rough voice screening on students.

  12. Computational method for general multicenter electronic structure calculations.

    PubMed

    Batcho, P F

    2000-06-01

    Here a three-dimensional fully numerical (i.e., chemical basis-set free) method [P. F. Batcho, Phys. Rev. A 57, 6 (1998)], is formulated and applied to the calculation of the electronic structure of general multicenter Hamiltonian systems. The numerical method is presented and applied to the solution of Schrödinger-type operators, where a given number of nuclei point singularities is present in the potential field. The numerical method combines the rapid "exponential" convergence rates of modern spectral methods with the multiresolution flexibility of finite element methods, and can be viewed as an extension of the spectral element method. The approximation of cusps in the wave function and the formulation of multicenter nuclei singularities are efficiently dealt with by the combination of a coordinate transformation and a piecewise variational spectral approximation. The complete system can be efficiently inverted by established iterative methods for elliptical partial differential equations; an application of the method is presented for atomic, diatomic, and triatomic systems, and comparisons are made to the literature when possible. In particular, local density approximations are studied within the context of Kohn-Sham density functional theory, and are presented for selected subsets of atomic and diatomic molecules as well as the ozone molecule.

  13. A Multivariate Computational Method to Analyze High-Content RNAi Screening Data.

    PubMed

    Rameseder, Jonathan; Krismer, Konstantin; Dayma, Yogesh; Ehrenberger, Tobias; Hwang, Mun Kyung; Airoldi, Edoardo M; Floyd, Scott R; Yaffe, Michael B

    2015-09-01

    High-content screening (HCS) using RNA interference (RNAi) in combination with automated microscopy is a powerful investigative tool to explore complex biological processes. However, despite the plethora of data generated from these screens, little progress has been made in analyzing HC data using multivariate methods that exploit the full richness of multidimensional data. We developed a novel multivariate method for HCS, multivariate robust analysis method (M-RAM), integrating image feature selection with ranking of perturbations for hit identification, and applied this method to an HC RNAi screen to discover novel components of the DNA damage response in an osteosarcoma cell line. M-RAM automatically selects the most informative phenotypic readouts and time points to facilitate the more efficient design of follow-up experiments and enhance biological understanding. Our method outperforms univariate hit identification and identifies relevant genes that these approaches would have missed. We found that statistical cell-to-cell variation in phenotypic responses is an important predictor of hits in RNAi-directed image-based screens. Genes that we identified as modulators of DNA damage signaling in U2OS cells include B-Raf, a cancer driver gene in multiple tumor types, whose role in DNA damage signaling we confirm experimentally, and multiple subunits of protein kinase A.

  14. A multivariate computational method to analyze high-content RNAi screening data

    PubMed Central

    Rameseder, Jonathan; Krismer, Konstantin; Dayma, Yogesh; Ehrenberger, Tobias; Hwang, Mun Kyung; Airoldi, Edoardo M.; Floyd, Scott R.; Yaffe, Michael B.

    2017-01-01

    High-content screening (HCS) using RNA interference (RNAi) in combination with automated microscopy is a powerful investigative tool to explore complex biological processes. However, despite the plethora of data generated from these screens, little progress has been made in analyzing HC data using multivariate methods that exploit the full richness of multidimensional data. We developed a novel multivariate method for HCS, Multivariate Robust Analysis Method (M-RAM), integrating image feature selection with ranking of perturbations for hit identification, and applied this method to a HC RNAi screen to discover novel components of the DNA damage response in an osteosarcoma cell line. M-RAM automatically selects the most informative phenotypic readouts and time points to facilitate the more efficient design of follow-up experiments and enhance biological understanding. Our method outperforms univariate hit identification and identifies relevant genes that these approaches would have missed. We found that statistical cell-to-cell variation in phenotypic responses is an important predictor of ‘hits’ in RNAi-directed image-based screens. Genes that we identified as modulators of DNA damage signaling in U2OS cells include B-Raf, a cancer driver gene in multiple tumor types, whose role in DNA damage signaling we confirm experimentally, and multiple subunits of protein kinase A. PMID:25918037

  15. Endocrine Disruptor Screening Program (EDSP) Universe of Chemicals and General Validation Principles

    EPA Pesticide Factsheets

    This document was developed by the EPA to provide guidance to staff and managers regarding the EDSP universe of chemicals and general validation principles for consideration of computational toxicology tools for chemical prioritization.

  16. One Question, Multiple Answers: Biochemical and Biophysical Screening Methods Retrieve Deviating Fragment Hit Lists.

    PubMed

    Schiebel, Johannes; Radeva, Nedyalka; Köster, Helene; Metz, Alexander; Krotzky, Timo; Kuhnert, Maren; Diederich, Wibke E; Heine, Andreas; Neumann, Lars; Atmanene, Cedric; Roecklin, Dominique; Vivat-Hannah, Valérie; Renaud, Jean-Paul; Meinecke, Robert; Schlinck, Nina; Sitte, Astrid; Popp, Franziska; Zeeb, Markus; Klebe, Gerhard

    2015-09-01

    Fragment-based lead discovery is gaining momentum in drug development. Typically, a hierarchical cascade of several screening techniques is consulted to identify fragment hits which are then analyzed by crystallography. Because crystal structures with bound fragments are essential for the subsequent hit-to-lead-to-drug optimization, the screening process should distinguish reliably between binders and non-binders. We therefore investigated whether different screening methods would reveal similar collections of putative binders. First we used a biochemical assay to identify fragments that bind to endothiapepsin, a surrogate for disease-relevant aspartic proteases. In a comprehensive screening approach, we then evaluated our 361-entry library by using a reporter-displacement assay, saturation-transfer difference NMR, native mass spectrometry, thermophoresis, and a thermal shift assay. While the combined results of these screening methods retrieve 10 of the 11 crystal structures originally predicted by the biochemical assay, the mutual overlap of individual hit lists is surprisingly low, highlighting that each technique operates on different biophysical principles and conditions.

  17. 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).

  18. Evaluation of Immunoassays and General Biological Indicator Tests for Field Screening of Bacillus anthracis and Ricin

    PubMed Central

    Bartholomew, Rachel A.; Ozanich, Richard M.; Arce, Jennifer S.; Engelmann, Heather E.; Heredia-Langner, Alejandro; Hofstad, Beth A.; Hutchison, Janine R.; Jarman, Kristin; Melville, Angela M.; Victry, Kristin D.

    2017-01-01

    There is little published data on the performance of biological indicator tests and immunoassays that could be used by first responders to determine if a suspicious powder contains a potential biothreat agent. We evaluated a range of biological indicator tests, including 3 protein tests, 2 ATP tests, 1 DNA test, and 1 FTIR spectroscopy instrument for their ability to screen suspicious powders for Bacillus anthracis (B. anthracis) spores and ricin. We also evaluated 12 immunoassays (mostly lateral flow immunoassays) for their ability to screen for B. anthracis and ricin. We used a cost-effective, statistically based test plan that allows instruments to be evaluated at performance levels ranging from 0.85 to 0.95 lower confidence bound of the probability of detection at confidence levels of 80% to 95%. We also assessed interference with 22 common suspicious powders encountered in the field. The detection reproducibility for the biological indicators was evaluated at 108 B. anthracis spores and 62.5 μg ricin, and the immunoassay detection reproducibility was evaluated at 107 spores/mL (B. anthracis) and 0.1 μg/mL (ricin). Seven out of 12 immunoassays met our most stringent criteria for B. anthracis detection, while 9 out of 12 met our most stringent test criteria for ricin detection. Most of the immunoassays also detected ricin in 3 different crude castor seed preparations. Our testing results varied across products and sample preparations, indicating the importance of reviewing performance data for specific instruments and sample types of interest for the application in order to make informed decisions regarding the selection of biodetection equipment for field use. PMID:28192054

  19. A vortex-lattice method for general, unsteady aerodynamics

    NASA Technical Reports Server (NTRS)

    Konstadinopoulos, P.; Thrasher, D. F.; Mook, D. T.; Nayfeh, A. H.; Watson, L.

    1985-01-01

    A general method of calculating unsteady, incompressible, inviscid, three-dimensional flows around arbitrary planforms has been developed. The method is an extension of the vortex-lattice technique. It is not limited by aspect ratio, camber, or angle of attack, as long as vortex breakdown does not occur above the surface of the wing and separation occurs only along sharp edges. As the wing performs arbitrary maneuvers, the position of the wake and the distribution of circulation on the wing and in the wake are obtained as functions of time. One desirable feature of the present method is its ability to treat steady lifting flows very efficiently. Several examples of steady and unsteady flows are presented. These include rectangular wings, with and without flaps, delta, and cropped delta wings.

  20. 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.

  1. A general method for determining secondary active transporter substrate stoichiometry.

    PubMed

    Fitzgerald, Gabriel A; Mulligan, Christopher; Mindell, Joseph A

    2017-01-25

    The number of ions required to drive substrate transport through a secondary active transporter determines the protein's ability to create a substrate gradient, a feature essential to its physiological function, and places fundamental constraints on the transporter's mechanism. Stoichiometry is known for a wide array of mammalian transporters, but, due to a lack of readily available tools, not for most of the prokaryotic transporters for which high-resolution structures are available. Here, we describe a general method for using radiolabeled substrate flux assays to determine coupling stoichiometries of electrogenic secondary active transporters reconstituted in proteoliposomes by measuring transporter equilibrium potentials. We demonstrate the utility of this method by determining the coupling stoichiometry of VcINDY, a bacterial Na(+)-coupled succinate transporter, and further validate it by confirming the coupling stoichiometry of vSGLT, a bacterial sugar transporter. This robust thermodynamic method should be especially useful in probing the mechanisms of transporters with available structures.

  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. A screening method for evaluating resistance to the spotted wing drosophilla (drosophilla suzukii)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of the study was to develop an effective screening method for evaluating resistance to the Spotted Wing Drosophilla (SWD, and to locate resistance in southern adapted blueberry germplasm including the hexaploid rabbiteye (Vaccinium asheii Reade = V. virgatum Aiton) and the tetraploid s...

  4. 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

  5. A novel screening method to assess developability of antibody-like molecules

    PubMed Central

    Kohli, Neeraj; Jain, Nidhi; Geddie, Melissa L; Razlog, Maja; Xu, Lihui; Lugovskoy, Alexey A

    2015-01-01

    Monoclonal antibodies and antibody-like molecules represent a fast-growing class of bio-therapeutics that has rapidly transformed patient care in a variety of disease indications. The discovery of antibodies that bind to particular targets with high affinity is now a routine exercise and a variety of in vitro and in vivo techniques are available for this purpose. However, it is still challenging to identify antibodies that, in addition to having the desired biological effect, also express well, remain soluble at different pH levels, remain stable at high concentrations, can withstand high shear stress, and have minimal non-specific interactions. Many promising antibody programs have ultimately failed in development due to the problems associated with one of these factors. Here, we present a simple high-performance liquid chromatography (HPLC)-based screening method to assess these developability factors earlier in discovery process. This method is robust and requires only microgram quantities of proteins. Briefly, we show that for antibodies injected on a commercially available pre-packed Zenix HPLC column, the retention times are inversely related to their colloidal stability with antibodies prone to precipitation or aggregation retained longer on the column with broader peaks. By simply varying the salt content of running buffer, we were also able to estimate the nature of interactions between the antibodies and the column. We believe this approach should generally be applicable to assessment of the developability of other classes of bio-therapeutic molecules, and that the addition of this simple tool early in the discovery process will lead to selection of molecules with improved developability characteristics. PMID:25961854

  6. Nonlinear generalization of Den Hartog's equal-peak method

    NASA Astrophysics Data System (ADS)

    Habib, G.; Detroux, T.; Viguié, R.; Kerschen, G.

    2015-02-01

    This study addresses the mitigation of a nonlinear resonance of a mechanical system. In view of the narrow bandwidth of the classical linear tuned vibration absorber, a nonlinear absorber, termed the nonlinear tuned vibration absorber (NLTVA), is introduced in this paper. An unconventional aspect of the NLTVA is that the mathematical form of its restoring force is tailored according to the nonlinear restoring force of the primary system. The NLTVA parameters are then determined using a nonlinear generalization of Den Hartog's equal-peak method. The mitigation of the resonant vibrations of a Duffing oscillator is considered to illustrate the proposed developments.

  7. Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results.

    PubMed

    Li, Yan; Han, Li; Liu, Zhihai; Wang, Renxiao

    2014-06-23

    Our comparative assessment of scoring functions (CASF) benchmark is created to provide an objective evaluation of current scoring functions. The key idea of CASF is to compare the general performance of scoring functions on a diverse set of protein-ligand complexes. In order to avoid testing scoring functions in the context of molecular docking, the scoring process is separated from the docking (or sampling) process by using ensembles of ligand binding poses that are generated in prior. Here, we describe the technical methods and evaluation results of the latest CASF-2013 study. The PDBbind core set (version 2013) was employed as the primary test set in this study, which consists of 195 protein-ligand complexes with high-quality three-dimensional structures and reliable binding constants. A panel of 20 scoring functions, most of which are implemented in main-stream commercial software, were evaluated in terms of "scoring power" (binding affinity prediction), "ranking power" (relative ranking prediction), "docking power" (binding pose prediction), and "screening power" (discrimination of true binders from random molecules). Our results reveal that the performance of these scoring functions is generally more promising in the docking/screening power tests than in the scoring/ranking power tests. Top-ranked scoring functions in the scoring power test, such as X-Score(HM), ChemScore@SYBYL, ChemPLP@GOLD, and PLP@DS, are also top-ranked in the ranking power test. Top-ranked scoring functions in the docking power test, such as ChemPLP@GOLD, Chemscore@GOLD, GlidScore-SP, LigScore@DS, and PLP@DS, are also top-ranked in the screening power test. Our results obtained on the entire test set and its subsets suggest that the real challenge in protein-ligand binding affinity prediction lies in polar interactions and associated desolvation effect. Nonadditive features observed among high-affinity protein-ligand complexes also need attention.

  8. Surface electromyography as a screening method for evaluation of dysphagia and odynophagia

    PubMed Central

    Vaiman, Michael; Eviatar, Ephraim

    2009-01-01

    Objective Patients suspected of having swallowing disorders, could highly benefit from simple diagnostic screening before being referred to specialist evaluations. The article analyzes various instrumental methods of dysphagia assessment, introduces surface electromyography (sEMG) to carry out rapid assessment of such patients, and debates proposed suggestions for sEMG screening protocol in order to identify abnormal deglutition. Data sources Subject related books and articles from 1813 to 2007 were obtained through library search, MEDLINE (1949–2007) and EMBASE (1975–2007). Methods Specifics steps for establishing the protocol for applying the technique for screening purposes (e.g., evaluation of specific muscles), the requirements for diagnostic sEMG equipment, the sEMG technique itself, and defining the tests suitable for assessing deglutition (e.g., saliva, normal, and excessive swallows and uninterrupted drinking of water) are presented in detail. SEMG is compared with other techniques in terms of cost, timing, involvement of radiation, etc. Results According to the published data, SEMG of swallowing is a simple and reliable method for screening and preliminary differentiation among dysphagia and odynophagia of various origins. This noninvasive radiation-free examination has a low level of discomfort, and is simple, time-saving and inexpensive to perform. The major weakness of the method seems to be inability for precise diagnostic of neurologically induced dysphagia. Conclusion With standardization of the technique and an established normative database, sEMG might serve as a reliable screening method for optimal patient management but cannot serve for proper investigation of neurogenic dysphagia. PMID:19232090

  9. Alizarin Red S for Online Pyrophosphate Detection Identified by a Rapid Screening Method

    PubMed Central

    Fischbach, Jens; Loh, Qiuting; Bier, Frank F.; Lim, Theam Soon; Frohme, Marcus; Glökler, Jörn

    2017-01-01

    We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity. In addition, the newly identified properties may also be useful in other enzymatic assays which do not generate nucleic acids but are based on inorganic pyrophosphate. Finally, we propose that our screening method may provide a blueprint for rapid screening of compounds for detecting inorganic pyrophosphate. PMID:28338022

  10. Thin-Film Thermoelectric Module for Power Generator Applications Using a Screen-Printing Method

    NASA Astrophysics Data System (ADS)

    Lee, Heon-Bok; Yang, Hyun Jeong; We, Ju Hyung; Kim, Kukjoo; Choi, Kyung Cheol; Cho, Byung Jin

    2011-05-01

    A new process for fabricating a low-cost thermoelectric module using a screen-printing method has been developed. Thermoelectric properties of screen-printed ZnSb films were investigated in an effort to develop a thermoelectric module with low cost per watt. The screen-printed Zn x Sb1- x films showed a low carrier concentration and high Seebeck coefficient when x was in the range of 0.5 to 0.57 and the annealing temperature was kept below 550°C. When the annealing temperature was higher than 550°C, the carrier concentration of the Zn x Sb1- x films reached that of a metal, leading to a decrease of the Seebeck coefficient. In the present experiment, the optimized carrier concentration of screen-printed ZnSb was 7 × 1018/cm3. The output voltage and power density of the ZnSb film were 10 mV and 0.17 mW/cm2, respectively, at Δ T = 50 K. A thermoelectric module was produced using the proposed screen-printing approach with ZnSb and CoSb3 as p-type and n-type thermoelectric materials, respectively, and copper as the pad metal.

  11. The WST survival assay: an easy and reliable method to screen radiation-sensitive individuals.

    PubMed

    Guertler, A; Kraemer, A; Roessler, U; Hornhardt, S; Kulka, U; Moertl, S; Friedl, A A; Illig, T; Wichmann, E; Gomolka, M

    2011-02-01

    An easy, fast and reliable method was developed to screen hundreds of Epstein-Barr virus-transformed cell lines (lymphoblastoid cell lines, LCLs) for radiation sensitivity that were generated from lymphocytes isolated from young lung cancer patients. The WST-1 test explores the metabolic activity of the mitochondria as an indicator for the vital status of cells. Cell proliferation as well as indirect cell death can be quantified by this method on a large scale in microtiter plates. Cell survival was measured at 24- and 48-h post-irradiation with 10 Gy ((137)Cs source) by the WST-1 assay and Trypan blue staining. To set up the experimental screening conditions and to establish a positive and a negative control, an ATM-mutated cell line from a radiation-sensitive ATM patient and an ATM proficient cell line from a healthy brother were compared. An optimal differentiation between the two cell lines was demonstrated for 10 Gy and 24- and 48-h cell growth after irradiation. Upon screening 120 LCLs of young lung cancer patients under these conditions, 5 of them were found to be radiation sensitive to a high degree of statistical significance. The results have been confirmed by a second laboratory by means of Trypan blue testing. The WST-1 test represents an efficient and reliable method by means of screening for radiation-sensitive cell lines.

  12. A general method for the quantitative assessment of mineral pigments.

    PubMed

    Ares, M C Zurita; Fernández, J M

    2016-01-01

    A general method for the estimation of mineral pigment contents in different bases has been proposed using a sole set of calibration curves, (one for each pigment), calculated for a white standard base, thus elaborating patterns for each utilized base is not necessary. The method can be used in different bases and its validity had ev en been proved in strongly tinted bases. The method consists of a novel procedure that combines diffuse reflectance spectroscopy, second derivatives and the Kubelka-Munk function. This technique has proved to be at least one order of magnitude more sensitive than X-Ray diffraction for colored compounds, since it allowed the determination of the pigment amount in colored samples containing 0.5 wt% of pigment that was not detected by X-Ray Diffraction. The method can be used to estimate the concentration of mineral pigments in a wide variety of either natural or artificial materials, since it does not requiere the calculation of each pigment pattern in every base. This fact could have important industrial consequences, as the proposed method would be more convenient, faster and cheaper.

  13. Intermediate electrostatic field for the generalized elongation method.

    PubMed

    Liu, Kai; Korchowiec, Jacek; Aoki, Yuriko

    2015-05-18

    An intermediate electrostatic field is introduced to improve the accuracy of fragment-based quantum-chemical computational methods by including long-range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms-in-molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO-3G, 6-31G, and 6-31G(d) basis sets and compared with reference Hartree-Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long-range polarization in electronic-structure calculations by fragmentation techniques.

  14. 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.

  15. Integrating Multiple Teaching Methods into a General Chemistry Classroom

    NASA Astrophysics Data System (ADS)

    Francisco, Joseph S.; Nicoll, Gayle; Trautmann, Marcella

    1998-02-01

    In addition to the traditional lecture format, three other teaching strategies (class discussions, concept maps, and cooperative learning) were incorporated into a freshman level general chemistry course. Student perceptions of their involvement in each of the teaching methods, as well as their perceptions of the utility of each method were used to assess the effectiveness of the integration of the teaching strategies as received by the students. Results suggest that each strategy serves a unique purpose for the students and increased student involvement in the course. These results indicate that the multiple teaching strategies were well received by the students and that all teaching strategies are necessary for students to get the most out of the course.

  16. General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models

    PubMed Central

    de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael

    2016-01-01

    Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population. PMID:27591750

  17. General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models.

    PubMed

    de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael

    2016-11-01

    Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population.

  18. A clone screening method using mRNA levels to determine specific productivity and product quality for monoclonal antibodies.

    PubMed

    Lee, Christina J; Seth, Gargi; Tsukuda, Joni; Hamilton, Robert W

    2009-03-01

    To meet increasing demands for efficient and streamlined production processes of therapeutic antibodies, improved methods of screening clones are required. In this article, we examined the potential of using antibody transcript levels as criteria for clone screening. We evaluated the QuantiGene Plex, a commercially available, high-throughput assay for simultaneously measuring multiple transcripts from cell lysate. Using the development of stable Chinese hamster ovary cell lines as examples, we investigated the relationship between transcript and antibody levels through several rounds of screening. First, we observed that measured heavy chain transcript levels are generally correlated with specific productivity, enabling the identification of high-producing clones from mRNA. Second, we observed that low ratios (< 1.5) of light to heavy chain transcript levels may be indicative of high antibody aggregation levels, allowing for the rapid identification and elimination of clones of questionable product quality. Therefore, an efficient process of identifying high-producing clones of desirable product quality is possible by using QuantiGene Plex assay to measure antibody transcript levels.

  19. Screening with faecal occult blood test (FOBT) for colorectal cancer: assessment of two methods that attempt to improve compliance.

    PubMed

    Ore, L; Hagoel, L; Lavi, I; Rennert, G

    2001-06-01

    Screening with the faecal occult blood test (FOBT) has been shown in randomized control trials to be effective in reducing mortality from colorectal cancer. Compliance to this test recommendation, however, by the general population is usually low. To evaluate different methods of increasing compliance with FOBT, using mailed test kits or order cards, with or without information leaflets, subjects were randomly assigned to receive a test kit or a kit request card. An information leaflet was included in half of the mailings. All participants were contacted for interview. Compliance was evaluated through the central computer system of the study's FOBT laboratory. Self-initiated compliance with FOBT in the year preceding the study was 0.6% of the study participants. The overall compliance rate with the programme invitation was 17.9%, with a somewhat higher, though non-significant response to the mailed kit (19.9%) over the kit request card (15.9%). Women complied with the test significantly more than men, older participants more than younger. Compliance to FOBT is low among the Israeli population aged 50-74 who receive a formal invitation to carry out this screening. Mailing a kit request card within the framework of a screening programme can achieve a substantial increase (to 17.9%) in the level of compliance for the relatively low cost of postage. More effort is needed to study additional means of convincing the non-responders to take part in this potentially life saving activity.

  20. First Principles Structure Calculations Using the General Potential Lapw Method

    NASA Astrophysics Data System (ADS)

    Wei, Su-Huai

    We have developed a completely general first principles self-consistent full-potential linearized-augmented-plane -wave (LAPW) method program within the density functional formalism to calculate electronic band structure, total energy, pressure and other quantities. No symmetry assumptions are used for the crystal structure. Shape unrestricted charge densities and potentials are calculated inside muffin -tin (MT) spheres as well as in the interstitial regions. All contributions to the Hamiltonian matrix elements are completely taken into account. The core states are treated fully relativistically using the spherical part of the potential only. Scalar relativistic effects are included for the band-states, and spin-orbit coupling is included using a second variation procedure. Both core states and valence states are treated self-consistently, the frozen core approximation is not required. The fast Fourier transformation method is used wherever it is applicable, and this greatly improves the efficiency. This state-of-the-art program has been tested extensively to check the accuracy and convergence properties by comparing calculated electronic band structures, ground state properties, equations of state and cohesive energies for bulk W and GaAs with other theoretical calculations and experimental results. It has been successfully applied to calculate and predict structural and metal-insulator phase transitions for close-packed crystal BaSe and BaTe and the geometric structure of the d-band metal W(001) surface. The results are in generally good agreement with experiment.

  1. 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.

  2. Laboratory investigation of monoclonal gammopathy during 10 years of screening in a general hospital.

    PubMed Central

    Malacrida, V; De Francesco, D; Banfi, G; Porta, F A; Riches, P G

    1987-01-01

    Protein electrophoresis was carried out on 102,000 samples from the patients of a district general hospital over 10 years, and a monoclonal protein was detected in 730 cases; of these, 114 could be classified as B cell malignancies and 261 as monoclonal gammopathy of undefined significance (MGUS). The various clinical and laboratory features of monoclonal gammopathy were examined with respect to distinguishing the malignant conditions from MGUS at first presentation. PMID:3114329

  3. [Intratesticular subcapsular assay, a simple method for the preliminary screening of male contraceptives].

    PubMed

    Xu, Y; Wang, Y; Zhang, Z T; Lin, N; Qian, S Z

    1993-01-01

    The MB-50 protocol worked out for long by the World Health Organization has been widely employed for the screening of male contraceptives. With this method, 40-80 rats will be used for 1 sample and the course of study will be about 3 months. In view of the high expenses and long duration of time needed, it seems to be not suitable for a preliminary screening. We have exploited a much simpler method, the intratesticular subcapsular assay. The method is as follows: Puncture the scrotal skin and the tunica albuginea at the equatorial plane of the testis just opposite to the epididymis with an intradermal needle fixed at a tuberculin syringe. Then push on the needle for 3-4 mm along the equator parallel to the tunica albuginea. Inject 100 microliters of solution containing 0.1-5 mg of the sample to each testis. To the controls, only the vehicle is injected. One week later the same procedure is repeated and 2 more weeks later, the animals are sacrificed and the data are observed (see Table 1 and 2). In this paper, 7 samples screened with this method were compared with results of the MB-50 method, no positive sample was missed except one false positive sample. These results indicate the coincidence between these two methods.

  4. Did the London Initiative Zone investment programme affect general practice structure and performance in East London? A time series analysis of cervical screening coverage and asthma prescribing.

    PubMed

    Naish, J; Eldridge, S; Moser, K; Sturdy, P

    2002-11-01

    A programme of incentives was set up in the London Initiative Zones to improve primary care in inner London based on the findings of the Tomlinson Enquiry in 1992. This descriptive study is a 4-y time series analysis of changes in general practice structure in East London as the result of London Initiative Zone investment, and an exploration of the possible effect of investment on practice performance. We used routinely available administrative data for the whole analysis. General practice characteristics and two selected performance indicators: the asthma prophylaxis to bronchodilator ratio and cervical cytology screening rate, for all practices in the East London and the City Health Authority for 4 y, 1993-1996, were used. Both reflect practice efficiency, but relate to different aspects of practice performance. The prescribing indicator is more indicative of the quality of clinical practise, whereas cervical screening coverage relates more to the characteristics of the practice population and to practice organisation. Repeated measures analyses were used to identify trends and to explore the relationship between changes in practice characteristics and performance. Graphical methods were used to compare East London trends with the rest of England. There were significant improvements in practice structure as the consequence of London Initiative Zone investment. There was a positive association with improvements in practice performance, but East London still lagged some way behind national patterns. The findings suggest that while improvements in asthma prescribing follow the national trend, practices have difficulty in achieving and sustaining the 80% target for cervical cytology screening, and that an overall population coverage of 80% may be in doubt.Increased investment in practice staffing may be influential in improving some aspects of performance. However, in common with other inner cities, a greater effort and more innovative strategies may be needed to

  5. Intimate partner violence among female drug users admitted to the general hospital: screening and prevalence.

    PubMed

    Caldentey, Clara; Tirado Muñoz, Judit; Ferrer, Tessie; Fonseca Casals, Francina; Rossi, Paola; Mestre-Pintó, Juan Ignacio; Torrens Melich, Marta

    2016-09-29

    Intimate partner violence (IPV) is a public health problem worldwide. Several factors have been found to be associated with an increased prevalence of IPV, such as substance use. A cross-sectional study was conducted with the aim of determining the prevalence of IPV among women entering Hospital del Mar (Barcelona) for any medical/surgical reason, and who had a diagnosis of substance use disorder. Secondly, it was intended to psychometrically validate the Spanish version of the Hurt, Insulted, Threatened with Harm, Screamed (HITS) questionnaire. All patients were assessed by two IPV questionnaires, the Composite Abuse Scale (CAS) and HITS. Out of 52 patients interviewed, 46 answered both questionnaires. According to the CAS questionnaire, 23 patients (50%) experienced IPV at some point in their lives and 11 (23.9%) in the last year. Cannabis consumption was also associated with an increased severity of IPV (95% CI 3.5-28.9, p = .013).According to the HITS questionnaire, there was a prevalence of 39.1% (18 patients) in the last 12 months. HITS had a specificity of 100% and a sensitivity of 78% relative to the CAS questionnaire. A cut-off score x∈ [6.7], derived through ROC analysis, correctly discriminated 91% of the victims and 100% of the non-victims. The results obtained showed that the prevalence of IPV was very high among women who suffered from more than one substance use disorder. Therefore, it is highly recommended to systematically screen for IPV victimization by putting the HITS questionnaire into practice.

  6. Automatic tailoring and transplanting: a practical method that makes virtual screening more useful.

    PubMed

    Li, Yan; Zhao, Yuan; Liu, Zhihai; Wang, Renxiao

    2011-06-27

    Docking-based virtual screening of large compound libraries has been widely applied to lead discovery in structure-based drug design. However, subsequent lead optimizations often rely on other types of computational methods, such as de novo design methods. We have developed an automatic method, namely automatic tailoring and transplanting (AutoT&T), which can effectively utilize the outcomes of virtual screening in lead optimization. This method detects suitable fragments on virtual screening hits and then transplants them onto a lead compound to generate new ligand molecules. Binding affinities, synthetic feasibilities, and drug-likeness properties are considered in the selection of final designs. In this study, our AutoT&T program was tested on three different target proteins, including p38 MAP kinase, PPAR-α, and Mcl-1. In the first two cases, AutoT&T was able to produce molecules identical or similar to known inhibitors with better potency than the given lead compound. In the third case, we demonstrated how to apply AutoT&T to design novel ligand molecules from scratch. Compared to the solutions generated by other two de novo design methods, i.e., LUDI and EA-Inventor, the solutions generated by AutoT&T were structurally more diverse and more promising in terms of binding scores in all three cases. AutoT&T also completed the assigned jobs more efficiently than LUDI and EA-Inventor by several folds. Our AutoT&T method has certain technical advantages over de novo design methods. Importantly, it expands the application of virtual screening from lead discovery to lead optimization and thus may serve as a valuable tool for many researchers.

  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. Amyloid oligomer structure characterization from simulations: a general method.

    PubMed

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

    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 Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

  10. Generalized Weighted Residual Method; Advancements and Current Studies

    NASA Astrophysics Data System (ADS)

    Scheffel, Jan; Lindvall, Kristoffer

    2016-10-01

    The Generalized Weighted Residual Method (GWRM) is a time-spectral method for solving initial value partial differential equations. The GWRM treats the temporal, spatial, and parameter domains by projecting the residual to a Chebyshev polynomial space, with the variational principle being that the residual is zero. This treatment provides a global semi-analytical solution. However, straightforward global solution is not economical. One remedy is the inclusion of spatial and temporal sub-domains with coupled internal boundary conditions, which decreases memory requirements and introduces sparse matrices. Only the equations pertaining to the boundary conditions need be solved globally, making the method parallelizable in time. Efficient solution of the linearized ideal MHD stability equations of screw-pinch equilibria are proved possible. The GWRM has also been used to solve strongly nonlinear ODEs such as the Lorenz equations (1984), and is capable of competing with finite time difference schemes in terms of both accuracy and efficiency. GWRM solutions of linear and nonlinear model problems of interest for stability and turbulence modelling will be presented, including detailed comparisons with time stepping methods.

  11. 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.

  12. 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

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

    PubMed

    Gaffron, Philine; Niemeier, Deb

    2015-02-11

    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.

  14. 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.

  15. 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

  16. A parallelized screen-based method for rendering polylines and polygons on terrain surfaces

    NASA Astrophysics Data System (ADS)

    She, Jiangfeng; Zhou, Yang; Tan, Xin; Li, Xingong; Guo, Xingchen

    2017-02-01

    Two dimensional (2D) vector features, when rendered on terrain as reference or highlight features, can improve the intelligibility of three dimensional (3D) scenes. This research proposes a new screen-space based method to render solid color 2D polylines and polygons on terrain. Using the z-buffer value and window coordinates in screen space, a pixel's spatial extent in real world coordinates can be calculated. The pixel's color is changed, if its spatial extent intersects with a polyline or polygon feature, to reflect the fact that there is a polyline going through or a polygon covering the pixel. Compared to other existing methods, our method eliminates undesirable rendering artifacts. A parallel computing schema was proposed and implemented as well to improve rendering performance.

  17. 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

  18. The incidence of monoclonal proteins during 7 years of screening in a District General Hospital.

    PubMed Central

    Adams, R A; Smith, L; Pickering, P E

    1984-01-01

    The aim of this study was to assess the incidence of monoclonal proteins, during a 7-year period, in the population served by a typical District General Hospital. 183,300 sera were electrophoresed and 804 monoclonal proteins were detected. Various biochemical prognostic criteria, such as the concentration of monoclonal protein, incidence of Bence-Jones protein and the presence of reduced polyclonal immunoglobulins, were studied in an attempt to assess the benign or malignant nature of the monoclonal protein. In this study, 75% of the patients with monoclonal proteins fulfilled at least one of these criteria, demonstrating the importance of long-term monitoring. PMID:6698575

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

    PubMed

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

    2014-10-07

    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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. A general method for determining secondary active transporter substrate stoichiometry

    PubMed Central

    Fitzgerald, Gabriel A; Mulligan, Christopher; Mindell, Joseph A

    2017-01-01

    The number of ions required to drive substrate transport through a secondary active transporter determines the protein’s ability to create a substrate gradient, a feature essential to its physiological function, and places fundamental constraints on the transporter’s mechanism. Stoichiometry is known for a wide array of mammalian transporters, but, due to a lack of readily available tools, not for most of the prokaryotic transporters for which high-resolution structures are available. Here, we describe a general method for using radiolabeled substrate flux assays to determine coupling stoichiometries of electrogenic secondary active transporters reconstituted in proteoliposomes by measuring transporter equilibrium potentials. We demonstrate the utility of this method by determining the coupling stoichiometry of VcINDY, a bacterial Na+-coupled succinate transporter, and further validate it by confirming the coupling stoichiometry of vSGLT, a bacterial sugar transporter. This robust thermodynamic method should be especially useful in probing the mechanisms of transporters with available structures. DOI: http://dx.doi.org/10.7554/eLife.21016.001 PMID:28121290

  7. 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.

  8. 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.

  9. Appropriate model selection methods for nonstationary generalized extreme value models

    NASA Astrophysics Data System (ADS)

    Kim, Hanbeen; Kim, Sooyoung; Shin, Hongjoon; Heo, Jun-Haeng

    2017-04-01

    Several evidences of hydrologic data series being nonstationary in nature have been found to date. This has resulted in the conduct of many studies in the area of nonstationary frequency analysis. Nonstationary probability distribution models involve parameters that vary over time. Therefore, it is not a straightforward process to apply conventional goodness-of-fit tests to the selection of an appropriate nonstationary probability distribution model. Tests that are generally recommended for such a selection include the Akaike's information criterion (AIC), corrected Akaike's information criterion (AICc), Bayesian information criterion (BIC), and likelihood ratio test (LRT). In this study, the Monte Carlo simulation was performed to compare the performances of these four tests, with regard to nonstationary as well as stationary generalized extreme value (GEV) distributions. Proper model selection ratios and sample sizes were taken into account to evaluate the performances of all the four tests. The BIC demonstrated the best performance with regard to stationary GEV models. In case of nonstationary GEV models, the AIC proved to be better than the other three methods, when relatively small sample sizes were considered. With larger sample sizes, the AIC, BIC, and LRT presented the best performances for GEV models which have nonstationary location and/or scale parameters, respectively. Simulation results were then evaluated by applying all four tests to annual maximum rainfall data of selected sites, as observed by the Korea Meteorological Administration.

  10. The usefulness of the Denver Developmental Screening Test to predict kindergarten problems in a general community population.

    PubMed Central

    Cadman, D; Chambers, L W; Walter, S D; Feldman, W; Smith, K; Ferguson, R

    1984-01-01

    The Denver Developmental Screening Test (DDST) was administered to 2,569 children five to seven months prior to starting kindergarten in September 1980 in a geographically well-defined community. The test was administered by trained public health nurses. At the end of the 1980-1981 school year, all 163 kindergarten teachers in the area completed a rating form for each child in their class. The rating form determined global ratings of: 1) learning abilities; 2) classroom behavior; 3) amount of special attention required; and 4) referrals to special education services outside the classroom. The specificity of the DDST in predicting kindergarten teacher ratings was 99 per cent for all areas. Test sensitivity varied from 5 per cent to 10 per cent in detecting problems in the four areas. The predictive values of an positive test varied from 31 per cent for behavior problems to 62 per cent for extra attention required in the classroom. Negative test predictive values varied from 79 per cent to 93 per cent. These results based on kindergarten teacher ratings suggest that, because of the low sensitivity and modest predictive value, the DDST may be relatively inefficient to use in a school entry screening program in a general community population of children. PMID:6206733

  11. A general radiochemical-color method for quantitation of immunoblots.

    PubMed

    Esmaeli-Azad, B; Feinstein, S C

    1991-12-01

    Quantitative interpretation of protein immunoblotting procedures is hampered by a variety of technical liabilities inherent in the use of photographic and densitometric methods. In this paper, we present a novel, simple, and generally applicable alternative procedure to acquire quantitative data from immunoblots. Our strategy employs both the standard alkaline phosphatase color reaction and radiolabelled Protein A. The color reaction is used to localize the polypeptide of interest after transfer to a solid support. The colored bands are then excised and the radioactivity in the colocalized Protein A is quantitated in a gamma counter. In addition to avoiding the problems associated with photographic and densitometric procedures, our assay also overcomes common problems associated with variable gel lane width and individual band distortion. The resulting data is linear over a range of at least 50-fold (10-500 ng of specific protein, for the example used in this study) and is highly reproducible.

  12. Optimal Methods to Screen Men and Women for Intimate Partner Violence: Results from an Internal Medicine Residency Continuity Clinic

    ERIC Educational Resources Information Center

    Kapur, Nitin A.; Windish, Donna M.

    2011-01-01

    Contradictory data exist regarding optimal methods and instruments for intimate partner violence (IPV) screening in primary care settings. The purpose of this study was to determine the optimal method and screening instrument for IPV among men and women in a primary-care resident clinic. We conducted a cross-sectional study at an urban, academic,…

  13. Screen detected high blood pressure under 40: a general practice population followed up for 21 years.

    PubMed Central

    Hart, J T; Edwards, C; Hart, M; Jones, J; Jones, M; Haines, A; Watt, G

    1993-01-01

    OBJECTIVE--To assess hypertension detected under 40 in a general practice population. DESIGN--Prospective case-control study. SETTING AND SUBJECTS--Former coal mining community in south Wales. Systematic case finding for hypertension and associated risk factors applied to a mean total population of 1945 from age 20 on a five year cycle through 21 years. Mean population aged 20-39, 227 men and 213 women. Case criteria: age < 40 and mean systolic pressure > or = 160 mm Hg or diastolic pressure > or = 100 mm Hg. Age and sex matched controls randomly sampled from the same population. MAIN OUTCOME MEASURES--Mean initial pressures and pressures at follow up in 1989 or preceding death, and all cardiovascular events. RESULTS--25 men and 16 women met criteria. Estimated five yearly inceptions were 26/1000 for men and 18/1000 for women. Male group mean initial blood pressure was 164/110 mm Hg for cases, falling to 148/89 mm Hg at follow up. Five male cases died at mean age 47.8, compared with two controls at 49.5. Female group mean initial pressure was 172/107 mm Hg for cases, falling to 145/86 mm Hg at follow up. One female case died aged 50, no controls. 10 male cases had non-fatal cardiovascular events at mean age 40.2, compared with two controls at mean age 50.5. Four female cases had non-fatal events at mean age 47.2, compared with one control aged 58. Male differences were statistically significant. CONCLUSIONS--Hypertension under 40 is dangerous, commoner in men than women, rarely secondary to classic causes, and may be controlled in general practice on a whole community basis. PMID:8461729

  14. Improved method for effective screening of ACC (1-aminocyclopropane-1-carboxylate) deaminase producing microorganisms.

    PubMed

    Patil, Chandrashekhar; Suryawanshi, Rahul; Koli, Sunil; Patil, Satish

    2016-12-01

    Aminocyclopropane-1-carboxylate deaminase (ACCD) producing microorganisms support plant growth under a variety of biotic and abiotic stress conditions such as drought, soil salinity, flooding, heavy metal pollution and phyto-pathogen attack. Available screening methods for ACCD give idea only about its primary microbial ACCD activity than the actual potential. In the present investigation, we have simply improved screening method by incorporating pH indicator dyes (phenol red and bromothymol blue) in ACC containing medium. This modification is based on the basic principle that ACCD action releases ammonia which can be detected by color change and zone around the bacterial colony. High color intensity and zone around the colony indicates most potent producer, colony showing only a color change indicates moderate potential and no change in colony color indicates least efficiency. Enzymatic bioassays as well as root elongation studies revealed that ACC-deaminase activity of Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Bacillus subtilis clearly corresponds to their growth on dye incorporated ACC medium. This method could be used to complement the existing screening methods and to speed up the targeted isolation of agriculturally important microorganisms.

  15. Real-time and online screening method for materials emitting volatile organic compounds

    NASA Astrophysics Data System (ADS)

    Kim, Changhyuk; Sul, Yong Tae; Pui, David Y. H.

    2016-09-01

    In the semiconductor industry, volatile organic compounds (VOCs) in the cleanroom air work as airborne molecular contamination, which reduce the production yield of semiconductor chips by forming nanoparticles and haze on silicon wafers and photomasks under ultraviolet irradiation during photolithography processes. Even though VOCs in outdoor air are removed by gas filters, VOCs can be emitted from many kinds of materials used in cleanrooms, such as organic solvents and construction materials (e.g., adhesives, flame retardants and sealants), threatening the production of semiconductors. Therefore, finding new replacements that emit lower VOCs is now essential in the semiconductor industry. In this study, we developed a real-time and online method to screen materials for developing the replacements by converting VOCs into nanoparticles under soft X-ray irradiation. This screening method was applied to measure VOCs emitted from different kinds of organic solvents and adhesives. Our results showed good repeatability and high sensitivity for VOCs, which come from aromatic compounds, some alcohols and all tested adhesives (Super glue and cleanroom-use adhesives). In addition, the overall trend of measured VOCs from cleanroom-use adhesives was well matched with those measured by a commercial thermal desorption-gas chromatography-mass spectrometry, which is a widely used off-line method for analyzing VOCs. Based on the results, this screening method can help accelerate the developing process for reducing VOCs in cleanrooms.

  16. 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

    2016-08-05

    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.

  17. 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

  18. 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

  19. 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

  20. A simple method to generate adipose stem cell-derived neurons for screening purposes.

    PubMed

    Bossio, Caterina; Mastrangelo, Rosa; Morini, Raffaella; Tonna, Noemi; Coco, Silvia; Verderio, Claudia; Matteoli, Michela; Bianco, Fabio

    2013-10-01

    Strategies involved in mesenchymal stem cell (MSC) differentiation toward neuronal cells for screening purposes are characterized by quality and quantity issues. Differentiated cells are often scarce with respect to starting undifferentiated population, and the differentiation process is usually quite long, with high risk of contamination and low yield efficiency. Here, we describe a novel simple method to induce direct differentiation of MSCs into neuronal cells, without neurosphere formation. Differentiated cells are characterized by clear morphological changes, expression of neuronal specific markers, showing functional response to depolarizing stimuli and electrophysiological properties similar to those of developing neurons. The method described here represents a valuable tool for future strategies aimed at personalized screening of therapeutic agents in vitro.

  1. 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.

  2. Medium-throughput profiling method for screening polysaccharide-degrading enzymes in complex bacterial extracts.

    PubMed

    Fer, Maude; Préchoux, Aurélie; Leroy, Andréa; Sassi, Jean-François; Lahaye, Marc; Boisset, Claire; Nyvall-Collén, Pi; Helbert, William

    2012-06-01

    Polysaccharides are the most abundant and the most diverse renewable materials found on earth. Due to the stereochemical variability of carbohydrates, polysaccharide-degrading enzymes - i.e. glycoside hydrolases and polysaccharide lyases - are essential tools for resolving the structure of these complex macromolecules. The exponential increase of genomic and metagenomic data contrasts sharply with the low number of proteins that have ascribed functions. To help fill this gap, we designed and implemented a medium-throughput profiling method to screen for polysaccharide-degrading enzymes in crude bacterial extracts. Our strategy was based on a series of filtrations, which are absolutely necessary to eliminate any reducing sugars not directly generated by enzyme degradation. In contrast with other protocols already available in the literature, our method can be applied to any panel of polysaccharides having known and unknown structures because no chemical modifications are required. We applied this approach to screen for enzymes that occur in Pseudoalteromonas carrageenovora grown in two culture conditions.

  3. 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.

  4. Histidine-containing peptide catalysts developed by a facile library screening method.

    PubMed

    Akagawa, Kengo; Sakai, Nobutaka; Kudo, Kazuaki

    2015-02-02

    Although peptide catalysts have a high potential for the use as organocatalysts, the optimization of peptide sequences is laborious and time-consuming. To address this issue, a facile screening method for finding efficient aminocatalysts from a peptide library has been developed. In the screening for the Michael addition of a malonate to an enal, a dye-labeled product is immobilized on resin-bound peptides through reductive amination to visualize active catalysts. This procedure allows for the monitoring of the reactivity of entire peptides without modifying the resin beads beforehand. Peptides containing histidine at an appropriate position were identified by this method. A novel function of the histidyl residue, which enhances the binding of a substrate to the catalyst by capturing an iminium intermediate, was indicated.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Generalized non-separable two-dimensional Dammann encoding method

    NASA Astrophysics Data System (ADS)

    Yu, Junjie; Zhou, Changhe; Zhu, Linwei; Lu, Yancong; Wu, Jun; Jia, Wei

    2017-01-01

    We generalize for the first time, to the best of our knowledge, the Dammann encoding method into non-separable two-dimensional (2D) structures for designing various pure-phase Dammann encoding gratings (DEGs). For examples, three types of non-separable 2D DEGs, including non-separable binary Dammann vortex gratings, non-separable binary distorted Dammann gratings, and non-separable continuous-phase cubic gratings, are designed theoretically and demonstrated experimentally. Correspondingly, it is shown that 2D square arrays of optical vortices with topological charges proportional to the diffraction orders, focus spots shifting along both transversal and axial directions with equal spacings, and Airy-like beams with controllable orientation for each beam, are generated in symmetry or asymmetry by these three DEGs, respectively. Also, it is shown that a more complex-shaped array of modulated beams could be achieved by this non-separable 2D Dammann encoding method, which will be a big challenge for those conventional separable 2D Dammann encoding gratings. Furthermore, the diffractive efficiency of the gratings can be improved around ∼10% when the non-separable structure is applied, compared with their conventional separable counterparts. Such improvement in the efficiency should be of high significance for some specific applications.

  10. Process Setting through General Linear Model and Response Surface Method

    NASA Astrophysics Data System (ADS)

    Senjuntichai, Angsumalin

    2010-10-01

    The objective of this study is to improve the efficiency of the flow-wrap packaging process in soap industry through the reduction of defectives. At the 95% confidence level, with the regression analysis, the sealing temperature, temperatures of upper and lower crimper are found to be the significant factors for the flow-wrap process with respect to the number/percentage of defectives. Twenty seven experiments have been designed and performed according to three levels of each controllable factor. With the general linear model (GLM), the suggested values for the sealing temperature, temperatures of upper and lower crimpers are 185, 85 and 85° C, respectively while the response surface method (RSM) provides the optimal process conditions at 186, 89 and 88° C. Due to different assumptions between percentage of defective and all three temperature parameters, the suggested conditions from the two methods are then slightly different. Fortunately, the estimated percentage of defectives at 5.51% under GLM process condition and the predicted percentage of defectives at 4.62% under RSM process condition are not significant different. But at 95% confidence level, the percentage of defectives under RSM condition can be much lower approximately 2.16% than those under GLM condition in accordance with wider variation. Lastly, the percentages of defectives under the conditions suggested by GLM and RSM are reduced by 55.81% and 62.95%, respectively.

  11. A novel generalized ridge regression method for quantitative genetics.

    PubMed

    Shen, Xia; Alam, Moudud; Fikse, Freddy; Rönnegård, Lars

    2013-04-01

    As the molecular marker density grows, there is a strong need in both genome-wide association studies and genomic selection to fit models with a large number of parameters. Here we present a computationally efficient generalized ridge regression (RR) algorithm for situations in which the number of parameters largely exceeds the number of observations. The computationally demanding parts of the method depend mainly on the number of observations and not the number of parameters. The algorithm was implemented in the R package bigRR based on the previously developed package hglm. Using such an approach, a heteroscedastic effects model (HEM) was also developed, implemented, and tested. The efficiency for different data sizes were evaluated via simulation. The method was tested for a bacteria-hypersensitive trait in a publicly available Arabidopsis data set including 84 inbred lines and 216,130 SNPs. The computation of all the SNP effects required <10 sec using a single 2.7-GHz core. The advantage in run time makes permutation test feasible for such a whole-genome model, so that a genome-wide significance threshold can be obtained. HEM was found to be more robust than ordinary RR (a.k.a. SNP-best linear unbiased prediction) in terms of QTL mapping, because SNP-specific shrinkage was applied instead of a common shrinkage. The proposed algorithm was also assessed for genomic evaluation and was shown to give better predictions than ordinary RR.

  12. 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.

  13. A simple, fast and sensitive screening LC-ESI-MS/MS method for antibiotics in fish.

    PubMed

    Guidi, Letícia Rocha; Santos, Flávio Alves; Ribeiro, Ana Cláudia S R; Fernandes, Christian; Silva, Luiza H M; Gloria, Maria Beatriz A

    2017-01-15

    The objective of this study was to develop and validate a fast, sensitive and simple liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method for the screening of six classes of antibiotics (aminoglycosides, beta-lactams, macrolides, quinolones, sulfonamides and tetracyclines) in fish. Samples were extracted with trichloroacetic acid. LC separation was achieved on a Zorbax Eclipse XDB C18 column and gradient elution using 0.1% heptafluorobutyric acid in water and acetonitrile as mobile phase. Analysis was carried out in multiple reaction monitoring mode via electrospray interface operated in the positive ionization mode, with sulfaphenazole as internal standard. The method was suitable for routine screening purposes of 40 antibiotics, according to EC Guidelines for the Validation of Screening Methods for Residues of Veterinary Medicines, taking into consideration threshold value, cut-off factor, detection capability, limit of detection, sensitivity and specificity. Real fish samples (n=193) from aquaculture were analyzed and 15% were positive for enrofloxacin (quinolone), one of them at a higher concentration than the level of interest (50µgkg(-1)), suggesting possible contamination or illegal use of that antibiotic.

  14. Terbium-sensitised luminescence screening method for fluoroquinolones in beef serum.

    PubMed

    Schneider, Marilyn J; Yun, Limei; Lehotay, Steven J

    2013-01-01

    Enrofloxacin and danofloxacin are the only fluoroquinolone antibiotics approved for use in cattle in the United States. 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 to detect fluoroquinolones in beef serum. This approach takes advantage of the DNA-enhanced luminescence signal of a fluoroquinolone-Tb⁺³ complex. In this method, serum samples were extracted with acidified acetonitrile in the presence of magnesium sulfate. After centrifugation, evaporation of the supernatant was followed by dissolution of the residue in buffer and filtration. Addition of Tb⁺³ and DNA then allowed a reading of the luminescence signal. The technique was illustrated using enrofloxacin, and provided good recoveries (73-88%) at 25, 50 and 100 ng ml⁻¹, with reasonable RSDs averaging at 11%. The LOD was 2.5 ng ml⁻¹ based on the variability of response of control serum samples from 18 different steers. The method provided no false-positive or false-negative results while screening blind samples for enrofloxacin and was demonstrated to be quantitative over a range of 0-100 ng ml⁻¹.

  15. Generalization of mixed multiscale finite element methods with applications

    SciTech Connect

    Lee, C S

    2016-08-01

    Many science and engineering problems exhibit scale disparity and high contrast. The small scale features cannot be omitted in the physical models because they can affect the macroscopic behavior of the problems. However, resolving all the scales in these problems can be prohibitively expensive. As a consequence, some types of model reduction techniques are required to design efficient solution algorithms. For practical purpose, we are interested in mixed finite element problems as they produce solutions with certain conservative properties. Existing multiscale methods for such problems include the mixed multiscale finite element methods. We show that for complicated problems, the mixed multiscale finite element methods may not be able to produce reliable approximations. This motivates the need of enrichment for coarse spaces. Two enrichment approaches are proposed, one is based on generalized multiscale finte element metthods (GMsFEM), while the other is based on spectral element-based algebraic multigrid (rAMGe). The former one, which is called mixed GMsFEM, is developed for both Darcy’s flow and linear elasticity. Application of the algorithm in two-phase flow simulations are demonstrated. For linear elasticity, the algorithm is subtly modified due to the symmetry requirement of the stress tensor. The latter enrichment approach is based on rAMGe. The algorithm differs from GMsFEM in that both of the velocity and pressure spaces are coarsened. Due the multigrid nature of the algorithm, recursive application is available, which results in an efficient multilevel construction of the coarse spaces. Stability, convergence analysis, and exhaustive numerical experiments are carried out to validate the proposed enrichment approaches. iii

  16. 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.

  17. 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.

  18. Effectiveness of vaccination with the pentavalent rotavirus vaccine in Nicaragua as determined using the screening method.

    PubMed

    Cardellino, Anna; Khawaja, Shazia; Sánchez Cruz, Edmundo; Mast, T Christopher

    2013-07-01

    The screening method is a surveillance tool to evaluate vaccine effectiveness (VE) using coverage data on cases and available administrative estimates of vaccine coverage in the population. The aim of this analysis was to evaluate the utility and limitations of using the screening methodology to estimate VE, particularly in a developing world country with a high coverage rate, and to compare it with the VE estimates from 2 case-control studies. Using data from 2008, the screening method employed in this study estimated that VE for 3 doses of RV5 among children<12 mo of age to prevent wild-type severe disease, resulting in hospitalization or emergency department visits, was 92% (95% confidence interval [CI]: 78-100%). Additional sensitivity analysis demonstrated that the point estimates of VE against severe disease ranged from 72% (95% CI: 62-83%) to 92% (95% CI: 78-100%); this range of VE estimates, although wide, is relatively consistent with results reported from 2 case-control studies in Nicaragua for the same time period. When the infrastructure is in place to collect reasonably robust case data, the use of the screening method to estimate VE is possible in the developing world setting. Cases of severe wild-type rotavirus gastroenteritis were obtained through an observational, hospital-based, prospective, surveillance program to assess rotavirus acute gastroenteritis. The proportion of cases vaccinated was estimated using the child's vaccination card or health record. The proportion of the population vaccinated was estimated using administrative population-based vaccination coverage estimates provided by the Nicaraguan Ministry of Health.

  19. Development of a rapid, one-step screening method for the isolation of presumptive proteolytic enterococci.

    PubMed

    Graham, Ken; Rea, Rosemary; Simpson, Paul; Stack, Helena

    2017-01-01

    Enterococci show higher proteolytic activities than other lactic acid bacteria and thus have received considerable attention in scientific literature in recent years. Proteolytic enzymes of enterococci have warranted the use of some species as starter, adjuncts or protective cultures and as probiotics, while in some strains they have also been linked with virulence. Consequently, the isolation and identification of proteolytic enterococci is becoming of increasing interest and importance. However, current screening methods for proteolytic enterococci can be time consuming, requiring a two-step procedure which may take up to 96h. This study describes a method, utilising Kanamycin Skim Milk Aesculin Azide (KSMEA) agar, for the isolation of proteolytic enterococci in one-step, thereby significantly reducing screening time. KSMEA combines the selective properties of Kanamycin Aesculin Azide Agar (KAA) with skim milk powder for the detection of proteolytic enterococci. Enterococci produced colonies with a black halo on KSMEA which were accompanied by a zone of clearing in the media when enterococci were proteolytic. KSMEA medium retained the selectivity of KAA, while proteolytic enterococci were easily distinguished from non-proteolytic enterococci when two known strains were propagated on KSMEA. KSMEA also proved effective at isolating and detecting enterococci in raw milk, faeces and soil. Isolates recovered from the screen were confirmed as enterococci using genus-specific primers. Proteolytic enterococci were present in the raw milk sample only and were easily distinguishable from non-proteolytic enterococci and other microorganisms. Therefore, KSMEA provides a rapid, one-step screening method for the isolation of presumptive proteolytic enterococci.

  20. A plate method for rapid screening of Ketogulonicigenium vulgare mutants for enhanced 2-keto-l-gulonic acid production.

    PubMed

    Yang, Weichao; Han, Litao; Mandlaa, Mandlaa; Zhang, Haihong; Zhang, Zhongze; Xu, Hui

    2017-02-21

    A new plate method was developed for rapid screening of Ketogulonicigenium vulgare mutants overproducing 2-keto-l-gulonic acid (2-KLG). The screening methodology took the advantage of the acidity caused by 2-KLG, which changes the color of bromothymol blue (pH indicator) from blue to yellow. Using the proposed method, a mutant, K. vulgare 65, was selected from 20,000 colonies produced by a strain subjected to spaceflight mutagenesis. When co-cultured with Bacillus megaterium 2980 in 20-L fermenters, K. vulgare 65 showed a high conversion rate (94.45%) of l-sorbose to 2-KLG. In contrast to the traditional screening method, this one significantly improved the frequency of obtaining positive mutants. The proposed plate screening method is cost-effective and easy to run and is thus useful for the isolation and screening of K. vulgare mutants overproducing 2-KLG.

  1. 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

    2015-04-03

    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.

  2. 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.

  3. Novel microscopy-based screening method reveals regulators of contact-dependent intercellular transfer

    PubMed Central

    Michael Frei, Dominik; Hodneland, Erlend; Rios-Mondragon, Ivan; Burtey, Anne; Neumann, Beate; Bulkescher, Jutta; Schölermann, Julia; Pepperkok, Rainer; Gerdes, Hans-Hermann; Kögel, Tanja

    2015-01-01

    Contact-dependent intercellular transfer (codeIT) of cellular constituents can have functional consequences for recipient cells, such as enhanced survival and drug resistance. Pathogenic viruses, prions and bacteria can also utilize this mechanism to spread to adjacent cells and potentially evade immune detection. However, little is known about the molecular mechanism underlying this intercellular transfer process. Here, we present a novel microscopy-based screening method to identify regulators and cargo of codeIT. Single donor cells, carrying fluorescently labelled endocytic organelles or proteins, are co-cultured with excess acceptor cells. CodeIT is quantified by confocal microscopy and image analysis in 3D, preserving spatial information. An siRNA-based screening using this method revealed the involvement of several myosins and small GTPases as codeIT regulators. Our data indicates that cellular protrusions and tubular recycling endosomes are important for codeIT. We automated image acquisition and analysis to facilitate large-scale chemical and genetic screening efforts to identify key regulators of codeIT. PMID:26271723

  4. 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.

  5. Rapid method to screen resistance of potato plants against Myzus persicae (Homoptera: Aphididae) in the laboratory.

    PubMed

    Le Roux, Vincent; Saguez, Julien; Vincent, Charles; Giordanengo, Philippe

    2004-12-01

    With the objective to develop a potato, Solanum tuberosum L., resistance program against aphids, we propose a rapid screening method with Myzus persicae (Sulzer) in the laboratory. We aimed to optimize the duration of the whole procedure and to decrease the frequency of measurements. In a first experiment, intrinsic rate of natural increase (r(m)) values were compared between adult aphids reared throughout their entire life and adults reared only during a period equivalent to their prereproductive period. No significant differences were observed. In a second experiment, four groups of aphids were distinguished according to the sampling frequency, i.e., those whose biological parameters were evaluated every single, second, third, and fourth day. Except for the fourth-day experiment, the r(m) values estimated on aphids reared on the three potato lines were not significantly different whatever sampling frequency of single, second, or third day used to check aphids. Thus, screening efforts in laboratory can be largely optimized by evaluating adult aphids only during a period equivalent to their prereproductive period and assessing M. persicae populations every third day. Our method is reliable and adapted to screen a large number of potato plants against M. persicae because it allows an average 70% reduction in the time required for the whole experimental process.

  6. 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

  7. 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

  8. 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

  9. 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

  10. Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods.

    PubMed

    Chen, T Scott; Keating, Amy E

    2012-07-01

    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.

  11. Generalization of the H - κ stacking method to anisotropic media

    NASA Astrophysics Data System (ADS)

    Kaviani, Ayoub; Rümpker, Georg

    2015-04-01

    The effect of anisotropy on the estimates of crustal thickness H and average bulk vP/vS-ratio κ can be significant in the presence of strong seismic anisotropy. Here we extend the stacking approach of Zhu and Kanamori (2000) to include all twenty P-to-S converted phases and their crustal reverberations that are generated in the anisotropic case - instead of only five phases in the isotropic case. The ray-based algorithm of Frederiksen and Bostock (2000) is used to calculate the amplitude and arrival time of each phase. Synthetic tests are performed to investigate the feasibility and robustness of the stacking approach. For simplicity, we assume hexagonal symmetry and a horizontal symmetry axis but more general anisotropy may be considered. The tests reveal that the estimates of H and κ can be significantly affected by the presence of crustal anisotropy. We verify the feasibility of the stacking approach for real data by applying the method to examples from three different tectonic regions. The results show that the anisotropic stacking scheme presented here can provide much better constraints on the estimation of H and κ in comparison to the isotropic stacking. The anisotropic stacking can also help to resolve ambiguities in the determination of H and κ when several maxima of stacked receiver-function amplitudes arise in cases of complex crustal structure.

  12. Cluster-cell calculation using the method of generalized homogenization

    SciTech Connect

    Laletin, N.I.; Boyarinov, V.F.

    1988-05-01

    The generalized-homogenization method (GHM), used for solving the neutron transfer equation, was applied to calculating the neutron distribution in the cluster cell with a series of cylindrical cells with cylindrically coaxial zones. Single-group calculations of the technological channel of the cell of an RBMK reactor were performed using GHM. The technological channel was understood to be the reactor channel, comprised of the zirconium rod, the water or steam-water mixture, the uranium dioxide fuel element, and the zirconium tube, together with the adjacent graphite layer. Calculations were performed for channels with no internal sources and with unit incoming current at the external boundary as well as for channels with internal sources and zero current at the external boundary. The PRAKTINETs program was used to calculate the symmetric neutron distributions in the microcell and in channels with homogenized annular zones. The ORAR-TsM program was used to calculate the antisymmetric distribution in the microcell. The accuracy of the calculations were compared for the two channel versions.

  13. 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.

  14. 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.

  15. From Classical to High Throughput Screening Methods for Feruloyl Esterases: A Review.

    PubMed

    Ramírez-Velasco, Lorena; Armendáriz-Ruiz, Mariana; Rodríguez-González, Jorge Alberto; Müller-Santos, Marcelo; Asaff-Torres, Ali; Mateos-Díaz, Juan Carlos

    2016-01-01

    Feruloyl esterases (FAEs) are a diverse group of hydrolases widely distributed in plants and microorganisms which catalyzes the cleavage and formation of ester bonds between plant cell wall polysaccharides and phenolic acids. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing highadded value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production, characterization and classification of FAEs, however only a few reports of suitable High Throughput Screening assays for this kind of enzymes have been reported. This review is focused on a concise but complete revision of classical to High Throughput Screening methods for FAEs, highlighting its advantages and disadvantages, and finally suggesting future perspectives for this important research field.

  16. 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.

  17. 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

  18. Case studies on screening soil samples for TNT and chlordane and practical aspects for bringing these field screening methods into the laboratory

    SciTech Connect

    Hooton, D.

    1995-12-31

    This paper shares specific experiences with screening soil samples for explosive (TNT) and pesticide (chlordane) residues. Suggestions for adapting analytical methods and associated QA/QC objectives for screening purposes are also discussed. Over the last several years, Midwest Research Institute (MRI) has analyzed hundreds of soil samples for environmental investigation programs. Quality control data are presented to show that reliable method performance (precision and recovery) has been achieved for this work. Comparative data are charted for representative samples which were subsequently reanalyzed using EPA methods to confirm non-contamination or to determine the exact concentration of the screened analytes. MRI has been successful in effectively controlling operational factors which impact cost and time for analysis completion. In the absence of a fully functional on-site laboratory, alternatives are suggested which make it possible to provide valid analysis results soon after sample collection. Sample documentation, data validation, and reporting are simplified using a 1-page form without sacrificing data quality and documentary evidence. Experimental data are presented which support the use of screening methods to improve a program`s effectiveness through evaluation of larger data sets and selective use of more rigorous and expensive EPA methods.

  19. 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.

  20. 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.

  1. 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.

  2. 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,...

  3. 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.

  4. [A new plate method for screening of polysaccharide-degrading enzymes and their producing microorganisms].

    PubMed

    Ma, Xiang-Dong; Ke, Tao; Xiong, Lan; Yan, Hong; Ma, Li-Xin

    2007-12-01

    A plate assay based on the formation of haloes on Petri dishes, containing the trypan blue dye and polysaccharides as substrates, provides a specific, reliable and rapid detection of corresponding polysaccharide degrading enzymes and their producing microorganisms. A blue complex was formed by mixing trypan blue and polysaccharides as substrates. It has been proved by testing three strains that the trypan blue was neither harmful to microorganisms nor enzymes and could stand the normal sterilization. It's optimum concentration was from 0.005% to 0.01% (W/V). It do not need to prepare dye-labelled polysaccharides, so is a money and time-consuming method. The sensitivity of trypan blue method was the same as traditional method and it has potential for increasing the efficacy of screening of microorganisms, utilizing different polysaccharides, especially for large-scale searching programs, such as screening of large numbers of natural samples and engineering bacteria. Using this method, polysaccharide-degrading enzyme genes also has potential of as a new kind of marker gene in gene engineering techniques. According to the result, this method is suitable for detecting cellulase, amylase, pullulanase and mannase, but not suitable for detecting xylanase and inulinase.

  5. 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.

  6. HPV detection methods and genotyping techniques in screening for cervical cancer.

    PubMed

    Eide, Maj Liv; Debaque, Hervé

    2012-12-01

    Human papillomaviruses (HPV), double-stranded DNA viruses, are causing many mucocutaneous diseases, benign or malignant, ranging from common warts to malignancies involving the upper aerodigestive tract and the anogenital sphere. The diagnosis of HPV infection is based primarily on the viral genome detection by molecular biological methods, given the difficulty in routine cultivation of these viruses. The current trend in screening against cervical cancer is to improve the sensitivity of screening with new methods and to propose new algorithms for diagnostic and therapeutic decisions. The development of liquid-based cytology facilitates the cytologic diagnosis and molecular assays from the same sample. There are two main types of HPV detection methods used on uterine cervical samples: signal amplification methods (hybridization techniques in liquid phase) and target amplification methods (the techniques of gene amplification or Polymerase Chain Reaction [PCR]). Genotyping techniques are also developed: they are based on an amplification technique followed by hybridization with probe specific types. In addition to the detection, genotyping techniques allow quantitative detection of viral DNA of HPV genotype and so monitor changes in viral load over time. Another approach relies on the detection of messenger RNA (mRNA) of HPV proteins E6 and E7 oncogenes, which would appear to be a relevant marker to identify and monitor women at risk of progression to a precancerous lesion or cervical cancer.

  7. An LC-MS screening method with library identification for the detection of steroids in dietary supplements.

    PubMed

    Becue, Ilse; Van Poucke, Christof; Van Peteghem, Carlos

    2011-03-01

    For many years anabolic-androgenic steroids (AAS) are by far the most frequently detected pharmacological substances in doping control. In order to improve their performances, professional sportsmen are often tempted to take dietary supplements. However, due to the frequent and widespread occurrence of contaminated supplements, the use of such products is not without risk for the athletes involved. In order to minimize the chances of an unattended positive doping test or serious health problems, fast and reliable screening methods for the detection of anabolic steroids in dietary supplements are needed. A general screening procedure requires the fast and unambiguous detection of a large range of steroids. Gas chromatography-mass spectrometry (GC-MS) has been used intensively in the detection of doping substances for the past 40 years. Over time, many laboratories have delivered spectra to be included in standard reference databases, one of which is maintained by the National Institute of Standards and Technology (NIST) (Gaithersburg, MD, USA). In recent years, however, liquid chromatography coupled to mass spectrometry (LC-MS) has gained popularity. Unfortunately, existing GC-MS libraries are not applicable to LC-MS analysis. In the present study, a new mass spectral library of 88 steroids was developed, along with a fast UPLC-MS method. For the construction of this mass spectral library, three different mass spectra were measured for each steroid, with a sample cone voltage of 30, 60 and 100 V, respectively. This method was then successfully tested on contaminated dietary supplements which had previously been tested by means of a targeted LC-MS/MS method. Overall, the library search was shown to identify the same compounds as the MRM method.

  8. Development of a facile method for high throughput screening with reporter gene assays.

    PubMed

    Goetz, A S; Andrews, J L; Littleton, T R; Ignar, D M

    2000-10-01

    This report describes a facile methodology for high throughput screening with stable mammalian cell reporter gene assays. We have adapted a 96-well adherent cell method to an assay in which cells propagated in suspension are dispensed into 96- or 384-well plates containing test compounds in 100% DMSO. The validation of a stable CHO cell line that expresses 6xCRE-luciferase for use as a reporter gene host cell line is described. The reporter gene, when expressed in this particular CHO cell line, appears to respond specifically to modulation of cAMP levels, thus the cell line is appropriate for screening and pharmacological analysis of Galpha(s)- and Galpha(i)-coupled seven-transmembrane receptors. The development of the new suspension cell assay in both 96- and 384-well formats was performed using a derivative of the CHO host reporter cell line that was stably transfected with human melanocortin-1 receptor. The response of this cell line to NDP-alpha-melanocyte-stimulating hormone and forskolin was nearly identical between the adherent and suspension methods. The new method offers improvements in cost, throughput, cell culture effort, compound stability, accuracy of compound delivery, and hands-on time. The 384-well assay can be performed at high capacity in any laboratory without the use of expensive automation systems such that a single person can screen 100 plates per day with 3.5-4 h hands-on time. Although the system has been validated using Galpha(s)-coupled receptor-mediated activation of a cAMP response element, the method can be applied to other types of targets and/or transcriptional response elements.

  9. 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.

  10. A newborn screening method for cerebrotendinous xanthomatosis using bile alcohol glucuronides and metabolite ratios.

    PubMed

    Vaz, Frédéric M; Bootsma, Albert H; Kulik, Willem; Verrips, Aad; Wevers, Ron A; Schielen, Peter C; DeBarber, Andrea E; Huidekoper, Hidde H

    2017-03-17

    Cerebrotendinous xanthomatosis (CTX) is a treatable neurodegenerative metabolic disorder of bile acid synthesis where symptoms can be prevented if treatment with chenodeoxycholic acid supplementation is initiated early in life, making CTX an excellent candidate for newborn screening. We developed a new dried blood spot screening assay for this disorder based on different ratios between the accumulating cholestanetetrol glucuronide (tetrol) and specific bile acids/bile acid intermediates, without the need for derivatization. A quarter-inch dried blood spot punch was extracted with methanol, internal standards were added and after concentration the extract was injected into the tandem mass spectrometer using a 2 minute flow injection analysis where specific transitions were measured for cholestanetetrol glucuronide, tauro-chenodeoxycholic acid (t-CDCA) and tauro-trihydroxycholestanoic acid (t-THCA). A proof of principle experiment was performed using 216 Guthrie cards from healthy term/preterm newborns, CTX patients and Zellweger patients. Using two calculated biomarkers, tetrol/t-CDCA and t-THCA/tetrol, this straightforward method achieved an excellent separation between dried blood spots of CTX patients and those of controls, Zellweger patients and newborns with cholestasis. The results of this small pilot study indicate that the tetrol/t-CDCA ratio is an excellent derived biomarker for CTX that has the potential to be used in neonatal screening programs.

  11. High-throughput transformation method for Yarrowia lipolytica mutant library screening.

    PubMed

    Leplat, Christophe; Nicaud, Jean-Marc; Rossignol, Tristan

    2015-09-01

    As a microorganism of major biotechnological importance, the oleaginous yeast Yarrowia lipolytica is subjected to intensive genetic engineering and functional genomic analysis. Future advancements in this area, however, require a system that will generate a large collection of mutants for high-throughput screening. Here, we report a rapid and efficient method for high-throughput transformation of Y. lipolytica in 96-well plates. We developed plasmids and strains for the large-scale screening of overexpression mutant strains, using Gateway® vectors that were adapted for specific locus integration in Y. lipolytica. As an example, a collection of mutants that overexpressed the alkaline extracellular protease (AEP) was obtained in a single transformation experiment. The platform strain that we developed to receive the overexpression cassette was designed to constitutively express a fluorescent protein as a convenient growth reporter for screening in non-translucid media. An example of growth comparison in skim milk-based medium between AEP overexpression and deletion mutants is provided.

  12. Comprehensive screening method for the qualitative detection of narcotics and stimulants using single step derivatisation.

    PubMed

    Van Thuyne, W; Van Eenoo, P; Delbeke, F T

    2007-10-01

    A selective and sensitive screening method for the detection of prohibited narcotic and stimulating agents in doping control is described and validated. This method is suitable for the detection of all narcotic agents mentioned on the World Anti-Doping Agency (WADA) doping list in addition to numerous stimulants. The analytes are extracted from urine by a combined extraction procedure using CH(2)Cl(2)/MeOH (9/1, v/v) and t-butylmethyl ether as extraction solvents at pH 9.5 and 14, respectively. Prior to GC-MS analysis the obtained residues are combined and derivatised with MSTFA. The mass spectrometer is operated in the full scan mode in the range between m/z 40 and 550. The obtained limits of detection (LOD) for all components included in this extensive screening method are in the range 20-500 ng/ml, which is in compliance with the requirements set by WADA. Besides narcotic and stimulating agents, this method is also capable of detecting several agents with anti-estrogenic activity and some beta-agonists. As an example, a positive identification of hydroxyl-methoxy-tamoxyfen is shown.

  13. [Effects of Different Pretreatment Methods on the Phenylketonuria Screening Model by FTIR/ATR Spectroscopy].

    PubMed

    Wang, Wei-wei; Wei, Wei-wei; Song, Xiang-gang; Cheng, Ya-ting; Chen, Chao; Wang, Shu-mei; Liang, Sheng-wang

    2015-05-01

    To establish a phenylketonuria screening model by FTIR/ATR spectroscopy, and to compare the effects of different pretreatment methods, such as baseline correction, smoothing, derivation, Fourier deconvolution, on the model quality. A consensus partial least squares regression method (cPLS) was used to build the quantitative model of phenylalanine in dried blood spots. The effects of different pretreatment methods on the model performance were investigated, using the correlation coefficient (r), root mean square error of prediction (RMSEP), mean relative error (MRE) and predictive accuracy (Acc). The nine-point smoothing coupled with the first differential was found to perform the best. Compared with the model by the original spectra, its r, RMSEP, MRE and Acc were improved from 0. 822 7, 115. 8, 0. 395 and 94. 6 to 0. 889 9, 102. 2, 0. 286 and 100, respectively. With the advantages of fast speed, easy process, no reagents consumption and environmental protection, the present method is expected to become a simple and green technology for rapidly screening the neonatal phenylketonuria in a large population.

  14. 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

  15. Screening, detection, and serotyping methods for toxin genes and enterotoxins in Staphylococcus strains.

    PubMed

    Hait, Jennifer M; Tallent, Sandra M; Bennett, Reginald W

    2014-01-01

    Staphylococcus aureus continues to play a significant role in foodborne outbreak investigations, with numerous individuals sickened each year after ingesting assorted foods contaminated with staphylococcal enterotoxins. The purpose of this study was to evaluate the use of several methods for the screening, detection, and enterotoxin serotyping of staphylococcal bacterial strains for classical staphylococcal enterotoxins (SEs; SEA, SEB, SEC, SED, and SEE) and the newly described SE and SE-like enterotoxin genes (seg, seh, sei, sej, sek, sel, sem, sen, seo, sep, seq, ser, ses, set, and seu). Inclusivity and exclusivity panels of staphylococcal strains were tested using a multiplex PCR method in addition to three polyvalent commercially prepared ELISA systems for the detection of SEA-SEE and one monovalent assay for the identification of classical SE serotypes. The results indicate an overall agreement between serological detection methods with a few exceptions, and molecular characterization identified an abundance of SE and SE-like enterotoxin genes including several potentially enterotoxigenic isolates that would have otherwise been missed by ELISA-based methods. These findings demonstrate the significance of PCR for future screening purposes and the use of ELISA systems for the detection and enterotoxin serotyping of staphylococcal bacterial strains.

  16. 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.

  17. Screening for antimicrobial resistance in normal bacterial flora of the skin using the replica plating method.

    PubMed

    Paavilainen, T; Osterblad, M; Leistevuo, T; Huovinen, P; Kotilainen, P

    2000-12-01

    The replica plating method was evaluated for detection of the antimicrobial resistance of normal bacterial flora of the skin and was compared with the results of a ten-colony method. If > or = 10% of the colonies from the master plate grew on a plate containing an antibiotic, the sensitivity of replica plating was comparable to that of a ten-colony method for samples containing resistant bacteria. However, this method classified significantly more samples as resistant to all eight antibiotics tested if the detection breakpoint was lowered to > or = 1% of the original colonies. Replica plating is an effective and practical tool for screening skin flora for resistance, also in samples with a low proportion of resistant strains.

  18. An objective method for screening and selecting personal cooling systems based on cooling properties.

    PubMed

    Elson, John; Eckels, Steve

    2015-05-01

    A method is proposed for evaluation and selection of a personal cooling system (PCS) incorporating PCS, subject, and equipment weights; PCS run time; user task time; PCS cooling power; and average metabolic rate. The cooling effectiveness method presented is derived from first principles and allows those who select PCSs for specific applications to compare systems based on their projected use. This can lower testing costs by screening for the most applicable system. Methods to predict cooling power of PCSs are presented and are compared to data taken through standard manikin testing. The cooling effectiveness ranking is presented and validated against human subject test data. The proposed method provides significant insight into the application of PCS on humans. However, the interaction a humans with a PCS is complex, especially considering the range of clothing ensembles, physiological issues, and end use scenarios, and requires additional analysis.

  19. 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.

  20. 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.

  1. 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.

  2. General Quality Control (QC) Guidelines for SAM Methods

    EPA Pesticide Factsheets

    Learn more about quality control guidelines and recommendations for the analysis of samples using the methods listed in EPA's Selected Analytical Methods for Environmental Remediation and Recovery (SAM).

  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.

  4. A cost/effective screening method for assessing the toxicity of nutrient rich effluents to algae.

    PubMed

    Carbonell, G; Fernández, C; Tarazona, J V

    2010-07-01

    Screening whole effluent toxicity tests are cost/effective methods for detecting the presence of toxic concentrations of unknown pollutants, but the application must solve the problem associated with the effect of high and variable concentrations of nutrients in the effluent on the results of algal toxicity tests. This work proposes a cost/effective test, based on three dilution levels measured at a single point time and a discriminant model for establishing if this kind of complex samples, with difficult interpretation of dilution-response curves, should be considered toxic to algae. This procedure identified properly around 85% of the samples considered toxic by expert judgement.

  5. 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.

  6. General unknown screening procedure for the characterization of human drug metabolites: Application to loratadine phase I metabolism.

    PubMed

    Picard, Nicolas; Dridi, Dorra; Sauvage, François-Ludovic; Boughattas, Naceur A; Marquet, Pierre

    2009-07-01

    This article describes the application of a recently developed general unknown screening (GUS) strategy based on LC coupled to a hybrid linear IT-triple quadrupole mass spectrometer (LC-MS/MS-LIT) for the simultaneous detection and identification of drug metabolites following in vitro incubation with human liver microsomes. The histamine H1 receptor antagonist loratadine was chosen as a model compound to demonstrate the interest of such approach, because of its previously described complex and extensive metabolism. Detection and mass spectral characterization were based on data-dependent acquisition, switching between a survey scan acquired in the ion-trapping Q3 scan mode with dynamic subtraction of background noise, and a dependent scan in the ion-trapping product ion scan mode of automatically selected parent ions. In addition, the MS(3) mode was used in a second step to confirm the structure of a few fragment ions. The sensitivity of the ion-trapping modes combined with the selectivity of the triple quadrupole modes allowed, with only one injection, the detection and identification of 17 phase I metabolites of loratadine. The GUS procedure used in this study may be applicable as a generic technique for the characterization of drug metabolites after in vitro incubation, as well as probably in vivo experiments.

  7. Non-high altitude methods for rapid screening of susceptibility to acute mountain sickness

    PubMed Central

    2013-01-01

    Background Acute mountain sickness (AMS) refers to the cerebral abnormalities typically triggered by exposure to hypobaric hypoxia at high altitude. Although AMS is not often life threatening, it can seriously impact health quality and decrease productivity. Thus, detection of potential susceptibility to AMS has become important for people arriving at high-altitude plateaus for the first time, including laborers and military staff. The aim of this review was to examine techniques which efficiently assess the susceptibility to AMS prior to exposure to high altitude. Methods By searching online databases, we retrieved studies with associations between AMS and methods to detect the susceptible people who were not exposed to high altitudes. Studies reporting significant correlation coefficients between screening methods and AMS scores were included. Results Several screening techniques of AMS susceptibility were found including cold pressor test, heart rate variability, and lung functions. Of these markers, heart rate variability was positively associated with AMS scores, while the rest were negatively associated with AMS scores. Conclusions We identified three physiological markers that were significantly associated with the risk of AMS. Although it is well known that simple sea level tests are not really helpful in predicting AMS currently, these markers, to some degree, may be employed as references in predicting susceptibility. PMID:24079477

  8. Efficient methods for screening of metal organic framework membranes for gas separations using atomically detailed models.

    PubMed

    Keskin, Seda; Sholl, David S

    2009-10-06

    Metal organic frameworks (MOFs) define a diverse class of nanoporous materials having potential applications in adsorption-based and membrane-based gas separations. We have previously used atomically detailed models to predict the performance of MOFs for membrane-based separations of gases, but these calculations require considerable computational resources and time. Here, we introduce an efficient approximate method for screening MOFs based on atomistic models that will accelerate the modeling of membrane applications. The validity of this approximate method is examined by comparison with detailed calculations for CH4/H2, CO2/CH4, and CO2/H2 mixtures at room temperature permeating through IRMOF-1 and CuBTC membranes. These results allow us to hypothesize a connection between two computationally efficient correlations predicting mixture adsorption and mixture self-diffusion properties and the validity of our approximate screening method. We then apply our model to six additional MOFs, IRMOF-8, -9, -10, and -14, Zn(bdc)(ted)0.5, and COF-102, to examine the effect of chemical diversity and interpenetration on the performance of metal organic framework membranes for light gas separations.

  9. 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.

  10. 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.

  11. 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.

  12. An EEG-based machine learning method to screen alcohol use disorder.

    PubMed

    Mumtaz, Wajid; Vuong, Pham Lam; Xia, Likun; Malik, Aamir Saeed; Rashid, Rusdi Bin Abd

    2017-04-01

    Screening alcohol use disorder (AUD) patients has been challenging due to the subjectivity involved in the process. Hence, robust and objective methods are needed to automate the screening of AUD patients. In this paper, a machine learning method is proposed that utilized resting-state electroencephalography (EEG)-derived features as input data to classify the AUD patients and healthy controls and to perform automatic screening of AUD patients. In this context, the EEG data were recorded during 5 min of eyes closed and 5 min of eyes open conditions. For this purpose, 30 AUD patients and 15 aged-matched healthy controls were recruited. After preprocessing the EEG data, EEG features such as inter-hemispheric coherences and spectral power for EEG delta, theta, alpha, beta and gamma bands were computed involving 19 scalp locations. The selection of most discriminant features was performed with a rank-based feature selection method assigning a weight value to each feature according to a criterion, i.e., receiver operating characteristics curve. For example, a feature with large weight was considered more relevant to the target labels than a feature with less weight. Therefore, a reduced set of most discriminant features was identified and further be utilized during classification of AUD patients and healthy controls. As results, the inter-hemispheric coherences between the brain regions were found significantly different between the study groups and provided high classification efficiency (Accuracy = 80.8, sensitivity = 82.5, and specificity = 80, F-Measure = 0.78). In addition, the power computed in different EEG bands were found significant and provided an overall classification efficiency as (Accuracy = 86.6, sensitivity = 95, specificity = 82.5, and F-Measure = 0.88). Further, the integration of these EEG feature resulted into even higher results (Accuracy = 89.3 %, sensitivity = 88.5 %, specificity = 91 %, and F-Measure = 0.90). Based

  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. 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

  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. Chronic Kidney Disease Screening Methods and Its Implication for Malaysia: An in Depth Review

    PubMed Central

    Almualm, Yasmin; Huri, Hasniza Zaman

    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

  17. 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.

  18. 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...

  19. 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…

  20. Aluminium tolerance in barley (Hordeum vulgare L.): physiological mechanisms, genetics and screening methods*

    PubMed Central

    Wang, Jun-ping; Raman, Harsh; Zhang, Guo-ping; Mendham, Neville; Zhou, Mei-xue

    2006-01-01

    Aluminium (Al) toxicity is one of the major limiting factors for barley production on acid soils. It inhibits root cell division and elongation, thus reducing water and nutrient uptake, consequently resulting in poor plant growth and yield. Plants tolerate Al either through external resistance mechanisms, by which Al is excluded from plant tissues or internal tolerance mechanisms, conferring the ability of plants to tolerate Al ion in the plant symplasm where Al that has permeated the plasmalemma is sequestered or converted into an innocuous form. Barley is considered to be most sensitive to Al toxicity among cereal species. Al tolerance in barley has been assessed by several methods, such as nutrient solution culture, soil bioassay and field screening. Genetic and molecular mapping research has shown that Al tolerance in barley is controlled by a single locus which is located on chromosome 4H. Molecular markers linked with Al tolerance loci have been identified and validated in a range of diverse populations. This paper reviews the (1) screening methods for evaluating Al tolerance, (2) genetics and (3) mechanisms underlying Al tolerance in barley. PMID:16972319

  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. 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.

  3. 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 Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE IMPORTATION OF SEED AND SCREENINGS UNDER THE FEDERAL SEED ACT § 361.2 Preemption of State and local...

  4. 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 Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE IMPORTATION OF SEED AND SCREENINGS UNDER THE FEDERAL SEED ACT § 361.2 Preemption of State and local...

  5. 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.

  6. The Influence Relevance Voter: An Accurate And Interpretable Virtual High Throughput Screening Method

    PubMed Central

    Swamidass, S. Joshua; Azencott, Chloé-Agathe; Lin, Ting-Wan; Gramajo, Hugo; Tsai, Sheryl; Baldi, Pierre

    2009-01-01

    Given activity training data from Hight-Throughput Screening (HTS) experiments, virtual High-Throughput Screening (vHTS) methods aim to predict in silico the activity of untested chemicals. We present a novel method, the Influence Relevance Voter (IRV), specifically tailored for the vHTS task. The IRV is a low-parameter neural network which refines a k-nearest neighbor classifier by non-linearly combining the influences of a chemical's neighbors in the training set. Influences are decomposed, also non-linearly, into a relevance component and a vote component. The IRV is benchmarked using the data and rules of two large, open, competitions, and its performance compared to the performance of other participating methods, as well as of an in-house Support Vector Machine (SVM) method. On these benchmark datasets, IRV achieves state-of-the-art results, comparable to the SVM in one case, and significantly better than the SVM in the other, retrieving three times as many actives in the top 1% of its prediction-sorted list. The IRV presents several other important advantages over SVMs and other methods: (1) the output predictions have a probabilistic semantic; (2) the underlying inferences are interpretable; (3) the training time is very short, on the order of minutes even for very large data sets; (4) the risk of overfitting is minimal, due to the small number of free parameters; and (5) additional information can easily be incorporated into the IRV architecture. Combined with its performance, these qualities make the IRV particularly well suited for vHTS. PMID:19391629

  7. 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.

  8. Exact Solutions for The Generalized Zakharov-Kuznetsov Equation with Variable Coefficients Using The Generalized (G'/G)-expansion Method

    NASA Astrophysics Data System (ADS)

    Zayed, Elsayed M. E.; Abdelaziz, Mahmoud A. M.

    2010-09-01

    In this article, the generalized G'/G-expansion method using a generalized wave transformation is applied to find exact traveling wave solutions of the generalized Zakharov-Kuznetsov equation with variable coefficients. As a result, hyperbolic, trigonometric and rational function solutions with parameters are obtained. When these parameters are taken special values, the solitary wave solutions are derived from the hyperbolic function solution. It is shown that the proposed method is direct, effective and can be applied to many other nonlinear evolution equations in mathematical physics.

  9. 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.

  10. Generalized dilatation operator method for non-relativistic holography

    NASA Astrophysics Data System (ADS)

    Chemissany, Wissam; Papadimitriou, Ioannis

    2014-10-01

    We present a general algorithm for constructing the holographic dictionary for Lifshitz and hyperscaling violating Lifshitz backgrounds for any value of the dynamical exponent z and any value of the hyperscaling violation parameter θ compatible with the null energy condition. The objective of the algorithm is the construction of the general asymptotic solution of the radial Hamilton-Jacobi equation subject to the desired boundary conditions, from which the full dictionary can be subsequently derived. Contrary to the relativistic case, we find that a fully covariant construction of the asymptotic solution for running non-relativistic theories necessitates an expansion in the eigenfunctions of two commuting operators instead of one. This provides a covariant but non-relativistic grading of the expansion, according to the number of time derivatives.

  11. Antimicrobial Screening of Actinobacteria using a Modified Cross-Streak Method

    PubMed Central

    Velho-Pereira, Sonashia; Kamat, N M

    2011-01-01

    Out of the 30 actinobacterial cultures screened for antimicrobial activity, 28 cultures were found to produce active products against various pathogenic microorganisms such as Gram-negative, Gram-positive bacteria and yeast, using a modified cross streak method. The modified method helped in easy quantification of results and also in ruling out probable mutual antibiosis. The actinobacterial strains that showed the ability to produce antimicrobial compounds belonged to Streptomyces (53%), Micromonospora (13%) and Actinomadura (10%) genera. Streptomyces sp. strain MMA-5 showed the highest multispecific antibiosis efficiency score value. Broad antibiotic spectrum activity was exhibited by Streptomyces sp. strain MMA-2 and Micromonospora sp. strain MMA-8. The multidrug resistant human pathogenic yeast strain Candida albicans was inhibited by 18 actinobacterial strains. PMID:22303068

  12. Slurry sampling electrothermal atomic absorption spectrometry as screening method for chromium in compost.

    PubMed

    Laborda, F; Górriz, M P; Castillo, J R

    2004-10-20

    Ultrasonic slurry sample introduction was applied to the determination of total chromium in composted materials by electrothermal atomic absorption spectrometry (ETAAS). The effect of grinding on the heterogeneity of the test samples and on the attainable precision was studied. The repeatability was influenced by the heterogeneity of the test samples at the mug-level, the R.S.D. of the measurements being 15%. The reproducibility depended on the heterogeneity of the test sample at the mg level, and it could be improved from 11 to 7% by increasing the grinding time. The characteristic mass was 2.6pg and the detection limit for the optimised procedure at the 0.04% (w/v) slurry concentration, 370ngg(-1). Good agreement with a certified reference material and with the conventional microwave assisted digestion method was found by using external calibration with aqueous standards. The performance of the method for screening purposes was evaluated.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. Two buffer PAGE system-based SSCP/HD analysis: a general protocol for rapid and sensitive mutation screening in cystic fibrosis and any other human genetic disease.

    PubMed

    Liechti-Gallati, S; Schneider, V; Neeser, D; Kraemer, R

    1999-07-01

    The large size of many disease genes and the multiplicity of mutations complicate the design of an adequate assay for the identification of disease-causing variants. One of the most successful methods for mutation detection is the single strand conformation polymorphism (SSCP) technique. By varying temperature, gel composition, ionic strength and additives, we optimised the sensitivity of SSCP for all 27 exons of the CFTR gene. Using simultaneously SSCP and heteroduplex (HD) analysis, a total of 80 known CF mutations (28 missense, 22 frameshift, 17 nonsense, 13 splicesite) and 20 polymorphisms was analysed resulting in a detection rate of 97.5% including the 24 most common mutations worldwide. The ability of this technique to detect mutations independent of their nature, frequency, and population specificity was confirmed by the identification of five novel mutations (420del9, 1199delG, R560S, A613T, T1299I) in Swiss CF patients, as well as by the detection of 41 different mutations in 198 patients experimentally analysed. We present a three-stage screening strategy allowing analysis of seven exons within 5 hours and analysis of the entire coding region within 1 week, including sequence analysis of the variants. Additionally, our protocol represents a general model for point mutation analysis in other genetic disorders and has already been successfully established for OTC deficiency, collagene deficiency, X-linked myotubular myopathy (XLMTM), Duchenne and Becker muscular dystrophy (DMD, BMD), Wilson disease (WD), Neurofibromatosis I and II, Charcot-Marie-Tooth disease, hereditary neuropathy with liability to pressure palsies, and defects in mitochondrial DNA. No other protocol published so far presents standard SSCP/HD conditions for mutation screening in different disease genes.

  19. 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.

  20. Generalized Newton Method for Energy Formulation in Image Processing

    DTIC Science & Technology

    2008-04-01

    Blurred (b) - Newton with LH (c) - Standard Newton (d) - Newton with Ls Fig. 5.2. Deblurring of the clown image with different Newton-like methods...proposed method, the inner product can be adapted to the problem at hand. In the second example, Figure 5.2, the 330 × 291 clown image was additionally

  1. [A hybrid volume rendering method using general hardware].

    PubMed

    Li, Bin; Tian, Lianfang; Chen, Ping; Mao, Zongyuan

    2008-06-01

    In order to improve the effect and efficiency of the reconstructed image after hybrid volume rendering of different kinds of volume data from medical sequential slices or polygonal models, we propose a hybrid volume rendering method based on Shear-Warp with economical hardware. First, the hybrid volume data are pre-processed by Z-Buffer method and RLE (Run-Length Encoded) data structure. Then, during the process of compositing intermediate image, a resampling method based on the dual-interpolation and the intermediate slice interpolation methods is used to improve the efficiency and the effect. Finally, the reconstructed image is rendered by the texture-mapping technology of OpenGL. Experiments demonstrate the good performance of the proposed method.

  2. 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

  3. Comparison of Mobile Laboratory screening method for the detection of high explosives with EPA SW 846 method 8330

    SciTech Connect

    Swanson, A.L.; Roberts, J.B.; Canavan, H.E.; Kelly, L.A.

    1996-03-01

    The current EPA SW-846 method for High Explosives (HE) analysis is not well suited to on-site analytical work. The method in general is too complex and time dependent to function well in a quick turn around mode. The Mobile Chemical Analytical Laboratory project at Los Alamos National Laboratory (LANL) has used a modified analytical method to generate quick turn around data to address Department of Transportation (DOT) shipping requirements, and with appropriate modifications to the QA/QC oversight of the method is well suited to deliver high quality quantitative data.

  4. An end-point method based on graphene oxide for RNase H analysis and inhibitors screening.

    PubMed

    Zhao, Chuan; Fan, Jialong; Peng, Lan; Zhao, Lijian; Tong, Chunyi; Wang, Wei; Liu, Bin

    2017-04-15

    As a highly conserved damage repair protein, RNase H can hydrolysis DNA-RNA heteroduplex endonucleolytically and cleave RNA-DNA junctions as well. In this study, we have developed an accurate and sensitive RNase H assay based on fluorophore-labeled chimeric substrate hydrolysis and the differential affinity of graphene oxide on RNA strand with different length. This end-point measurement method can detect RNase H in a range of 0.01 to 1 units /mL with a detection limit of 5.0×10(-3) units/ mL under optimal conditions. We demonstrate the utility of the assay by screening antibiotics, resulting in the identification of gentamycin, streptomycin and kanamycin as inhibitors with IC50 of 60±5µM, 70±8µM and 300±20µM, respectively. Furthermore, the assay was reliably used to detect RNase H in complicated biosamples and found that RNase H activity in tumor cells was inhibited by gentamycin and streptomycin sulfate in a concentration-dependent manner. The average level of RNase H in serums of HBV infection group was similar to that of control group. In summary, the assay provides an alternative tool for biochemical analysis for this enzyme and indicates the feasibility of high throughput screening inhibitors of RNase H in vitro and in vivo.

  5. 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

  6. 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

    2016-10-04

    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.

  7. 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.

  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

    2016-02-09

    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. 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.

  10. A generalized modal shock spectra method for spacecraft loads analysis

    NASA Technical Reports Server (NTRS)

    Trubert, M.; Salama, M.

    1979-01-01

    Unlike the traditional shock spectra approach, the generalization presented in this paper permits elastic interaction between the spacecraft and launch vehicle in order to obtain accurate bounds on the spacecraft response and structural loads. In addition, the modal response from a previous launch vehicle transient analysis - with or without a dummy spacecraft - is exploited in order to define a modal impulse as a simple idealization of the actual forcing function. The idealized modal forcing function is then used to derive explicit expressions for an estimate of the bound on the spacecraft structural response and forces.

  11. [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.

  12. 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

  13. Development and evaluation of an improved method for screening of amphetamines.

    PubMed

    Shindelman, J; Mahal, J; Hemphill, G; Pizzo, P; Coty, W A

    1999-10-01

    We developed a homogeneous immunoassay method to eliminate false-positive amphetamine results caused by cross-reactive substances, including over-the-counter allergy and cold medications. This method uses a neutralizing antibody that binds to amphetamines but does not bind to the labeled amphetamine conjugate used in the assay. The amount of neutralizing antibody is sufficient to reduce the assay signal resulting from authentic amphetamine and methamphetamine, but not the signal resulting from cross-reactants. This concept was implemented using the CEDIA DAU Amphetamines assay on Hitachi 747 and 717 clinical chemistry analyzers. Urine samples were tested using the standard, unmodified reagents in one channel and reagents containing the neutralizing antibody in a second channel. The difference in rate between the two tests was calculated by the analyzer; true-positive samples showed a significantly greater decrease in assay signal in response to neutralizing antibody as compared with false-positive samples. The neutralization method was evaluated in two studies using 448 samples that tested positive in the initial CEDIA DAU Amphetamines screening test. The samples were separated into categories of 154 true-positive samples and 294 false-positive samples based upon a secondary screen with the Abbott FPIA Amphetamines assay followed by gas chromatography-mass spectrometry (GC-MS) testing using the HHS (SAMHSA) cutoff criteria. The CEDIA neutralization test successfully identified all 154 of the GC-MS confirmed positive samples. The test successfully identified as false positive 251 out of the 294 (85.4%) samples that failed to confirm by GC-MS.

  14. 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

  15. 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.

  16. 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.

  17. Physical methods of nucleic acid transfer: general concepts and applications

    PubMed Central

    Villemejane, Julien; Mir, Lluis M

    2009-01-01

    Physical methods of gene (and/or drug) transfer need to combine two effects to deliver the therapeutic material into cells. The physical methods must induce reversible alterations in the plasma membrane to allow the direct passage of the molecules of interest into the cell cytosol. They must also bring the nucleic acids in contact with the permeabilized plasma membrane or facilitate access to the inside of the cell. These two effects can be achieved in one or more steps, depending upon the methods employed. In this review, we describe and compare several physical methods: biolistics, jet injection, hydrodynamic injection, ultrasound, magnetic field and electric pulse mediated gene transfer. We describe the physical mechanisms underlying these approaches and discuss the advantages and limitations of each approach as well as its potential application in research or in preclinical and clinical trials. We also provide conclusions, comparisons, and projections for future developments. While some of these methods are already in use in man, some are still under development or are used only within clinical trials for gene transfer. The possibilities offered by these methods are, however, not restricted to the transfer of genes and the complementary uses of these technologies are also discussed. As these methods of gene transfer may bypass some of the side effects linked to viral or biochemical approaches, they may find their place in specific clinical applications in the future. This article is part of a themed section on Vector Design and Drug Delivery. For a list of all articles in this section see the end of this paper, or visit: http://www3.interscience.wiley.com/journal/121548564/issueyear?year=2009 PMID:19154421

  18. A new general 1-D vadose zone flow solution method

    NASA Astrophysics Data System (ADS)

    Ogden, Fred L.; Lai, Wencong; Steinke, Robert C.; Zhu, Jianting; Talbot, Cary A.; Wilson, John L.

    2015-06-01

    We have developed an alternative to the one-dimensional partial differential equation (PDE) attributed to Richards (1931) that describes unsaturated porous media flow in homogeneous soil layers. Our solution is a set of three ordinary differential equations (ODEs) derived from unsaturated flux and mass conservation principles. We used a hodograph transformation, the Method of Lines, and a finite water-content discretization to produce ODEs that accurately simulate infiltration, falling slugs, and groundwater table dynamic effects on vadose zone fluxes. This formulation, which we refer to as "finite water-content", simulates sharp fronts and is guaranteed to conserve mass using a finite-volume solution. Our ODE solution method is explicitly integrable, does not require iterations and therefore has no convergence limits and is computationally efficient. The method accepts boundary fluxes including arbitrary precipitation, bare soil evaporation, and evapotranspiration. The method can simulate heterogeneous soils using layers. Results are presented in terms of fluxes and water content profiles. Comparing our method against analytical solutions, laboratory data, and the Hydrus-1D solver, we find that predictive performance of our finite water-content ODE method is comparable to or in some cases exceeds that of the solution of Richards' equation, with or without a shallow water table. The presented ODE method is transformative in that it offers accuracy comparable to the Richards (1931) PDE numerical solution, without the numerical complexity, in a form that is robust, continuous, and suitable for use in large watershed and land-atmosphere simulation models, including regional-scale models of coupled climate and hydrology.

  19. 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.

  20. A general method for saturation mutagenesis of cloned DNA fragments.

    PubMed

    Myers, R M; Lerman, L S; Maniatis, T

    1985-07-19

    A new procedure for generating and isolating random single-base substitutions in cloned DNA fragments is presented. The mutations are generated by treatment of single-stranded DNA with various chemicals, followed by the synthesis of the complementary strand with reverse transcriptase. Misincorporation frequently occurs when the enzyme encounters a damaged base in the mutagenized template DNA. The resulting duplex DNA fragments containing random single-base substitutions are cloned, amplified as a population, and isolated from wild-type DNA by preparative denaturing gradient gel electrophoresis. The physical separation of mutant DNA fragments makes it possible to isolate and characterize large numbers of site-directed single-base substitutions in the absence of a phenotypic selection. This procedure should be generally applicable to the fine-structure genetic analysis of regulatory and protein-coding sequences.

  1. A High-Throughput Screening Method for Identification of Inhibitors of the Deubiquitinating Enzyme USP14

    PubMed Central

    Lee, Byung-Hoon; Finley, Daniel; King, Randall W.

    2013-01-01

    Deubiquitinating enzymes (DUBs) reverse the process of ubiquitination, and number nearly 100 in humans. In principle, DUBs represent promising drug targets, as several of the enzymes have been implicated in human diseases. The isopeptidase activity of DUBs can be selectively inhibited by targeting the catalytic site with drug-like compounds. Notably, the mammalian 26S proteasome is associated with three major DUBs: RPN11, UCH37 and USP14. Because the ubiquitin ‘chain-trimming’ activity of USP14 can inhibit proteasome function, inhibitors of USP14 can stimulate proteasomal degradation. We recently established a high-throughput screening (HTS) method to discover small-molecule inhibitors specific for USP14. The protocols in this article cover the necessary procedures for preparing assay reagents, performing HTS for USP14 inhibitors, and carrying out post-HTS analysis. PMID:23788557

  2. Simple method for screening aflatoxin-producing molds by UV photography.

    PubMed Central

    Yabe, K; Ando, Y; Ito, M; Terakado, N

    1987-01-01

    UV absorption by aflatoxins was monitored in GY agar medium by UV photography. In the UV photographs, aflatoxin-producing molds were identified as gray or black colonies, whereas aflatoxin-nonproducing molds appeared as white colonies. By cellophane transplantation experiments and silica gel thin-layer chromatography, the products absorbing UV light substantially were found to be mainly aflatoxins B1 and G1 excreted from the mold mycelium into the agar medium. UV absorption did not occur when the agar medium contained aflatoxin-noninducible carbon sources instead of glucose. Various inhibitors of aflatoxin production, such as dichlorovos and dimethyl sulfoxide, also decreased the intensity of UV absorption. These results indicate that this technique can be used as a simple, safe, and rapid method of screening aflatoxin-producing molds. Images PMID:3105453

  3. Infrared thermography based on artificial intelligence as a screening method for carpal tunnel syndrome diagnosis.

    PubMed

    Jesensek Papez, B; Palfy, M; Mertik, M; Turk, Z

    2009-01-01

    This study further evaluated a computer-based infrared thermography (IRT) system, which employs artificial neural networks for the diagnosis of carpal tunnel syndrome (CTS) using a large database of 502 thermal images of the dorsal and palmar side of 132 healthy and 119 pathological hands. It confirmed the hypothesis that the dorsal side of the hand is of greater importance than the palmar side when diagnosing CTS thermographically. Using this method it was possible correctly to classify 72.2% of all hands (healthy and pathological) based on dorsal images and > 80% of hands when only severely affected and healthy hands were considered. Compared with the gold standard electromyographic diagnosis of CTS, IRT cannot be recommended as an adequate diagnostic tool when exact severity level diagnosis is required, however we conclude that IRT could be used as a screening tool for severe cases in populations with high ergonomic risk factors of CTS.

  4. 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.

  5. 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.

  6. General advancing front packing algorithm for the discrete element method

    NASA Astrophysics Data System (ADS)

    Morfa, Carlos A. Recarey; Pérez Morales, Irvin Pablo; de Farias, Márcio Muniz; de Navarra, Eugenio Oñate Ibañez; Valera, Roberto Roselló; Casañas, Harold Díaz-Guzmán

    2016-11-01

    A generic formulation of a new method for packing particles is presented. It is based on a constructive advancing front method, and uses Monte Carlo techniques for the generation of particle dimensions. The method can be used to obtain virtual dense packings of particles with several geometrical shapes. It employs continuous, discrete, and empirical statistical distributions in order to generate the dimensions of particles. The packing algorithm is very flexible and allows alternatives for: 1—the direction of the advancing front (inwards or outwards), 2—the selection of the local advancing front, 3—the method for placing a mobile particle in contact with others, and 4—the overlap checks. The algorithm also allows obtaining highly porous media when it is slightly modified. The use of the algorithm to generate real particle packings from grain size distribution curves, in order to carry out engineering applications, is illustrated. Finally, basic applications of the algorithm, which prove its effectiveness in the generation of a large number of particles, are carried out.

  7. 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…

  8. 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…

  9. 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

  10. SUDOSCAN: A Simple, Rapid, and Objective Method with Potential for Screening for Diabetic Peripheral Neuropathy.

    PubMed

    Selvarajah, Dinesh; Cash, Tom; Davies, Jennifer; Sankar, Adithya; Rao, Ganesh; Grieg, Marni; Pallai, Shillo; Gandhi, Rajiv; Wilkinson, Iain D; Tesfaye, Solomon

    2015-01-01

    Clinical methods of detecting diabetic peripheral neuropathy (DPN) are not objective and reproducible. We therefore evaluated if SUDOSCAN, a new method developed to provide a quick, non-invasive and quantitative assessment of sudomotor function can reliably screen for DPN. 70 subjects (45 with type 1 diabetes and 25 healthy volunteers [HV]) underwent detailed assessments including clinical, neurophysiological and 5 standard cardiovascular reflex tests (CARTs). Using the American Academy of Neurology criteria subjects were classified into DPN and No-DPN groups. Based on CARTs subjects were also divided into CAN, subclinical-CAN and no-CAN. Sudomotor function was assessed with measurement of hand and foot Electrochemical Skin Conductance (ESC) and calculation of the CAN risk score. Foot ESC (μS) was significantly lower in subjects with DPN [n = 24; 53.5(25.1)] compared to the No-DPN [77.0(7.9)] and HV [77.1(14.3)] groups (ANCOVA p<0.001). Sensitivity and specificity of foot ESC for classifying DPN were 87.5% and 76.2%, respectively. The area under the ROC curve (AUC) was 0.85. Subjects with CAN had significantly lower foot [55.0(28.2)] and hand [53.5(19.6)] ESC compared to No-CAN [foot ESC, 72.1(12.2); hand ESC 64.9(14.4)] and HV groups (ANCOVA p<0.001 and 0.001, respectively). ROC analysis of CAN risk score to correctly classify CAN revealed a sensitivity of 65.0% and specificity of 80.0%. AUC was 0.75. Both foot and hand ESC demonstrated strong correlation with individual parameters and composite scores of nerve conduction and CAN. SUDOSCAN, a non-invasive and quick test, could be used as an objective screening test for DPN in busy diabetic clinics, insuring adherence to current recommendation of annual assessments for all diabetic patients that remains unfulfilled.

  11. SUDOSCAN: A Simple, Rapid, and Objective Method with Potential for Screening for Diabetic Peripheral Neuropathy

    PubMed Central

    Selvarajah, Dinesh; Cash, Tom; Davies, Jennifer; Sankar, Adithya; Rao, Ganesh; Grieg, Marni; Pallai, Shillo; Gandhi, Rajiv; Wilkinson, Iain D.; Tesfaye, Solomon

    2015-01-01

    Clinical methods of detecting diabetic peripheral neuropathy (DPN) are not objective and reproducible. We therefore evaluated if SUDOSCAN, a new method developed to provide a quick, non-invasive and quantitative assessment of sudomotor function can reliably screen for DPN. 70 subjects (45 with type 1 diabetes and 25 healthy volunteers [HV]) underwent detailed assessments including clinical, neurophysiological and 5 standard cardiovascular reflex tests (CARTs). Using the American Academy of Neurology criteria subjects were classified into DPN and No-DPN groups. Based on CARTs subjects were also divided into CAN, subclinical-CAN and no-CAN. Sudomotor function was assessed with measurement of hand and foot Electrochemical Skin Conductance (ESC) and calculation of the CAN risk score. Foot ESC (μS) was significantly lower in subjects with DPN [n = 24; 53.5(25.1)] compared to the No-DPN [77.0(7.9)] and HV [77.1(14.3)] groups (ANCOVA p<0.001). Sensitivity and specificity of foot ESC for classifying DPN were 87.5% and 76.2%, respectively. The area under the ROC curve (AUC) was 0.85. Subjects with CAN had significantly lower foot [55.0(28.2)] and hand [53.5(19.6)] ESC compared to No-CAN [foot ESC, 72.1(12.2); hand ESC 64.9(14.4)] and HV groups (ANCOVA p<0.001 and 0.001, respectively). ROC analysis of CAN risk score to correctly classify CAN revealed a sensitivity of 65.0% and specificity of 80.0%. AUC was 0.75. Both foot and hand ESC demonstrated strong correlation with individual parameters and composite scores of nerve conduction and CAN. SUDOSCAN, a non-invasive and quick test, could be used as an objective screening test for DPN in busy diabetic clinics, insuring adherence to current recommendation of annual assessments for all diabetic patients that remains unfulfilled. PMID:26457582

  12. A screening pattern recognition method finds new and divergent targets for drugs and natural products.

    PubMed

    Wassermann, Anne Mai; Lounkine, Eugen; Urban, Laszlo; Whitebread, Steven; Chen, Shanni; Hughes, Kevin; Guo, Hongqiu; Kutlina, Elena; Fekete, Alexander; Klumpp, Martin; Glick, Meir

    2014-07-18

    Computational target prediction methods using chemical descriptors have been applied exhaustively in drug discovery to elucidate the mechanisms-of-action (MOAs) of small molecules. To predict truly novel and unexpected small molecule-target interactions, compounds must be compared by means other than their chemical structure alone. Here we investigated predictions made by a method, HTS fingerprints (HTSFPs), that matches patterns of activities in experimental screens. Over 1,400 drugs and 1,300 natural products (NPs) were screened in more than 200 diverse assays, creating encodable activity patterns. The comparison of these activity patterns to an MOA-annotated reference panel led to the prediction of 5,281 and 2,798 previously unknown targets for the NP and drug sets, respectively. Intriguingly, there was limited overlap among the targets predicted; the drugs were more biased toward membrane receptors and the NPs toward soluble enzymes, consistent with the idea that they represent unexplored pharmacologies. Importantly, HTSFPs inferred targets that were beyond the prediction capabilities of standard chemical descriptors, especially for NPs but also for the more explored drug set. Of 65 drug-target predictions that we tested in vitro, 48 (73.8%) were confirmed with AC50 values ranging from 38 nM to 29 μM. Among these interactions was the inhibition of cyclooxygenases 1 and 2 by the HIV protease inhibitor Tipranavir. These newly discovered targets that are phylogenetically and phylochemically distant to the primary target provide an explanation for spontaneous bleeding events observed for patients treated with this drug, a physiological effect that was previously difficult to reconcile with the drug's known MOA.

  13. Mitigating unwanted amorphisation: A screening method for the selection of suitable excipients.

    PubMed

    Amharar, Youness; Curtin, Vincent; Gallagher, Kieran H; O'Siochru, Eoin; O'Connell, Peter; Healy, Anne-Marie

    2016-01-01

    Co-processing an active pharmaceutical ingredient (API) with a low Tg excipient has been previously reported to be an effective strategy for preventing drug amorphisation on milling. This technique relies on the ability of the excipient to form a molecular dispersion with the amorphous API during the milling process. The presence of the excipient within the amorphous phase induces a reduction of the Tg. Hence, the molecular dispersion becomes less stable than the amorphous API alone and recrystallises upon milling. The objective of this study was to develop a screening method for the selection of suitable excipients to prevent amorphisation, based on two criteria: the Tg of the excipient and the solubility of the excipient in the amorphous API. The ability of the excipients to induce Tg reduction was first assessed by measuring the Tg of the amorphous composite by thermal analysis and comparing it with that of the pure API (griseofulvin). A predicted ability for mitigation of amorphisation upon milling was then deduced from these observations for each excipient and assessed against experimental results. The same excipients were then studied with regard to their expected solubility in another amorphous API (budesonide) by Hildebrand solubility parameter calculations in order to evaluate their capacity to form an amorphous composite with the drug. The predicted effects of the excipients on comilling were compared with the amorphous content of the processed API. The screening method as applied to both APIs showed good agreement with the experimental results and were shown to be efficient for the selection of the most appropriate excipient. This approach revealed that the two key parameters involved are the Tg of the excipient and the ability of the API to form an amorphous molecular dispersion with the excipients. This work confirms and completes our previously published results on the mitigation of the amorphisation by comilling with low Tg excipients and constitutes

  14. 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.

  15. Fluorometric method for inorganic pyrophosphatase activity detection and inhibitor screening based on click chemistry.

    PubMed

    Xu, Kefeng; Chen, Zhonghui; Zhou, Ling; Zheng, Ou; Wu, Xiaoping; Guo, Longhua; Qiu, Bin; Lin, Zhenyu; Chen, Guonan

    2015-01-06

    A fluorometric method for pyrophosphatase (PPase) activity detection was developed based on click chemistry. Cu(II) can coordinate with pyrophosphate (PPi), the addition of pyrophosphatase (PPase) into the above system can destroy the coordinate compound because PPase catalyzes the hydrolysis of PPi into inorganic phosphate and produces free Cu(II), and free Cu(II) can be reduced by sodium ascorbate (SA) to form Cu(I), which in turn initiates the ligating reaction between nonfluorescent 3-azidocoumarins and terminal alkynes to produce a highly fluorescent triazole complex, based on which, a simple and sensitive turn on fluorometric method for PPase can be developed. The fluorescence intensity of the system has a linear relationship with the logarithm of the PPase concentration in the range of 0.5 and 10 mU with a detection limit down to 0.2 mU (S/N = 3). This method is cost-effective and convenient without any labels or complicated operations. The proposed system was applied to screen the potential PPase inhibitor with high efficiency. The proposed method can be applied to diagnosis of PPase-related diseases.

  16. The Split-Spectrum Method for Differential InSAR Ionospheric Phase Screen Correction

    NASA Astrophysics Data System (ADS)

    Gomba, G.; Eineder, M.

    2015-12-01

    The differential ionospheric path delay is a major error source in L-band interferograms. It is superimposed to topography and ground deformation signals hindering the measurement of geophysical processes like earthquakes. Exploiting the ionosphere dispersive nature of the ionosphere, the method separates the ionospheric component of the interferometric phase from the non-dispersive component, related to topography, ground motion and tropospheric path delay. An implementation of the split-spectrum method is in this work exposed in detail and its performance is analyzed. We test the method using various ALOS PALSAR interferometric pairs with different characteristics: high to low coherence, moving and non-moving terrain, with and without topography and different ionosphere states. Ionospheric errors of almost one meter have been corrected to a centimeter or millimeter level. The results show how the method is able to systematically compensate the ionospheric phase in interferograms. In this work we also present ALOS PALSAR ionospheric-free interferograms and the related ionospheric phase screens for the 2015 Nepal earthquake, the 2008 Wenchuan earthquake, the 2008 Kyrgyzstan earthquake, and the 2011 Myanmar earthquke.

  17. Multi-laboratory testing of a screening method for world trade center (WTC) collapse dust.

    PubMed

    Rosati, Jacky A; Bern, Amy M; Willis, Robert D; Blanchard, Fredrick T; Conner, Teri L; Kahn, Henry D; Friedman, David

    2008-02-15

    The September 11, 2001 attack on the World Trade Center (WTC) covered a large area of downtown New York City with dust and debris. This paper describes the testing of an analytical method designed to evaluate whether sampled dust contains dust that may have originated from the collapse of the WTC. Using dust samples collected from locations affected and not affected (referred to as 'background' locations) by the collapse, a scanning electron microscopy (SEM) analysis method was developed to screen for three materials that are believed to be present in large quantities in WTC dusts: slag wool, concrete, and gypsum. An inter-laboratory evaluation of the method was implemented by having eight laboratories analyze a number of 'blind' dust samples, consisting of confirmed background dust and confirmed background dust spiked with varying amounts of dust affected by the WTC collapse. The levels of gypsum and concrete in the spiked samples were indistinguishable from the levels in the background samples. Measurements of slag wool in dust demonstrated potential for distinguishing between spiked and background samples in spite of considerable within and between laboratory variability. Slag wool measurements appear to be sufficiently sensitive to distinguish dust spiked with 5% WTC-affected dust from 22 out of 25 background dust samples. Additional development work and inter-laboratory testing of the slag wool component will be necessary to improve the precision and accuracy of the method and reduce inter- and intra-laboratory variability from levels observed in the inter-laboratory evaluation.

  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. A General Quantum Mechanical Method to Predict Positron Spectroscopy

    DTIC Science & Technology

    2007-06-01

    70 6.2.3 Positronic Systems for Modeling and Experiment 71 Appendix A. Electron-Positron Annihilation Observables from NEO-HF and NEO-MP2...spectroscopy (PAS) experiments are widely used to study materials defects, including point defects in semiconductors and voids in composite materials...addition to traditional PAS techniques, experiments involving VFRs are also discussed. In Section 2.2, methods for modeling positron interaction with

  20. A general method for modeling population dynamics and its applications.

    PubMed

    Shestopaloff, Yuri K

    2013-12-01

    Studying populations, be it a microbe colony or mankind, is important for understanding how complex systems evolve and exist. Such knowledge also often provides insights into evolution, history and different aspects of human life. By and large, populations' prosperity and decline is about transformation of certain resources into quantity and other characteristics of populations through growth, replication, expansion and acquisition of resources. We introduce a general model of population change, applicable to different types of populations, which interconnects numerous factors influencing population dynamics, such as nutrient influx and nutrient consumption, reproduction period, reproduction rate, etc. It is also possible to take into account specific growth features of individual organisms. We considered two recently discovered distinct growth scenarios: first, when organisms do not change their grown mass regardless of nutrients availability, and the second when organisms can reduce their grown mass by several times in a nutritionally poor environment. We found that nutrient supply and reproduction period are two major factors influencing the shape of population growth curves. There is also a difference in population dynamics between these two groups. Organisms belonging to the second group are significantly more adaptive to reduction of nutrients and far more resistant to extinction. Also, such organisms have substantially more frequent and lesser in amplitude fluctuations of population quantity for the same periodic nutrient supply (compared to the first group). Proposed model allows adequately describing virtually any possible growth scenario, including complex ones with periodic and irregular nutrient supply and other changing parameters, which present approaches cannot do.

  1. Systematic and general method for quantifying localization in microscopy images

    PubMed Central

    Sheng, Huanjie; Stauffer, Weston

    2016-01-01

    ABSTRACT Quantifying the localization of molecules with respect to other molecules, cell structures and intracellular regions is essential to understanding their regulation and actions. However, measuring localization from microscopy images is often difficult with existing metrics. Here, we evaluate a metric for quantifying localization termed the threshold overlap score (TOS), and show it is simple to calculate, easy to interpret, able to be used to systematically characterize localization patterns, and generally applicable. TOS is calculated by: (i) measuring the overlap of pixels that are above the intensity thresholds for two signals; (ii) determining whether the overlap is more, less, or the same as expected by chance, i.e. colocalization, anti-colocalization, or non-colocalization; and (iii) rescaling to allow comparison at different thresholds. The above is repeated at multiple threshold combinations to generate a TOS matrix to systematically characterize the relationship between localization and signal intensities. TOS matrices were used to identify and distinguish localization patterns of different proteins in various simulations, cell types and organisms with greater specificity and sensitivity than common metrics. For all the above reasons, TOS is an excellent first line metric, particularly for cells with mixed localization patterns. PMID:27979831

  2. Screening for Parental Depression in Urban Primary Care Practices: A Mixed Methods Study.

    PubMed

    Guevara, James P; Gerdes, Marsha; Rothman, Brooke; Igbokidi, Victor; Doughterty, Susan; Localio, Russell; Boyd, Rhonda C

    2016-01-01

    We sought to determine feasibility and acceptability of parental depression screening in urban pediatric practices. We recruited seven practices to participate. Patient Health Questionnaire-2, a validated two-item screening tool, was used to screen for depressive symptoms at 1-3 year old well visits. We conducted semi-structured interviews with clinicians to identify barriers and facilitators to screening. Of 8,621 eligible parents, 21.1% completed screening with site-specific rates ranging from 10.1% to 48.5%. Among those screened, 8.1% screened positive for depressive symptoms with site-specific rates ranging from 1.2% to 16.9%. Electronic alerts improved screening rates from 45 / month to 170 / month. Fifteen clinicians completed interviews and endorsed screening to provide help for families, build stronger ties with parents, and improve outcomes for children. However, insufficient time, need to complete activities with higher priority, lack of mental health availability, few resources for parents with limited English proficiency, and discomfort addressing depression were thought to limit screening.

  3. 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.

  4. Efficient production of Clostridium botulinum exotoxin C3 in bacteria: a screening method to optimize production yields.

    PubMed

    Gadea, Gilles; Boublik, Yvan; Delga, Stephanie; Roux, Pierre

    2005-03-01

    Clostridium botulinum exoenzyme C3 is responsible for the inactivation of members of the Rho GTPase family that are implicated in actin-cytoskeleton reorganization. This property has been extensively used in the field to investigate the functionality of the Rho GTPases. However, systematic analysis of Rho GTPase functions requires large amounts of such inhibitors and consequently an optimization of the production yield of these proteins. Bacterial production of soluble proteins often requires a refolding step that noticeably affects the production yields and necessitates additional experiments to verify functional activity. This is particularly true for TAT-C3, the production yields of which are generally low. In this report, we describe a rapid and efficient method for the production of soluble C3 exoenzyme developed by screening a collection of bacterial strains. The recombinant C3 protein was fused to the TAT protein-transduction domain from HIV, to allow protein delivery into cells, and to a hexahistidine tag, that permitted purification by Nickel affinity chromatography. We have demonstrated the production of large amounts of soluble and functional protein using the bacterial strain AD494 (DE3)pLysS. This rapid and efficient method for the production of soluble C3 exoenzyme could also be useful for the production of other proteins with solubility problems.

  5. A Colony Multiplex Quantitative PCR-Based 3S3DBC Method and Variations of It for Screening DNA Libraries

    PubMed Central

    An, Yang; Toyoda, Atsushi; Zhao, Chen; Fujiyama, Asao; Agata, Kiyokazu

    2015-01-01

    A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC) method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements. PMID:25646755

  6. 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 ...

  7. 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.

  8. Generalized spectral method for near-field optical microscopy

    SciTech Connect

    Jiang, B.-Y.; Zhang, L. M.; Basov, D. N.; Fogler, M. M.; Castro Neto, A. H.

    2016-02-07

    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.

  9. 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.

  10. Conductor-like screening model for relaxed excited states: Implementation in the semiempirical method MSINDO.

    PubMed

    Krause, Katharina; Bredow, Thomas

    2014-03-15

    Two approaches to treat solvent polarization and reorientation effects for excited states of molecules and surfaces have been implemented in the recently developed MSINDO-sCIS method (Gadaczek, Krause, Hintze, Bredow, J. Chem. Theory Comput. 2011, 7, 3675). They allow for an efficient calculation of analytical energy gradients and hence open the opportunity to investigate fluorescence effects or photochemical reactions in solution for large molecules that are difficult to treat with high-level methods. Both approaches are based on the conductor-like screening model (COSMO) (Klamt and Schüürmann, J. Chem. Soc., Perkin Trans. 1993, 2, 799) in combination with the configuration interaction singles (CIS) method (Foresman, Head-Gordon, Pople, and Frisch, J. Phys. Chem. 1992, 96, 135). The paper gives a brief outline of the theoretical background. As a first application, solvent shifts of three well-studied, environment-sensitive fluorescent dyes (Kucherak, Didier, Mély, and Klymchenko, J. Phys. Chem. Lett. 2010, 1, 616) have been calculated and compared with experimental results and standard time-dependent density functional theory. A statistical evaluation of MSINDO-COSMO-sCIS is provided for a set of 39 molecules suggested recently by Jacquemin et al. (Jacquemin, Planchat, Adamo, and Mennucci, J. Chem. Theory Comput. 2012, 8, 2359). Calculated vertical and adiabatic excitation energies and fluorescence energies are compared to experimental data.

  11. LC-MS method for screening unknown microbial carotenoids and isoprenoid quinones.

    PubMed

    Kaiser, Philipp; Geyer, Roland; Surmann, Peter; Fuhrmann, Herbert

    2012-01-01

    The structure of secondary metabolites from microorganisms provides a useful tool for microbial characterization and chemotaxonomic classification. Microbial isoprenoid quinones, for example, are well described and used to distinguish among photosynthetic microorganism groups. In addition, isoprenoid quinones can also be found, together with carotenoids, in non-photosynthetic microorganisms. The aim of the present study was to develop a LC-MS/MS method which can analyze and identify these microbial isoprenoids. Positive atmospheric pressure chemical ionization (APCI) together with collisionally induced dissociation was applied for generation of informative fragment spectra by mass spectrometry. Enhanced product ion (EPI) scan in a linear ion trap with information dependent data acquisition (IDA) enabled generation of MS fragment data even from minor isoprenoids. The developed liquid chromatography method enabled separation of isoprenoid patterns from their ester derivatives. Discovery and structural characterization of isoprenoid quinones and carotenoids were carried out by comparing characteristics of fragment spectra from unknown compounds with fragment spectra of a range of isoprenoid standard compounds and using published data. Throughout the study 17 microorganisms (e.g., Acremonium butyri, Arthrobacter spp., Brevibacterium linens, Bullera variabilis, Exophiala dermatitidis, Lecythophora hoffmannii, Panthoea agglomerans, Rhodotorula spp., Xanthophyllomyces dendrorhous) were screened and probable structures of isoprenoid quinones and carotenoids were suggested. The method lays some foundations on the analysis of yet unknown isoprenoids in microorganisms by using LCMS/MS techniques.

  12. Screening possible solid electrolytes by calculating the conduction pathways using Bond Valence method

    NASA Astrophysics Data System (ADS)

    Gao, Jian; Chu, Geng; He, Meng; Zhang, Shu; Xiao, RuiJuan; Li, Hong; Chen, LiQuan

    2014-08-01

    Inorganic solid electrolytes have distinguished advantages in terms of safety and stability, and are promising to substitute for conventional organic liquid electrolytes. However, low ionic conductivity of typical candidates is the key problem. As connective diffusion path is the prerequisite for high performance, we screen for possible solid electrolytes from the 2004 International Centre for Diffraction Data (ICDD) database by calculating conduction pathways using Bond Valence (BV) method. There are 109846 inorganic crystals in the 2004 ICDD database, and 5295 of them contain lithium. Except for those with toxic, radioactive, rare, or variable valence elements, 1380 materials are candidates for solid electrolytes. The rationality of the BV method is approved by comparing the existing solid electrolytes' conduction pathways we had calculated with those from experiments or first principle calculations. The implication for doping and substitution, two important ways to improve the conductivity, is also discussed. Among them Li2CO3 is selected for a detailed comparison, and the pathway is reproduced well with that based on the density functional studies. To reveal the correlation between connectivity of pathways and conductivity, α/ γ-LiAlO2 and Li2CO3 are investigated by the impedance spectrum as an example, and many experimental and theoretical studies are in process to indicate the relationship between property and structure. The BV method can calculate one material within a few minutes, providing an efficient way to lock onto targets from abundant data, and to investigate the structure-property relationship systematically.

  13. Methods for transforming and expression screening of filamentous fungal cells with a DNA library

    DOEpatents

    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.

  14. Nonmevalonate terpene biosynthesis enzymes as antiinfective drug targets: substrate synthesis and high-throughput screening methods.

    PubMed

    Illarionova, Victoria; Kaiser, Johannes; Ostrozhenkova, Elena; Bacher, Adelbert; Fischer, Markus; Eisenreich, Wolfgang; Rohdich, Felix

    2006-11-10

    The nonmevalonate isoprenoid pathway is an established target for antiinfective drug development. This paper describes high-throughput methods for the screening of 2C-methyl-D-erythritol synthase (IspC protein), 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (IspD protein), 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (IspE protein), and 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF protein) against large compound libraries. The assays use up to three auxiliary enzymes. They are all monitored photometrically at 340 nm and are robust as documented by Z-factors of >or=0.86. 13C NMR assays designed for hit verification via direct detection of the primary reaction product are also described. Enzyme-assisted methods for the preparation, on a multigram scale, of isoprenoid biosynthesis intermediates required as substrates for these assays are reported. Notably, these methods enable the introduction of single or multiple 13C labels as required for NMR-monitored assays. The preparation of 4-diphosphosphocytidyl-2C-methyl-D-erythritol 2-phosphate in multigram quantities is described for the first time.

  15. How to benchmark methods for structure-based virtual screening of large compound libraries.

    PubMed

    Christofferson, Andrew J; Huang, Niu

    2012-01-01

    Structure-based virtual screening is a useful computational technique for ligand discovery. To systematically evaluate different docking approaches, it is important to have a consistent benchmarking protocol that is both relevant and unbiased. Here, we describe the designing of a benchmarking data set for docking screen assessment, a standard docking screening process, and the analysis and presentation of the enrichment of annotated ligands among a background decoy database.

  16. 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.

  17. A general method for sifting linguistic knowledge from structured terminologies.

    PubMed Central

    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. PMID:11079895

  18. A generalized self-consistent mechanics method for microcracked solids

    NASA Astrophysics Data System (ADS)

    Huang, Y.; Hu, K. X.; Chandra, A.

    1994-08-01

    A CRACK-MATRIX-COMPOSITE model is proposed and studied for microcracked solids. The model properly accounts for the effect of crack interactions on the effective moduli of microcracked solids. Approximate formulas for randomly distributed penny-shaped cracks and tunnel cracks are given. The difference between the crack-matrix-composite model and that of the dilute or non-interacting solution is of the order ɛ {5}/{2} for penny-shaped cracks and ɛ 2 for tunnel cracks, where ɛ is the crack density. The results from an accurate numerical method for arbitrarily distributed cracks, based on a pseudo-traction approach, verify the present crack-matrix-composite model.

  19. Generalized Derivation of the RRV Method and Its Application

    NASA Astrophysics Data System (ADS)

    Lin, F. R.; Peng, Q. Y.; Wang, N.; Peng, H. W.; Zhang, Q. F.; Li, Z.

    2016-12-01

    Very recently, Heinze & Metchev proposed a novel method for calculating precise distances to the main-belt asteroids using only two nights of data from a single observatory. In this paper, we re-derive the solution but use easily understood spherical astronomy. Our derivation is based on the premise that the geocentric angular velocity of an asteroid changes linearly with time, which is closer to the real situation. Therefore, a possible extra error of rotational reflex velocity, in some cases, is eliminated. A total of 193 frames of CCD images over four nights for 10 asteroids in a conventional stare mode taken with the 1 m telescope at Yunnan Observatory were used to test the improved solution and precise distances were evaluated.

  20. 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…

  1. 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

  2. Identification of imprinted genes using a novel screening method based on asynchronous DNA replication

    SciTech Connect

    Kawame, H.; Hansen, R.S.; Gartler, S.M.

    1994-09-01

    Genomic imprinting refers to the process of epigenetic change that occurs during germ cell development that results in either maternal- or paternal-specific gene expression. Identification of imprinted genes is of primary importance to the understanding of imprinting mechanisms and the role of specific imprinted genes in human disease. Recently, it has been established that chromosomal regions known to contain imprinted genes replicate asynchronously. We propose a novel screening method to identify imprinted genes based on replication asynchrony as a marker for imprinted domains. Dividing human cells were pulse-labeled with BrdU and separated into different fractions of S-phase by flow cytometry. A library of late-replicating inter-Alu sequences should be enriched in gene-associated sequences that replicate early on one chromosome and late on the other homologue. Clones were analyzed for replication timing by hybridization to inter-Alu replication profiles. Candidates for replication asynchrony exhibited broad or biphasic replication timing, and these were analyzed for chromosomal location by hybridizations to inter-Alu products from a hybrid mapping panel. Initial screening of 123 clones resulted in 3 asynchronously-replicating clones that localized to single chromosomes. Chromosome 17 and chromosome 19 candidates might be located in regions thought to be imprinted by synteny with mouse chromosomes. A chromosome 15 clone was further characterized because of its possible localization to the Prader-Willi/Angelman locus. This sequence was localized outside the region deleted in Prader-Willi patients, and was found to be expressed in human cell lines. Replication asynchrony for this sequence appears to be polymorphic because cells derived from some individuals indicated synchronous replication. This appears to be the first example of a polymorphism in replication asynchrony.

  3. 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%.

  4. Efficacy of ACL injury risk screening methods in identifying high-risk landing patterns during a sport-specific task.

    PubMed

    Fox, A S; Bonacci, J; McLean, S G; Saunders, N

    2016-06-12

    Screening methods sensitive to movement strategies that increase anterior cruciate ligament (ACL) loads are likely to be effective in identifying athletes at-risk of ACL injury. Current ACL injury risk screening methods are yet to be evaluated for their ability to identify athletes' who exhibit high-risk lower limb mechanics during sport-specific maneuvers associated with ACL injury occurrences. The purpose of this study was to examine the efficacy of two ACL injury risk screening methods in identifying high-risk lower limb mechanics during a sport-specific landing task. Thirty-two female athletes were screened using the Landing Error Scoring System (LESS) and Tuck Jump Assessment. Participants' also completed a sport-specific landing task, during which three-dimensional kinematic and kinetic data were collected. One-dimensional statistical parametric mapping was used to examine the relationships between screening method scores, and the three-dimensional hip and knee joint rotation and moment data from the sport-specific landing. Higher LESS scores were associated with reduced knee flexion from 30 to 57 ms after initial contact (P = 0.003) during the sport-specific landing; however, no additional relationships were found. These findings suggest the LESS and Tuck Jump Assessment may have minimal applicability in identifying athletes' who exhibit high-risk landing postures in the sport-specific task examined.

  5. 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.

  6. Developing a UHPLC-QTOF-MS and Automated Library Search Method for Screening Drugs and Toxic Compounds in Postmortem Specimens.

    PubMed

    Liu, Hsiu-Chuan; Yang, Chu-An; Liu, Ray H; Lin, Dong-Liang

    2017-03-24

    Screening and confirming the presence of drugs and toxic compounds in various matrices are important and challenging tasks routinely faced by forensic and clinical laboratories. Recent advances in the liquid chromatographic and mass spectrometric technologies have provided an opportunity for the development of more specific and effective approaches to achieve the "screening" and "confirmation" goals in a single analytical step. The objectives of this study are: (i) the establishment of an ultra-high performance liquid chromatographic, quadrupole time-of-flight mass spectrometric mass spectrometric and MS-MS spectral database, including 1,200 compounds of interest; and (ii) the development of an effective protocol, using this database and three searching algorithms, for general unknown screening of these compounds. The established database and protocol were evaluated through the analysis of 30 external proficiency test and 100 postmortem samples and found to be significantly more effective than the LC-IT-MS and GC-MS approaches previously established in our laboratory.

  7. Assessment of Sediment Heavy Metals Pollution Using Screening Methods (XRF, TGA/MS, XRPD and Earthworms Bioassay)

    NASA Astrophysics Data System (ADS)

    Findoráková, Lenka; Šestinová, Ol'ga; Hančul'ák, Jozef; Fedorová, Erika; Zorkovská, Anna

    2016-10-01

    The aim of this study is focused on the use of screening methods (TG/DTA coupled with MS, XRF, AAS, XRPD and earthworm bioassay) for sediments pollution assessing by heavy metals (Cu, Zn, Pb, Hg) coming from the former mining workloads in the central Spis, Eastern Slovakia. The screening methods (XRF, AAS) indicated pollution of studied sediments by Cu, Zn, Pb, Hg. The earthworms Dendrobaena veneta caused in some studied samples decrease of heavy metals concentration after their 7 days’ exposure in sediments. The other screening methods such as thermal analysis and XRPD analysis, does not confirm the specifically changes in physicochemical properties comparing the properties before and after 7 days’ earthworm's exposure.

  8. Observational methods used to assess rat behavior: general activity.

    PubMed

    Paul, Carol Ann; Beltz, Barbara; Berger-Sweeney, Joanne

    2007-09-01

    INTRODUCTIONThe activity-inactivity continuum is an important parameter of behavior, and quantification of overall locomotor activity in the rat should identify it as a naturally nocturnal animal. Disruptions in nocturnal activity can be caused by damage in visual inputs to the brain or damage in the hypothalamus. Many commercial devices are available to measure activity automatically; some can be integrated with a computer to allow overnight monitoring in the absence of an observer. A less sophisticated but still accurate method of measuring activity is to create a home-made activity chamber by replacing the bottom of a box with Plexiglas or by marking lines on the bottom of a clean rat cage so that the observer can record rat activity by noting when the lines are crossed, while simultaneously recording other behaviors. Activity in rat pups can be observed as soon as they are 10 days old using smaller activity chambers. This protocol describes the construction of a home-made activity chamber and how to measure four activities: locomotion, rearing, circling, and grooming.

  9. 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.

  10. Causal co-expression method with module analysis to screen drugs with specific target.

    PubMed

    Yu, Shuhao; Zheng, Lulu; Li, Yixue; Li, Chunyan; Ma, Chenchen; Yu, Yang; Li, Xuan; Hao, Pei

    2013-04-10

    The considerable increase of investment in research and development by the pharmaceutical industry over the past three decades has not added the number of approved new drugs. An important issue ignored by drug discovery practice is the multi-dimensional interaction network between drugs and their targets. Thus, it is essential to view drug actions through the lens of network biology. In the current study, based on the co-expression network of transcription factors and their downstream genes, we proposed a novel approach, called causal co-expression method with module analysis, to screen drugs with specific target and fewer side effects. We presented a causal co-expression method with module analysis and it could be used in analyzing the microarray data of different drug candidates. At first, the differential wiring value (DW) was calculated to find some causal transcription factors (TFs) by combining with differential expression genes in the regulated networks. After the discovery of the causal TFs, co-expression module analysis method was applied to mine molecular pharmacology pathways around these causal TFs at molecular level. We applied our methods to two drug candidates, Argyrin A and Bortezomib, both with anti-cancer activities. We first obtained some differentially expressed transcription factors of cells treated with Argyrin A or Bortezomib. Nearly all these transcription factors are associated with the tumor suppressor protein p27kip1. Furthermore, module analysis showed that Bortezomib inhibited tumor growth not specifically by cell cycle and cell proliferation pathway, but through many basic metabolic processes which result in cell toxicity. In contrast, Argyrin A had influence on cell cycle, and was involved in DNA damage repair at the same time, showing that Argyrin A was a more suitable drug for anti-cancer treatment. Our study revealed that the causal co-expression method with module analysis was effective and can be used as a tool to evaluate drug

  11. Flow-cytometric screening of aggregation-inhibitors using a fluorescence-assisted intracellular method.

    PubMed

    Lindberg, Hanna; Sandersjöö, Lisa; Meister, Sebastian W; Uhlén, Mathias; Löfblom, John; Ståhl, Stefan

    2017-01-01

    Aggregation of misfolded peptides and proteins is a key event in several neurodegenerative diseases. Suggested treatments of such disorders aim to inhibit the initial aggregation process. Here, we have developed an intracellular, function-based screening method, intended for isolation of aggregation-inhibitors from combinatorial protein libraries by flow-cytometric cell sorting. The method is based on fusion of aggregation-prone peptides to a fluorescent protein, functioning as a solubility reporter. Co-expression of a protein-based aggregation-inhibitor should prevent aggregation and thus increase the whole-cell fluorescence. We evaluated the method using the aggregation-prone Alzheimer's-related amyloid-β (Aβ) peptide in fusion to green-fluorescent protein (GFP), and an Aβ aggregation-inhibiting Affibody molecule. To adapt the method for library applications, the inhibitor was linked to an mCherry reporter for normalization of protein expression levels. We found that aggregation propensity correlates with fluorescence intensity, as co-expression of the Affibody-inhibitor increased the whole-cell fluorescence relative to a non-inhibitor. Employing improved cultivation parameters, we furthermore demonstrated efficient rescue from aggregation of an α-synuclein-derived protein using a different type of aggregation-inhibitor. Importantly, we also showed that the Aβ aggregation-inhibiting Affibody molecule could be isolated from a 1:10,000 background of non-inhibitors, with around 3,500-fold enrichment, in one cycle of fluorescence-based cell sorting. In conclusion, our new method represents a promising approach for generation of novel protein-based aggregation-inhibitors.

  12. 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.

  13. 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.

  14. 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.

  15. Screening Brazilian C gasoline quality: application of the SIMCA chemometric method to gas chromatographic data.

    PubMed

    Flumignan, Danilo Luiz; Tininis, Aristeu G; Ferreira, Fabrício de O; de Oliveira, José Eduardo

    2007-07-09

    A total of 2400 samples of commercial Brazilian C gasoline were collected over a 6-month period from different gas stations in the São Paulo state, Brazil, and analysed with respect to 12 physicochemical parameters according to regulation 309 of the Brazilian Government Petroleum, Natural Gas and Biofuels Agency (ANP). The percentages (v/v) of hydrocarbons (olefins, aromatics and saturated) were also determined. Hierarchical cluster analysis (HCA) was employed to select 150 representative samples that exhibited least similarity on the basis of their physicochemical parameters and hydrocarbon compositions. The chromatographic profiles of the selected samples were measured by gas chromatography with flame ionisation detection and analysed using soft independent modelling of class analogy (SIMCA) method in order to create a classification scheme to identify conform gasolines according to ANP 309 regulation. Following the optimisation of the SIMCA algorithm, it was possible to classify correctly 96% of the commercial gasoline samples present in the training set of 100. In order to check the quality of the model, an external group of 50 gasoline samples (the prediction set) were analysed and the developed SIMCA model classified 94% of these correctly. The developed chemometric method is recommended for screening commercial gasoline quality and detection of potential adulteration.

  16. 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.

  17. 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

  18. 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

  19. 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. |

  20. 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…

  1. An effective method for controlling false discovery and false nondiscovery rates in genome-scale RNAi screens.

    PubMed

    Zhang, Xiaohua Douglas

    2010-10-01

    In most genome-scale RNA interference (RNAi) screens, the ultimate goal is to select siRNAs with a large inhibition or activation effect. The selection of hits typically requires statistical control of 2 errors: false positives and false negatives. Traditional methods of controlling false positives and false negatives do not take into account the important feature in RNAi screens: many small-interfering RNAs (siRNAs) may have very small but real nonzero average effects on the measured response and thus cannot allow us to effectively control false positives and false negatives. To address for deficiencies in the application of traditional approaches in RNAi screening, the author proposes a new method for controlling false positives and false negatives in RNAi high-throughput screens. The false negatives are statistically controlled through a false-negative rate (FNR) or false nondiscovery rate (FNDR). FNR is the proportion of false negatives among all siRNAs examined, whereas FNDR is the proportion of false negatives among declared nonhits. The author also proposes new concepts, q*-value and p*-value, to control FNR and FNDR, respectively. The proposed method should have broad utility for hit selection in which one needs to control both false discovery and false nondiscovery rates in genome-scale RNAi screens in a robust manner.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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

  8. Directed evolution of mandelate racemase by a novel high-throughput screening method.

    PubMed

    Yang, Chengcheng; Ye, Lidan; Gu, Jiali; Yang, Xiaohong; Li, Aipeng; Yu, Hongwei

    2017-02-01

    Optically pure methyl (R)-o-chloromandelate and (R)-acetyl-o-mandelic acid are key intermediates for the synthesis of (S)-clopidogrel, which could be prepared with 100 % theoretical yield by sequential hydrolysis and racemization. At the moment, efficient sequential hydrolysis and racemization are hindered by the low catalytic activity of mandelate racemase (MR) toward (S)-o-chloromandelic acid ((S)-2-CMA). In the present work, we proposed to improve the catalytic performance of MR toward (S)-2-CMA by directed evolution and developed an enantioselective oxidation system for high-throughput screening (HTS) of MR libraries. Based on this HTS method, a triple mutant V22I/V29I/Y54F (MRDE1) with 3.5-fold greater relative activity as compared to the native MR was obtained. Kinetic analysis indicated that the enhanced catalytic efficiency mainly arose from the elevated k cat. Further insight into the source of improved catalytic activity was gained by molecular simulations, finding that substrate binding and product release were possibly made easier by decreased steric bulk and increased hydrophobicity of substrate binding sites. In addition, the substrate (S)-2-CMA in the enzyme-substrate complex of MRDE1 seemed to have a lower binding free energy comparing with the complex of wild-type MR. The HTS method developed in this work and the successful directed evolution of MR based on this method provide an example for racemase engineering and may inspire directed evolution of other racemases toward enhanced catalytic performance on non-natural substrates.

  9. Debye screening

    NASA Astrophysics Data System (ADS)

    Brydges, David C.; Federbush, Paul

    1980-10-01

    The existence and exponential clustering of correlation functions for a classical coulomb system at low density or high temperature are proven using methods from constructive quantum field theory, the sine gordon transformation and the Glimm, Jaffe, Spencer expansion about mean field theory. This is a vindication of a belief of long standing among physicists, known as Debye screening. That is, because of special properties of the coulomb potential, the configurations of significant probability are those in which the long range parts of r -1 are mostly cancelled, leaving an effective exponentially decaying potential acting between charge clouds. This paper generalizes a previous paper of one of the authors in which these results were obtained for a special lattice system. The present treatment covers the continuous mechanics situation, with essentially arbitrary short range forces and charge species. Charge symmetry is not assumed.

  10. 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.

  11. A bivariate binormal ROC methodology for comparing new methods to an existing standard for screening applications

    NASA Astrophysics Data System (ADS)

    Abbey, Craig K.; Insana, Michael F.; Eckstein, Miguel P.; Boone, John M.

    2007-03-01

    Validating the use of new imaging technologies for screening large patient populations is an important and very challenging area of diagnostic imaging research. A particular concern in ROC studies evaluating screening technologies is the problem of verification bias, in which an independent verification of disease status is only available for a subpopulation of patients, typically those with positive results by a current screening standard. For example, in screening mammography, a study might evaluate a new approach using a sample of patients that have undergone needle biopsy following a standard mammogram and subsequent work-up. This case sampling approach provides accurate independent verification of ground truth and increases the prevalence of disease cases. However, the selection criteria will likely bias results of the study. In this work we present an initial exploration of an approach to correcting this bias within the parametric framework of binormal assumptions. We posit conditionally bivariate normal distributions on the latent decision variable for both the new methodology as well as the screening standard. In this case, verification bias can be seen as the effect of missing data from an operating point in the screening standard. We examine the magnitude of this bias in the setting of breast cancer screening with mammography, and we derive a maximum likelihood approach to estimating bias corrected ROC curves in this model.

  12. 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.

  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...

  14. Transmission rates, screening methods and costs of MRSA--a systematic literature review related to the prevalence in Germany.

    PubMed

    Tübbicke, A; Hübner, C; Kramer, A; Hübner, N-O; Fleßa, S

    2012-10-01

    Methicillin-resistant Staphylococcus aureus (MRSA) infections represent a serious challenge for health care institutions, which is inherent in the combination of prevalence, transmission rates and costs. Furthermore, performing an MRSA screening requires information on the complex system of effectiveness, accuracy and costs of different screening methods. The purpose of this study was to give an overview of parameters with decisive significance for the burden of MRSA and the selection of a specific MRSA screening strategy. A systematic literature search for peer-reviewed health economic studies associated with MRSA was performed (from 1995 to the present). Eighty-seven different studies met all inclusion and exclusion criteria. Primary outcomes included the prevalence of MRSA, MRSA transmission rates, performance characteristics of MRSA screening methods, costs for pre-emptive isolation precautions and costs per MRSA case. The prevalence rates reported for all inpatients (1.2-5.3 %) as well as for inpatients with risk factors or patients in risk areas (3.85-20.6 %) vary greatly. The range of cross-transmission rates per day reported for patients with MRSA in isolation is 0.00081-0.009 and for carriers not in isolation is 0.00137-0.140, respectively. For polymerase chain reaction (PCR) methods, the mean sensitivity and specificity were 91.09 and 95.79 %, respectively. Culture methods show an average sensitivity of 89.01 % and an average specificity of 93.21 %. The turn-around time for PCR methods averages 15 h, while for the culture method, it can only be estimated as 48-72 h. This review filtered important parameters and cost drivers, and covered them with literature-based averages. These findings serve as an ideal evidence base for further health economic considerations of the cost-effectiveness of different MRSA screening methods.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Optically Based Rapid Screening Method for Proven Optimal Treatment Strategies Before Treatment Begins

    DTIC Science & Technology

    2015-08-01

    development, by reducing the number of animals , cost, and time required to screen new drugs and drug combinations. The feasibility of OMI measurements...24). 1a. Regulatory review and approval for animal studies (months 1-2). Completed. 1b. Measure mouse organoid response to drug treatments...can therefore be used to streamline pre-clinical drug development, by reducing the number of animals , cost, and time required to screen new drugs and

  7. 20 CFR 404.240 - Old-start method-general.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Old-start method-general. 404.240 Section 404.240 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL OLD-AGE, SURVIVORS AND DISABILITY INSURANCE (1950- ) Computing Primary Insurance Amounts Old-Start Method of Computing Primary Insurance Amounts § 404.240 Old-start method—general....

  8. A high-throughput colourimetric method for the determination of pH in crystallization screens.

    PubMed

    Kirkwood, Jobie; Wilson, Julie; O'Keefe, Simon; Hargreaves, David

    2014-09-01

    The crystallization of proteins is dependent on the careful control of numerous parameters, one of these being pH. The pH of crystallization is generally reported as that of the buffer; however, the true pH has been found to be as many as four pH units away. Measurement of pH with a meter is time-consuming and requires the reformatting of the crystallization solution. To overcome this, a high-throughput method for pH determination of buffered solutions has been developed with results comparable to those of a pH meter.

  9. 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

  10. The Future of Toxicity Testing: A Focus on In Vitro Methods Using a Quantitative High Throughput Screening Platform

    PubMed Central

    Shukla, Sunita J.; Huang, Ruili; Austin, Christopher P.; Xia, Menghang

    2010-01-01

    The U.S. Tox21 collaborative program represents a paradigm shift in toxicity testing of chemical compounds from traditional in vivo tests to less expensive and higher throughput in vitro methods to prioritize compounds for further study, identify mechanisms of action, and ultimately develop predictive models for adverse health effects in humans. The NIH Chemical Genomics Center (NCGC) is an integral component of the Tox21 collaboration due to its quantitative high throughput screening (qHTS) paradigm, in which titration-based screening is used to profile hundreds of thousands of compounds per week. Here, we describe the Tox21 collaboration, qHTS-based compound testing, and the various Tox21 screening assays that have been validated and tested at the NCGC to date. PMID:20708096

  11. Evaluation of a QuECHERS-like extraction approach for the determination of PBDEs in mussels by immuno-assay-based screening methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A sample preparation method was evaluated for the determination of polybrominated diphenyl ethers (PBDEs) in mussel samples, by using colorimetric and electrochemical immunoassay-based screening methods. A simple sample preparation in conjunction with a rapid screening method possesses the desired c...

  12. 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.

  13. 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

  14. 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

    2014-12-08

    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.

  15. Approximate Method of Calculating Heating Rates at General Three-Dimensional Stagnation Points During Atmospheric Entry

    NASA Technical Reports Server (NTRS)

    Hamilton, H. H., II

    1982-01-01

    An approximate method for calculating heating rates at general three dimensional stagnation points is presented. The application of the method for making stagnation point heating calculations during atmospheric entry is described. Comparisons with results from boundary layer calculations indicate that the method should provide an accurate method for engineering type design and analysis applications.

  16. 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

  17. Validation approach for a fast and simple targeted screening method for 75 antibiotics in meat and aquaculture products using LC-MS/MS.

    PubMed

    Dubreil, Estelle; Gautier, Sophie; Fourmond, Marie-Pierre; Bessiral, Mélaine; Gaugain, Murielle; Verdon, Eric; Pessel, Dominique

    2017-04-01

    An approach is described to validate a fast and simple targeted screening method for antibiotic analysis in meat and aquaculture products by LC-MS/MS. The strategy of validation was applied for a panel of 75 antibiotics belonging to different families, i.e., penicillins, cephalosporins, sulfonamides, macrolides, quinolones and phenicols. The samples were extracted once with acetonitrile, concentrated by evaporation and injected into the LC-MS/MS system. The approach chosen for the validation was based on the Community Reference Laboratory (CRL) guidelines for the validation of screening qualitative methods. The aim of the validation was to prove sufficient sensitivity of the method to detect all the targeted antibiotics at the level of interest, generally the maximum residue limit (MRL). A robustness study was also performed to test the influence of different factors. The validation showed that the method is valid to detect and identify 73 antibiotics of the 75 antibiotics studied in meat and aquaculture products at the validation levels.

  18. An approximate-reasoning-based method for screening high-level waste tanks for flammable gas

    SciTech Connect

    Eisenhawer, S.W.; Bott, T.F.; Smith, R.E.

    1998-07-01

    The in situ retention of flammable gas produced by radiolysis and thermal decomposition in high-level waste can pose a safety problem if the gases are released episodically into the dome space of a storage tank. Screening efforts at Hanford have been directed at identifying tanks in which this situation could exist. Problems encountered in screening motivated an effort to develop an improved screening methodology. Approximate reasoning (AR) is a formalism designed to emulate the kinds of complex judgments made by subject matter experts. It uses inductive logic structures to build a sequence of forward-chaining inferences about a subject. AR models incorporate natural language expressions known as linguistic variables to represent evidence. The use of fuzzy sets to represent these variables mathematically makes it practical to evaluate quantitative and qualitative information consistently. The authors performed a pilot study to investigate the utility of AR for flammable gas screening. They found that the effort to implement such a model was acceptable and that computational requirements were reasonable. The preliminary results showed that important judgments about the validity of observational data and the predictive power of models could be made. These results give new insights into the problems observed in previous screening efforts.

  19. An approximate reasoning-based method for screening high-level-waste tanks for flammable gas

    SciTech Connect

    Eisenhawer, S.W.; Bott, T.F.; Smith, R.E.

    2000-06-01

    The in situ retention of flammable gas produced by radiolysis and thermal decomposition in high-level waste can pose a safety problem if the gases are released episodically into the dome space of a storage tank. Screening efforts at the Hanford site have been directed at identifying tanks in which this situation could exist. Problems encountered in screening motivated an effort to develop and improved screening methodology. Approximate reasoning (AR) is a formalism designed to emulate the kinds of complex judgments made by subject matter experts. It uses inductive logic structures to build a sequence of forward-chaining inferences about a subject. Approximate-reasoning models incorporate natural language expressions known as linguistic variables to represent evidence. The use of fuzzy sets to represent these variables mathematically makes it practical to evaluate quantitative and qualitative information consistently. In a pilot study to investigate the utility of AR for flammable gas screening, the effort to implement such a model was found to be acceptable, and computational requirements were found to be reasonable. The preliminary results showed that important judgments about the validity of observational data and the predictive power of models could be made. These results give new insights into the problems observed in previous screening efforts.

  20. Riemannian Optimization Method on Generalized Flag Manifolds for Complex and Subspace ICA

    NASA Astrophysics Data System (ADS)

    Nishimori, Yasunori; Akaho, Shotaro; Plumbley, Mark D.

    2006-11-01

    In this paper we introduce a new class of manifolds, generalized flag manifolds, for the complex and subspace ICA problems. A generalized flag manifold is a manifold consisting of subspaces which are orthogonal to each other. The class of generalized flag manifolds include the class of Grassmann manifolds. We extend the Riemannian optimization method to include this new class of manifolds by deriving the formulas for the natural gradient and geodesics on these manifolds. We show how the complex and subspace ICA problems can be solved by optimization of cost functions on a generalized flag manifold. Computer simulations demonstrate our algorithm gives good performance compared with the ordinary gradient descent method.

  1. A Special Investigation to Develop a General Method for Three-dimensional Photoelastic Stress Analysis

    NASA Technical Reports Server (NTRS)

    Frocht, M M; Guernsey, R , Jr

    1953-01-01

    The method of strain measurement after annealing is reviewed and found to be satisfactory for the materials available in this country. A new general method is described for the photoelastic determination of the principal stresses at any point of a general body subjected to arbitrary load. The method has been applied to a sphere subjected to diametrical compressive loads. The results show possibilities of high accuracy.

  2. Generalized source method in curvilinear coordinates for 2D grating diffraction simulation

    NASA Astrophysics Data System (ADS)

    Shcherbakov, Alexey A.; Tishchenko, Alexandre V.

    2017-01-01

    The article presents a curvilinear coordinate Fourier space integral method for linear optical rigorous grating diffraction simulation in 3D (crossed grating diffraction). The presented formulation extends our previous work on a related method for 1D periodic grating diffraction. Following this previous work we exploit a concept of the generalized metric sources to efficiently solve the Maxwell's equations. The article provides a general description of the method together with a detailed formulation and analysis of sinusoidal corrugation crossed grating diffraction.

  3. The Development of Screening Methods to Identify Drugs to Limit ER Stress Using Wild-type and Mutant Serotonin Transporter

    PubMed Central

    Katarao, Kazusa; Murakawa, Seiya; Asano, Masaya; Usuki, Naoto; Yamamoto, Hikaru; Shirafuji, Toshihiko; Tanaka, Shigeru; Hide, Izumi; Sakai, Norio

    2016-01-01

    The function of the serotonin transporter (SERT) is regulated by its membrane trafficking. Previously, we showed that the C-terminus-deleted mutant of SERT (SERTΔCT) exhibited an aberrant membrane trafficking and subsequent retention at the endoplasmic reticulum (ER). In addition, we found that proteasome inhibitor-induced ER stress resulted in the impairment of SERT membrane trafficking and retention of SERT at the ER, an impairment very similar to that of SERTΔCT. Based on the result that the chemical chaperone 4-phnylbutulic acid (4-PBA), which relieves ER stress, accelerated the membrane trafficking and upregulated SERT activity, we hypothesized that drugs that facilitate the membrane trafficking of SERT would have potential therapeutic effects on an ER stress-related disease. In this study, we aimed to develop simple screening methods for such drugs using SERT. We first validated the serotonin uptake assay using fluorescent substrates. This simple and reliable assay method was useful for screening for drugs that affected the wild-type SERT but not SERTΔCT. In addition, we verified an assay focusing on the formation of SERTΔCT aggregates. The drugs 4-PBA and SKF-10047 facilitated the trafficking of SERT to the membrane and reduced SERTΔCT aggregates, indicating that the drugs with such characters could be potential candidates for ER stress relief. For both assays, we clarified the usefulness of a high-content screening microscope. These results could pave the way for high-throughput screening for such drugs. PMID:28127108

  4. Incorporating Virtual Reactions into a Logic-based Ligand-based Virtual Screening Method to Discover New Leads.

    PubMed

    Reynolds, Christopher R; Muggleton, Stephen H; Sternberg, Michael J E

    2015-09-01

    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 1.21×10(12) 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.

  5. 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.

  6. 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.

  7. An efficient screening method for the isolation of heterotrophic bacteria influencing growth of diatoms under photoautotrophic conditions.

    PubMed

    Zecher, Karsten; Jagmann, Nina; Seemann, Philipp; Philipp, Bodo

    2015-12-01

    Interactions between photoautotrophic diatoms and heterotrophic bacteria are important for the biogeochemical C-cycle in the oceans. Additionally, biofilms formed by diatoms and bacteria are the initiating step of biofouling processes, which causes high costs in shipping. Despite this ecological and economical importance, the knowledge about biochemical and molecular mechanisms underlying these interkingdom interactions is relatively small. For analyzing these mechanisms, laboratory model systems are required. In this study, an efficient screening method for isolating bacteria influencing photoautotrophic diatom growth was established. First, diatom cultures of Phaeodactylum tricornutum and Thalassiosira pseudonana were made axenic by applying β-lactam antibiotics. Second, a non-invasive method for measuring growth of multiple parallel diatom cultures by chlorophyll fluorescence was established. This method allowed semi-quantitative chlorophyll determination of cultures with up to 3 μg (chlorophyll) ml(-1). Axenic diatom cultures were then used for enriching bacteria and led to the isolation of 24 strains influencing growth of both diatom strains in various ways. For example, Rheinheimera sp. strain Tn16 inhibited growth of T. pseudonana, while it stimulated growth and cell aggregation of P. tricornutum. Thus, this screening method is appropriate for isolating heterotrophic bacteria showing different interactions with different diatom species ranging from synergistic to antagonistic. In consecutive applications, this method will be useful to screen for bacterial mutants with altered phenotypes regarding the influence on diatom growth.

  8. National Newborn Screening and Genetics Resource Center

    MedlinePlus

    ... GENERAL INFORMATION Conditions Screened by US Programs General Resources Genetics Birth Defects Hearing Screening FOR PROFESSIONALS ACT Sheets(ACMG) General Resources Newborn Screening Genetics Birth Defects FOR FAMILIES FAQs ...

  9. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods.

    PubMed

    Bernacki, Katarzyna; Kalyanaraman, Chakrapani; Jacobson, Matthew P

    2005-10-01

    Motivated by their participation in the McMaster Data-Mining and Docking Competition, the authors developed 2 new computational technologies and applied them to docking against Escherichia coli dihydrofolate reductase: a receptor preparation procedure that incorporates rotamer optimization of side chains and a physics-based rescoring procedure for estimating relative binding affinities of the protein-ligand complexes. Both methods use the same energy function, consisting of the all-atom OPLS-AA force field and a generalized Born solvent model, which treats the protein receptor and small-molecule ligands in a consistent manner. Thus, the energy function is similar to that used in more sophisticated approaches, such as free-energy perturbation and the molecular mechanics Poisson-Boltzmann/surface area, but sampling during the rescoring procedure is limited to simple energy minimization of the ligand. The use of a highly efficient minimization algorithm permitted the authors to apply this rescoring procedure to hundreds of thousands of protein-ligand complexes during the competition, using a modest Linux cluster. To test these methods, they used the 12 competitive inhibitors identified in the training set, plus methotrexate, as positive controls in enrichment studies with both the training and test sets, each containing 50,000 compounds. The key conclusion is that combining the receptor preparation and rescoring methods makes it possible to identify most of the positive controls within the top few tenths of a percent of the rank-ordered training and test set libraries.

  10. A New DEM Generalization Method Based on Watershed and Tree Structure

    PubMed Central

    Chen, Yonggang; Ma, Tianwu; Chen, Xiaoyin; Chen, Zhende; Yang, Chunju; Lin, Chenzhi; Shan, Ligang

    2016-01-01

    The DEM generalization is the basis of multi-dimensional observation, the basis of expressing and analyzing the terrain. DEM is also the core of building the Multi-Scale Geographic Database. Thus, many researchers have studied both the theory and the method of DEM generalization. This paper proposed a new method of generalizing terrain, which extracts feature points based on the tree model construction which considering the nested relationship of watershed characteristics. The paper used the 5 m resolution DEM of the Jiuyuan gully watersheds in the Loess Plateau as the original data and extracted the feature points in every single watershed to reconstruct the DEM. The paper has achieved generalization from 1:10000 DEM to 1:50000 DEM by computing the best threshold. The best threshold is 0.06. In the last part of the paper, the height accuracy of the generalized DEM is analyzed by comparing it with some other classic methods, such as aggregation, resample, and VIP based on the original 1:50000 DEM. The outcome shows that the method performed well. The method can choose the best threshold according to the target generalization scale to decide the density of the feature points in the watershed. Meanwhile, this method can reserve the skeleton of the terrain, which can meet the needs of different levels of generalization. Additionally, through overlapped contour contrast, elevation statistical parameters and slope and aspect analysis, we found out that the W8D algorithm performed well and effectively in terrain representation. PMID:27517296

  11. Liver (Hepatocellular) Cancer Screening

    MedlinePlus

    ... Treatment Liver Cancer Prevention Liver Cancer Screening Research Liver (Hepatocellular) Cancer Screening (PDQ®)–Patient Version What is ... These are called diagnostic tests . General Information About Liver (Hepatocellular) Cancer Key Points Liver cancer is a ...

  12. Revision of FMM-Yukawa: An adaptive fast multipole method for screened Coulomb interactions

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai

    2010-12-01

    FMM-YUKAWA is a mathematical software package primarily for rapid evaluation of the screened Coulomb interactions of N particles in three dimensional space. Since its release, we have revised and re-organized the data structure, software architecture, and user interface, for the purpose of enabling more flexible, broader and easier use of the package. The package and its documentation are available at http://www.fastmultipole.org/, along with a few other closely related mathematical software packages. New version program summaryProgram title: FMM-Yukawa Catalogue identifier: AEEQ_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEQ_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL 2.0 No. of lines in distributed program, including test data, etc.: 78 704 No. of bytes in distributed program, including test data, etc.: 854 265 Distribution format: tar.gz Programming language: FORTRAN 77, FORTRAN 90, and C. Requires gcc and gfortran version 4.4.3 or later Computer: All Operating system: Any Classification: 4.8, 4.12 Catalogue identifier of previous version: AEEQ_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 2331 Does the new version supersede the previous version?: Yes 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: The new version of fast multipole method (FMM) that diagonalizes the multipole-to-local translation operator is applied with the tree structure adaptive to sample particle locations. Reasons for new version: To handle much larger particle ensembles, to enable the iterative use of the subroutines in a solver, and to remove potential contention in assignments for parallelization. Summary of revisions: The software package FMM-Yukawa has been

  13. Methods for Effective Virtual Screening and Scaffold-Hopping in Chemical Compounds

    DTIC Science & Technology

    2007-04-04

    1999. [7] J. M. Bland. An introduction to medical statistics. (1995) 2nd edn. Oxford University Press. [8] H.J. Bohm and G. Schneider. Virtual screening...2005. [26] Jamal C. Saeh, Paul D. Lyne, Bryan K. Takasaki, and David A. Cosgrove. Lead hopping using svm and 3d pharmacophore fingerprints. J. Chem

  14. 18 CFR 385.403 - Methods of discovery; general provisions (Rule 403).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Methods of discovery... Discovery Procedures for Matters Set for Hearing Under Subpart E § 385.403 Methods of discovery; general provisions (Rule 403). (a) Discovery methods. Participants may obtain discovery by data requests,...

  15. Finite element Fourier and Abbe transform methods for generalization of aperture function and geometry in Fraunhofer diffraction theory

    SciTech Connect

    Kraus, H.G. )

    1991-08-01

    This paper discusses methods for calculating Fraunhofer intensity fields resulting from diffraction through one- and two-dimensional apertures are presented. These methods are based on the geometric concept of finite elements and on Fourier and Abbe transforms. The geometry of the two-dimensional diffracting aperture(s) is based on biquadratic isoparametric elements, which are used to define aperture(s) of complex geometry. These elements are also used to build complex amplitude and phase functions across the aperture(s) which may be of continuous or discontinuous form. The transform integrals are accurately and efficiently integrated numerically using Gaussian quadrature. The power of these methods is most evident in two dimensions, where several examples are presented which include secondary obstructions, straight and curved secondary spider supports, multiple-mirror arrays, synthetic aperture arrays, segmented mirrors, apertures covered by screens, apodization, and phase plates. Typically, the finite element Abbe transform method results in significant gains in computational efficiency over the finite element Fourier transform method, but is also subject to some loss in generality.

  16. Rapid screening method for determination of Ecstasy and amphetamines in urine samples using gas chromatography-chemical ionisation mass spectrometry.

    PubMed

    Pellegrini, M; Rosati, F; Pacifici, R; Zuccaro, R; Romolo, F S; Lopez, A

    2002-04-05

    The need for analytical screening tests more reliable and valid to detect amphetamine and related "designer drugs" in biological samples is becoming critical, due to the increasing diffusion of these drugs on the European illegal market. The most common screening procedures based on immunoassays suffer a number of limitations, including low sensitivity, lack of specificity and limited number of detectable substances. This paper describes a screening method based on gas-chromatography-mass-spectrometry (GC/MS) using positive chemical ionisation (PCI) detection. Methanol was used as reactant gas in the ionisation chamber. Molecular ions of different compounds were monitored, allowing a sensitivity of 5-10 ng/ml with high selectivity. The sensitivity of the method gives positive results in samples taken 48-72 h after intake of one dose of 50-100 mg. The method is simple and rapid. Sample preparation was limited to one liquid-liquid extraction, without any hydrolysis and derivatisation. Hydrolysis is critical to identify metabolites excreted as conjugates. Blank urine samples spiked with known amounts of amphetamine (AM), methylamphetamine (MA), methylenedioxyamphetamine (MDA), methylenedioxymethylamphetamine (MDMA), methylenedioxyethylamphetamine (MDEA) and methylenedioxyphenyl-N-methyl-2-butanamine (MBDB) were analysed. The method was successfully tested on real samples of urine from people, whose use of amphetamine was suspected, and results were compared with results obtained with immunoassays.

  17. Validation of nutritional risk index method against patient-generated subjective global assessment in screening malnutrition in colorectal cancer patients

    PubMed Central

    Faramarzi, Elnaz; Mohammad-Zadeh, Mohammad; Nasirimotlagh, Behnam

    2013-01-01

    Objective To validate malnutrition screening tool of nutrition risk index (NRI) against patient-generated subjective global assessment (PG-SGA) as a gold standard tool in colorectal cancer patients before radiotherapy. Methods Nutritional status of 52 volunteer colorectal cancer patients with a mean age of 54.1±16.8 years who referred to radiotherapy center were assessed by PG-SGA (gold standard method) and NRI. Serum albumin levels of patients were determined by colorimetric method. A contingency table was used to determine the sensitivity, specificity, and predictive value of the NRI in screening patients at risk of malnutrition, in comparison with the PG-SGA in patients before radiotherapy. Results The findings of PG-SGA and NRI showed that 52% and 45% of patients in our study were moderately or severely malnourished respectively. The NRI had a sensitivity of 66% and a specificity of 60% against PG-SGA. The positive predictive value was 64% and the negative predicative value was 62%. The agreement between NRI and PG-SGA was statistically insignificant (kappa =0.267; P>0.05). Conclusions The findings of present study showed that the prevalence of malnutrition was high in patients with colorectal cancer. Moreover, NRI method had low sensitivity and specificity in assessing nutritional status of patients with cancer. It seems that the combination of anthropometric, laboratory parameters and a subjective scoring system may be helpful tools in screening of malnutrition in cancer patients. PMID:24255578

  18. A Generalized Method of Image Analysis from an Intercorrelation Matrix which May Be Singular.

    ERIC Educational Resources Information Center

    Yanai, Haruo; Mukherjee, Bishwa Nath

    1987-01-01

    This generalized image analysis method is applicable to singular and non-singular correlation matrices (CMs). Using the orthogonal projector and a weaker generalized inverse matrix, image and anti-image covariance matrices can be derived from a singular CM. (SLD)

  19. Field analytical screening program: PCP method. Innovative technology evaluation report. Report for 1 July-31 August 1993

    SciTech Connect

    Hess, E.; Hamilton, D.

    1995-08-01

    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 pentachlorophenol (PCP) contamination in soil and water. This method was demonstrated in Norrisville, North Carolina, in August 1993. The FASP PCP Method was developed by the EPA Superfund Branch for use at Superfund sites. The method uses a gas chromatograph (GC) equipped with a megabore capillary column and either a flame ionization detector (FID) or an electron capture detector (ECD). Gas chromatography is an EPA-approved method for determining PCP concentrations in soil, water, and waste samples. The FASP PCP Method is an abbrevaited, modified version of approved methods. Soil and water samples require extraction before GC analysis. To remove interferences caused by petroleum hydrocarbons, an acid-base partition cleanup step is used during the FASP PCP Method.

  20. A novel derivatization procedure and chiral gas chromatographic method for enantiomeric purity screening of L-carnitine.

    PubMed

    Albreht, Alen; Zupančič, Borut; Vovk, Irena

    2014-01-01

    L-Carnitine is used extensively in functional foods and food supplements; consequently, the control of its enantiomeric purity is of paramount importance. A new derivatization procedure and chiral gas chromatographic method with flame ionization detection, using a cyclodextrin based stationary phase, enables prompt, simple, and inexpensive screening of the enantiomeric ratio of L- and D-carnitine in samples with different matrices. Conversion of carnitine to beta-acetoxy-gama-butyrolactone was optimized for maximum conversion (98% of the desired product lactone was formed and 2% of the side product gama-crotonolactone) and minimum racemization (no changes at the chiral center were detected) and time consumption. As it is shown in this study, a fast gas chromatographic method, with total run time of 7 min, together with the new derivatization procedure enables an effective enantiomeric purity screening of L-carnitine in real samples such as food supplements and L-carnitine raw ingredient.